bluuebunny/crossref_metadata_2025 huggingface dataset:
Glutton: large-scale integration of non-model organism transcriptome data for comparative analysis
Authors: Medlar Alan , Laakso Laura , Miraldo Andreia , Löytynoja Ari
Published: September 2016

High-throughput RNA-seq data has become ubiquitous in the study of non-model organisms, but its use in comparative analysis remains a challenge. Without a reference genome for mapping, sequence data has to bede novoassembled, producing large numbers of short, highly redundant contigs. Preparing these assemblies for comparative analyses requires the removal of redundant isoforms, assignment of orthologs and converting fragmented transcripts into gene alignments. In this article we present Glutton, a novel tool to process transcriptome assemblies for downstream evolutionary analyses. Glutton takes as input a set of fragmented, possibly erroneous transcriptome assemblies. Utilising phylogeny-aware alignment and reference data from a closely related species, it reconstructs one transcript per gene, finds orthologous sequences and produces accurate multiple alignments of coding sequences. We present a comprehensive analysis of Glutton’s performance across a wide range of divergence times between study and reference species. We demonstrate the impact choice of assembler has on both the number of alignments and the correctness of ortholog assignment and show substantial improvements over heuristic methods, without sacrificing correctness. Finally, using inference of Darwinian selection as an example of downstream analysis, we show that Glutton-processed RNA-seq data give results comparable to those obtained from full length gene sequences even with distantly related reference species. Glutton is available fromhttp://wasabiapp.org/software/glutton/and is licensed under the GPLv3.
Nuclear and structural dynamics during the establishment of a specialized effector-secreting cell byMagnaporthe oryzaein living rice cells
Authors: Shipman Emma N. , Jones Kiersun , Jenkinson Cory B. , Kim Dong Won , Zhu Jie , Khang Chang Hyun
Published: September 2016

Background

To cause an economically important blast disease on rice, the filamentous fungusMagnaporthe oryzaeforms a specialized infection structure, called an appressorium, to penetrate host cells. Once inside host cells, the fungus produces a filamentous primary hypha that differentiates into multicellular bulbous invasive hyphae (IH), which are surrounded by a host-derived membrane. These hyphae secrete cytoplasmic effectors that enter host cells presumably via the biotrophic interfacial complex (BIC). The first IH cell, also known as the side BIC-associated cell, is a specialized effector-secreting cell essential for a successful infection. This study aims to determine cellular processes that lead to the development of this effector-secreting first IH cell inside susceptible rice cells.

Results

Using live-cell confocal imaging, we determined a series of cellular events by which the appressorium gives rise to the first IH cell in live rice cells. The filamentous primary hypha extended from the appressorium and underwent asymmetric swelling at its apex. The single nucleus in the appressorium divided, and then one nucleus migrated into the swollen apex. Septation occurred in the filamentous region of the primary hypha, establishing the first IH cell. The tip BIC that was initially associated with the primary hypha becomes the side BIC on the swollen apex prior to nuclear division in the appressorium. The average distance between the early side BIC and the nearest nucleus in the appressorium was estimated to be more than 32 µm. These results suggest an unknown mechanism by which effectors that are expressed in the appressorium are transported through the primary hypha for their secretion to the distantly located BIC. WhenM. oryzaewas inoculated on heat-killed rice cells, penetration proceeded as normal, but there was no differentiation of a bulbous IH cell, suggesting its specialization for establishment of biotrophic infection.

Conclusions

Our studies reveal cellular dynamics associated with the development of the effector-secreting first IH cell. Our data raise new mechanistic questions concerning hyphal differentiation in response to host environmental cues and effector trafficking from the appressorium to the BIC.
Expression and crystallographic studies of theArabidopsis thalianaGDP-D-mannose pyrophosphorylase VTC1
Authors: Zhao Shun , Liu Lin
Published: September 2016

GDP-D-mannose pyrophosphorylase catalyzes the production of GDP-D-mannose, an intermediate product in the plant ascorbic acid (AsA) biosynthetic pathway. This enzyme is a key regulatory target in AsA biosynthesis and is encoded byVITAMIN C DEFECTIVE 1(VTC1) in theArabidopsis thalianagenome. Here, recombinant VTC1 was expressed, purified and crystallized. Diffraction data were obtained from VTC1 crystals grown in the absence and presence of substrate using X-rays. The ligand-free VTC1 crystal diffracted X-rays to 3.3 Å resolution and belonged to space groupR32, with unit-cell parametersa=b= 183.6,c= 368.5 Å, α = β = 90, γ = 120°; the crystal of VTC1 in the presence of substrate diffracted X-rays to 1.75 Å resolution and belonged to space groupP21, with unit-cell parametersa= 70.8,b= 83.9,c= 74.5 Å, α = γ = 90.0, β = 114.9°.
Crystal structure of a mixed-ligand silver(I) complex of the non-steroidal anti-inflammatory drug diclofenac and pyrimidine
Authors: Hamamci Alisir Sevim , Dege Necmi
Published: September 2016

In the title mixed-ligand silver(I) coordination polymeric complex with the non-steroidal anti-inflammatory drug diclofenac (C14H11Cl2NO2) (diclH) and pyrimidine (pym), namely poly[{μ2-2-[2-(2,6-dichloroanilino)phenyl]acetato-κ2
O:O′}(μ2-pyrimidine-κ2
N
1:N
3)silver(I)], [Ag(C14H10Cl2NO2)(C4H4N2)]
n
or [Ag(μ-dicl)(μ-pym)]
n
, the very distorted tetrahedral AgN2O2 coordination centres comprise two N-atom donors from bridging pym ligands [Ag—N = 2.381 (3) and 2.412 (3) Å] and two carboxylate O-atom donors from dicl ligands [Ag—O = 2.279 (2) and 2.280 (2) Å], which bridge Ag atoms, giving a centrosymmetric dinuclear units with a short Ag...Ag separation [2.8931 (5) Å]. Within the units are short intraligand C—Cl...π(pym) interactions [3.6409 (15) Å]. The units are linked through the bridging N atoms of the pym ligand into a two-dimensional sheet–polymer structure lying parallel to (100) and stabilized by inter-ring π–π interactions between the pym ligands [Cg...Cg = 3.4199 (17) Å]. Additional inter-unit C—H...O and C—H...Cg hydrogen-bonding interactions between the sheets give an overall three-dimensional structure.
2-(6-Methyl-1-benzofuran-3-yl)acetic acid
Authors: Ramprasad N. , Gowda K. V. Arjuna , Gowda Ramakrishna , Basanagouda Mahantesha , Kantharaj K. S. , Gowda G. V. Jagadeesha
Published: September 2016

The asymmetric unit of the title compound, C11H10O3, contains two crystallographically independent molecules (AandB) with nearly matching conformations. Both molecules are almost planar [r.m.s. overlay fit for the non-hydrogen atoms = 0.011 (1) Å] and in each molecule there is a short intramolecular C—H...O contact. In both molecules, the OH group of the acetic acid residue occupies a position approximately antiperiplanar to the C atom of the heterocycle. In the crystal, the two molecules are linked by a pair of O—H...O hydrogen bonds, enclosing anR22(8) ring motif and forming anA–Bdimer. The dimers are linked by C—H...π interactions, forming columns along the [010] direction.
2-Methyl-N-(pyrazin-2-yl)propanamide–1,2,4,5-tetrafluoro-3,6-diiodobenzene (2/1)
Authors: Dziuk Błażej , Ośmiałowski Borys , Zarychta Bartosz , Ejsmont Krzysztof
Published: September 2016

In the title compound, C8H11N3O·0.5C6F4I2, molecules ofiPr-substituted pyrazine are co-crystallized with 1,4-diiodo-2,3,5,6-tetrafluorobenzene. The complete molecule of 1,4-diiodo-2,3,5,6-tetrafluorobenzene is generated by an inversion centre at the middle of the aromatic ring. Both molecules have normal geometry and theiPr acylamine group is disordered over two sets of sites with an occupancy ratio of 0.51:0.49. In the crystal, the components are linked by I...N halogen bonds [2.830 (2) Å] and C—H...F interactions are observed.
(E)-2-[(2,3-Dibromoallyl)sulfanyl]-1-methyl-1H-imidazol-3-ium bromide
Authors: Oberparleiter Stefan , Laus Gerhard , Wurst Klaus , Schottenberger Herwig
Published: September 2016

The title salt, C7H9Br2N2S+·Br−, was obtained from methimazole (1-methyl-3H-imidazole-2-thione) byS-allylation using 1,2,3-tribromopropene. A positional disorder of the bromine atoms at the allyl chain was observed, with each Br atom equally disordered over two positions. N—H...Br and C—H...Br interactions were identified.
Directed dispersal by an abiotic vector: wetland plants disperse their seeds selectively to suitable sites along the hydrological gradient via water
Authors: Soons Merel B. , de Groot G. Arjen , Cuesta Ramirez M. Teresa , Fraaije Rob G. A. , Verhoeven Jos T. A. , de Jager Monique
Published: September 2016

Plant species around the world invest in seed dispersal by producing large numbers of seeds, with a wide range of morphological adaptations that facilitate dispersal. Not all dispersed seeds reach suitable sites, however, and plants can significantly improve their fitness by increasing the proportion of seeds arriving at suitable sites for germination and establishment. Disproportionate dispersal to suitable sites is known as ‘directed dispersal’. Yet, mechanisms of directed dispersal are only known for a limited number of animal‐dispersed plant species.

We tested the hypothesis that directed dispersal can also be driven by abiotic vectors, such as water or wind. We used a tiered approach, combining analyses of experimental, field and literature data on wetland plant species and evaluating the potential for evolution of directed dispersal with a spatially explicit individual‐based model.

The data collected demonstrate that wetland plants produce seeds with adaptations to promote transportation and deposition by water towards microsites along the hydrological gradient where they germinate and establish best. Aquatic species produce seeds that sink and are transported by water as bed load towards inundated sites. In contrast, shoreline species produce seeds that float for very long periods of time so that they are eventually entrapped by shoreline vegetation or deposited at the waterline. Our model simulations confirm that the patterns we observed in nature can evolve under natural selection through adaptations in seed buoyancy.

For wind dispersal, the situation is more complex. Wind does not provide directed dispersal in the strictest sense but, rather, simply appears to be the best available dispersal vector for more terrestrial wetland plant species to reach drier areas in a wet environment.

Synthesis. We show that directed dispersal towards specific, suitable microsites is not exclusive to animal‐dispersed plant species, but may be far more common in plants – also in species dispersed by abiotic vectors, in particular water. As water and wind are very common dispersal vectors throughout the plant kingdom, directed dispersal (and not just dispersal distance) seems to be of general importance for the ecology of plants.

A lay summary is available for this article.
Does biomass growth increase in the largest trees? Flaws, fallacies and alternative analyses
Authors: Sheil Douglas , Eastaugh Chris S. , Vlam Mart , Zuidema Pieter A. , Groenendijk Peter , van der Sleen Peter , Jay Alex , Vanclay Jerome
Published: September 2016

The long‐standing view that biomass growth in trees typically follows a rise‐and‐fall unimodal pattern has been challenged by studies concluding that biomass growth increases with size even among the largest stems in both closed forests and in open competition‐free environments. We highlight challenges and pitfalls that influence such interpretations.

The ability to observe and calibrate biomass change in large stems requires adequate data regarding these specific stems.

Data checking and control procedures can bias estimates of biomass growth and generate false increases with stem size.

It is important to distinguish aggregate and individual‐level trends: a failure to do so results in flawed interpretations.

Our assessment of biomass growth in 706 tropical forest stems indicates that individual biomass growth patterns often plateau for extended periods, with no significant difference in the number of stems indicating positive and negative trends in all but one of the 14 species. Nonetheless, when comparing aggregate growth during the most recent five years, 13 out of our 14 species indicate that biomass growth increases with size even among the largest sizes. Thus, individual and aggregate patterns of biomass growth with size are distinct.

Claims concerning general biomass growth patterns for large trees remain unconvincing. We suggest how future studies can improve our knowledge of growth patterns in and among large trees.

Alay summaryis available for this article.
LGBTI organizations navigating imperial contexts: the Kaleidoscope Trust, the Commonwealth and the need for a decolonizing, intersectional politics
Authors: Waites Matthew
Published: September 2016

This article presents the first sustained social analysis of the Kaleidoscope Trust, the UK’s leading social movement organization on LGBTI issues internationally, and its engagement with the Commonwealth – particularly through forming The Commonwealth Equality Network, comprising national NGOs. A contribution is made to sociological and critical analysis of transnational LGBTI movements, through argument for a new analytical framework combining the sociology of human rights with a decolonizing, intersectional approach – beyond the division between optimistic theories extending Western LGBTI progressive politics, or pessimistic postcolonial queer analyses. To investigate organizations’ strategies leading to the Malta 2015 Commonwealth Heads of Government Meeting, the research utilizes sources of data including event observation and website sources, initiating analysis of online environments. The analysis deploys social movement theory to examine how and why Kaleidoscope selected the Commonwealth as a political opportunity structure to engage through strategies of framing and articulation of human rights. Invention of The Commonwealth Equality Network, shaped online and offline by imperial relations between core and periphery, is analysed via transnational public sphere and critical theories and argued to indicate a significant restructuring of global queer politics. It is contended that a consistently decolonizing and intersectional articulation of human rights is needed.
Embodied narratives of disaster: the expression of bodily experience in Aceh, Indonesia
Authors: Samuels Annemarie
Published: September 2016

The devastating Indian Ocean tsunami of 26 December 2004 caused massive destruction to coastal Aceh, Indonesia, and left countless numbers of people dead or wounded. This article focuses on the embodied narratives of three Acehnese women who survived the disaster and, like many others in Aceh, told their stories ‘through’ their bodies. A detailed ethnographic account of their narratives reveals how the body stretches temporally between the ‘narrated event’ and the ‘narrative event’, both through the representation of the body in narratives and through the embodied performance of narratives. Moving beyond meaning‐centred analyses of narratives, I argue that the central accomplishment of these narratives is that they convey poignant bodily experiences to others and thereby create a shared, post‐disaster, world. Ultimately, through these embodied narratives of disaster people remake their world, with others, in the wake of its ‘unmaking’.
Longing: A Patient and Caregiver Focused Clinical Diagnostic Validity (CDV) Study
Authors: Pehler Shelley‐Rae
Published: September 2016

PURPOSE

To gather data from patients and caregivers about their personal experiences with longing.

METHODS

Using Fehring's Clinical Diagnostic Validity model, patients and caregivers were surveyed for their experiences with longing. The survey was developed based on two previous research projects (a content analysis and survey of expert nurses). Approval for the study was received from the University of Wisconsin‐Eau Claire Institutional Review Board.

FINDINGS

None of the 84 attributes met major criteria (weighted ratios ≥ 0.8), but 19 met minor (weighted ratios of 0.60–0.79) across patients, caregivers, and combined scores. The proposed definition was supported by the respondents.

CONCLUSIONS

The phenomenon of longing may exist.

IMPLICATIONS FOR NURSING PRACTICE

There is evidence justifying the submission to NANDA‐I for a new nursing diagnosis for longing.
Energy Drink Use Patterns Among Young Adults: Associations with Drunk Driving
Authors: Arria Amelia M. , Caldeira Kimberly M. , Bugbee Brittany A. , Vincent Kathryn B. , O'Grady Kevin E.
Published: September 2016

Background

Highly caffeinated “energy drinks” (ED) are commonly consumed and sometimes mixed with alcohol. Associations between ED consumption, risk‐taking, and alcohol‐related problems have been observed. This study examines the relationship between ED consumption—both with and without alcohol—and drunk driving.

Methods

Data were derived from a longitudinal study of college students assessed annually via personal interviews. In Year 6 (modal age 23; n = 1,000), participants self‐reported their past‐year frequency of drunk driving, ED consumption patterns (frequency of drinking alcohol mixed with energy drinks [AmED] and drinking energy drinks without alcohol [ED]), alcohol use (frequency, quantity), and other caffeine consumption. Earlier assessments captured suspected risk factors for drunk driving. Structural equation modeling was used to develop an explanatory model for the association between ED consumption patterns and drunk driving frequency while accounting for other suspected risk factors.

Results

More than half (57%) consumed ED at least once during the past year. Among ED consumers, 71% drank AmED and 85% drank ED alone; many (56%) engaged in both styles of ED consumption while others specialized in one or the other (29% drank ED alone exclusively, while, 15% drank AmED exclusively). After accounting for other risk factors, ED consumption was associated with drunk driving frequency in 2 ways. First, a direct path existed from ED frequency (without alcohol) to drunk driving frequency. Second, an indirect path existed from AmED frequency through alcohol quantity to drunk driving frequency.

Conclusions

Among this sample, ED consumption with and without alcohol was common, and both styles of ED consumption contributed independently to drunk driving frequency. Results call for increased attention to the impact of different patterns of ED consumption on alcohol‐related consequences, such as drunk driving.
Alcohol Involvement in Homicide Victimization in the United States
Authors: Naimi Timothy S. , Xuan Ziming , Cooper Susanna E. , Coleman Sharon M. , Hadland Scott E. , Swahn Monica H. , Heeren Timothy C.
Published: September 2016

Background

Although the association between alcohol and homicide is well documented, there has been no recent study of alcohol involvement in homicide victimization in U.S. states. The objective of this article was to determine the prevalence of alcohol involvement in homicide victimization and to identify socio demographic and other factors associated with alcohol involvement in homicide victimization.

Methods

Data from homicide victims with a reported blood alcohol content (BAC) level were analyzed from 17 states from 2010 to 2012 using the National Violent Death Reporting System. Logistic regression was used to investigate factors associated with the odds of homicide victims having a BAC ≥ 0.08%.

Results

Among all homicide victims, 39.9% had a positive BAC including 13.7% with a BAC between 0.01% and 0.79% and 26.2% of victims with a BAC ≥ 0.08%. Males were twice as likely as females to have a BAC ≥ 0.08% (29.1% vs. 15.2%; p < 0.001). Characteristics that were independent predictors of homicide victims having a BAC ≥ 0.08 included male sex, American Indian/Alaska Native race, Hispanic ethnicity, history of intimate partner violence, and nonfirearm homicides.

Conclusions

Alcohol is present in a substantial proportion of homicide victims in the United States, with substantial variation by state, demographic, and circumstantial characteristics. Future studies should explore the relationships between state‐level alcohol policies and alcohol involvement among perpetrators and victims of homicide.
The protective effects of moderate drinking: lies, damned lies, and… selection biases?
Authors: Britton Annie , Bell Steven
Published: September 2016

Commentary to: Selection biases in observational studies affect associations between ‘moderate’ alcohol consumption and mortality
Referral patterns of special needs patients at the Royal Dental Hospital of Melbourne, Victoria, Australia
Authors: Mohamed Rohani M , Calache H , Borromeo GL
Published: September 2016

Background

Special Needs Dentistry (SND) has been recognized as a dental specialty in Australia since 2003 but there have been no studies addressing the profile of patients for specialist care. The purpose of this study is to identify, via referrals received, the profile of patients and quality of referrals at the largest public SND unit in Victoria, Australia.

Methods

All referrals received over a 6‐month period (1 January–30 June 2013) by the integrated SND unit (ISNU) were reviewed prior to allocation to the outpatient clinic (OP), domiciliary (DOM) or general anaesthetic (GA) services.

Results

Six‐hundred and eighty‐eight referrals were received with the majority for the OP clinic (68.3%), followed by DOM (22.4%) and GA services (9.3%) (χ2 = 360.2, P < 0.001). A referral may have specified more than one special needs condition with the most common category being those who were medically compromised (81.7%). The reasons for referral included lack of compliance (27.2%), further management due to multiple medical conditions or GA services required (9.9%), or for multiple other reasons (62.9%).

Conclusions

A diverse pattern of SND patients was referred to the ISNU with a majority of referrals having no specific referral reason cited, suggesting poor quality of referrals.
Staging research of human lung cancer tissues by high‐resolution magic angle spinning proton nuclear magnetic resonance spectroscopy (HRMAS 1H NMR) and multivariate data analysis
Authors: Chen Wenxue , Lu Shaohua , Wang Guifang , Chen Fener , Bai Chunxue
Published: September 2016

Aim

High‐resolution magic‐angle spinning proton nuclear magnetic resonance (HRMAS 1H NMR) spectroscopy technique was employed to analyze the metabonomic characterizations of lung cancer tissues in hope to identify potential diagnostic biomarkers for malignancy detection and staging research of lung tissues.

Methods

HRMAS 1H NMR spectroscopy technique can rapidly provide important information for accurate diagnosis and staging of cancer tissues owing to its noninvasive nature and limited requirement for the samples, and thus has been acknowledged as an excellent tool to investigate tissue metabolism and provide a more realistic insight into the metabonomics of tissues when combined with multivariate data analysis (MVDA) such as component analysis and orthogonal partial least squares‐discriminant analysis in particular.

Results

HRMAS 1H NMR spectra displayed the metabonomic differences of 32 lung cancer tissues at the different stages from 32 patients. The significant changes (P < 0.05) of some important metabolites such as lipids, aspartate and choline‐containing compounds in cancer tissues at the different stages had been identified. Furthermore, the combination of HRMAS 1H NMR spectroscopy and MVDA might potentially and precisely provided for a high sensitivity, specificity, prediction accuracy in the positive identification of the staging for the cancer tissues in contrast with the pathological data in clinic.

Conclusion

This study highlighted the potential of metabonomics in clinical settings so that the techniques might be further exploited for the diagnosis and staging prediction of lung cancer in future.
Fatty acids profiling reveals potential candidate markers of semen quality
Authors: Zerbinati C. , Caponecchia L. , Rago R. , Leoncini E. , Bottaccioli A. G. , Ciacciarelli M. , Pacelli A. , Salacone P. , Sebastianelli A. , Pastore A. , Palleschi G. , Boccia S. , Carbone A. , Iuliano L.
Published: September 2016

Previous reports showed altered fatty acid content in subjects with altered sperm parameters compared to normozoospermic individuals. However, these studies focused on a limited number of fatty acids, included a short number of subjects and results varied widely. We conducted a case–control study involving 155 patients allocated into four groups, including normozoospermia (n = 33), oligoasthenoteratozoospermia (n = 32), asthenozoospermia (n = 25), and varicocoele (n = 44). Fatty acid profiling, including 30 species, was analyzed by a validated gas chromatography (GC) method on the whole seminal fluid sample. Multinomial logistic regression modeling was used to identify the associations between fatty acids and the four groups. Specimens from 15 normozoospermic subjects were also analyzed for fatty acids content in the seminal plasma and spermatozoa to study the distribution in the two compartments. Fatty acids lipidome varied markedly between the four groups. Multinomial logistic regression modeling revealed that high levels of palmitic acid, behenic acid, oleic acid, and docosahexaenoic acid (DHA) confer a low risk to stay out of the normozoospermic group. In the whole population, seminal fluid stearic acid was negatively correlated (r = −0.53), and DHA was positively correlated (r = 0.65) with sperm motility. Some fatty acids were preferentially accumulated in spermatozoa and the highest difference was observed for DHA, which was 6.2 times higher in spermatozoa than in seminal plasma. The results of this study highlight complete fatty acids profile in patients with different semen parameters. Given the easy‐to‐follow and rapid method of analysis, fatty acid profiling by GC method can be used for therapeutic purposes and to measure compliance in infertility trials using fatty acids supplements.
Spermatozoa from normozoospermic fertile and infertile individuals convey a distinct miRNA cargo
Authors: Salas‐Huetos A. , Blanco J. , Vidal F. , Grossmann M. , Pons M. C. , Garrido N. , Anton E.
Published: September 2016

Deciphering the underlying causes of idiopathic male infertility is one of the main challenges in reproductive medicine. This is especially relevant in infertile patients displaying normal seminal parameters and no urogenital or genetic abnormalities. In these cases, the search for additional sperm biomarkers is of high interest. This study was aimed to determine the implications of the sperm miRNA expression profiles in the reproductive capacity of normozoospermic infertile individuals. The expression level of 736 miRNAs was evaluated in spermatozoa from eight normozoospermic infertile males using TaqMan® qRT‐PCR. Results were contrasted with data from 10 control normozoospermic fertile individuals analyzed under the same conditions. Clustering analysis of miRNA expression data separated the individuals according to their fertility condition (fertile and infertile). Fifty‐seven miRNAs were differentially expressed (DE‐miRNAs) between populations; 20 of them was regulated by a host gene promoter that in three cases comprised genes involved in fertility. The predicted targets of the DE‐miRNAs (n = 8,606) unveiled a significant enrichment of biological processes related to embryonic morphogenesis and chromatin modification. Normozoospermic infertile individuals exhibit a specific sperm miRNA expression profile clearly differentiated from normozoospermic fertile individuals. This miRNA cargo has potential implications in the individuals' reproductive competence.
Addition of different concentrations of prostasome‐like vesicles at neutral or slightly alkaline pH decreases canine sperm motility
Authors: Zelli R. , Orlandi R. , Verstegen J. , Troisi A. , Elad Ngonput A. , Menchetti L. , Cardinali L. , Polisca A.
Published: September 2016

Prostasome‐like vesicles (PV) are components of the canine prostatic fluid during ejaculation and despite some enzymatic activities have been identified recently, their functions in the reproductive events in this species are still poorly understood. In this study, we evaluated at neutral or slightly alkaline pH, the effects of different concentrations of purified PV on sperm cell motility characteristics and the impact on the short‐ and long‐term preservation of preserved semen maintained at room temperature. Two different experiments were performed. In the first experiment, purified PV were added at increasing concentration (1.25, 2.5, 5, 10, and 20 μL equivalent to 1, 2, 4, 8, and 16 μg of protein, respectively) to aliquots of 100 μL of preserved semen maintained at 22 °C at the following time points: 0, 30, 60, 120, 240, and 480 min. Computer‐assisted sperm motility characteristics and pH were assessed three times at each time points, for each sample and for every concentrations. In the second experiment, the purified PV were added with the same methods as described above but only at time 0. Sperm motility characteristics and pH were assessed over the time. This study showed how the addition of purified PV to preserved semen affects negatively (p < 0.05) at neutral and alkaline pH, both total and progressive motility in a concentration depending manner. Furthermore, prostasome addition was demonstrated to change the quality of sperm movement which may represent a mechanism facilitating sperm cells attachment to the uterine epithelium and facilitating energy preservation before fertilization.
Effects of baseline abdominal pain and bloating on response to lubiprostone in patients with irritable bowel syndrome with constipation
Authors: Chang L. , Chey W. D. , Drossman D. , Losch‐Beridon T. , Wang M. , Lichtlen P. , Mareya S.
Published: September 2016

Background

Lubiprostone (8 μg b.d.) received US Food and Drug Administration (FDA) approval in 2008 for the treatment of constipation‐predominant irritable bowel syndrome (IBS‐C) in women aged ≥18 years. In 2012, the FDA issued new guidance for IBS‐C clinical trials, recommending a composite endpoint incorporating both abdominal pain and stool frequency.

Aim

In a post hoc analysis, similar criteria were applied to data from two pivotal, phase 3, double‐blind, randomised trials of lubiprostone in patients with IBS‐C.

Methods

Included patients had a baseline spontaneous bowel movement (SBM) frequency <3/week and abdominal pain or bloating ratings ≥1.36 on a 5‐point scale [0 (absent) to 4 (very severe)]. Responders (composite endpoint) had a mean pain reduction ≥30% compared with baseline, and an increase from baseline of ≥1 SBM/week for ≥6 of the 12 treatment weeks. Lubiprostone effects on abdominal pain alone were also evaluated, as were bloating alone and in a composite endpoint with stool frequency.

Results

In pooled data, 325 patients received lubiprostone and 180 received placebo. Rates of response were higher with lubiprostone vs. placebo for the composite endpoint of improved pain and stool frequency (26.3% vs. 15.3%, respectively; P = 0.008) and the composite endpoint of improved bloating and stool frequency (23.8% vs. 12.6%, respectively; P = 0.012). Response rates were also higher with lubiprostone vs. placebo for abdominal pain alone (P = 0.005) and bloating alone (P = 0.012).

Conclusion

Lubiprostone was significantly more effective than placebo in improving abdominal pain or bloating, and also in composite endpoints that included stool frequency.
Viral neurotropism, peripheral neuropathy and other morphological abnormalities in bovine ephemeral fever virus‐infected downer cattle
Authors: Barigye R , Davis S , Hunt R , Hunt N , Walsh S , Elliott N , Burnup C , Aumann S , Day C , Dyrting K , Weir R , Melville LF
Published: September 2016

Objective

This study assessed the neurotropism of bovine ephemeral fever (BEF) virus (BEFV) and described histomorphological abnormalities of the brain, spinal cord and peripheral nerves that may causally contribute to paresis or paralysis in BEF.

Methods

Four paralysed and six asymptomatic but virus‐infected cattle were monitored, and blood and serum samples screened by qRT‐PCR, virus isolation and neutralisation tests. Fresh brain, spinal cord, peripheral nerve and other tissues were qRT‐PCR‐tested for viral RNA, while formalin‐fixed specimens were processed routinely and immunohistochemically evaluated for histomorphological abnormalities and viral antigen distribution, respectively.

Results

The neurotropism of BEFV was immunohistochemically confirmed in the brain and peripheral nerves and peripheral neuropathy was demonstrated in three paralysed but not the six aneurological but virus‐infected animals. Wallerian degeneration (WD) was present in the ventral funicular white matter of the lumbar spinal cord of a paralysed steer and in cervical and thoracic spinal cord segments of three paralysed animals. Although no spinal cord lesions were seen in the steer euthanased within 7 days of illness, peripheral neuropathy was present and more severe in nerves of the brachial plexuses than in the gluteal or fibular nerves. The only steer with WD in the lumbar spinal cord also showed intrahistiocytic cell viral antigen that was spatially distributed within areas of moderate brain stem encephalitis.

Conclusion

The data confirmed neurotropism of BEFV in cattle and documented histomorphological abnormalities in peripheral nerves and brain which, together with spinal cord lesions, may contribute to chronic paralysis in BEFV‐infected downer cattle.
Live and inactivated vaccine regimens against caecal Salmonella Typhimurium colonisation in laying hens
Authors: Groves PJ , Sharpe SM , Muir WI , Pavic A , Cox JM
Published: September 2016

Objective

In Australia, Salmonella serovar Typhimurium (S. Typhimurium) is the predominant zoonotic serovar in humans and is frequently isolated from layer hens. Vaccination against this serovar has been previously shown to be effective in broilers and the aim of this current study was to assess and determine the best vaccination strategy (live or inactivated) to minimise caecal colonisation by S. Typhimurium.

Methods

A long‐term experiment (56 weeks) was conducted on ISABROWN pullets using a commercial live aroA deleted mutant S. Typhimurium vaccine and an autogenous inactivated multivalent Salmonella vaccine (containing serovars Typhimurium, Infantis, Montevideo and Zanzibar). These vaccines were administered PO or by SC or IM injection, either alone or in combination. Pullets were vaccinated throughout rearing (to 18 weeks of age) and sequentially bled for antibody titre levels. The birds, vaccinated and controls, were challenged orally with a field isolate of S. Typhimurium at different ages, held for 21 days post‐challenge, then euthanased and their caeca cultured for the presence of Salmonella.

Results

None of the oral live‐vaccinated groups exhibited lasting protection. When administered twice, the inactivated vaccine gave significant protection at 17 weeks of age and the live vaccine given by SC injection given twice produced significant protection at 17, 25 and 34 weeks.

Conclusions

Vaccination regimens that included parenteral administration of live or inactivated vaccines and thus achieved positive serum antibody levels were able to provide protection against challenge. Hence, vaccination may play a useful role in a management strategy for Salmonella carriage in layer flocks.
Giving meaning to Ellenberg nutrient values: National Forest Soil Inventory yields frequency‐based scaling
Authors: Ewald Jörg , Ziche Daniel
Published: September 2016

Questions

Ellenberg nutrient values based on indicator plant species composition of vegetation plots (mN) are widely used to measure temporal and spatial patterns of nutrient deficiency and eutrophication. The widespread use is in contrast to the lack of direct calibration against soil chemical proxies of nutrient availability. Lack of calibration and range contraction due to averaging of a bounded ordinal scale hinder the interpretation of mN across studies. Based on a large set of concomitant vegetation–soil data we asked: (1) which is the best single soil predictor of mN, (2) which combination of soil variables best explains mN; and (3) can a meaningful relative scale of mN be provided for comparative purposes?

Location

Forests in Germany, sampled in a systematic 8 km × 8 km grid.

Methods

The German National Forest Soil Inventory (NFSI) provides a large, representative sample of joint soil and vegetation plots, which were additionally intersected with modelled background N deposition. Values of mN of vegetation plots were related to measured 36 soil and three deposition variables by correlation and multiple regression. The distribution of mN was partitioned based on quantiles.

Results

In NFSI mN was most closely related to the C/N ratio of the topsoil (r² = 0.31). Multiple analysis regression showed that soil acidity, soil P and K, humus quality and deposition were complementary predictors (multiple r² = 0.47) of mN.

Conclusions

Values of mN are moderately, but consistently, related to measurable chemical properties of forest soils. The 10, 30, 70 and 90% quantiles of the frequency distribution of mN in the NFSI data are proposed to define a relative scale of macronutrient availability in forest soils, distinguishing very oligotrophic (mN < 3.38), oligotrophic (3.38–4.8), mesotrophic (4.80–5.75), eutrophic (5.75–6.21) and highly eutrophic (>6.21) sites, which broadly correspond to conventional classes of C/N ratio used in forest site mapping. This proposed five‐class trophic scale can be used to compare mN and its trends across studies in forest vegetation of Central Europe.
A multifaceted intervention to reduce drug‐related complications in surgical patients
Authors: Bos Jacqueline M. , van den Bemt Patricia M. L. A. , Kievit Wietske , Pot Johan L. W. , Nagtegaal J. Elsbeth , Wieringa André , van der Westerlaken Monique M. L. , van der Wilt Gert Jan , de Smet Peter A. G. M. , Kramers Cornelis
Published: September 2016

Aim

The P‐REVIEW study was a prospective, multicenter, open intervention study, designed to determine whether a multifaceted intervention of educating the prescriber combined with medication review and pharmaceutical visits to the ward by the hospital pharmacist could lead to a reduction in drug‐related complications among surgical patients.

Methods

A total of 6780 admissions of 5940 patients to surgical, urological and orthopaedic wards during the usual care period and 6484 admissions of 5711 patients during the intervention period were included. An educational programme covering pain management, antithrombotics, fluid and electrolyte management, prescription in case of renal insufficiency and antibiotics was developed. National and local hospital guidelines were included. Hospital pharmacists performed medication safety consultations, combining medication review of high‐risk patients and a visit to the physician on the ward.

Results

A significantly lower proportion of admissions with one or more clinically relevant, potentially preventable, drug‐related problems (including death, temporary or sustained disability, increased length of hospital stay or readmission within 30 days) occurred in the intervention period (1.1% (73/6484) compared to the usual care period [1.6% (106/6780)] (P = 0.029). The relative risk (RR) was 0.72 (95% CI 0.53–0.97). Several types of drug‐related problems occurred less frequently. Costs incurred as result of time spent on study‐related activities were not different before and after the intervention.

Conclusions

The P‐REVIEW study shows that education and support of the prescribing physician with respect to high‐risk patients in surgical departments leads to a significant, clinically relevant benefit for patients without generating additional costs.
Apoptotic properties of the type 1 interferon induced family of human mitochondrial membrane ISG12 proteins
Authors: Gytz Heidi , Hansen Mariann F. , Skovbjerg Signe , Kristensen Anders C. M. , Hørlyck Sofie , Jensen Mette B. , Fredborg Marlene , Markert Lotte D. , McMillan Nigel A. , Christensen Erik I. , Martensen Pia M.
Published: September 2016

Background information

Interferons are a family of cytokines with growth inhibitory and antiviral functions, which exert their biological actions through the expression of interferon‐stimulated genes (ISGs). The human ISG12 family of proteins comprises ISG12A, ISG12B, ISG12C and ISG6‐16. Due to differential splicing and a gene variation, the human ISG12A protein exists as a full‐length ISG12A form and three ISG12A variants. ISG12 genes have been found transcriptionally dysregulated in many disorders. High levels of ISG12A mRNA have been found in breast and ovarian cancers. Loss of heterozygosity at the position of the ISG12 genes often occurs in ovarian carcinomas and lymphoblastic leukemias. Both ISG12A and ISG6‐16 are up‐regulated in psoriasis.

Results

We demonstrate here that expression of the human full‐length ISG12A protein sensitises cells for TNFα and the BH3 mimetic gossypol induced apoptosis, and the other ISG12A variants as well as ISG12B and ISG12C can induce apoptosis directly in HEK293 cells. Also ISG6‐16 sensitises HEK293 cells for gossypol‐induced apoptosis. In the ISG12 motif, two putative Bcl‐2 homology (BH)3 like motifs were found, which may be decisive for the apoptotic properties of the ISG12 proteins. A series of BH3 mutants was made in ISG12AΔ‐S, the smallest apoptosis‐inducing ISG12A variant and our results indicate that ISG12AΔ‐S indeed possesses features resembling those of BH3‐only proteins. Supporting this notion are our findings that the full‐length ISG12A co‐immunoprecipitates with the Bcl‐2 protein, and the apoptotic properties of the ISG12A variants are reduced in Bcl‐2 expressing HEK293 cells. In addition, full‐length ISG12A is able to form homodimers, which suggests a possible involvement in pore formation during apoptosis. The full‐length ISG12A, the three ISG12A variants and the ISG12B proteins were found to be localised in the mitochondria.

Conclusions

Our results suggest that the ISG12 family of proteins has an important role for the apoptotic properties induced by type 1 interferon.

Significance

The ISG12 family constitute small hydrophic proteins involved in apoptosis. This is the first comparison of the apoptotic potentials of the full‐length ISG12A protein and the three ISG12A variants. The differential apoptotic potentials of these proteins might have an impact on the strategies to monitor and interpret their dysregulation associated with many disorders.
Socio‐economics, food habits and the prevalence of childhood obesity in Spain
Authors: Gil J. M. , Takourabt S.
Published: September 2016

Background

In 2012, the prevalence of obesity and overweight statuses among children in Spain was 9% and 26%, respectively. Concerns about childhood obesity have increased over the past few years, as obesity developed during childhood can persist throughout an individual's lifetime (cohort effect). This study aims to develop a better understanding of the factors influencing the prevalence of obesity in Spain.

Methods

Microdata from the 2012 National Health Survey are used, and the methodological framework is based on the estimation of a sample selection model.

Results

Results suggest that the prevalence of obesity increases among children who live in households of a lower socio‐economic status and households in which parents are obese. Lower levels of childhood physical activity are positively related to the probability of being obese. Finally, there exists a positive relationship between children's body mass index and an inappropriate intake of fresh fruits, fish, pasta and rice, legumes, sweets and soft drinks.

Conclusions

The methodological framework used in this study is flexible enough to be used in traditional longitudinal studies. Children's and households' lifestyles play a pivotal role in the prevalence of obesity. Policies should be oriented toward changing lifestyles, which would require more multidisciplinary research in the future to reduce childhood obesity.
Data‐Driven Shape Interpolation and Morphing Editing
Authors: Gao Lin , Chen Shu‐Yu , Lai Yu‐Kun , Xia Shihong
Published: September 2016

Shape interpolation has many applications in computer graphics such as morphing for computer animation. In this paper, we propose a novel data‐driven mesh interpolation method. We adapt patch‐based linear rotational invariant coordinates to effectively represent deformations of models in a shape collection, and utilize this information to guide the synthesis of interpolated shapes. Unlike previous data‐driven approaches, we use a rotation/translation invariant representation which defines the plausible deformations in a global continuous space. By effectively exploiting the knowledge in the shape space, our method produces realistic interpolation results at interactive rates, outperforming state‐of‐the‐art methods for challenging cases. We further propose a novel approach to interactive editing of shape morphing according to the shape distribution. The user can explore the morphing path and select example models intuitively and adjust the path with simple interactions to edit the morphing sequences. This provides a useful tool to allow users to generate desired morphing with little effort. We demonstrate the effectiveness of our approach using various examples.
Tracking Multiple Statistics: Simultaneous Learning of Object Names and Categories in English and Mandarin Speakers
Authors: Chen Chi‐hsin , Gershkoff‐Stowe Lisa , Wu Chih‐Yi , Cheung Hintat , Yu Chen
Published: September 2016

Two experiments were conducted to examine adult learners' ability to extract multiple statistics in simultaneously presented visual and auditory input. Experiment 1 used a cross‐situational learning paradigm to test whether English speakers were able to use co‐occurrences to learn word‐to‐object mappings and concurrently form object categories based on the commonalities across training stimuli. Experiment 2 replicated the first experiment and further examined whether speakers of Mandarin, a language in which final syllables of object names are more predictive of category membership than English, were able to learn words and form object categories when trained with the same type of structures. The results indicate that both groups of learners successfully extracted multiple levels of co‐occurrence and used them to learn words and object categories simultaneously. However, marked individual differences in performance were also found, suggesting possible interference and competition in processing the two concurrent streams of regularities.
Naturally occurring compounds acting as potent anti‐metastatic agents and their suppressing effects on Hedgehog and WNT/β‐catenin signalling pathways
Authors: Farahmand L. , Darvishi B. , Majidzadeh‐A K. , Madjid Ansari A.
Published: September 2016

Despite numerous remarkable achievements in the field of anti‐cancer therapy, tumour relapse and metastasis still remain major obstacles in improvement of overall cancer survival, which may be at least partially owing to epithelial‐mesenchymal transition (EMT). Multiple signalling pathways have been identified in EMT; however, it appears that the role of the Hedgehog and WNT/β‐catenin pathways are more prominent than others. These are well‐known preserved intracellular regulatory pathways of different cellular functions including proliferation, survival, adhesion and differentiation. Over the last few decades, several naturally occurring compounds have been identified to significantly obstruct several intermediates in Hedgehog and WNT/β‐catenin signalling, eventually resulting in suppression of signal transduction. This article highlights the current state of knowledge associated with Hedgehog and WNT/β‐catenin, their involvement in metastasis through EMT processes and introduction of the most potent naturally occurring agents with capability of suppressing them, eventually overcoming tumour relapse, invasion and metastasis.