bluuebunny/crossref_metadata_2025 huggingface dataset:
258 THE PRELIMINARY RESULTS OF IN VITRO PRODUCTION OF THE WISENT HYBRID EMBRYOS
Authors: Duszewska A. M. , Olech W. , Trzeciak P. , Krzysiak M. , Rapala L. , Nowak Z. , Dabrowski S.
Published: December 2014

Wisent (Bison bonasus), also called the European bison, is listed as vulnerable on the International Union for the Conservation of Nature Red List of Threatened Species. In Poland, a program for protection in situ and ex situ is being implemented. One new approach is the use of the in vitro embryo production (IVP) procedures to obtain wisent offspring. In contrast to previous successes with cattle IVP, use of IVP with wisent is limited by the small size of the population (only ~5000 individuals in more than 200 herds in Europe) and seasonal reproduction. The aim of this preliminary study was to obtain hybrid embryos (Bison bonasus × Bos taurus) in vitro. Ovaries were isolated from wisent females outside the reproductive season and eliminated from breeding for reasons other than infertility. Cumulus-oocytes complexes (COC) were isolated from all follicles above 2 mm in diameter. All COC were matured in TCM 199 supplemented with 10% fetal bovine serum, 0.02 IU mL–1 of porcine FSH, 17 β-oestradiol, 0.2 mM Na pyruvate, and antibiotics. The COC were cultured for 24 h at 38.5°C and 5% CO2 in humidified air. The matured COC (Bison bonasus) were fertilized in vitro with sperm from Jersey bulls (Bos taurus) in TALP supplemented with 6 mg mL–1 of fatty acid free BSA (BSA FAF), 0.2 mM Na pyruvate, 20 µM penicillamine,10 µM hypotaurine, 1 µM epinephrine, 2 µg mL–1 heparin, and antibiotics. Spermatozoa were used at a final concentration of 1 × 105 per oocyte and were co-cultured for 18 h at 38.5°C and 5% CO2 in humidified air. The hybrid zygotes were cultured in KSOM supplemented with 5 µg mL–1 of MEM Nonessential Amino Acid Solution (100×), 3 mg mL–1 of BSA FAF, and antibiotic for 192 h at 38.5°C and 5% CO2 in humidified air. The medium was partly replaced by fresh medium after 48 and 144 h of culture. Development was evaluated every day. From 25 COC isolated from wisent ovaries, only 18 COC were qualified for in vitro maturation (60%). Of these, 15 COC (83.3%) matured. The percentage of hybrid embryos that cleaved was 80% after 48 h of culture, and the percentage of embryos that developed up to the 8-cell stage was 33% after 96 h of culture. The morula/blastocyst rate was 26.6% after 192 h of culture, as represented by 1 early blastocyst, 2 compact morulae, and 1 morula. The use of the cattle IVP procedure allowed to receive hybrid embryos (Bison bonasus × Bos taurus), but they developed slower than cattle embryos under the same conditions, based on our previous studies. This research will be continued and may make a contribution to the protection of this threatened species.
276 PHOSPHOINOSITIDE 3-KINASE REGULATES EXPRESSION OF KEY ENZYMES AND CELLULAR TRANSPORTERS OF GLUCOSE METABOLISM IN CUMULUS CELLS OF BOVINE COCs CULTURED IN VITRO
Authors: Kaiser de Souza D. , Salles L. P. , Camargo R. , Dolabela de Lima B. , Torres F. A. G. , Rosa e Silva A. A. M.
Published: December 2014

The aim was to analyse the function of the PI3K pathway during oocyte maturation in bovine by use of the specific inhibitor, LY294002. Genes studied in cumulus cells (CC) were PDH, G6PDH, GLUT1, and GLUT4. PDH is an important enzyme for oxidative metabolism, G6PDH is related to resumption and progression of oocyte meiosis, and GLUT1 and GLUT4 are glucose transporters. This study was performed in defined medium (MIV B) in absence or presence of 10 ng mL–1 of FSH. Polar body extrusion was analysed after culture and correlated with gene expression. Experimental methods were bovine COC (n = 35–40/well, n = 3 replicates) collected from ovaries obtained from abattoirs (DF, Brazil) and cultivated in either 400 µL of medium MIV B, or MIV B + 100 µM of LY294002, or MIV B + 10 ng mL–1 of FSH; or MIV B + 10 ng mL–1 of FSH + 100 µM of LY294002 during 22 to 24 h. After culture, COC were mechanically denuded and CC from 20 COC/group were isolated. Gene expression of GLUT1, GLUT4, G6PDH, and PDH were measured by real time PCR. The CC of immature COC were also collected and analysed as the calibrator group. Student-Newman-Keuls was performed as a statistical test. The percentage of oocytes that extruded the polar body was determined. Two-way ANOVA, followed by Bonferroni test, and t-test were performed to determine statistical significance. In MIV B, the polar body extrusion rate was 25.48 ± 7.64%, while FSH increased it up to 74.52 ± 10.58% (P < 0.05). The extrusion of polar body was inhibited by LY294002 in the absence or presence of FSH (67.51 ± 6.13 and 31.02 ± 16.97%, respectively, P < 0.05). Gene expression of PDH was not altered by any culture medium in contrast to GLUT1, GLUT4, and G6PDH expression (Table 1). Only G6PDH expression showed the same pattern as the polar body extrusion, in absence or presence of FSH. In conclusion, PI3-K inhibition affects polar body extrusion and expression of genes related to glucose metabolism in CC. Lower G6PDH expression in CC may be related to low rates of polar body extrusion in treated oocytes.

Table 1.Gene expression of GLUT1, GLUT4, and G6PDH in CC of COC after culture

The authors thank FAP-DF (193.000.577/2009), CNPq, CAPES and Ponte Alta abattoir, Brasilia.
308 VERBASCOSIDE TREATMENT DURING IN VITRO MATURATION IMPROVES THE EMBRYO DEVELOPMENT OF PREPUBERTAL OVINE OOCYTES
Authors: Dell'Aquila M. E. , Ariu F. , Martino N. A. , Minervini F. , Cardinali A. , Bogliolo L.
Published: December 2014

Verbascoside (VB), a bioactive polyphenol from olive mill wastewater with known antioxidant activity, was shown to act as a pro-oxidant molecule, by impairing energy/redox status and embryo developmental competence of prepubertal ovine oocytes when added at micromolar concentrations in a continuative 24-h in vitro maturation (IVM) exposure protocol (1). The aim of the present study was to determine whether a lower (nanomolar) VB concentration and a shorter exposure time (2 v. 24 h) during IVM may improve the maturation rates of prepubertal ovine oocytes and their subsequent embryonic development in vitro. Cumulus-oocyte complexes derived from the ovaries of slaughtered 1-mo-old prepubertal sheep oocytes underwent IVM in TCM 199 with 10% oestrus sheep serum, 0.1 IU mL–1 of FSH/LH, and 100 µM cysteamine, in 5% CO2 in air at 38.5°C for 24 h. Based on our previous results (Dell'Aquila et al. 2014 Biomed. Res. Int. 2014, 878062), VB was added in the IVM medium at 1.03 nM, and 2 incubation times (24 and 2 h) were tested. In the 2-h exposure group, after 2 h of exposure to VB, oocytes were washed and cultured up to 24 h without VB. A group of oocytes were cultured in absence of VB, as controls. Matured oocytes were fertilized with frozen-thawed ram semen in SOF medium for 22 h and zygotes were cultured in vitro for 8 days. Metaphase II (MII) cleavage and blastocyst rates were analysed by Chi-squared test. Embryo quality was evaluated by staining and total cell count of the blastocyst and analysis of variance (ANOVA) was applied. Differences were considered to be significant when P < 0.05. Compared to controls, VB treatment at the concentration of 1.03 nM and 24 h of exposure had no effect on MII rates (196/268, 73% v. 226/323, 70% MII/cultured oocytes; P > 0.05). However, this treatment allowed to obtain significantly higher rates of cleaved embryos/MII oocytes (156/196, 80% v. 165/226, 73%; respectively; P < 0.05), blastocyst yield/cleaved embryos (59/156, 38% v. 45/165, 27%, respectively; P < 0.05), and total blastocyst cell numbers (108.62 ± 19.87 v. 89.61 ± 26.32, respectively; P < 0.05) compared to control oocytes. The VB treatment at the same concentration but for 2 h induced only significantly higher cleavage rate (196/210, 93% v. 165/226, 73%; P < 0.05). In conclusion, our results showed that VB treatment at 1.03 nM during 24 h of IVM exerted a positive effect on in vitro embryo development of prepubertal ovine oocytes by increasing the blastocyst yield and their quality. The hypothesis that VB at nanomolar concentrations may improve cumulus-oocyte energy/redox status is under investigation.The authors acknowledge support by the Regione Autonoma della Sardegna (LR 7, Agosto 2007, no. 7, CRP-17602). The authors thank Dr D. Bebbere and L. Falchi, Dept. Veterinary Medicine, Sassari, for statistical analysis.
91 SILDENAFIL CITRATE MODIFIES FETOPLACENTAL DEVELOPMENT IN A RABBIT MODEL OF INTRAUTERINE GROWTH RESTRICTION
Authors: López-Tello J. , Arias-Alvarez M. , González-Bulnes A. , Astiz S. , García-García R. M. , Rodríguez M. , Lorenzo P. L. , Rebollar P.
Published: December 2014

The failure of fetuses to achieve their full growth potential is known as intrauterine growth restriction (IUGR). Sildenafil citrate (SC) is a phosphodiesterase 5 (PDE-5) inhibitor, which enhances nitric oxide (NO)-dependent vasodilatation, and it may have a potential therapeutic role in the treatment of IUGR. The aim of this study was to evaluate the effect of SC on placental and fetal development in a diet-induced rabbit model of IUGR. A total of 24 rabbits does weighing 4.3 ± 0.49 kg on average were used. At Day 9 of pregnancy, females were randomly allocated into 3 experimental groups: one group was fed ad libitum during pregnancy (Group C; n = 8); the rest of the does had 50% restricted daily intake and were treated or not with 20 mg of SC daily from Day 22 of pregnancy until parturition (Groups SC and R, respectively, n = 8 for both). At Day 28 of pregnancy, half of the pregnant does from each group were euthanised to study fetoplacental development, while the remaining does were allowed to deliver. At Day 28, weight, length, and thickness of fetal and maternal placentas, and fetal weight and size [crown-rump length (CRL), and transversal thoracic diameter (TD)] were assessed. A fetus was considered IUGR when it weighted less than the 10th percentile for its normal gestational weight. Statistical analysis was performed using the PROC GLM procedure. Nutritional restriction induced a higher rate of fetuses IUGR than control group (31.0% v. 15.1%; P < 0.05). The percentage of fetuses with IUGR was 23% in SC group (no significant differences with groups C and R). However, SC increased the thickness of maternal and fetal placentas compared to group R (0.4 ± 0.02 v. 0.2 ± 0.02 cm; 0.6 ± 0.02 v. 0.3 ± 0.02 cm; P < 0.05 respectively), being similar to group C (0.4 ± 0.02 and 0.5 ± 0.03 cm). Maternal placental weight in group C showed higher values (1.5 ± 0.08 g; P < 0.05) than both restricted groups (1.2 ± 0.07 g). CRL in group SC was larger than in group R (10.5 ± 0.12 v. 10.0 ± 0.12 cm; P < 0.05) and similar to that in group C (10.5 ± 0.15 cm). The neonates in group SC showed higher values for CRL (10.9 ± 0.15 cm) than those from groups R and C (10.5 ± 0.11, 10.2 ± 0.20 cm; P = 0.05). Regarding TD, fetuses in group SC showed higher values than group R (2.3 ± 0.04 v. 2.1 ± 0.03 cm; P < 0.05) and equaled that of group C (2.3 ± 0.03 cm). In conclusion, maternal malnutrition prejudices fetoplacental development, causing IUGR. Treatment with SC in the last third of gestation counteracts fetal growth retardation by favouring placental development and function and, thus, fetal growth. These results confirm that administration of SC may have a potential benefit in pregnancies complicated by placental insufficiency and IUGR.We acknowledge CM, FSE, and AGL2011-23822 for funding.
Anaerobic methane oxidation coupled to denitrification is the dominant methane sink in a deep lake
Authors: Deutzmann Joerg S. , Stief Peter , Brandes Josephin , Schink Bernhard
Published: December 2014

Significance

Evidence whether the recently discovered denitrification-dependent methane oxidation (nitrate/nitrite-dependent anaerobic methane oxidation, n-damo) represents a major methane sink or an insignificant side aspect in the global methane cycle is scarce. High-resolution microprofiles measured in intact sediment cores close to in situ conditions, anoxic incubations of intact sediments, and quantification of the responsible microorganisms with molecular techniques proved n-damo to be the major methane sink in Lake Constance, one of the best-studied freshwater lakes. The n-damo process has long been overlooked because of the close proximity of aerobic and anaerobic activities. Our study documents that a large part of methane previously thought to be oxidized aerobically is in fact oxidized anaerobically by physiologically entirely different organisms.
Ill-posedness for the nonlinear Schrödinger equation with quadratic non-linearity in low dimensions
Authors: Iwabuchi Tsukasa , Ogawa Takayoshi
Published: December 2014

We consider the ill-posedness issue for the nonlinear Schrödinger equation with a quadratic nonlinearity. We refine the Bejenaru-Tao result by constructing an example in the following sense. There exist a sequence of time

T
N

→
0

T_N\to 0

and solution

u
N

(
t
)

u_N(t)

such that

u
N

(

T
N

)
→
∞

u_N(T_N)\to \infty

in the Besov space

B

2
,
σ

−
1

(

R

)

B_{2,\sigma }^{-1}(\mathbb {R})

(

σ
>
2

\sigma >2

) for one space dimension. We also construct a similar ill-posed sequence of solutions in two space dimensions in the scaling critical Sobolev space

H

−
1

(

R

2

)

H^{-1}(\mathbb {R}^2)

. We systematically utilize the modulation space

M

2
,
1

0

M_{2,1}^0

for one dimension and the scaled modulation space

(

M

2
,
1

0

)
N

(M_{2,1}^0)_N

for two dimensions.
Single-cell variation leads to population invariance in NF-κB signaling dynamics
Authors: Hughey Jacob J. , Gutschow Miriam V. , Bajar Bryce T. , Covert Markus W.
Published: December 2014

The activation dynamics of nuclear factor (NF)-κB have been shown to affect downstream gene expression. On activation, NF-κB shuttles back and forth across the nuclear envelope. Many dynamic features of this shuttling have been characterized, and most features vary significantly with respect to ligand type and concentration. Here, we report an invariant feature with regard to NF-κB dynamics in cellular populations: the distribution—the average, as well as the variance—of the time between two nuclear entries (the period). We find that this period is conserved, regardless of concentration and across several different ligands. Intriguingly, the distributions observed at the population level are not observed in individual cells over 20-h time courses. Instead, the average period of NF-κB nuclear translocation varies considerably among single cells, and the variance is much smaller within a cell than that of the population. Finally, analysis of daughter-cell pairs and isogenic populations indicates that the dynamics of the NF-κB response is heritable but diverges over multiple divisions, on the time scale of weeks to months. These observations are contrary to the existing theory of NF-κB dynamics and suggest an additional level of control that regulates the overall distribution of translocation timing at the population level.
LigDig: a web server for querying ligand–protein interactions
Authors: Fuller Jonathan C. , Martinez Michael , Henrich Stefan , Stank Antonia , Richter Stefan , Wade Rebecca C.
Published: November 2014

Summary: LigDig is a web server designed to answer questions that previously required several independent queries to diverse data sources. It also performs basic manipulations and analyses of the structures of protein–ligand complexes. The LigDig webserver is modular in design and consists of seven tools, which can be used separately, or via linking the output from one tool to the next, in order to answer more complex questions. Currently, the tools allow a user to: (i) perform a free-text compound search, (ii) search for suitable ligands, particularly inhibitors, of a protein and query their interaction network, (iii) search for the likely function of a ligand, (iv) perform a batch search for compound identifiers, (v) find structures of protein–ligand complexes, (vi) compare three-dimensional structures of ligand binding sites and (vii) prepare coordinate files of protein–ligand complexes for further calculations.

Availability and implementation: LigDig makes use of freely available databases, including ChEMBL, PubChem and SABIO-RK, and software programs, including cytoscape.js, PDB2PQR, ProBiS and Fconv. LigDig can be used by non-experts in bio- and chemoinformatics. LigDig is available at: http://mcm.h-its.org/ligdig.

Contact:  jonathan.fuller@h-its.org, rebecca.wade@h-its.org

Supplementary information:  Supplementary data are available at Bioinformatics online.
Computer-assisted curation of a human regulatory core network from the biological literature
Authors: Thomas Philippe , Durek Pawel , Solt Illés , Klinger Bertram , Witzel Franziska , Schulthess Pascal , Mayer Yvonne , Tikk Domonkos , Blüthgen Nils , Leser Ulf
Published: November 2014

Motivation: A highly interlinked network of transcription factors (TFs) orchestrates the context-dependent expression of human genes. ChIP-chip experiments that interrogate the binding of particular TFs to genomic regions are used to reconstruct gene regulatory networks at genome-scale, but are plagued by high false-positive rates. Meanwhile, a large body of knowledge on high-quality regulatory interactions remains largely unexplored, as it is available only in natural language descriptions scattered over millions of scientific publications. Such data are hard to extract and regulatory data currently contain together only 503 regulatory relations between human TFs.

Results: We developed a text-mining-assisted workflow to systematically extract knowledge about regulatory interactions between human TFs from the biological literature. We applied this workflow to the entire Medline, which helped us to identify more than 45 000 sentences potentially describing such relationships. We ranked these sentences by a machine-learning approach. The top-2500 sentences contained ∼900 sentences that encompass relations already known in databases. By manually curating the remaining 1625 top-ranking sentences, we obtained more than 300 validated regulatory relationships that were not present in a regulatory database before. Full-text curation allowed us to obtain detailed information on the strength of experimental evidences supporting a relationship.

Conclusions: We were able to increase curated information about the human core transcriptional network by >60% compared with the current content of regulatory databases. We observed improved performance when using the network for disease gene prioritization compared with the state-of-the-art.

Availability and implementation: Web-service is freely accessible at http://fastforward.sys-bio.net/.

Contact: leser@informatik.hu-berlin.de or nils.bluethgen@charite.de

Supplementary information: Supplementary data are available at Bioinformatics online.
Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms
Authors: Ahmed Zeeshan , Mayr Michel , Zeeshan Saman , Dandekar Thomas , Mueller Martin J. , Fekete Agnes
Published: November 2014

Summary: A major challenge for mass spectrometric-based lipidomics, aiming at describing all lipid species in a biological sample, lies in the computational and bioinformatic processing of the large amount of data that arises after data acquisition. Lipid-Pro is a software tool that supports the identification of lipids by interpreting large datasets generated by liquid chromatography—tandem mass spectrometry (LC–MS/MS) using the advanced data-independent acquisition mode MSE. In the MSE mode, the instrument fragments all molecular ions generated from a sample and records time-resolved molecular ion data as well as fragment ion data for every detectable molecular ion. Lipid-Pro matches the retention time-aligned mass-to-charge ratio data of molecular- and fragment ions with a lipid database and generates a report on all identified lipid species. For generation of the lipid database, Lipid-Pro provides a module for construction of lipid species and their fragments using a flexible building block approach. Hence, Lipid-Pro is an easy to use analysis tool to interpret complex MSE lipidomics data and also offers a module to generate a user-specific lipid database.

Availability and implementation:  Lipid-Pro is freely available at: http://www.neurogenetics.biozentrum.uni-wuerzburg.de/en/project/services/lipidpro/

Contact:  zeeshan.ahmed@uni-wuerzburg.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
Exploiting hidden information interleaved in the redundancy of the genetic code without prior knowledge
Authors: Zur Hadas , Tuller Tamir
Published: November 2014

Motivation: Dozens of studies in recent years have demonstrated that codon usage encodes various aspects related to all stages of gene expression regulation. When relevant high-quality large-scale gene expression data are available, it is possible to statistically infer and model these signals, enabling analysing and engineering gene expression. However, when these data are not available, it is impossible to infer and validate such models.

Results: In this current study, we suggest Chimera—an unsupervised computationally efficient approach for exploiting hidden high-dimensional information related to the way gene expression is encoded in the open reading frame (ORF), based solely on the genome of the analysed organism. One version of the approach, named Chimera Average Repetitive Substring (ChimeraARS), estimates the adaptability of an ORF to the intracellular gene expression machinery of a genome (host), by computing its tendency to include long substrings that appear in its coding sequences; the second version, named ChimeraMap, engineers the codons of a protein such that it will include long substrings of codons that appear in the host coding sequences, improving its adaptation to a new host’s gene expression machinery. We demonstrate the applicability of the new approach for analysing and engineering heterologous genes and for analysing endogenous genes. Specifically, focusing on Escherichia coli, we show that it can exploit information that cannot be detected by conventional approaches (e.g. the CAI—Codon Adaptation Index), which only consider single codon distributions; for example, we report correlations of up to 0.67 for the ChimeraARS measure with heterologous gene expression, when the CAI yielded no correlation.

Availability and implementation: For non-commercial purposes, the code of the Chimera approach can be downloaded from http://www.cs.tau.ac.il/∼tamirtul/Chimera/download.htm.

Contact:  tamirtul@post.tau.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Radiation fields of intermediate-age stellar populations with binaries as ionizing sources of H ii regions
Authors: Zhang F. , Li L. , Cheng L. , Wang L. , Kang X. , Zhuang Y. , Han Z.
Published: November 2014

Radiation fields emitted by O- and B-type stars or young stellar populations (SPs) are generally considered as significant central ionizing sources (CISs) of classic H ii regions. In our previous studies, we showed that the inclusion of binary interactions in stellar population synthesis models can significantly increase the ultraviolet spectrum hardness and the number of ionizing photons of intermediate-age (IA) SPs (7 ≲ log(t/yr) ≲ 8). In this work, we present photoionization models of H ii regions ionized by radiation fields emitted by IA SPs, including binary systems, and show that these fields are in theory possible candidates for significant CISs of classic H ii regions. When radiation fields of IA SPs comprising binary systems are used as the CISs of classic H ii regions, the theoretical strengths of a number of lines (such as [O iii] λ4959′, [S ii] λ6716′, etc.), which are weaker than observations, are increased; the border or selection-criterion lines between star-forming galaxies and active galactic nuclei (AGNs) in the diagnostic diagrams (for example, [N ii] λ6583/Hα versus [O iii] λ5007/Hβ), move into the region occupied originally by AGNs; and the He ii λ1640 line, observed in Lyman break and high-redshift gravitationally lensed galaxies, also can be produced.
Rotation measure synthesis revisited
Authors: Schnitzeler D. H. F. M. , Lee K. J.
Published: November 2014

We reformulate rotation measure (RM) synthesis for data sets with discrete frequency channels and an arbitrary channel response function. The most commonly used version of the formalism by Brentjens & De Bruyn assumes a top-hat response function in wavelength squared, while real data sets can often be approximated better with a top-hat in frequency. We simulate mock data sets for various source geometries, using a top-hat response function in frequency, and we compare the quality of the RM spectra that are found with both formalisms. We include the response function of the simulated data to calculate exact RM spectra using our formalism. We show that the formalism by Brentjens & De Bruyn produces accurate results even if depolarization at the lowest frequencies in the observing band is severe. If RMs are large, our formalism reconstructs the emitted signal more accurately, with a higher amplitude and (in most cases) a narrower RM spread function. Our formalism can also detect sources with larger (absolute) RMs for a given sensitivity level of the observations.
Responsibility and the sense of agency enhance empathy for pain
Authors: Lepron Evelyne , Causse Michaël , Farrer Chlöé
Published: December 2014

Being held responsible for our actions strongly determines our moral judgements and decisions. This study examined whether responsibility also influences our affective reaction to others' emotions. We conducted two experiments in order to assess the effect of responsibility and of a sense of agency (the conscious feeling of controlling an action) on the empathic response to pain. In both experiments, participants were presented with video clips showing an actor's facial expression of pain of varying intensity. The empathic response was assessed with behavioural (pain intensity estimation from facial expressions and unpleasantness for the observer ratings) and electrophysiological measures (facial electromyography). Experiment 1 showed enhanced empathic response (increased unpleasantness for the observer and facial electromyography responses) as participants' degree of responsibility for the actor's pain increased. This effect was mainly accounted for by the decisional component of responsibility (compared with the execution component). In addition, experiment 2 found that participants' unpleasantness rating also increased when they had a sense of agency over the pain, while controlling for decision and execution processes. The findings suggest that increased empathy induced by responsibility and a sense of agency may play a role in regulating our moral conduct.
Division of Labor: A Democratic Approach to Understanding Manual Asymmetries in Non-Human Primates
Authors: Mangalam Madhur , Desai Nisarg , Singh Mewa
Published: November 2014

A consequence of the ‘gold rush’ like hunch for human-like handedness in non-human primates has been that researchers have been continually analyzing observations at the level of the population, ignoring the analysis at the level of an individual and, consequently, have potentially missed revelations on the forms and functions of manual asymmetries. Recently, consecutive studies on manual asymmetries in bonnet macaques, Macaca radiata [Mangalam et al., 2014a; Mangalam et al., 2014b] revealed both the functional and the adaptive significance of manual asymmetries respectively, and pointed towards the division of labor as being the general principle underlying the observed hand-usage patterns. We review the studies on manual asymmetries in capuchin monkeys, Cebus spp. and argue that the observed hand-usage patterns might reflect specialization of the two hands for accomplishing tasks that require different dexterity types (i.e., maneuvering in three dimensional space or physical strength). To this end, we do a step-by-step analysis of the various tasks used in the studies on manual asymmetries in capuchin monkeys, wherein we: (a) analyze the different manual tasks that have been used to study manual asymmetries in non-human primates on the basis of the attributes such as the number of hands required to solve a given task (i.e., unimanual, pseudo unimanual, or bimanual) and the spatiotemporal progression of manual actions (i.e., sequential or concurrent). (b) Determine the forms and functions of manual asymmetries that these tasks can potentially elicit within the broader scope of the behavioral repertoire of an individual, a population, or a species. (c) Qualify the scope of the inter-individual, -population, or -species comparisons. We then describe the division of labor as a general principle underlying manual asymmetries in non-human primates, and propose experimental designs that would elaborate the forms and functions of manual asymmetries in non-human primates, and the associated adaptive value.
Division of Labor in Hand Usage Is Associated with Higher Hand Performance in Free-Ranging Bonnet Macaques,Macaca radiata
Authors: Mangalam Madhur , Desai Nisarg , Singh Mewa
Published: November 2014

A practical approach to understanding lateral asymmetries in body, brain, and cognition would be to examine the performance advantages/disadvantages associated with the corresponding functions and behavior. In the present study, we examined whether the division of labor in hand usage, marked by the preferential usage of the two hands across manual operations requiring maneuvering in three-dimensional space (e.g., reaching for food, grooming, and hitting an opponent) and those requiring physical strength (e.g., climbing), as described by Mangalam et al. [1], is associated with higher hand performance in free-ranging bonnet macaques, Macaca radiata. We determined the extent to which (a) the macaques exhibit laterality in hand usage in an experimental unimanual and a bimanual food-reaching task, and (b) manual laterality is associated with hand performance in an experimental hand-performance-differentiation task. We found strong negative relationships between (a) the performance of the preferred hand in the hand-performance-differentiation task (measured as the latency in food extraction; lower latency = higher performance), the preferred hand determined using the bimanual food-reaching task, and the normalized difference in the performance between the two hands (measured as the difference in the latency in food extraction between them normalized by the latency in food extraction using the preferred hand), and (b) the normalized difference in the performance between the two hands and the manual specialization (measured as the absolute difference in the laterality in hand usage between the unimanual and the bimanual food-reaching tasks; lesser difference = higher manual specialization). These observations demonstrate that the division of labor between the two hands is associated with higher hand performance.
An Integrated Modelling Framework for the Forest-based Bioeconomy
Authors: Mubareka Sarah , Jonsson Ragnar , Rinaldi Francesca , Fiorese Giulia , San-Miguel-Ayanz Jesús , Sallnäs Ola , Baranzelli Claudia , Pilli Roberto , Lavalle Carlo , Kitous Alban
Published: November 2014

This paper describes the conceptual design of a regional modelling framework to assess scenarios for the forest-based bioeconomy. The framework consists of a core set of tools: a partial equilibrium model for the forest sector, a forestry dynamics model for forest growth and harvest and a wood resources balance sheet. The framework can be expanded to include an energy model, a land use model and a forest owner decision model. This partially integrated, multi-disciplinary modelling framework is described, with particular emphasis on the structure of the variables to be exchanged between the framework tools. The data exchange is subject to a series of integrity checks to ensure that the model is computing the correct information in the correct format and order of elements.
NODE DETECTION USING HIGH-DIMENSIONAL FUZZY PARCELLATION APPLIED TO THE INSULAR CORTEX
Authors: Vercelli Ugo , Diano Matteo , Costa Tommaso , Duca Sergio , Geminiani Giuliano , Vercelli Alessandro , Cauda Franco
Published: November 2014

Several functional connectivity approaches require the definition of a set of ROIs that act as network nodes. Different methods have been developed to define these nodes and to derive their functional and effective connections, most of which are rather complex. Here we aim to propose a relatively simple “one-step” border detection and ROI estimation procedure employing the fuzzy c-mean clustering algorithm. To test this procedure and to explore insular connectivity beyond the two/three-region model currently proposed in the literature, we parcellated the insular cortex of a group of twenty healthy right-handed volunteers (10 females) scanned in a resting state condition. Employing a high-dimensional functional connectivity-based clustering process, we confirmed the two patterns of connectivity previously described. This method revealed a complex pattern of functional connectivity where the two previously detected insular clusters are subdivided into several other networks, some of which not commonly associated with the insular cortex, such as the default mode network and parts of the dorsal attentional network. Finally, the detection of nodes was reliable
Comparative performances of the new chronic kidney disease epidemiology equations incorporating cystatin C for use in cancer patients
Authors: Chew‐Harris Janice SC , Florkowski Christopher M , George Peter M , Endre Zoltan H
Published: December 2014

Aim

In cancer patients receiving chemotherapy treatment, accurate assessment of kidney function is required. The aim of our study was to investigate whether the inclusion of cystatin C together with creatinine in prediction equations would improve the prediction of glomerular filtration rate (GFR).

Methods

Plasma creatinine and cystatin C were analyzed in 155 patients (cancer, n = 80, kidney donors, n = 75) undergoing 99mTechnetium diethylenepentaacetic (Tc‐DTPA) GFR clearance. Equations by the CKD‐EPI (chronic kidney disease epidemiology) group (creatinine‐, creatinine + cystatin C‐, cystatin C‐based, respectively) and Cockcroft–Gault were compared with Tc‐DTPA GFR by difference plots, receiver operator characteristics curve analysis, root mean square error, chi‐squared analysis and percentage concordance according to carboplatin dosage. Comparisons between two creatinine methodologies (enzymatic vs Jaffe) were also performed.

Results

In the overall group, the combination creatinine and cystatin C equation had 69% of results within 20% of GFR (P20), a sensitivity of 86.3% and a specificity of 73.1% to detect reduced GFR at <90 mL/min/1.73 m2, and a concordance of 78%. In contrast, the traditional Cockcroft–Gault equation had a P20 of 38.0%, with a large underestimation to predict GFR, thereby accounting for approximately 45% of dosing discordance. No obvious differences were obtained when comparing the performance of equations using the two creatinine methodologies.

Conclusion

The inclusion of cystatin C in the CKD‐EPI equations improved the prediction of kidney function in the overall population, although probably not sufficiently for it to be favored over radioisotopic GFR for guiding chemotherapy. More research is warranted to further improve estimated GFR equations for these purposes.
Identification and examination of a novel 9‐bp insert/deletion polymorphism on porcine SFTPA1 exon 2 associated with acute lung injury using an oleic acid‐acute lung injury model
Authors: Zhang Yuebo , Zhang Longchao , Wang Ligang , Qiao Lijuan , Liang Jing , Yan Hua , Zhao Kebin , Liu Xin , Wang Lixian
Published: November 2014

The pulmonary surfactant‐associated protein (SFTPA1, SP‐A) gene has been studied as a candidate gene for lung disease resistance in humans and livestock. The objective of the present study was to identify polymorphisms of the porcine SFTPA1 gene coding region and its association with acute lung injury (ALI). Through DNA sequencing and the PCR‐single‐strand conformation polymorphism method, a novel 9‐bp nucleotide insertion (+) or deletion (‐) was detected on exon 2 of SFTPA1, which causes a change in three amino acids, namely, alanine (Ala), glycine (Gly) and proline (Pro). Individuals of three genotypes (−/−, +/− and +/+) were divided into equal groups from 60 Rongchang pigs that were genotyped. These pigs were selected for participation in the oleic acid (OA)‐ALI model by 1‐h and 3‐h injections of OA, and there were equal numbers of pigs in the control and injection groups. The lung water content, a marker for acute lung injury, was measured in this study; there is a significant correlation between high lung water content and the presence of the 9‐bp indel polymorphism (P < 0.01). The lung water content of the OA injection group was markedly higher than that of the control group and lung water content for the +/+ genotype was significantly higher than that of the others in the 1‐h group (P < 0.01). No differences in the expression of the SFTPA1 gene were found among individuals with different SFTPA1 genotypes, indicating that the trait is not caused by a linked polymorphism causing altered expression of the gene. The individuals with the −/− genotype showed lower lung water content than the +/+ genotype pigs, which suggests that polymorphism could be a potential marker for lung disease‐resistant pig breeding and that pig can be a potential animal model for human lung disease resistance in future studies.
Burnout prevalence and correlates amongst Colombian dental students: the STRESSCODE study
Authors: Mafla A. C. , Villa‐Torres L. , Polychronopoulou A. , Polanco H. , Moreno‐Juvinao V. , Parra‐Galvis D. , Durán C. , Villalobos M. J. , Divaris K.
Published: December 2014

Introduction

Accumulating evidence amongst dental students indicates an alarming prevalence of stress, which can precipitate the development of burnout – a state of mental or physical exhaustion and disengagement. Understanding individual and educational correlates of burnout is necessary for its prevention. The aims of this study were to determine the prevalence of burnout amongst a large sample of Colombian dental undergraduates and investigate its psychosocial and educational correlates.

Materials and methods

Survey data collected from 5647 students participating in the Stress in Colombian Dental Education study were used for this analysis. Burnout was measured using the Maslach Burnout Inventory–Student Survey (MBI‐SS). Covariates included participants’ socio‐demographic characteristics and perceived stress, as well as educational environment factors. Descriptive, bivariate and multivariate methods based on multilevel mixed‐effects logistic regression modelling were used for data analysis.

Results

Seven per cent of the students surveyed met the criteria for burnout. The prevalence of burnout was higher amongst upper classes, older and married students, those who reported not having passed all required courses and not having dentistry as their first career choice, as well as students in public institutions and those with large class sizes. Moreover, students’ perceived stress in the domains of workload and self‐efficacy was significantly and positively associated with burnout.

Conclusions

Both personal and educational environment characteristics were found to be associated with burnout. Irrespective of these factors, students’ perceived stress with regard to workload and self‐efficacy was a strong influence on burnout and its alleviation may be a promising avenue to prevent psychological morbidity.
New Financial Alternatives in Seeding Entrepreneurship: Microfinance, Crowdfunding, and Peer–to–Peer Innovations
Authors: Bruton Garry , Khavul Susanna , Siegel Donald , Wright Mike
Published: December 2014

New financing alternatives, such as microfinance, crowdfunding, and peer–to–peer lending, have expanded rapidly. To date, few studies have investigated the antecedents and consequences of these financing mechanisms. This special issue provides an academic foundation for understanding new financial options that entrepreneurs can now use to start and grow ventures. In the introductory article, we integrate strands of the literature on emerging innovations in entrepreneurial finance and provide a framework for a systematic approach to new research questions. We conclude with a discussion of the six papers in the special issue and demonstrate how they contribute to the framework.
Combination of CD160 and CD200 as a useful tool for differential diagnosis between chronic lymphocytic leukemia and other mature B‐cell neoplasms
Authors: Lesesve J.‐F. , Tardy S. , Frotscher B. , Latger‐Cannard V. , Feugier P. , De Carvalho Bittencourt M.
Published: December 2014

Introduction

Chronic lymphocytic leukemia is usually diagnosed through the characteristic morphology/immunophenotype of the lymphocytes, but some CLL cases remain atypical resulting in diagnostic uncertainty.

Methods

Using flow cytometry analysis, we investigated the expression of CDs160/200 on B cells from 124 patients (82 CLL, 42 other B‐cell neoplasms) and nine controls. CDs160/200 measurements were determined as a ratio of the mean fluorescence intensities of leukemic cells/controls and were considered positive when the ratios were ≥2 and 20, respectively.

Results

Sixty and 83% CLL expressed CDs160/200 as compared to 5% and 10% of other B‐cell neoplasms, respectively. None of the controls showed CDs160/200 expressions. Combination of both markers was observed in 55% of CLL but only in 2% of other B‐cell neoplasms, and absence of both markers occurred in 12% of CLL but in 86% of other B‐cell neoplasms.

Conclusion

CDs160/200 were associated with markers of the gold standard ‘Matutes score’ and could be useful markers to differentiate atypical CLL from other B‐cell neoplasms in the absence of available biopsies or cytogenetics and molecular studies.
Development of a clinical score system for the diagnosis of photoallergic contact dermatitis using a consensus process: item selection and reliability
Authors: Cazzaniga S. , Lecchi S. , Bruze M. , Chosidow O. , Diepgen T. , Gonçalo M. , Hercogova J. , Pigatto P.D. , Naldi L.
Published: December 2014

Background

Photoallergic contact dermatitis (PACD) is an uncommon condition, and there is a lack of validated criteria for its diagnosis.

Objective

To identify a set of relevant criteria to be considered when suspecting a diagnosis of PACD and to assess the reproducibility of these criteria.

Methods

This was a diagnostic item selection and reliability study performed between July 2012 and October 2012. A panel of seven recognized experts was invited to consecutive rounds of a Delphi survey and to a conclusive face‐to‐face meeting with the aim of obtaining an agreement on criteria for the diagnosis of PACD. The panel was also provided with a series of 16 reports of suspected PACDs to be classified according to a five‐point likelihood scale. Identified criteria with the weights attributed by experts were used to develop a score system for the diagnosis of PACD. Consensus was measured by calculating the Intraclass Correlation Coefficient (ICC). The performance of the score system was evaluated in terms of overall classification accuracy.

Results

Seven criteria were identified by experts as relevant for the diagnosis of PACD. The criteria were related to the type of skin lesions, accompanying symptoms, skin area involved, general medical history, modality of exposure to the culprit substance, history of exposure to the sun or other light sources and photopatch test results. Experts reached a moderate agreement on PACD cases classification, with ICC = 0.69 (95% Confidence Interval, CI, 0.50–0.86). The score system enabled discrimination of probable and definite PACD cases from possible and unlikely or excluded ones, with a nearly perfect agreement being observed between the score system classification and judgment by experts.

Conclusion

A diagnostic score was proposed. The score should receive a comprehensive validation on a larger series of cases and with multiple evaluators.
Parents' experiences of healthcare provider actions when their child dies: An integrative review of the literature
Authors: Butler Ashleigh , Hall Helen , Willetts Georgina , Copnell Beverley
Published: November 2014

Purpose

To review, critique and synthesise current research studies that examine parental perceptions of healthcare provider actions during and after the death of a child.

Conclusions

Five main themes were synthesised from the literature: staff attitudes and affect; follow‐up care and ongoing contact; communication; attending to the parents; and continuity of care.

Practice Implications

This review helps to identify important aspects of paediatric end‐of‐life care as recognised by parents, with the intention of placing the family at the centre of any future end‐of‐life care education or policy/protocol development.
Sylvia's Similes: A Stylistic Approach to Sylvia Townsend Warner
Authors: Swaab Peter
Published: December 2014

This essay notes the prevalence and analyses the excellence of similes in the writing of Sylvia Townsend Warner. Discussing instances from different genres and periods of her work, it argues that the author's imagination, humour and critical intelligence are especially evident in her similes. It goes on to illustrate how and to what ends these similes are often drawn from the natural world, and how they express a range of attitudes to sexuality and homosexuality. The essay proposes that Warner's similes are characteristically what grammarians term ‘catachretic’ and not ‘illustrative’, and that they often function to complicate the stories and disconcert or shock the reader. It suggests that Warner's might be thought a queer practice of simile. The essay concludes that the propositional force of similes, asserting relations of likeness, gives us a window onto the views and perspectives of Warner's narrators.