bluuebunny/crossref_metadata_2025 huggingface dataset:
Scoring a backstage pass: Mechanisms of ciliogenesis and ciliary access
Authors: Garcia-Gonzalo Francesc R. , Reiter Jeremy F.
Published: June 2012

Cilia are conserved, microtubule-based cell surface projections that emanate from basal bodies, membrane-docked centrioles. The beating of motile cilia and flagella enables cells to swim and epithelia to displace fluids. In contrast, most primary cilia do not beat but instead detect environmental or intercellular stimuli. Inborn defects in both kinds of cilia cause human ciliopathies, diseases with diverse manifestations such as heterotaxia and kidney cysts. These diseases are caused by defects in ciliogenesis or ciliary function. The signaling functions of cilia require regulation of ciliary composition, which depends on the control of protein traffic into and out of cilia.
Unitary 𝑁-dilations for tuples of commuting matrices
Authors: McCarthy John , Shalit Orr
Published: June 2012

We show that whenever a contractive

k
k

-tuple

T
T

on a finite dimensional space

H
H

has a unitary dilation, then for any fixed degree

N
N

there is a unitary

k
k

-tuple

U
U

on a finite dimensional space so that

q
(
T
)
=

P
H

q
(
U
)

|

H

q(T) = P_H q(U) |_H

for all polynomials

q
q

of degree at most

N
N

.
How networks change with time
Authors: Park Yongjin , Bader Joel S.
Published: June 2012

Motivation: Biological networks change in response to genetic and environmental cues. Changes are reflected in the abundances of biomolecules, the composition of protein complexes and other descriptors of the biological state. Methods to infer the dynamic state of a cell would have great value for understanding how cells change over time to accomplish biological goals.

Results: A new method predicts the dynamic state of protein complexes in a cell, with protein expression inferred from transcription profile time courses and protein complexes inferred by joint analysis of protein co-expression and protein–protein interaction maps. Two algorithmic advances are presented: a new method, DHAC (Dynamical Hierarchical Agglomerative Clustering), for clustering time-evolving networks; and a companion method, MATCH-EM, for matching corresponding clusters across time points. With link prediction as an objective assessment metric, DHAC provides a substantial advance over existing clustering methods. An application to the yeast metabolic cycle demonstrates how waves of gene expression correspond to individual protein complexes. Our results suggest regulatory mechanisms for assembling the mitochondrial ribosome and illustrate dynamic changes in the components of the nuclear pore.

Availability: All source code and data are available under the Boost Software License as supplementary material, at www.baderzone.org, and at sourceforge.net/projects/dhacdist

Contact: joel.bader@jhu.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Joint stage recognition and anatomical annotation of drosophila gene expression patterns
Authors: Cai Xiao , Wang Hua , Huang Heng , Ding Chris
Published: June 2012

Motivation: Staining the mRNA of a gene via in situ hybridization (ISH) during the development of a Drosophila melanogaster embryo delivers the detailed spatio-temporal patterns of the gene expression. Many related biological problems such as the detection of co-expressed genes, co-regulated genes and transcription factor binding motifs rely heavily on the analysis of these image patterns. To provide the text-based pattern searching for facilitating related biological studies, the images in the Berkeley Drosophila Genome Project (BDGP) study are annotated with developmental stage term and anatomical ontology terms manually by domain experts. Due to the rapid increase in the number of such images and the inevitable bias annotations by human curators, it is necessary to develop an automatic method to recognize the developmental stage and annotate anatomical terms.

Results: In this article, we propose a novel computational model for jointly stage classification and anatomical terms annotation of Drosophila gene expression patterns. We propose a novel Tri-Relational Graph (TG) model that comprises the data graph, anatomical term graph, developmental stage term graph, and connect them by two additional graphs induced from stage or annotation label assignments. Upon the TG model, we introduce a Preferential Random Walk (PRW) method to jointly recognize developmental stage and annotate anatomical terms by utilizing the interrelations between two tasks. The experimental results on two refined BDGP datasets demonstrate that our joint learning method can achieve superior prediction results on both tasks than the state-of-the-art methods.

Availability:  http://ranger.uta.edu/%7eheng/Drosophila/

Contact:  heng@uta.edu
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss
Authors: Bansal Mukul S. , Alm Eric J. , Kellis Manolis
Published: June 2012

Motivation: Gene family evolution is driven by evolutionary events such as speciation, gene duplication, horizontal gene transfer and gene loss, and inferring these events in the evolutionary history of a given gene family is a fundamental problem in comparative and evolutionary genomics with numerous important applications. Solving this problem requires the use of a reconciliation framework, where the input consists of a gene family phylogeny and the corresponding species phylogeny, and the goal is to reconcile the two by postulating speciation, gene duplication, horizontal gene transfer and gene loss events. This reconciliation problem is referred to as duplication-transfer-loss (DTL) reconciliation and has been extensively studied in the literature. Yet, even the fastest existing algorithms for DTL reconciliation are too slow for reconciling large gene families and for use in more sophisticated applications such as gene tree or species tree reconstruction.

Results: We present two new algorithms for the DTL reconciliation problem that are dramatically faster than existing algorithms, both asymptotically and in practice. We also extend the standard DTL reconciliation model by considering distance-dependent transfer costs, which allow for more accurate reconciliation and give an efficient algorithm for DTL reconciliation under this extended model. We implemented our new algorithms and demonstrated up to 100 000-fold speed-up over existing methods, using both simulated and biological datasets. This dramatic improvement makes it possible to use DTL reconciliation for performing rigorous evolutionary analyses of large gene families and enables its use in advanced reconciliation-based gene and species tree reconstruction methods.

Availability: Our programs can be freely downloaded from http://compbio.mit.edu/ranger-dtl/.

Contact:  mukul@csail.mit.edu; manoli@mit.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Leveraging input and output structures for joint mapping of epistatic and marginal eQTLs
Authors: Lee Seunghak , Xing Eric P.
Published: June 2012

Motivation: As many complex disease and expression phenotypes are the outcome of intricate perturbation of molecular networks underlying gene regulation resulted from interdependent genome variations, association mapping of causal QTLs or expression quantitative trait loci must consider both additive and epistatic effects of multiple candidate genotypes. This problem poses a significant challenge to contemporary genome-wide-association (GWA) mapping technologies because of its computational complexity. Fortunately, a plethora of recent developments in biological network community, especially the availability of genetic interaction networks, make it possible to construct informative priors of complex interactions between genotypes, which can substantially reduce the complexity and increase the statistical power of GWA inference.

Results: In this article, we consider the problem of learning a multitask regression model while taking advantage of the prior information on structures on both the inputs (genetic variations) and outputs (expression levels). We propose a novel regularization scheme over multitask regression called jointly structured input–output lasso based on an ℓ1/ℓ2 norm, which allows shared sparsity patterns for related inputs and outputs to be optimally estimated. Such patterns capture multiple related single nucleotide polymorphisms (SNPs) that jointly influence multiple-related expression traits. In addition, we generalize this new multitask regression to structurally regularized polynomial regression to detect epistatic interactions with manageable complexity by exploiting the prior knowledge on candidate SNPs for epistatic effects from biological experiments. We demonstrate our method on simulated and yeast eQTL datasets.

Availability: Software is available at http://www.sailing.cs.cmu.edu/.

Contact:  epxing@cs.cmu.edu
Identifying disease sensitive and quantitative trait-relevant biomarkers from multidimensional heterogeneous imaging genetics data via sparse multimodal multitask learning
Authors: Wang Hua , Nie Feiping , Huang Heng , Risacher Shannon L. , Saykin Andrew J. , Shen Li ,   For the Alzheimer's Disease Neuroimaging Initiative
Published: June 2012

Motivation: Recent advances in brain imaging and high-throughput genotyping techniques enable new approaches to study the influence of genetic and anatomical variations on brain functions and disorders. Traditional association studies typically perform independent and pairwise analysis among neuroimaging measures, cognitive scores and disease status, and ignore the important underlying interacting relationships between these units.

Results: To overcome this limitation, in this article, we propose a new sparse multimodal multitask learning method to reveal complex relationships from gene to brain to symptom. Our main contributions are three-fold: (i) introducing combined structured sparsity regularizations into multimodal multitask learning to integrate multidimensional heterogeneous imaging genetics data and identify multimodal biomarkers; (ii) utilizing a joint classification and regression learning model to identify disease-sensitive and cognition-relevant biomarkers; (iii) deriving a new efficient optimization algorithm to solve our non-smooth objective function and providing rigorous theoretical analysis on the global optimum convergency. Using the imaging genetics data from the Alzheimer's Disease Neuroimaging Initiative database, the effectiveness of the proposed method is demonstrated by clearly improved performance on predicting both cognitive scores and disease status. The identified multimodal biomarkers could predict not only disease status but also cognitive function to help elucidate the biological pathway from gene to brain structure and function, and to cognition and disease.

Availability: Software is publicly available at: http://ranger.uta.edu/%7eheng/multimodal/

Contact:  heng@uta.edu; shenli@iupui.edu
Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease
Authors: Patel Chirag J. , Chen Rong , Butte Atul J.
Published: June 2012

Motivation: Complex diseases, such as Type 2 Diabetes Mellitus (T2D), result from the interplay of both environmental and genetic factors. However, most studies investigate either the genetics or the environment and there are a few that study their possible interaction in context of disease. One key challenge in documenting interactions between genes and environment includes choosing which of each to test jointly. Here, we attempt to address this challenge through a data-driven integration of epidemiological and toxicological studies. Specifically, we derive lists of candidate interacting genetic and environmental factors by integrating findings from genome-wide and environment-wide association studies. Next, we search for evidence of toxicological relationships between these genetic and environmental factors that may have an etiological role in the disease. We illustrate our method by selecting candidate interacting factors for T2D.

Contact:  abutte@stanford.edu
Xenome—a tool for classifying reads from xenograft samples
Authors: Conway Thomas , Wazny Jeremy , Bromage Andrew , Tymms Martin , Sooraj Dhanya , Williams Elizabeth D. , Beresford-Smith Bryan
Published: June 2012

Motivation: Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Classifying the read mixture to separate the two allows for more precise analysis to be performed.

Results: We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets.

Availability:  Xenome is available for non-commercial use from http://www.nicta.com.au/bioinformatics

Contact:  tom.conway@nicta.com.au
Processing multiple non-adjacent dependencies: evidence from sequence learning
Authors: de Vries Meinou H. , Petersson Karl Magnus , Geukes Sebastian , Zwitserlood Pienie , Christiansen Morten H.
Published: June 2012

Processing non-adjacent dependencies is considered to be one of the hallmarks of human language. Assuming that sequence-learning tasks provide a useful way to tap natural-language-processing mechanisms, we cross-modally combined serial reaction time and artificial-grammar learning paradigms to investigate the processing of multiple nested (A1A2A3B3B2B1) and crossed dependencies (A1A2A3B1B2B3), containing either three or two dependencies. Both reaction times and prediction errors highlighted problems with processing the middle dependency in nested structures (A1A2A3B3_B1), reminiscent of the ‘missing-verb effect’ observed in English and French, but not with crossed structures (A1A2A3B1_B3). Prior linguistic experience did not play a major role: native speakers of German and Dutch—which permit nested and crossed dependencies, respectively—showed a similar pattern of results for sequences with three dependencies. As for sequences with two dependencies, reaction times and prediction errors were similar for both nested and crossed dependencies. The results suggest that constraints on the processing of multiple non-adjacent dependencies are determined by the specific ordering of the non-adjacent dependencies (i.e. nested or crossed), as well as the number of non-adjacent dependencies to be resolved (i.e. two or three). Furthermore, these constraints may not be specific to language but instead derive from limitations on structured sequence learning.
High-pressure phase transitions and equations of state in NiSi. II. Experimental results
Authors: Lord Oliver T. , Vočadlo Lidunka , Wood Ian G. , Dobson David P. , Clark Simon M. , Walter Michael J.
Published: June 2012

The high-pressure structures of nickel monosilicide (NiSi) have been investigated to 124 GPa by synchrotron-based X-ray powder diffraction studies of quenched samples from laser-heated diamond anvil cell experiments, and the equations of state of three of these phases have been determined at room temperature. NiSi transforms from the MnP (B31) structure (space groupPnma) to the ∊-FeSi (B20) structure (space groupP213) at 12.5 ± 4.5 GPa and 1550 ± 150 K. Upon further compression, the CsCl (B2) structure (space groupPm3m) becomes stable at 46 ± 3 GPa and 1900 ± 150 K. Thus, NiSi will be in the B2 structure throughout the majority of the Earth's mantle and its entire core, and will likely form a solid solution with FeSi, which is already known to undergo a B20 → B2 transition at high pressure. Data from the quenched (room-temperature) samples of all three phases have been fitted to the third-order Birch–Murnaghan equation of state. For the MnP (B31) structure this yieldsK0= 165 ± 3 GPa withK0′ fixed at 4 andV0fixed at 12.1499 Å3 atom−1[V0from unpublished neutron diffraction measurements on the same batch of starting material; Wood (2011), personal communication]. For the ∊-FeSi (B20) structure,K0=161± 3 GPa andK0′ = 5.6 ± 0.2 withV0fixed at 11.4289 Å3 atom−1. For the CsCl (B2) structure,K0 = 200 ± 9 GPa,K0′ = 4.6 ± 0.1 andV0= 11.09 ± 0.05 Å3 atom−1. The ambient volume of NiSi, therefore, decreases by 6% at the first phase transition and then by a further 3% at the transition to the CsCl structure. Traces of additional NiSi structures predicted by Vočadlo, Wood & Dobson [J. Appl. Cryst. (2012),45, 186–196; part I], and labelled therein asPbma-I,Pnma-II, and possibly alsoPnma-III andP4/nmm, have been detected.
Randomised clinical trial: Lactobacillus reuteri DSM 17938 vs. placebo in children with acute diarrhoea ‐ a double‐blind study
Authors: Francavilla R. , Lionetti E. , Castellaneta S. , Ciruzzi F. , Indrio F. , Masciale A. , Fontana C. , La Rosa M. M. , Cavallo L. , Francavilla A
Published: June 2012

Background

Probiotics may be of help for the management of acute diarrhoea, however, the effect is strain specific and efficacy needs to be proven.

Aim

To test the efficacy and safety of
Lactobacillus reuteri
DSM 17938 derived from
L. reuteri
ATCC 55730 in children with acute diarrhoea. Primary outcomes were the rate of unresolved diarrhoea after 3 days of treatment and duration of diarrhoea.

Methods

Children (6–36 months), hospitalised in three paediatric hospitals in Southern Italy for acute diarrhoea with clinical signs of dehydration were randomised to receive in a double‐blind fashion either
L. reuteri (dose of 4 × 108 colony‐forming units/die) or placebo.

Results

Out of 96 eligible children, 74 were enrolled, five patients were withdrawn; 35 in the
L. reuteri group and 34 in the placebo group.
Lactobacillus reuteri significantly reduced the duration of watery diarrhoea as compared with placebo (2.1 ± 1.7 days vs. 3.3 ± 2.1 days; P < 0.03); on day two and three of treatment watery diarrhoea persisted in 82% and 74% of the placebo and 55% and 45% of the
L. reuteri recipients respectively (P < 0.01; P < 0.03). Finally, children receiving
L. reuteri had a significantly lower relapse rate of diarrhoea (15% vs. 42%; P < 0.03). There was not a significant difference in hospital stay between the groups. No adverse events were recorded.

Conclusion

Our study shows that
L
. reuteri
DSM 17938 as an adjunct to rehydration therapy is efficacious in the treatment of acute diarrhoea reducing the frequency, duration and recrudescence rate of the disease.
A randomised controlled trial comparing two insertion techniques for the Laryngeal Mask Airway Flexible™ in patients undergoing dental surgery
Authors: Choo C. Y. , Koay C. K. , Yoong C. S.
Published: June 2012

The Laryngeal Mask Airway FlexibleTM (LMA Flexible) has been widely utilised for dental, ophthalmology and otorhinolaryngology‐related procedures. Our study evaluates two different techniques of inserting the LMA Flexible for patients undergoing day‐case dental surgery. One hundred and eight patients were randomly assigned into two groups based on the LMA Flexible insertion technique – either laryngoscopy‐guided (n = 54) or digital manipulation (standard technique; n = 54). Patient and airway characteristics were recorded before induction of anaesthesia. The primary outcome was success rate at first insertion. Other outcomes assessed included fibreoptic assessment of laryngeal mask airway placement, haemodynamic changes, need for airway adjustment during surgery and sore throat. The success rate of insertion on the first attempt was higher for the laryngoscopy‐assisted technique compared with the standard technique (96.3% vs 81.5%, respectively, p < 0.05). Fibreoptic assessment showed that the former group had better placement of the laryngeal mask airway than the latter (59.3% vs 37% p < 0.05). There were no significant differences between the two groups for haemodynamic changes. Sore throat was more common in the group with the standard technique (35.2% vs 16.7%, p < 0.05). Our study suggests the use of the laryngoscope to guide insertion of the LMA Flexible for dental surgery is a better option compared with the standard technique of digital manipulation.
Influence of CYP2B6 and ABCB1 SNPs on nevirapine plasma concentrations in Burundese HIV‐positive patients using dried sample spot devices
Authors: Calcagno Andrea , D'Avolio Antonio , Simiele Marco , Cusato Jessica , Rostagno Roberto , Libanore Valentina , Baietto Lorena , Siccardi Marco , Bonora Stefano , Di Perri Giovanni
Published: June 2012

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Nevirapine pharmacokinetics are affected by several factors including CYP2B6 single nucleotide polymorphisms (SNPs). These genetic profiles are more common in African patients and they affect the drug clearance being associated with higher trough concentrations. Pharmacokinetic/pharmacogenetic (PK/PG) studies are difficult to perform in remote areas where refrigeration is not available, although dried plasma and dried blood methods have been validated.

WHAT THIS STUDY ADDS

• Dried plasma spots are useful tools for studying nevirapine PK with a good association to plasma concentrations and they can be used in rural areas since a cold chain is not necessary. Dried blood spots can be used to store and analyze patients' DNA for PG polymorphisms. Nevirapine trough concentrations in Burundese patients, not studied so far, are above the target concentration (3000 ng ml−1) in 84% of patients. CYP2B6 (both at position 516 and 983) but not ABCB1 (3435 and 1236) SNPs as well as age correlate with higher nevirapine exposure.

AIMS The pharmacokinetics (PK) and pharmacogenetics (PG) of nevirapine have been studied in rich and limited‐resource countries. CYP2B6 single nucleotide polymorphisms (SNPs) have been associated with decreased drug clearance. We evaluated the PG determinants of nevirapine trough concentrations in a rural cohort in Burundi using easy to store and transport dried sample spot devices.

METHODS A cross‐sectional analysis in HIV‐positive nevirapine‐treated patients in Kiremba, north of Burundi, was performed in 2009. After blood withdrawal whole blood was stored on dried blood spots and plasma (after centrifugation) was placed on dried plasma spot devices and stored at room temperature. Nevirapine plasma and dried sample spot concentrations were compared to test the clinical usefulness of this method. SNPs in CYP2B6 and ABCB1 (using a real time PCR technique) were analyzed and associated with nevirapine plasma trough concentrations.

RESULTS Nevirapine concentrations measured on dried plasma spot devices were highly related to plasma concentrations in 60 patients, although a negative bias was observed (−18%). Nevirapine trough concentrations were above the target concentration (3000 ng ml−1) in 84% of patients and they were associated with CYP2B6 SNPs (both at position 516 and 983). No effect of ABCB1 SNPs was noted.

CONCLUSIONS Dried plasma spot devices are accurate tools for measuring nevirapine concentrations in rural settings where refrigeration is not available, despite a moderate underestimation bias. They allowed the evaluation of nevirapine concentrations in a cohort of HIV‐infected people in rural Burundi, confirming very good exposure and correlation with PG polymorphisms in the CYP2B6 encoding gene.
Novel Δ9‐tetrahydrocannabinol formulation Namisol® has beneficial pharmacokinetics and promising pharmacodynamic effects
Authors: Klumpers Linda E. , Beumer Tim L. , van Hasselt Johan G. C. , Lipplaa Astrid , Karger Lennard B. , Kleinloog H. Daniël , Freijer Jan I. , de Kam Marieke L. , van Gerven Joop M. A.
Published: June 2012

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• Cannabis based medicines are registered as a treatment for various indications, such as pain and spasms in multiple sclerosis (MS) patients, and anorexia and nausea in patients with HIV or receiving cancer treatment.

• the pharmacokinetics of the various administration routes of cannabis and cannabis based medicines are variable and dosing is hard to regulate.

WHAT THIS STUDY ADDS

• Namisol is a new tablet containing pure THC (>98%) that has a beneficial pharmacokinetic profile after oral administration.

• Namisol gives a quick onset of pharmacodynamic effects in healthy volunteers, which implies a rapid initiation of therapeutic effects in patients.

AIMS Among the main disadvantages of currently available Δ9‐tetrahydrocannabinol (THC) formulations are dosing difficulties due to poor pharmacokinetic characteristics. Namisol® is a novel THC formulation, designed to improve THC absorption. The study objectives were to investigate the optimal administration route, pharmacokinetics (PK), pharmacodynamics (PD) and tolerability of Namisol®.

METHODS This first in human study consisted of two parts. Panel I included healthy males and females (n = 6/6) in a double‐blind, double‐dummy, randomized, crossover study with sublingual (crushed tablet) and oral administration of Namisol® (5 mg THC). Based on these results, male and female (n = 4/5) participants from panel I received oral THC 6.5 and 8.0 mg or matching placebo in a randomized, crossover, rising dose study during panel II. PD measurements were body sway; visual analogue scales (VAS) mood, psychedelic and heart rate. THC and 11‐OH‐THC population PK analysis was performed.

RESULTS Sublingual administration showed a flat concentration profile compared with oral administration. Oral THC apparent t1/2 was 72–80 min, tmax was 39–56 min and Cmax 2.92–4.69 ng ml−1. THC affected body sway (60.8%, 95% CI 29.5, 99.8), external perception (0.078 log mm, 95% CI 0.019, 0.137), alertness (−2.7 mm, 95% CI −4.5, −0.9) feeling high (0.256 log mm, 95% CI 0.093, 0.418) and heart rate (5.6 beats min–1, 95% CI 2.7, 6.5). Namisol® was well tolerated.

CONCLUSIONS Oral Namisol® showed promising PK and PD characteristics. Variability and tmax of THC plasma concentrations were smaller for Namisol® than reported for studies using oral dronabinol and nabilone. This study was performed in a limited number of healthy volunteers. Therefore, future research on Namisol® should study clinical effects in patient populations.
Identifying high‐risk babies born in the community using foot length measurement at birth in Uganda
Authors: Nabiwemba E. , Marchant T. , Namazzi G. , Kadobera D. , Waiswa P.
Published: June 2012

Background  Low birthweight and prematurity are risk factors for neonatal mortality. Identifying low birthweight and premature babies at birth and giving them appropriate care could increase their chances of survival. This study aimed at assessing the use of foot length as a surrogate for low birthweight and prematurity, and recommending an operational cut‐off for identifying high‐risk babies at the community level in low resource settings.

Methods  A hospital‐based cross‐sectional study was carried out between 1 September and 17 December 2009 in Uganda. Foot length of 711 newborns was measured using three different methods and their weight taken using a digital salter scale within 24 h of life. Gestational age of the newborns was also estimated using the Eregie method. Non‐parametric receiver operating characteristic curve analysis was carried out to determine the foot length method with the highest predictive value to predict low birthweight and premature newborns. Sensitivity, specificity and predictive values for a range of foot lengths were estimated to determine the optimal cut‐off to predict low birthweight and prematurity in this setting.

Results  Of the 711 babies recruited on day 1, 85 (12%) babies were low birthweight (<2500 g) and 29 (4%) premature (<37 weeks). The operational cut‐off for foot length to detect small babies was defined as 7.6 cm, with sensitivity 85% [95% confidence interval (CI) 75–92] and specificity 81% (95% CI 78–84) for low birthweight, and sensitivity 96% (95% CI 82–100) and specificity 76% (95% CI 73–79) for premature babies.

Conclusion  Foot length in the first days of life can predict low birthweight and prematurity among newborn babies in this setting. Further evaluation is needed to assess the feasibility of its use by community health workers to identify babies that need extra care.
Plasmablastic lymphoma of the elderly: a clinicopathological comparison with age‐related Epstein–Barr virus‐associated B cell lymphoproliferative disorder
Authors: Liu Fang , Asano Naoko , Tatematsu Akiko , Oyama Takashi , Kitamura Kunio , Suzuki Kotaro , Yamamoto Kazuhito , Sakamoto Natsumi , Taniwaki Masafumi , Kinoshita Tomohiro , Nakamura Shigeo
Published: June 2012

Liu F, Asano N, Tatematsu A, Oyama T, Kitamura K, Suzuki K, Yamamoto K, Sakamoto N, Taniwaki M, Kinoshita T & Nakamura S  (2012) Histopathology Plasmablastic lymphoma of the elderly: a clinicopathological comparison with age‐related Epstein–Barr virus‐associated B cell lymphoproliferative disorder

Aims:  Plasmablastic lymphoma (PBL) is an aggressive lymphoma with a terminally differentiated B cell phenotype; half of patients with this disease have Epstein–Barr virus (EBV) infection. The majority of PBL cases are associated with human immunodeficiency virus (HIV) infection, while the remaining HIV‐negative cases were accompanied by other immunodeficiency conditions or immunosenescence in the elderly.

Methods and results:  To characterize HIV‐negative PBL of the elderly (PBL‐E), we compared the clinicopathological characteristics of 10 cases of PBL‐E and 124 cases with age‐related EBV‐associated B cell lymphoproliferative disorder (AR‐EBVLPD). The 10 PBL‐E (eight men, two women; median age: 68 years) were associated with a more indolent clinical behaviour and a better overall survival than AR‐EBVLPD. Extranodal involvement was higher in PBL‐E (50%) than AR‐EBVLPD; notably, the nasal cavity was affected most frequently in PBL‐E (60%). Immunoglobulin heavy chain/(IGH)/MYC translocation was detected in half of the PBL‐E cases.

Conclusions:  PBL‐E shares some clinical features with AR‐EBVLPD, such as HIV negativity, old age, and EBV infection, no known immunosuppressive condition but there are some differences such as a higher ratio of extranodal involvement and better prognosis. PBL‐E is a newly recognized condition and should be distinguished from HIV‐positive PBL, sharing features with AR‐EBVLPD in particular, immunosenescence of the elderly.
Metals in organic and conventional wheat flours determined by an optimised and validated ICP‐MS method
Authors: Vrček Valerije , Vinković Vrček Ivana
Published: June 2012

This study was undertaken (i) to optimise and validate a suitable method for multi‐element determination in cereal products and (ii) to evaluate multi‐element content differences in commercially available conventional vs. organic wheat flours. Presented ICP‐MS method is simple and accurate for the determination of eighteen elements in cereal food. Obtained results show differences in metal content between conventional and organic wheat flours and confirm that both types of production are well within the toxicological safety limits regarding the metal contents. The significant differences among conventional vs. organic wheat flours were obtained for As, Cd, Cr, Fe, Mg, Mo, Ni and V. Toxic metals (Al, As, Cd and Pb) input was higher in conventional compared with organic wheat flours. However, further and long‐term research is needed to clearly underline the effects of organic agricultural practice on the quality of food products.
Preparation of rice analogues using extrusion technology
Authors: Mishra Abhinav , Mishra Hari Niwas , Srinivasa Rao Pavuluri
Published: June 2012

Rice is considered as staple food in many parts of the world. An issue of concern is the breakage of rice kernels in milling processes, and these broken kernels are not generally accepted by consumers. These broken kernels can be mixed with some desired additives to improve their quality and extruded for the preparation of reconstituted rice kernels or rice analogues. Various studies have been conducted for the preparation of the rice analogues in the past few decades, and recently attempts have been made to fortify these analogues with protein, certain vitamins and minerals. The main features such as colour, shape, size, texture, and cooking characteristics and cooking time of these rice‐like grains can be tailored to the requirements of specific applications by modification of the extrusion parameters. Various organisations, such as Wuxi NutriRice Co. (DSM/Buhler) and China National Cereals, Oils and Foodstuffs Corporate (COFCO), Superlative Snacks Inc., Vigui and PATH, have utilised this technique to prepare fortified and reconstituted rice. Studies have shown that it is possible to improve the nutritional quality of rice by fortified rice analogues. This article reviews research results of the many approaches to the formation of fortified rice analogues by extrusion‐based technologies.
Effects of salts of organic acids on the survival of Listeria monocytogenes in soft cheeses
Authors: Silva Elaine N. G. , Almeida Rogeria C.C. , Figueiredo Ana Cláudia L. , Miranda Fernanda A.
Published: June 2012

The purpose of this study was to determine the effect of sodium lactate and sodium propionate, both in combination with sodium acetate, on strains of Listeria monocytogenes in artificially inoculated soft cheeses. Minas Frescal and Coalho cheeses, inoculated with a mix of L. monocytogenes 1/2a and Scott A, underwent two treatments: 2% (w/v) sodium lactate in combination with 0.25% (w/v) sodium acetate and 2% (w/v) sodium propionate in combination with 0.25% (w/v) sodium acetate. The samples were analysed immediately and after 7 days at 10 °C. The growth of the pathogen was inhibited in cheeses containing the salts of organic acids, and the effects of treatment were statistically significant (P < 0.05). However, there was no difference between the types of treatment applied. Our data demonstrate that the effectiveness of the salts of organic acids depended on the initial concentration of L. monocytogenes and that a higher concentration of the salts is necessary to ensure sustained inactivation of target pathogens because they are weakly antilisterial when the soft cheeses are stored at 10 °C.
Influence of some oenological practices on the aromatic and sensorial characteristics of white Verdejo wines
Authors: Losada Manuel M. , López Jorge F. , Añón Ana , Andrés Jesús , Revilla Eugenio
Published: June 2012

Changes in the aromatic composition as well as sensory characteristics in Verdejo white wines were analysed based on two factors: the winemaking methodology and the storing time of wine in bottles. The volatile components were determined by GLC‐MS, and the sensory profile was designed and assessed according to the ISO 11035 standard. The results showed that when wines were made in oak barrels, either completely or partially, which means the wines were in contact with the lees, the levels of 1‐octanol, ethyl heptanoate and ethyl decanoate were significantly affected (P < 0.05); the softness sensation was also influenced (P < 0.05). However, the amount of time the wines were stored in bottles significantly affected (P < 0.05) the levels of 1‐hexanol, ethyl heptanoate, ethyl octanoate, ethyl decanoate, hexyl acetate, isoamyl acetate and isoamyl lactate and also an odour note (tropical fruit). The compounds with higher OAV values belong to the groups of esters and fatty acids. For these reasons, the composition and the quality of the aroma of Verdejo white wines appear to be significantly affected both by use of oak barrels in winemaking and the time the wines are stored in bottles.
Bioconversion of shrimp shell waste for the production of antioxidant and chitosan used as fruit juice clarifier
Authors: Ghorbel‐Bellaaj Olfa , Jridi Mourad , Khaled Hayet Ben , Jellouli Kemel , Nasri Moncef
Published: June 2012

The pH, proteolytic activity, extent of demineralisation and deprotenisation of shrimp waste were studied during 7 days of fermentation using Pseudomonas aeruginosa A2. After 3 days, pH dropped from 7.0 to 4.4 and then remained constant. Simultaneously, a demineralisation of 92% was achieved. However, protease activity reached its highest level (1230 U mL−1) after 1 day of incubation, and a protein removal of 90% was achieved. Chitin obtained was converted to chitosan. This chitosan, with 73% deacetylation, was tested for clarification of different fruit juices. It was observed that low concentrations of chitosan (below to 1%) greatly increase the clarity of juices without affecting the nutritional value. The antioxidant activity of the hydrolysates produced during fermentation was tested. Hydrolysate obtained after 3 days showed the strongest scavenging activity (90%), which was comparable to the positive control BHA; however, that obtained after 1 day exhibited the highest ferric‐reducing antioxidant power (OD 700 nm = 1.7).
RecA mediates MgpB and MgpC phase and antigenic variation in Mycoplasma genitalium, but plays a minor role in DNA repair
Authors: Burgos Raul , Wood Gwendolyn E. , Young Lei , Glass John I. , Totten Patricia A.
Published: June 2012

Mycoplasma genitalium, a sexually transmitted human pathogen, encodes MgpB and MgpC adhesins that undergo phase and antigenic variation through recombination with archived ‘MgPar’ donor sequences. The mechanism and molecular factors required for this genetic variation are poorly understood. In this study, we estimate that sequence variation at the mgpB/C locus occurs in vitro at a frequency of > 1.25 × 10−4 events per genome per generation using a quantitative anchored PCR assay. This rate was dramatically reduced in a recA deletion mutant and increased in a complemented strain overexpressing RecA. Similarly, the frequency of haemadsorption‐deficient phase variants was reduced in the recA mutant, but restored by complementation. Unlike Escherichia coli, inactivation of recA in M. genitalium had a minimal effect on survival after exposure to mitomycin C or UV irradiation. In contrast, a deletion mutant for the predicted nucleotide excision repair uvrC gene showed growth defects and was exquisitely sensitive to DNA damage. We conclude that M. genitalium RecA has a primary role in mgpB/C–MgPar recombination leading to antigenic and phase variation, yet plays a minor role in DNA repair. Our results also suggest that M. genitalium possesses an active nucleotide excision repair system, possibly representing the main DNA repair pathway in this minimal bacterium.
Antimicrobial resistance of Staphylococcus pseudintermedius
Authors: Kadlec Kristina , Schwarz Stefan
Published: June 2012

Staphylococcus pseudintermedius, Staphylococcus intermedius and Staphylococcus delphini together comprise the S. intermedius group (SIG). Within the SIG, S. pseudintermedius represents the major pathogenic species and is involved in a wide variety of infections, mainly in dogs, but to a lesser degree also in other animal species and humans.

Antimicrobial agents are commonly applied to control S. pseudintermedius infections; however, during recent years S. pseudintermedius isolates have been identified that are meticillin‐resistant and have also proved to be resistant to most of the antimicrobial agents approved for veterinary applications.

This review deals with the genetic basis of antimicrobial resistance properties in S. pseudintermedius and other SIG members. A summary of the known resistance genes and their association with mobile genetic elements is given, as well as an update of the known resistance‐mediating mutations. These data show that, in contrast to other staphylococcal species, S. pseudintermedius seems to prefer transposon‐borne resistance genes, which are then incorporated into the chromosomal DNA, over plasmid‐located resistance genes.
Evaluation of methylprednisolone and triamcinolone for the induction and maintenance treatment of pruritus in allergic cats: a double‐blinded, randomized, prospective study
Authors: Ganz Eva C. , Griffin Craig E. , Keys Deborah A. , Flatgard Tami A.
Published: June 2012

Background –  Oral triamcinolone (T) and methylprednisolone (M) have been recommended at various dosages for the control of pruritus associated with feline allergic dermatitis.

Objectives –  The first objective was to determine effective dosages of methylprednisolone (Pfizer, New York, NY, USA) and triamcinolone (Boehringer Ingelheim Vetmedica, Inc., St Joseph, MO, USA) required to induce remission from pruritus associated with feline allergic dermatitis. The second objective was to compare efficacy of several different alternate day maintenance dosages. The third objective was to determine whether laboratory abnormalities occurred at effective dosages.

Animals –  Thirty‐two client‐owned allergic cats were randomly assigned to the M or T groups.

Methods –  Owners reported weekly on pruritus score and behavioural changes. Remission was defined as a pruritus score of ≤2/10, with 0 as the least and 10 as the most pruritic. Serum chemistry, complete blood count, fructosamine and urinalysis were assessed on day 0, at the end of the 7–14 day induction phase and at study completion.

Results –  Mean once daily doses required for induction were 1.41 mg/kg for M and 0.18 mg/kg for T. Mean alternate day maintenance doses were 0.54 mg/kg for M and 0.08 mg/kg for T. There was a statistically significant decrease in eosinophils and increase in fructosamine for both groups from baseline to study completion. Fructosamine levels did not exceed the reference range in any case.

Conclusions –  These results suggest that triamcinolone is approximately seven times as potent as methylprednisolone, and that these dosages are efficacious and well tolerated for the control of pruritus in allergic cats.
Detecting asymptomatic ink‐diseased chestnut trees by the composition of the ectomycorrhizal community
Authors: Scattolin L. , Dal Maso E. , Mutto Accordi S. , Sella L. , Montecchio L.
Published: June 2012

The research was performed in a new and isolated ink disease outbreak. Nine sweet chestnuts of comparable age, growing under same environmental and site conditions, and belonging to three phytosanitary classes (healthy, infected but asymptomatic and symptomatic) were randomly selected. Their ectomycorrhizal community was monitored during two periods, with regard to species abundance, to verify whether the community composition can be useful as an ink disease bioindicator. From the 216 samples, 29 ectomycorrhizal species were recorded, with abundances that changed with the health status of the tree. The results demonstrated that the mycorrhizal community composition was highly related to the ink disease level, allowing the consideration of the use of this parameter as a tool for the quick detection and control of the early stages of the disease.
Cryopreservation of the Bovine Oocyte: Current Status and Perspectives
Authors: Díez C , Muñoz M , Caamaño JN , Gómez E
Published: June 2012

Contents

This review presents some of the most noticeable aspects related with the oocyte cryopreservation procedures, emphasizing their evolution in the bovine, which points towards the critical points determining the reduced survival rates of female gametes to freezing and vitrification. Factors such as the maturation status, the cytoskeleton and membrane sensitivity, the role of the cumulus cells, the impact of the cryoprotectants agents and the protocols utilized and the future of this tool have been extensively reviewed.
The Membrane of the Mammalian Spermatozoa: Much More Than an Inert Envelope
Authors: Tapia JA , Macias‐Garcia B , Miro‐Moran A , Ortega‐Ferrusola C , Salido GM , Peña FJ , Aparicio IM
Published: June 2012

Contents

Sperm plasma membrane is a very important structure that functions to protect sperm against extracellular injuries and to respond to physiological challenges. It plays a crucial role during sperm capacitation, in sperm–egg interaction and, finally, in fertilization. Concerning sperm technology, possibly the most important factors causing damage in mammalian spermatozoa membranes are initiated by the osmotic stress generated by dehydration of the cells during freezing and thawing. These changes are rapidly derived to the plasma and organelle membranes that gradually experiment loss of membrane architecture, causing unbalanced production of reactive oxygen species and increased lipid peroxidation. Other procedures such as sperm sorting or liquid storage of sperm also induce harmful changes in the integrity of the membrane. The specific composition of lipids of the sperm membranes may provide clues for understanding the mechanisms behind the differences found in the response to stress in different species. In the present review, we deal with the composition, architecture and organization of the sperm plasma membrane, emphasizing the factors that can affect membrane integrity. The intracellular signalling pathways related with membrane reorganization during capacitation and acrosome reaction are also reviewed.
“Micromere” formation and expression of endomesoderm regulatory genes during embryogenesis of the primitive echinoid Prionocidaris baculosa
Authors: Yamazaki Atsuko , Kidachi Yumi , Minokawa Takuya
Published: June 2012

Blastomere composition and expression profiles of wnt8 and hox11/13b orthologues were examined in the primitive indirect‐developing echinoid Prionocidaris baculosa. We found that blastomere composition in the 16‐cell‐stage Prionocidaris embryos was different from that of the indirect‐developing echinoids belonging to Euechinoidea, a derived group of the echinoids. The sizes of the blastomeres in the 16‐cell‐stage embryo varied, and no embryos formed a “micromere quartet,” a group of four equal‐sized micromeres. The smallest blastomere was usually located around the vegetal pole. We also found significant differences in early expression profiles of wnt8 orthologues of the Prionocidaris and euechinoids. Unlike euechinoids, the expression of wnt8 orthologue of Prionocidaris was not detected at the 16‐cell stage; it began at the 32‐cell stage in the broad area containing the vegetal pole. However, in later stages, the expression profiles of hox11/13b and wnt8 orthologues of Prionocidaris were similar to that of euechinoid orthologues. The present study suggests that there are considerable differences between Prionocidaris and euechinoids in early developmental mechanisms in the vicinity of the vegetal pole.
Mineral chemistry and geothermobarometry of Moshirabad pluton, Qorveh, Kurdistan, western Iran
Authors: SEPAHI ALI A. , MAANIJOU MOHAMMAD , SALAMI SEDDIGHEH , GARDIDEH SARA , KHAKSAR TAYEBEH
Published: June 2012

The Moshirabad pluton is located southwest of the Sanandaj–Sirjan Metamorphic Belt, Qorveh, western Iran. The pluton is composed of diorite, monzodiorite, quartz diorite, quartz monzodiorite, tonalite, granodiorite, granite, aplite, and pegmatite. In this study 31 samples from various rocks were chosen for whole‐rock analyses and 15 samples from different lithologies were chosen for mineral chemical studies. The compositions of minerals are used to describe the nature of magma and estimate the pressure and temperature at which the Moshirabad pluton was emplaced. Feldspar compositions are near the binary systems in which plagioclase compositions range from An5 to An53 and alkali‐feldspar compositions range from Or91 to Or97. Mafic minerals in the plutonic rocks are biotite and hornblende. Based on the composition of biotites and whole‐rock chemistry, the Moshirabad pluton formed from a calc‐alkaline magma. Amphiboles are calcic amphiboles (magnesio‐hornblende or edenite). Temperatures of crystallization, calculated with the hornblende–plagioclase thermometer, range 550–750°C. These temperatures indicate that plutonic rocks have undergone some retrogressive changes in their mineral compositions. Aluminum‐in‐hornblende geobarometry indicates that the Moshirabad pluton was emplaced at pressures of 2.3–6.0 kbar, equal to depths of 7–20 km, but with consideration of regional geology, lower pressures than the above pressure range are more probable. Alteration of amphiboles can be the reason for some overestimation of pressures.