bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative study of nemertean complete mitochondrial genomes, including two new ones for Nectonemertes cf. mirabilis and Zygeupolia rubens, may elucidate the fundamental pattern for the phylum Nemertea
Authors: Chen Hai-Xia , Sun Shi-Chun , Sundberg Per , Ren Wei-Cheng , Norenburg Jon L 
Published: April 2012

Abstract

Background
The mitochondrial genome is important for studying genome evolution as well as reconstructing the phylogeny of organisms. Complete mitochondrial genome sequences have been reported for more than 2200 metazoans, mainly vertebrates and arthropods. To date, from a total of about 1275 described nemertean species, only three complete and two partial mitochondrial DNA sequences from nemerteans have been published. Here, we report the entire mitochondrial genomes for two more nemertean species: Nectonemertes cf. mirabilis and Zygeupolia rubens.

Results
The sizes of the entire mitochondrial genomes are 15365 bp for N. cf. mirabilis and 15513 bp for Z. rubens. Each circular genome contains 37 genes and an AT-rich non-coding region, and overall nucleotide composition is AT-rich. In both species, there is significant strand asymmetry in the distribution of nucleotides, with the coding strand being richer in T than A and in G than C. The AT-rich non-coding regions of the two genomes have some repeat sequences and stem-loop structures, both of which may be associated with the initiation of replication or transcription. The 22 tRNAs show variable substitution patterns in nemerteans, with higher sequence conservation in genes located on the H strand. Gene arrangement of N. cf. mirabilis is identical to that of Paranemertes cf. peregrina, both of which are Hoplonemertea, while that of Z. rubens is the same as in Lineus viridis, both of which are Heteronemertea. Comparison of the gene arrangements and phylogenomic analysis based on concatenated nucleotide sequences of the 12 mitochondrial protein-coding genes revealed that species with closer relationships share more identical gene blocks.

Conclusion
The two new mitochondrial genomes share many features, including gene contents, with other known nemertean mitochondrial genomes. The tRNA families display a composite substitution pathway. Gene order comparison to the proposed ground pattern of Bilateria and some lophotrochozoans suggests that the nemertean ancestral mitochondrial gene order most closely resembles the heteronemertean type. Phylogenetic analysis proposes a sister-group relationship between Hetero- and Hoplonemertea, which supports one of two recent alternative hypotheses of nemertean phylogeny.
Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin
Authors: Bourguiba Hedia , Audergon Jean-Marc , Krichen Lamia , Trifi-Farah Neila , Mamouni Ali , Trabelsi Samia , D’Onofrio Claudio , Asma Bayram M , Santoni Sylvain , Khadari Bouchaib 
Published: April 2012

AbstractBackgroundDomestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniacaL.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin.ResultsAccording to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: ‘Irano-Caucasian’, ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the ‘Irano-Caucasian’ gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the ‘North Mediterranean Basin’ and ‘South Mediterranean Basin’ to the secondary centre of diversification.ConclusionsA marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the ‘Irano-Caucasian’ gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits.
Expression and purification of the p75 neurotrophin receptor transmembrane domain using a ketosteroid isomerase tag
Authors: Li Qingxin , Chen Angela Shuyi , Gayen Shovanlal , Kang CongBao 
Published: April 2012

AbstractBackgroundReceptors with a single transmembrane (TM) domain are essential for the signal transduction across the cell membrane. NMR spectroscopy is a powerful tool to study structure of the single TM domain. The expression and purification of a TM domain inEscherichia coli(E.coli) is challenging due to its small molecular weight. Although ketosteroid isomerase (KSI) is a commonly used affinity tag for expression and purification of short peptides, KSI tag needs to be removed with the toxic reagent cyanogen bromide (CNBr).ResultThe purification of the TM domain of p75 neurotrophin receptor using a KSI tag with the introduction of a thrombin cleavage site is described herein. The recombinant fusion protein was refolded into micelles and was cleaved with thrombin. Studies showed that purified protein could be used for structural study using NMR spectroscopy.ConclusionsThese results provide another strategy for obtaining a single TM domain for structural studies without using toxic chemical digestion or acid to remove the fusion tag. The purified TM domain of p75 neurotrophin receptor will be useful for structural studies.
Patient-oriented simulation based on Monte Carlo algorithm by using MRI data
Authors: Chuang Ching-Cheng , Lee Yu-Tzu , Chen Chung-Ming , Hsieh Yao-Sheng , Liu Tsan-Chi , Sun Chia-Wei 
Published: April 2012

AbstractBackgroundAlthough Monte Carlo simulations of light propagation in full segmented three-dimensional MRI based anatomical models of the human head have been reported in many articles. To our knowledge, there is no patient-oriented simulation for individualized calibration with NIRS measurement. Thus, we offer an approach for brain modeling based on image segmentation process within vivoMRI T1 three-dimensional image to investigate the individualized calibration for NIRS measurement with Monte Carlo simulation.MethodsIn this study, an individualized brain is modeled based onin vivoMRI 3D image as five layers structure. The behavior of photon migration was studied for this individualized brain detections based on three-dimensional time-resolved Monte Carlo algorithm. During the Monte Carlo iteration, all photon paths were traced with various source-detector separations for characterization of brain structure to provide helpful information for individualized design of NIRS system.ResultsOur results indicate that the patient-oriented simulation can provide significant characteristics on the optimal choice of source-detector separation within 3.3 cm of individualized design in this case. Significant distortions were observed around the cerebral cortex folding. The spatial sensitivity profile penetrated deeper to the brain in the case of expanded CSF. This finding suggests that the optical method may provide not only functional signal from brain activation but also structural information of brain atrophy with the expanded CSF layer. The proposed modeling method also provides multi-wavelength for NIRS simulation to approach the practical NIRS measurement.ConclusionsIn this study, the three-dimensional time-resolved brain modeling method approaches the realistic human brain that provides useful information for NIRS systematic design and calibration for individualized case with prior MRI data.
Tubulobulbar complex: Cytoskeletal remodeling to release spermatozoa
Authors: Upadhyay Rahul D , Kumar Anita V , Ganeshan Malti , Balasinor Nafisa H 
Published: April 2012

AbstractTubulobulbar complexes (TBCs) are actin-based structures that help establish close contact between Sertoli–Sertoli cells or Sertoli–mature germ cells (spermatids) in the seminiferous tubules of the testes. They are actin-rich push-through devices that eliminate excess spermatid cytoplasm and prepare mature spermatids for release into the tubular lumen. Just prior to spermiation, the elongated spermatid interacts with the Sertoli cell via an extensive structure comprising various adhesion molecules called the apical ectoplasmic specialization which is partially replaced by the apical TBC, on the concave surface of the spermatid head. The sperm release process involves extensive restructuring, namely the disassembly and reassembly of junctions at the Sertoli–spermatid interface in the seminiferous epithelium. Based on the presence of different classes of molecules in the TBCs or the defects observed in the absence of TBCs, the main functions attributed to TBCs are elimination of excess spermatid cytoplasm, endocytosis and recycling of junctional molecules, shaping of the spermatid acrosome, and forming transient anchoring devices for mature spermatids before they are released. This review summarizes the recent findings that focus on the role of TBCs in cell cytoskeleton restructuring during sperm release in the testes and the molecular mechanism involved.
Fixed point results for multivalued contractive maps
Authors: Bin Dehaish B A , Latif Abdul 
Published: April 2012

Abstract
Using the concept of u-distance, we prove a fixed point theorem for multivalued contractive maps. We also establish a multivalued version of the Caristi's fixed point theorem and common fixed point result. Consequently, several known fixed point results are either improved or generalized including the corresponding fixed point results of Caristi, Mizoguchi-Takahashi, Kada et al., Suzuki-Takahashi, Suzuki, and Ume.

Mathematics Subject Classification (2000): 47H10; 54H25.
Inhibition of Ca2+/Calmodulin-Dependent Protein Kinase II Reverses Oxaliplatin-Induced Mechanical Allodynia in Rats
Authors: Shirahama Masafumi , Ushio Soichiro , Egashira Nobuaki , Yamamoto Shota , Sada Hikaru , Masuguchi Ken , Kawashiri Takehiro , Oishi Ryozo 
Published: April 2012

Background: Oxaliplatin is a key drug in the treatment of colorectal cancer, but it causes severe peripheral neuropathy. We previously reported that oxaliplatin (4 mg/kg, i.p., twice a week) induces mechanical allodynia in the late phase in rats, and that spinal NR2B-containig N-methyl-D-aspartate (NMDA) receptors are involved in the oxaliplatin-induced mechanical allodynia. In the present study, we investigated the involvement of Ca2+/calmodulin dependent protein kinase II (CaMKII), which is a major intracellular protein kinase and is activated by NMDA receptor-mediated Ca2+ influx, in the oxaliplatin-induced mechanical allodynia in rats. Results: An increase of CaMKII phosphorylation was found in the spinal cord (L4-6) of oxaliplatin-treated rats. This increased CaMKII phosphorylation was reversed by intrathecal injection of a selective CaMKII inhibitor KN-93 (50 nmol, i.t.) and a selective NR2B antagonist Ro 25–6981 (300 nmol, i.t.). Moreover, acute administration of KN-93 (50 nmol, i.t.) strongly reversed the oxaliplatin-induced mechanical allodynia in von Frey test, while it did not affect the oxaliplatin-induced cold hyperalgesia in acetone test. Similarly, oral administration of trifluoperazine (0.1 and 0.3 mg/kg, p.o.), which is an antipsychotic drug and inhibits calmodulin, reduced both mechanical allodynia and increased CaMKII phosphorylation. On the other hand, trifluoperazine at the effective dose (0.3 mg/kg) had no effect on the paw withdrawal threshold in intact rats. In addition, trifluoperazine at the same dose did not affect the motor coordination in rota-rod test in intact and oxaliplatin-treated rats. Conclusions: These results suggest that CaMKII is involved in the oxaliplatin-induced mechanical allodynia, and trifluoperazine may be useful for the treatment of oxaliplatin-induced peripheral neuropathy in clinical setting.
Clinicopathological significance of SOX4 expression in primary gallbladder carcinoma
Authors: Wang Chengguo , Zhao Huadong , Lu Jianguo , Yin Jikai , Zang Li , Song Nuan , Dong Rui , Wu Tao , Du Xilin 
Published: April 2012

Abstract

Aim
SOX4, as a member of the SRY-related HMG-box (SOX) transcription factor family, has been demonstrated to be involved in tumorigenesis of many human malignancies; however, its role in primary gallbladder carcinoma (PGC) is still largely unknown. The aim of this study was to investigate SOX4 expression in PGC and its prognostic significance.

Methods
From 1997 to 2006, 136 patients underwent resection for PGC. The median follow-up was 12.8 months. Immunostainings for SOX4 were performed on these archival tissues. The correlation of SOX4 expression with clinicopathological features including survival was analyzed.

Results
SOX4 was expressed in 75.0% (102/136) of PGC but not in the normal epithelium of the gallbladder. In addition, the over-expression of SOX4 was significantly associated with low histologic grade (P = 0.02), low pathologic T stage (P = 0.02), and early clinical stage (P = 0.03). The levels of SOX4 immunostainings in PGC tissues with positive nodal metastasis were also significantly lower than those without (P = 0.01). Moreover, Kaplan-Meier curves showed that SOX4 over-expression was significantly related to better overall (P = 0.008) and disease-free survival (P = 0.01). Furthermore, multivariate analyses showed that SOX4 expression was an independent risk factor for both overall (P = 0.03, hazard ratio, 3.682) and disease-free survival (P = 0.04, hazard ratio, 2.215).

Conclusion
Our data indicate for the first time that the over-expression of SOX4 in PGC was significantly correlated with favorable clinicopathologic features and was an independent prognostic factor for better overall and disease-free survival in patients. Therefore, SOX4 might be an auxiliary parameter for predicting malignant behavior for PGC.

Virtual slides
The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1534825818694957.
The influence of oestrous substances on cyclicity and oestrous behaviour in dairy heifers
Authors: Nordéus Kristina , Båge Renée , Gustafsson Hans , Humblot Patrice , Söderquist Lennart 
Published: April 2012

Abstract

Background
Declining fertility is a major concern for dairy farmers today. One explanation is shorter and weaker expression of oestrus in dairy cows making it difficult to determine optimal time for artificial insemination (AI). Chemical communication is of interest in the search for tools to detect oestrus or to synchronise or enhance oestrous periods. Pheromones, used in chemical communication within species, can influence reproduction in different ways. The aim here was to investigate whether oestrous cycle length, and duration and intensity of oestrous expression in dairy heifers could be manipulated through exposure to pheromones in oestrual substances from other females.

Methods
Beginning on day 16 of two consecutive control oestrous cycles, ten heifers of the Swedish Red Breed (SRB) were exposed to water. During the two following cycles the heifers were exposed to urine and vaginal mucus, obtained from cows in oestrus. Cyclicity parameters were monitored through hormone measurements, oestrus detection and ultrasonographic examination.

Results
We found no difference in cycle length or in duration of standing oestrus between control and treatment. We did, however, find a tendency of interaction between type of exposure (control or treatment) and cycle number within type of exposure for cycle length (p = 0.068), with the length differing less between the treatment cycles. We also found a tendency of effect of type of exposure on maximal concentration (p = 0.073) and sum of concentrations (p = 0.063) of LH during the LH surge, with values being higher for the control cycles. There were also significant differences in when the different signs of oestrus occurred and in the intensity of oestrous expression. The score for oedema and hyperaemia of external genitalia was significantly higher (p = 0.004) for the control cycles and there was also a significant interaction between type of exposure and time period for restlessness (p = 0.011), with maximum score occurring earlier for treatment cycles.

Conclusions
No evidence of altered oestrous cycle length or duration of oestrus after exposure of females to oestrous substances from other females was found. Expression of oestrus, and maybe also LH secretion, however, seemed influenced by the exposure, with the effect of treatment being suppressive rather than enhancing.
An observational study of compliance with the Scandinavian guidelines for management of minimal, mild and moderate head injury
Authors: Heskestad Ben , Waterloo Knut , Ingebrigtsen Tor , Romner Bertil , Harr Marianne Efskind , Helseth Eirik 
Published: April 2012

Abstract

Background
The Scandinavian guidelines for management of minimal, mild and moderate head injuries were developed to provide safe and cost effective assessment of head injured patients. In a previous study conducted one year after publication and implementation of the guidelines (2003), we showed low compliance, involving over-triage with computed tomography (CT) and hospital admissions. The aim of the present study was to investigate guideline compliance after an educational intervention.

Methods
We evaluated guideline compliance in the management of head injured patients referred to the University Hospital of Stavanger, Norway. The findings from the previous study in 2003 were communicated to the hospitals physicians, and a feed-back loop training program for guideline implementation was conducted. All patients managed during the months January through June in the years 2005, 2007 and 2009 were then identified with an electronic search in the hospitals patient administrative database, and the patient files were reviewed. Patients were classified according to the Head Injury Severity Scale, and the management was classified as compliant or not with the guideline.

Results
The 1 180 patients were 759 (64%) males and 421 (36%) females with a mean age of 31.5 (range 0-97) years. Over all, 738 (63%) patients were managed in accordance with the guidelines and 442 (37%) were not. Compliance was not significantly different between minimal (56%) and mild (59%) injuries, while most moderate (93%) injuries were managed in accordance with the guidelines (p < 0.05). Noncompliance was caused by overtriage in 362 cases (30%) and undertriage in 80 (7%). Guideline compliance was 54% in 2005, 71% in 2007, and 64% in 2009.

Conclusions
This study shows higher guideline compliance after an educational intervention involving feed-back on performance. A substantial number of patients are exposed to over-triage, involving unnecessary radiation from CT examinations, and unnecessary costs from hospital admissions.
Kinematic and dynamic gait compensations resulting from knee instability in a rat model of osteoarthritis
Authors: Allen Kyle D , Mata Brian A , Gabr Mostafa A , Huebner Janet L , Adams Samuel B , Kraus Virginia B , Schmitt Daniel O , Setton Lori A 
Published: April 2012

Abstract
Introduction
Osteoarthritis (OA) results in pain and disability; however, preclinical OA models often focus on joint-level changes. Gait analysis is one method used to evaluate both preclinical OA models and OA patients. The objective of this study is to describe spatiotemporal and ground reaction force changes in a rat medial meniscus transection (MMT) model of knee OA and to compare these gait measures with assays of weight bearing and tactile allodynia.

Methods
Sixteen rats were used in the study. The medial collateral ligament (MCL) was transected in twelve Lewis rats (male, 200 to 250 g); in six rats, the medial meniscus was transected, and the remaining six rats served as sham controls. The remaining four rats served as naïve controls. Gait, weight-bearing as measured by an incapacitance meter, and tactile allodynia were assessed on postoperative days 9 to 24. On day 28, knee joints were collected for histology. Cytokine concentrations in the serum were assessed with a 10-plex cytokine panel.

Results
Weight bearing was not affected by sham or MMT surgery; however, the MMT group had decreased mechanical paw-withdrawal thresholds in the operated limb relative to the contralateral limb (P = 0.017). The gait of the MMT group became increasingly asymmetric from postoperative days 9 to 24 (P = 0.020); moreover, MMT animals tended to spend more time on their contralateral limb than their operated limb while walking (P < 0.1). Ground reaction forces confirmed temporal shifts in symmetry and stance time, as the MMT group had lower vertical and propulsive ground reaction forces in their operated limb relative to the contralateral limb, naïve, and sham controls (P < 0.05). Levels of interleukin 6 in the MMT group tended to be higher than naïve controls (P = 0.072). Histology confirmed increased cartilage damage in the MMT group, consistent with OA initiation. Post hoc analysis revealed that gait symmetry, stance time imbalance, peak propulsive force, and serum interleukin 6 concentrations had significant correlations to the severity of cartilage lesion formation.

Conclusion
These data indicate significant gait compensations were present in the MMT group relative to medial collateral ligament (MCL) injury (sham) alone and naïve controls. Moreover, these data suggest that gait compensations are likely driven by meniscal instability and/or cartilage damage, and not by MCL injury alone.