bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel network-based method for measuring the functional relationship between gene sets
Authors: Wang Qianghu , Sun Jie , Zhou Meng , Yang Haixiu , Li Yan , Li Xiang , Lv Sali , Li Xia , Li Yixue
Published: March 2011

Motivation: In the functional genomic era, a large number of gene sets have been identified via high-throughput genomic and proteomic technologies. These gene sets of interest are often related to the same or similar disorders or phenotypes, and are commonly presented as differentially expressed gene lists, co-expressed gene modules, protein complexes or signaling pathways. However, biologists are still faced by the challenge of comparing gene sets and interpreting the functional relationships between gene sets into an understanding of the underlying biological mechanisms.

Results: We introduce a novel network-based method, designated corrected cumulative rank score (CCRS), which analyzes the functional communication and physical interaction between genes, and presents an easy-to-use web-based toolkit called GsNetCom to quantify the functional relationship between two gene sets. To evaluate the performance of our method in assessing the functional similarity between two gene sets, we analyzed the functional coherence of complexes in functional catalog and identified protein complexes in the same functional catalog. The results suggested that CCRS can offer a significant advance in addressing the functional relationship between different gene sets compared with several other available tools or algorithms with similar functionality. We also conducted the case study based on our method, and succeeded in prioritizing candidate leukemia-associated protein complexes and expanding the prioritization and analysis of cancer-related complexes to other cancer types. In addition, GsNetCom provides a new insight into the communication between gene modules, such as exploring gene sets from the perspective of well-annotated protein complexes.

Availability and Implementation: GsNetCom is a freely available web accessible toolkit at http://bioinfo.hrbmu.edu.cn/GsNetCom.

Contact:  lixia@hrbmu.edu.cn

Supplementary information:  Supplementary data are available at Bioinformatics online.
Inference of transcriptional regulatory network by bootstrapping patterns
Authors: Wang Hei-Chia , Chen Yi-HSiu , Kao Hung-Yu , Tsai Shaw-Jenq
Published: March 2011

Motivation: Transcriptional regulatory networks, which consist of linkages between transcription factors (TF) and target genes (TGene), control the expression of a genome and play important roles in all aspects of an organism's life cycle. Accurate prediction of transcriptional regulatory networks is critical in providing useful information for biologists to determine what to do next. Currently, there is a substantial amount of fragmented gene regulation information described in the medical literature. However, current related text analysis methods designed to identify protein–protein interactions are not entirely suitable for finding transcriptional regulatory networks.

Result: In this article, we propose an automatic regulatory network inference method that uses bootstrapping of description patterns to predict the relationship between a TF and its TGenes. The proposed method differs from other regulatory network generators in that it makes use of both positive and negative patterns for different vector combinations in a sentence. Moreover, the positive pattern learning process can be fully automatic. Furthermore, patterns for active and passive voice sentences are learned separately. The experiments use 609 HIF-1 expert-tagged articles from PubMed as the gold standard. The results show that the proposed method can automatically generate a predicted regulatory network for a transcription factor. Our system achieves an F-measure of 72.60%.

Availability: The software, training/test datasets and learned patterns are available at http://140.116.99.138/∼hcw0901/PubMedSearch.php

Contact:  seantsai@mail.ncku.edu.tw

Supplementary information:  Supplementary data are available at Bioinformatics online.
Development and Validation of the Questionnaire of Satisfaction with Perioperative Anesthetic Care for General and Regional Anesthesia in Taiwanese Patients
Authors: Mui Wui-Chiu , Chang Chia-Ming , Cheng Kong-Fah , Lee Tak-Yu , Ng Kwok-On , Tsao Kao-Rong , Hwang Fang-Ming
Published: March 2011

Background

To fulfill the increasing demand of service quality improvement in recent years, it is imperative to develop a proper instrument to evaluate patient satisfaction with perioperative anesthetic care for many institutes in Taiwan.

Methods

We used a six-factor 32-item pilot questionnaire developed in our previous study as our starting point in this study. Exploratory factor analysis of the pilot questionnaire for factor structure generation was performed in general anesthesia patients (group 1, n = 320) and resulted in the generation of the Patient Satisfaction with Perioperative Anesthetic Care questionnaire (PSPACq). Confirmatory factor analysis of the PSPACq in general anesthesia (group 2, n = 565) and regional anesthesia (group 3, n = 225) patients was performed for validation and cross-validation of the PSPACq model, respectively. The confounding variables and the patient loyalty effects on PSPACq scores were analyzed to evaluate the nomological validity of the PSPACq.

Result

Exploratory factor analysis of the pilot questionnaire in group 1 resulted in the development of the PSPACq (a seven-factor 30-item model). The standardized coefficients and indexes for the assessment of fit of the PSPACq model in group 2 (validation) and group 3 (cross-validation) patients revealed a well-fitting model. The results of the loyalty scores and confounding variables support the nomological validity of the PSPACq.

Conclusions

A valid and reliable questionnaire (PSPACq) with Taiwanese culture characteristics was developed and is suitable for testing of patient satisfaction with perioperative anesthesia care for patients receiving general or regional anesthesia for their surgery.
Regurgitation and remastication in the foregut-fermenting proboscis monkey (
Nasalis larvatus
)
Authors: Matsuda Ikki , Murai Tadahiro , Clauss Marcus , Yamada Tomomi , Tuuga Augustine , Bernard Henry , Higashi Seigo
Published: March 2011

Although foregut fermentation is often equated with rumination in the literature, functional ruminants (ruminants, camelids) differ fundamentally from non-ruminant foregut fermenters (e.g. macropods, hippos, peccaries). They combine foregut fermentation with a sorting mechanism that allows them to remasticate large particles and clear their foregut quickly of digested particles; thus, they do not only achieve high degrees of particle size reduction but also comparatively high food intakes. Regurgitation and remastication of stomach contents have been described sporadically in several non-ruminant, non-primate herbivores. However, this so-called ‘merycism’ apparently does not occur as consistently as in ruminants. Here, to our knowledge we report, for the first time, regurgitation and remastication in 23 free-ranging individuals of a primate species, the foregut-fermenting proboscis monkey (
Nasalis larvatus
). In one male that was observed continuously during 169 days, the behaviour was observed on 11 different days occurring mostly in the morning, and was associated with significantly higher proportions of daily feeding time than on days when it was not observed. This observation is consistent with the concept that intensified mastication allows higher food intake without compromising digestive efficiency, and represents an expansion of the known physiological primate repertoire that converges with a strategy usually associated with ruminants only.
Identification, sequencing and molecular analysis of Chp4, a novel chlamydiaphage of Chlamydophila abortus belonging to the family Microviridae
Authors: Sait Michelle , Livingstone Morag , Graham Rebecca , Inglis Neil F. , Wheelhouse Nick , Longbottom David
Published: March 2011

Members of the familyMicroviridaehave been identified in a number of chlamydial species infecting humans (phage CPAR39 inChlamydophila pneumoniae), other mammals (φCPG1 inChlamydophila caviae, Chp2 inChlamydophila abortusand Chp3 inChlamydophila pecorum) and birds (Chp1 inChlamydophila psittaci). This study describes the identification and genome sequencing of Chp4, an icosahedral, 4530 bp, ssDNA phage inC. abortus. Chp4 is predicted to contain eight ORFs, six of which could be assigned putative functions based on sequence similarity to characterized bacteriophage. Gene order and content were highly conserved amongst chlamydiaphage, with the highest sequence variability occurring in the IN5 and INS variable regions of the VP1 major coat protein, which has been associated with host cell recognition and binding. Phylogenetic analysis of VP1 indicated that Chp4 is a member of theChlamydiamicrovirus, and is most closely related to phage φCPG1 and CPAR39.
The tail-elicited tail withdrawal reflex of Aplysia is mediated centrally at tail sensory-motor synapses and exhibits sensitization across multiple temporal domains
Authors: Philips Gary T. , Sherff Carolyn M. , Menges Steven A. , Carew Thomas J.
Published: March 2011

The defensive withdrawal reflexes of Aplysia californica have provided powerful behavioral systems for studying the cellular and molecular basis of memory formation. Among these reflexes the tail-elicited tail withdrawal reflex (T-TWR) has been especially useful. In vitro studies examining the monosynaptic circuit for the T-TWR, the tail sensory-motor (SN-MN) synapses, have identified the induction requirements and molecular basis of different temporal phases of synaptic facilitation that underlie sensitization in this system. They have also permitted more recent studies elucidating the role of synaptic and nuclear signaling during synaptic facilitation. Here we report the development of a novel, compartmentalized semi-intact T-TWR preparation that allows examination of the unique contributions of processing in the SN somatic compartment (the pleural ganglion) and the SN-MN synaptic compartment (the pedal ganglion) during the induction of sensitization. Using this preparation we find that the T-TWR is mediated entirely by central connections in the synaptic compartment. Moreover, the reflex is stably expressed for at least 24 h, and can be modified by tail shocks that induce sensitization across multiple temporal domains, as well as direct application of the modulatory neurotransmitter serotonin. This preparation now provides an experimentally powerful system in which to directly examine the unique and combined roles of synaptic and nuclear signaling in different temporal domains of memory formation.
Integration of Auxin and Salt Signals by the NAC Transcription Factor NTM2 during Seed Germination in Arabidopsis
Authors: Park Jungmin , Kim Youn-Sung , Kim Sang-Gyu , Jung Jae-Hoon , Woo Je-Chang , Park Chung-Mo
Published: March 2011

Seed germination is regulated through elaborately interacting signaling networks that integrate diverse environmental cues into hormonal signaling pathways. Roles of gibberellic acid and abscisic acid in germination have been studied extensively using Arabidopsis (Arabidopsis thaliana) mutants having alterations in seed germination. Auxin has also been implicated in seed germination. However, how auxin influences germination is largely unknown. Here, we demonstrate that auxin is linked via the IAA30 gene with a salt signaling cascade mediated by the NAM-ATAF1/2-CUC2 transcription factor NTM2/Arabidopsis NAC domain-containing protein 69 (for NAC with Transmembrane Motif1) during seed germination. Germination of the NTM2-deficient ntm2-1 mutant seeds exhibited enhanced resistance to high salinity. However, the salt resistance disappeared in the ntm2-1 mutant overexpressing the IAA30 gene, which was induced by salt in a NTM2-dependent manner. Auxin exhibited no discernible effects on germination under normal growth conditions. Under high salinity, however, whereas exogenous application of auxin further suppressed the germination of control seeds, the auxin effects were reduced in the ntm2-1 mutant. Consistent with the inhibitory effects of auxin on germination, germination of YUCCA 3-overexpressing plants containing elevated levels of active auxin was more severely influenced by salt. These observations indicate that auxin delays seed germination under high salinity through cross talk with the NTM2-mediated salt signaling in Arabidopsis.
Assessing the overlap between the diet of a coastal shark and the surrounding prey communities in a sub‐tropical embayment
Authors: Gutteridge A. N. , Bennett M. B. , Huveneers C. , Tibbetts I. R.
Published: March 2011

An elasmobranch survey of sub‐tropical Hervey Bay, Australia, captured the slit‐eye shark Loxodon macrorhinus at only one of three sites sampled. The dietary composition of this small shark species was compared to the prey communities within Hervey Bay to test whether prey availability was driving this observation. Dietary analysis of prey groups revealed that teleosts dominated the diet, per cent index of relative importance, % IRI (79·5%) and per cent geometric index of importance, % GII (52·7%), with shrimp‐like invertebrates and cephalopods identified as the most important invertebrate prey groups. Baited remote underwater video (BRUV) used to sample prey communities at each site, demonstrated a highly diverse and significantly different community composition among the sites. There was no significant overlap between the diet of L. macrorhinus and any of the prey communities detected by BRUVs according to one‐way analysis of similarities and the simplified Morisita index. Habitat electivity analysis revealed affinity of L. macrorhinus for the site with the highest water clarity (Secchi disc depth), opposing that of three other shark species. Overall, the results suggest that the distribution of L. macrorhinus is not driven by prey availability but other factors such as water clarity, predator avoidance or a reduction in interspecies competition.
Macrophage infiltration and its prognostic relevance in clear cell renal cell carcinoma
Authors: Komohara Yoshihiro , Hasita Horlad , Ohnishi Koji , Fujiwara Yukio , Suzu Shinya , Eto Masatoshi , Takeya Motohiro
Published: March 2011

Most malignant tumors evidence infiltration of many macrophages. In this study, we investigated an anti‐inflammatory macrophage phenotype (M2) in clear cell renal cell carcinoma (RCC) using CD163 and CD204 as markers. Immunostaining showed a correlation between the number of CD163+ cells and age, sex, nuclear grade, and TNM classification. High infiltration of CD163+ cells was significantly associated with poor clinical prognosis in univariate analysis but not in multivariate analysis. We also carried out in vitro studies to examine cell–cell interactions between macrophages and cancer cells. Culture supernatants from RCC cell lines induced polarization of macrophages toward the M2 phenotype. Coculture of macrophages with cancer cells significantly induced activation of signal transducers and activators of transcription‐3 (Stat3) in the cancer cells. Direct coculture of RCC cells with macrophages led to stronger activation of Stat3 in the cancer cells than did indirect coculture using Transwell chamber dishes. Because RCC cells expressed membrane‐type macrophage colony‐stimulating factor (mM‐CSF) on the cell surface, we suggested that this mM‐CSF plays an important role in direct cell–cell interactions. Stat3 activation in cancer cells that was induced by coculture with macrophages was suppressed by downregulation of the M‐CSF receptor (M‐CSFR) in macrophages and by an inhibitor of M‐CSFR. In conclusion, investigation of CD163+ tumor‐associated macrophages would be useful for assessment of the clinical prognosis of patients with ccRCC. Cell–cell interactions mediated by mM‐CSF and M‐CSFR binding could contribute to cancer cell activation. (Cancer Sci 2011; 102: 1424–1431)
Detection of HTLV‐1 by means of HBZ gene in situ hybridization in formalin‐fixed and paraffin‐embedded tissues
Authors: Shimizu‐Kohno Kei , Satou Yorifumi , Arakawa Fumiko , Kiyasu Junichi , Kimura Yoshizo , Niino Daisuke , Sugita Yasuo , Ishikawa Fumihiko , Matsuoka Masao , Ohshima Koichi
Published: March 2011

Adult T‐cell leukemia/lymphoma (ATLL) is a T‐cell malignancy associated with HTLV‐1. The HTLV‐1 provirus genome has the pX region that encodes tax and HTLV‐1 basic leucine zipper factor (HBZ). Previous studies have reported that the tax gene is expressed in few ATLL cases, but the HBZ gene in all ATLL cases. In this study, we used HBZ gene in situ hybridization (HBZ‐ISH) for detection of the HBZ gene in formalin‐fixed paraffin‐embedded tissues. This method showed that all cases (n = 19) were positive for the ATLL cell line (MT‐1, MT‐2, and MT‐4) and ATLL mouse model (HBZ‐Tg mice and NOD/SCID/β2‐microglobulinnull mice with ATLL transplanted), and the HBZ gene was also detected in all human ATLL cases (n = 16). The percentage of positive cells in HBZ‐ISH was 5–70%. Immunohistochemical staining for Tax protein showed positivity in seven of 11 cases in NOD/SCID/β2‐microglobulinnull mice with ATLL transplanted and in six of eight human ATLL cases, but the percentage of positive cells was very low (range, 1–5%). Although HBZ‐ISH is unsuitable to detect HTLV‐1 clonality, this method is convenient and can be useful for the histological diagnosis of ATLL in HTLV‐1 sero‐indeterminate patients. (Cancer Sci 2011; 102: 1432–1436)
Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake
Authors: Chen Y. , Gondro C. , Quinn K. , Herd R. M. , Parnell P. F. , Vanselow B.
Published: March 2011

Feed efficiency is an economically important trait in beef production. It can be measured as residual feed intake. This is the difference between actual feed intake recorded over a test period and the expected feed intake of an animal based on its size and growth rate. DNA‐based marker‐assisted selection would help beef breeders to accelerate genetic improvement for feed efficiency by reducing the generation interval and would obviate the high cost of measuring residual feed intake. Although numbers of quantitative trait loci and candidate genes have been identified with the advance of molecular genetics, our understanding of the physiological mechanisms and the nature of genes underlying residual feed intake is limited. The aim of the study was to use global gene expression profiling by microarray to identify genes that are differentially expressed in cattle, using lines genetically selected for low and high residual feed intake, and to uncover candidate genes for residual feed intake. A long‐oligo microarray with 24 000 probes was used to profile the liver transcriptome of 44 cattle selected for high or low residual feed intake. One hundred and sixty‐one unique genes were identified as being differentially expressed between animals with high and low residual feed intake. These genes were involved in seven gene networks affecting cellular growth and proliferation, cellular assembly and organization, cell signalling, drug metabolism, protein synthesis, lipid metabolism, and carbohydrate metabolism. Analysis of functional data using a transcriptional approach allows a better understanding of the underlying biological processes involved in residual feed intake and also allows the identification of candidate genes for marker‐assisted selection.
Does β‐adrenoceptor blocker therapy improve cancer survival? Findings from a population‐based retrospective cohort study
Authors: Shah Sunil M. , Carey Iain M. , Owen Christopher G. , Harris Tess , DeWilde Stephen , Cook Derek G.
Published: March 2011

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT

• In vitro studies suggest that β‐adrenoceptor blocker therapy inhibits cancer cell proliferation and migration leading to their consideration as novel therapeutic agents for cancer.

• While trials in humans have suggested β‐adrenoceptor blockers have no effect on cancer incidence, their effect on cancer survival has not been studied.

• Recent limited evidence in breast cancer patients suggests that β‐adrenoceptor blockers may improve cancer‐specific survival.

WHAT THIS STUDY ADDS

• This study is the first to examine cancer survival in patients receiving β‐adrenoceptor blockers across a range of common cancers in a large population‐based sample.

• For common tumour sites, including lung, breast and colon, there was no evidence that β‐adrenoceptor blocker treatment modified overall survival but poorer survival was seen in patients with prostate and pancreatic cancer.

• Our findings do not support development of clinical trials on β‐adrenoceptor blocker therapy for cancer without further evidence of a beneficial effect in humans.

AIMS To examine the effect of β‐adrenoceptor blocker treatment on cancer survival.

METHODS In a UK primary care database, we compared patients with a new cancer diagnosis receiving β‐adrenoceptor blockers regularly (n= 1406) with patients receiving other antihypertensive medication (n= 2056).

RESULTS Compared with cancer patients receiving other antihypertensive medication, patients receiving β‐adrenoceptor blocker therapy experienced slightly poorer survival (HR = 1.18, 95% CI 1.04, 1.33 for all β‐adrenoceptor blockers; HR = 1.21, 95% CI 0.94, 1.55 for non‐selective β‐adrenoceptor blockers). This poorer overall survival was explained by patients with pancreatic and prostate cancer with no evidence of an effect on survival for patients with lung, breast or colorectal cancer. Analysis in a cancer‐free matched parallel cohort did not suggest selection bias masked a beneficial effect.

CONCLUSION Our study does not support the hypothesis that β‐adrenoceptor blockers improve survival for common cancers.
Warming climate advances breeding and improves synchrony of food demand and food availability in a boreal passerine
Authors: VATKA EMMA , ORELL MARKKU , RYTKÖNEN SEPPO
Published: March 2011

Global climate change affects ecosystems via several trophic levels. We investigated changes in the timing of breeding in the willow tit (Poecile montanus) and timing of its caterpillar food resource in relation to warming springs in a boreal forest. We used generalized linear mixed effect models to study the importance of synchrony between the timing of breeding in willow tits and the caterpillar food availability on the breeding success, measured as nestling survival rate and mean nestling weight. Both the timing of breeding and the timing of the caterpillar peak advanced during the last decades, and were well explained by spring temperatures. Unlike in most passerine populations studied, synchrony has improved with rising spring temperatures. However, it had only a modest although statistically significant positive influence on breeding success. Spring temperatures do not seem to be used as cues for the timing of caterpillar food availability by willow tits. We conclude that responses to climatic warming seem to be population, species and habitat specific, necessitating research in a wide range of taxa in different climatic zones.
Insights into the climate of safety towards the prevention of falls among hospital staff
Authors: Black Alex A , Brauer Sandra G , Bell Rebecca AR , Economidis Alyssia J , Haines Terry P
Published: March 2011

Aims and objectives.  To explore the climate of safety towards falls prevention among frontline hospital staff.

Background.  Falls represent a serious threat to patient safety in hospitals. A positive safety climate is vital in healthcare organisations to promote safe care and reduce patient harm, yet little is known about the safety climate towards falls prevention among frontline staff in the hospital setting.

Design.  An observational descriptive study.

Methods.  Frontline staff working in five acute and subacute wards at two metropolitan hospitals in Australia were sampled. Safety climate towards falls prevention was measured using the Patient Safety Climate in Healthcare Organizations survey. The item‐specific, dimension‐specific and overall percentage of problematic responses were calculated, based on the frequency of responses inconsistent with a positive safety climate. Higher percentage of problematic responses values reflects a weaker safety climate.

Results.  The overall percentage of problematic responses towards falls prevention was 15%. Dimensions that were most inconsistent with a positive safety climate included ‘provision of safe care’ (percentage of problematic responses 42·1%) and ‘unit recognition and support for safety efforts’ (percentage of problematic responses 26·9%). The overall and dimension‐specific percentage of problematic responses scores did not vary by hospital, or between nursing and allied health disciplines.

Conclusions.  The study provides important insights into the safety climate towards falls prevention among frontline hospital staff. Further research is required to improve the problematic areas of safety climate towards falls prevention, to promote and deliver safe patient care by hospital healthcare teams.

Relevance to clinical practice.  Identifying problematic areas in the safety climate towards falls prevention is a first step in guiding the development of targeted strategies to promote a positive atmosphere towards preventing falls and reducing patient harm in the hospital setting.
‘We’re just not getting it right’– how should we provide care to the older person with multi‐morbid chronic conditions?
Authors: Lupari Marina , Coates Vivien , Adamson Gary , Crealey Grainne E
Published: March 2011

Aims and objectives.  The aim was to review available literature on research and service evaluation evidence of nurse‐led case management services targeting older people with multiple chronic conditions in their own homes. This was anticipated to highlight important issues for nursing practice, healthcare policy, service provision and health service research.

Background.  Enhanced roles for nurses have developed in response to demands for increased efficiency in the provision of healthcare especially in the area of chronic disease management. It is apparent that the evidence to support nurses providing a case management approach for patients with multimorbid chronic conditions in their home environment is ambiguous.

Design.  A systematic review of the literature.

Methods.  The review was carried out across multiple sources including search and alert engines, electronic databases, relevant journal websites and grey literature. The inclusion criteria applied concentrated on articles in the English language, case management intervention involving nurses providing care in the patients’ own home and older people (aged over 65 years) with multiple chronic illnesses. Of a total of 568 papers identified, eight were of relevance and included in the review.

Results.  The qualitative data derived from this systematic review suggests that access to case management services had a positive impact on the patient, the carer and the healthcare staff particularly the General Practitioner. In contrast the more robust quantitative data does not demonstrate a significant impact on emergency admissions, bed days, nor costs.

Conclusions.  Further research is needed to understand how case management can most effectively improve service effectiveness for patients and their carers and reduce cost of care.

Relevance to clinical practice.  A new emphasis on comparative effectiveness research is required which has the potential to reshape the whole system of healthcare provision for patients with complex needs.
Integrating stress‐related ventricular functional and angiographic data in preventive cardiology: a unified approach implementing a Bayesian network
Authors: Berchialla Paola , Foltran Francesca , Bigi Riccardo , Gregori Dario
Published: March 2011

Background  Identification of key factors associated with the risk of adverse cardiovascular events and quantification of this risk using multivariable prediction algorithms are among the major advances made in preventive cardiology and cardiovascular epidemiology.

Methods  In the present paper, we examined clinical predictors of adverse cardiovascular events among 228 individuals with symptoms suggestive of coronary artery disease (CAD) undergoing functional (stress echocardiography) and anatomical (coronary angiography) assessment of CAD. Particularly, we evaluate the possibility to integrate simple measures that have known prognostic value and more recently discovered predictors of risk, such as stress‐related ventricular function data and angiographic data, in a unique model implementing a Bayesian network (BN). Moreover, we compared the performance of BN and the covariates hierarchy with those obtained from logistic regression model and from a set of alternative tools becoming popular in various clinical settings, including random forest classification tree analysis, artificial neural networks and support vector machine.

Results  Network graph and results coming from sensitivity analysis, where variables are ranked according to the gain they provided in variance reduction, seem have an easily intuitive lecture: variables that are measure of ventricular disfunction or of the extent of CAD show a greater impact in predicting event. On the other hand, anamnestic data such as diabetes, dyslipidaemia, hypertension, smoke habits, which are related to the outcome throughout a process of intermediate variables, per se have a small role in outcome prediction. BNs are able to explain a relevant part of variance (70%) and have discrimination ability superior or comparable with those to random forest classification tree analysis, artificial neural networks and support vector machine.

Discussion  Despite the complexity of interactions, model obtained implementing a BN seems to be able to adequately describe the relationships existing among the analysed variables. BN, being able to predict scenarios in which new variables can be incorporated as health process evolves, can measure individual's risks for adverse cardiovascular events, providing a permanent second opinion to the medical practitioner and assisting diagnostic and therapeutic process.
Loss of neurofilaments in the neuromuscular junction in a rat model of proximal axonopathy
Authors: Soler‐Martín C. , Vilardosa Ú. , Saldaña‐Ruíz S. , Garcia N. , Llorens J.
Published: March 2011

C. Soler‐Martín, Ú. Vilardosa, S. Saldaña‐Ruíz, N. Garcia and J. Llorens (2012) Neuropathology and Applied Neurobiology38, 61–71

Loss of neurofilaments in the neuromuscular junction in a rat model of proximal axonopathy

Aims: Rodents exposed to 3,3′‐iminodipropionitrile (IDPN) develop an axonopathy similar to that observed in amyotrophic lateral sclerosis motor neurones, in which neurofilaments accumulate in swollen proximal axon segments. This study addressed the hypotheses that this proximal axonopathy is associated with loss of neurofilament proteins in the neuromuscular junctions and a progressive loss of neurofilaments advancing in a distal‐proximal direction from the distal motor nerve. Methods: Adult male Long‐Evans rats were exposed to 0 or 15 mM of IDPN in drinking water for 1, 3 or 5 weeks, and their distal axons and neuromuscular junction organization studied by immunohistochemistry. Quantitative data were obtained by confocal microscopy on whole mounts of the Levator auris longus. Results: Muscles showed no change in the distribution of acetylcholine receptor labelling in the neuromuscular junctions after IDPN. In contrast, the amount of neurofilament labelling in the junctions was significantly reduced by IDPN, assessed with two different anti‐neurofilament antibodies. In preterminal axons and in more proximal axon levels, no statistically significant reductions in neurofilament content were observed. Conclusions: The proximal neurofilamentous axonopathy induced by IDPN is associated with an abnormally low content of neurofilaments in the motor terminals, with a potential impact in the function or stability of the neuromuscular junction. In contrast, neurofilaments are significantly maintained in the distal axon.
Clinical characteristics of pediatric patients evaluated for primary immunodeficiency
Authors: MacGinnitie Andrew , Aloi Frank , Mishra Seema
Published: March 2011

To cite this article: MacGinnitie A, Aloi F, Mishra S. Clinical characteristics of pediatric patients evaluated for primary immunodeficiency. Pediatric Allergy Immunology 2011; 22: 671–675.

Objective:  When to evaluate a child for possible immune deficiency is a challenge, as many children have frequent infections for which they are treated with antibiotics. We aimed to describe the clinical characteristics of children evaluated for possible primary immunodeficiency in a specialist clinic. We specifically aimed to evaluate widely promulgated ‘warning signs of primary immunodeficiency’ and to evaluate the relationship between primary immunodeficiency and atopy.

Methods:  A retrospective analysis of 141 children who underwent testing for possible primary immunodeficiency was undertaken.

Results:  Thirty‐two (23%) children were diagnosed with an underlying primary immunodeficiency, and published warning signs were neither sensitive nor specific for primary immunodeficiency. Patients with allergy as determined by the presence of antigen‐specific IgE were more likely to be diagnosed with immunodeficiency.

Conclusions:  Widely promulgated warning signs did not distinguish between patients with and without primary immunodeficiency. Likewise, primary immunodeficiency and allergy may coexist.
HLA antibodies in pediatric heart transplantation
Authors: Ho Eric K. , Vasilescu Elena R. , Vlad George , Marboe Charles C. , Addonizio Linda J. , Suciu‐Foca Nicole
Published: March 2011

Ho EK, Vasilescu ER, Vlad G, Marboe CC, Addonizio LJ, Suciu‐Foca N. HLA antibodies in pediatric heart transplantation. Pediatr Transplantation 2011: 15: 458–464. © 2011 John Wiley & Sons A/S.

Abstract:  We have analyzed the impact of anti‐HLA antibodies present in the patients’ circulation prior and/or following heart transplantation in a population of 108 pediatric recipients. Anti‐HLA class I and class II antibodies were monitored by traditional CDC using donor and panel T and B lymphocytes and by SPA for detection of DSA. There was a highly significant correlation between the development of AMR and presence of CDC‐ or SPA‐detected DSA. However, the fraction of the transplant population which remained AMR‐free was much higher among patients with SPA‐detected compared to CDC‐detected DSA. Furthermore, long‐term graft survival was negatively affected only by cytotoxic, complement‐fixing anti‐HLA class I antibodies developing following transplantation. Anti‐HLA class I or class II antibodies detected by SPA had no effect on long‐term survival rates.
Effects of rural status on health outcomes in pediatric liver transplantation: A single center analysis of 388 patients
Authors: Park K. T. , Nanda Pranav , Bensen Rachel , Strichartz Debra , Esquivel Carlos , Cox Kenneth
Published: March 2011

Park KT, Nanda P, Bensen R, Strichartz D, Esquivel C, Cox K. Effects of rural status on health outcomes in pediatric liver transplantation: A single center analysis of 388 patients. Pediatr Transplantation 2011: 15: 300–305. © 2011 John Wiley & Sons A/S.

Abstract:  Rural status of patients may impact health before and after pediatric LT. We used UI codes published by the USDA to stratify patients as urban or rural depending county residence. A total of 388 patients who had LT and who met criteria were included. Rejection, PTLD, and survival were used as primary outcome measures of post‐LT health. UNOS Status 1 and PELD/MELD scores >20 were used as secondary outcome measures of poorer pre‐LT health. Logistic regression models were run to determine associations. We did not find any statistically significant differences in pre‐ or post‐LT outcomes with respect to rurality. Among rural patients, there was a general trend for decreased incidence of rejection (25.0% vs. 33.4%; OR 0.64, 95% CI 0.29–1.44), increased risk of PTLD (5.6% vs. 3.4%; OR 1.86, 95% CI 0.36–3.31), and decreased survival (OR 0.85, 95% CI 0.34–2.13) after LT. Rural patients also tended to be sicker at the time of LT than patients from urban areas, with increased proportion of Status 1 (OR 1.17, 95% CI 0.51–2.70) and PELD/MELD scores >20 (OR 1.20, 95% CI 0.59–2.45). From a single center experience, we conclude that rurality did not significantly affect health outcomes after LT, although a larger study may validate the general trends that rural patients may have decreased rejection, increased PTLD, and mortality, and be in poorer health at the time of LT.
Unrelated cord blood transplantation can restore hematologic and immunologic functions in patients with Chediak–Higashi syndrome
Authors: Rihani Rawad , Barbar Maha , Faqih Nesreen , Halalsheh Hadeel , Hussein Ayad Ahmad , Al‐Zaben Abdul Hadi , Rahman Fawzi Abdel , Sarhan Mahmoud
Published: March 2011

Rihani R, Barbar M, Faqih N, Halalsheh H, Hussein A, Al‐Zaben AH, Rahman FA, Sarhan M. Unrelated cord blood transplantation can restore hematologic and immunologic functions in patients with Chediak–Higashi syndrome.

Abstract:  CHS is a rare hereditary fatal disease, if not treated. APs occur in 85% of patients and are usually the main cause of mortality, and HSCT from HLA‐matched related and unrelated donors is the only effective treatment for CHS and prevents recurrences of APs. We reviewed the records of three patients with CHS who underwent UCBT at KHCC. Records were examined for clinical features at the time of UCBT, conditioning regimens, morbidities, and outcomes. Conditioning comprised BU, cyclophosphamide, horse ATG, and etoposide. All patients tolerated the conditioning well. Two patients are alive, one with mixed and the other with full donor chimerism; hematologic and immunologic defects of CHS have been corrected in both patients. They show no evidence of recurrences of APs and have normal growth and development. In patients with CHS who lack HLA‐matched related and unrelated donors, UCBT is a suitable alternative source of stem cells to restore immunologic and hematologic functions and prevent AP relapses, even in mixed chimeric states. Long follow‐up and close monitoring are essential to evaluate the long‐term benefits of using UCBT in patients with CHS.
Studies on the Transmission of Theileria annulata to Cattle by the Tick Hyalomma lusitanicum
Authors: Viseras J. , Hueli L. E. , Adroher F. J. , García‐Fernández P.
Published: March 2011

The role of the ixodid tick Hyalomma lusitanicum Koch 1844 as a vector of Mediterranean or tropical theileriosis (caused by the protozoan parasite Theileria annulata Dschunkowsky et Luhs 1904) in southern Spain was studied. Hyalomma lusitanicum was the most common tick, and the only species of the genus Hyalomma L., found on T. annulata‐infected cattle from the theileriosis enzootic area studied (province of Cádiz, southern Spain). Likewise, we found that all sera of the cattle previously considered as suspected of theileriosis by clinical signs, tested for T. annulata antibodies, were positive and all blood samples of these suspected cattle examined had infected erythrocytes. Partially fed H. lusitanicum adults were collected in the field on T. annulata‐infected cattle in this enzootic area and fed on an uninfected calf in an experimental farm free of theileriosis and ticks. At approximately 3 weeks post‐tick feeding on the calf, this became positive for T. annulata antibodies and T. annulata merozoites were found in erythrocytes from blood smears. These results show the ability of H. lusitanicum to transmit the protozoan parasite T. annulata to susceptible cattle and indicate that H. lusitanicum is probably an important vector of T. annulata in the enzootic area surveyed.
A Case of an Embryo Transfer Calf Infected with Bovine Leukemia Virus from the Recipient Cow
Authors: Fukai K. , Sato M. , Kawara M. , Hoshi Z. , Ueno S. , Chyou N. , Akashi H.
Published: March 2011

A case was discovered where the embryo transfer (ET) calf had been infected with bovine leukemia virus (BLV) from the recipient cow. The embryo was transferred from the BLV‐uninfected donor cow to the recipient cow. However, the BLV test had not been performed to the recipient cow before ET was performed. The ET calf was raised in a calf hatch from birth to 1‐month old and was given the recipient cow's colostrum and milk artificially. The ET calf was raised with the two other calves from a 1‐month old to a 6‐month old. The BLV test was performed to the ET calf by agar gel precipitation (AGP) and passive haemagglutination (PHA) assay when the ET calf was 6 months old. Because the ET calf was positive, the BLV test was performed to the recipient cow, the two other calves raised with the ET calf and the two dams of the two other calves. Because the recipient cow only was positive at the time of the first test, we judged that the ET calf had been infected with BLV from the recipient cow. The importance of the BLV test being carried out on the recipient cow for the prevention of enzootic bovine leukemia in a case of ET was recognised.
Serological Survey for Antibodies against Selected Infectious Agents among Fallow Deer (Dama dama) in Central Italy
Authors: Cuteri V. , Diverio S. , Carnieletto P. , Turilli C. , Valente C.
Published: March 2011

Sera were collected from 224 fallow deer (Dama dama) in reserves in central Italy. Samples were tested for antibodies against Chlamydia spp., Brucella spp. and Coxiella spp. with the complement fixation (CF) test. Indirect immunofluorescence was used to test for antibodies against Borrelia spp. and agglutination tests were conducted for Leptospira interrogans antibodies. Enzyme‐linked immunosorbent assay (ELISA) tests were used to detect antibodies against bovine herpesvirus‐1 (BHV‐1) and bovine viral diarrhoea virus (BVDV). All samples were negative for antibodies against Brucella spp., L. interrogans, Coxiella spp. and BHV‐1. Four samples (1.8%) had antibodies against Chlamydia spp., nine (4%) against Borrelia spp. and 10 (4.5%) against BVDV. These results indicate that fallow deer in central Italy have a low rate of exposure to pathogens typical of domestic livestock.
Benign mucinous cystadenoma with stromal luteinization responsible for maternal virilization and fetal intrauterine growth restriction
Authors: Bolat Filiz , Parlakgumus Ayse , Canpolat Tuba , Tuncer Ilhan
Published: March 2011

Virilization caused by ovarian tumors with functioning stroma during pregnancy is extremely rare and has been reported to be due to different types of ovarian tumors. In mucinous cystadenomas with maternal virilization during pregnancy, the stromal cells responsible for hormone secretion resemble lutein or Leydig cells and have been referred to as luteinized stromal cells.

Here we present a rare case of mucinous cystadenoma accompanied by virilization, which was also the cause of fetal intrauterine growth restriction during pregnancy and discuss the mechanisms of hormone production in these tumors in the light of the literature.
Torsion of a rudimentary uterine horn at 22 weeks of gestation
Authors: Wang Bo , Zhou Jian‐hong , Jin Hang‐mei
Published: March 2011

Rudimentary uterine horn is an uncommon abnormality of the female reproductive tract. Torsion of rudimentary uterine horn in pregnancy is even rarer. A case of successful excision of distorted rudimentary uterine horn in the second trimester, which caused severe abdominal pain, is described. A congenital absence of the right kidney was discovered simultaneously. The pregnancy continued uneventfully until term delivery.
Growing teratoma syndrome of the Ovary: A case report with FDG ‐PET findings
Authors: Kikawa Satomi , Todo Yukiharu , Minobe Shinichiro , Yamashiro Katsushige , Kato Hidenori , Sakuragi Noriaki
Published: March 2011

Growing teratoma syndrome (GTS) is defined as enlarging masses during or after chemotherapy for germ cell tumors, and containing only mature teratoma components. A surgical resection is important to confirm a diagnosis and thereby result in the resection of the most appropriate therapeutic management. GTS is a rare event in association with ovarian germ cell tumors. This report presents a case of a 36‐year‐old female treated surgically for GTS found during the follow‐up after chemotherapy and the primary surgical resection of a malignant immature teratoma. Those masses showed fluorodeoxyglucose positron emission tomography positivity and elevated serum CA19‐9 prior to the second operation. The histology revealed a mature teratoma. The patient has been disease free for 6 months after the second operation.
Yellowstone Lake: high‐energy geochemistry and rich bacterial diversity
Authors: Clingenpeel Scott , Macur Richard E. , Kan Jinjun , Inskeep William P. , Lovalvo Dave , Varley John , Mathur Eric , Nealson Kenneth , Gorby Yuri , Jiang Hongchen , LaFracois Toben , McDermott Timothy R.
Published: March 2011

Yellowstone Lake is central to the balanced functioning of the Yellowstone ecosystem, yet little is known about the microbial component of its food chain. A remotely operated vehicle provided video documentation (http://www.tbi.montana.edu/media/videos/) and allowed sampling of dilute surface zone waters and enriched lake floor hydrothermal vent fluids. Vent emissions contained substantial H2S, CH4, CO2 and H2, although CH4 and H2 levels were also significant throughout the lake. Pyrosequencing and near full‐length sequencing of Bacteria 16S rRNA gene diversity associated with two vents and two surface water environments demonstrated that this lake contains significant bacterial diversity. Biomass was size‐fractionated by sequentially filtering through 20‐µm‐, 3.0‐µm‐, 0.8‐µm‐ and 0.1‐µm‐pore‐size filters, with the > 0.1 to < 0.8 µm size class being the focus of this study. Major phyla included Acidobacteria, Actinobacteria, Bacteroidetes, α‐ and β‐Proteobacteria and Cyanobacteria, with 21 other phyla represented at varying levels. Surface waters were dominated by two phylotypes: the Actinobacteria freshwater acI group and an α‐Proteobacteria clade tightly linked with freshwater SAR11‐like organisms. We also obtained evidence of novel thermophiles and recovered Prochlorococcus phylotypes (97–100% identity) in one near surface photic zone region of the lake. The combined geochemical and microbial analyses suggest that the foundation of this lake's food chain is not simple. Phototrophy presumably is an important driver of primary productivity in photic zone waters; however, chemosynthetic hydrogenotrophy and methanotrophy are likely important components of the lake's food chain.