bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of landscape features on population genetic structure in Yunnan snub‐nosed monkeys (Rhinopithecus bieti) implies an anthropogenic genetic discontinuity
Authors: LIU ZHIJIN , REN BAOPING , WU RUIDONG , ZHAO LIANG , HAO YANLI , WANG BOSHI , WEI FUWEN , LONG YONGCHENG , LI MING 
Published: September 2009

AbstractThe Tibetan Plateau is one of the top 10 biodiversity hotspots in the world and acts as a modern harbour for many rare species because of its relatively pristine state. In this article, we report a landscape genetic study on the Yunnan snub‐nosed monkey (Rhinopithecus bieti), a primate endemic to the Tibetan Plateau. DNA was extracted from blood, tissue and fecal samples of 135 wild individuals representing 11 out of 15 extant monkey groups. Ten microsatellite loci were used to characterize patterns of genetic diversity. The most striking feature of the population structure is the presence of five subpopulations with distinct genetic backgrounds and unique spatial regions. The population structure of R. bieti appears to be shaped by anthropogenic landscape features as gene flow between subpopulations is strongly impeded by arable land, highways and human habitation. A partial Mantel test showed that 36.23% (r = 0.51, P = 0.01) of the genetic distance was explained by habitat gaps after controlling for the effect of geographical distance. Only 4.92% of the genetic distance was explained by geographical distance in the partial Mantel test, and no significant correlation was found. Estimation of population structure history indicates that environmental change during the last glacial maximum and human impacts since the Holocene, or a combination of both, have shaped the observed population structure of R. bieti. Increasing human activity on the Plateau, especially that resulting in habitat fragmentation, is becoming an important factor in shaping the genetic structure and evolutionary potential of species inhabiting this key ecosystem.
Specific and pleiotropic patterns of mRNA regulation by ArcZ, a conserved, Hfq‐dependent small RNA
Authors: Papenfort Kai , Said Nelly , Welsink Tim , Lucchini Sacha , Hinton Jay C. D. , Vogel Jörg 
Published: September 2009

SummaryThe small RNA, ArcZ (previously RyhA/SraH), was discovered in several genome‐wide screens in Escherichia coli and Salmonella. Its high degree of genomic conservation, its frequent recovery by shotgun sequencing, and its association with the RNA chaperone, Hfq, identified ArcZ as an abundant enterobacterial ‘core’ small RNA, yet its function remained unknown. Here, we report that ArcZ acts as a post‐transcriptional regulator in Salmonella, repressing the mRNAs of the widely distributed sdaCB (serine uptake) and tpx (oxidative stress) genes, and of STM3216, a horizontally acquired methyl‐accepting chemotaxis protein (MCP). Both sdaCB and STM3216 are regulated by sequestration of the ribosome binding site. In contrast, the tpx mRNA is targeted in the coding sequence (CDS), arguing that CDS targeting is more common than appreciated. Transcriptomic analysis of an arcZ deletion strain further argued for the existence of a distinct set of Salmonella loci specifically regulated by ArcZ. In contrast, increased expression of the sRNA altered the steady‐state levels of > 16% (> 750) of all Salmonella mRNAs, and rendered the bacteria non‐motile. Deep sequencing detected a dramatically changed profile of Hfq‐bound sRNAs and mRNAs, suggesting that the unprecedented pleiotropic effects by a single sRNA might in part be caused by altered post‐transcriptional regulation.
Alexander Fleming, citrated blood and penicillin: paths not pursued and applications delayed
Authors: Mortimer P. P. 
Published: September 2009

summary.Ninety years ago Alexander Fleming (later to discover penicillin) jointly wrote a description of the use of indirect transfusions of citrated blood at a World War 1 (WW1) base hospital. It was the longest series yet to be published, incorporating what was then a novel procedure for treating war casualties. Returning to civilian life Fleming, a qualified surgeon and bacteriologist, chose a different career path, and not until the wars of the late 1930s were the advances in transfusion in WW1 fully incorporated into the management of trauma and haemorrhage. Like penicillin, the benefits of indirect transfusion were only slowly realised.
Growth and photosynthesis of four invasive aquatic plant species in Europe
Authors: HUSSNER A 
Published: September 2009

Summary Crassula helmsii, Hydrocotyle ranunculoides, Ludwigia grandiflora and Myriophyllum aquaticum are four well known invasive aquatic plants in European waters. In this study, plant growth at different nutrient availabilities, regeneration capacity and photosynthesis were investigated. Results show high relative growth rates (RGR) of the species of up to 0.132 ± 0.008 g g−1 dry weight (dw) day−1 (H. ranunculoides) and a significant increase in RGR with increasing nutrient availability. All species show a high regeneration capacity and the ability to form new shoots from single nodes, even though it differs between the species. Ludwigia grandiflora and M. aquaticum also show regeneration from single leaves. Species differed in maximal amounts, and in temperature and light optima of net assimilation rates: H. ranunculoides leaves reach maximum photosynthetic rates of up to 3500 μmol CO2 × h−1 g−1 dw, L. grandiflora (leaves) up to 2200 μmol CO2 × h−1 g−1 dw, M. aquaticum (shoots) 400 μmol CO2 × h−1 g−1 dw and C. helmsii (shoots) up to 200 μmol CO2 × h−1 g−1 dw. Hydrocotyle ranunculoides, L. grandiflora and M. aquaticum preferred high light intensity and high temperatures, whilst C. helmsii was negatively affected by intense sunlight. Summarising, it can be assumed that at least H. ranunculoides, L. grandiflora and M. aquaticum can grow well under current and likely future central European climate conditions.
An on‐farm approach to investigate the impact of diversified crop rotations on weed species richness and composition in winter wheat
Authors: ULBER L , STEINMANN H‐H , KLIMEK S , ISSELSTEIN J 
Published: September 2009

SummaryWeed species diversity may benefit from organic farming due to enhanced temporal diversification of crop species in a rotation and omission of herbicide applications. However, in intensively managed conventional systems, little evidence exists as to what extent diversified crop rotations contribute to higher weed species richness. Using an on‐farm approach, the effect of crop rotation (organic, conventional diverse (CD) and conventional simple (CS) crop rotations) and weed control (with vs. without) on weed species richness, cover, community composition and crop biomass, was analysed in 24 winter wheat fields. Weed species with beneficial functions for invertebrates and birds were analysed separately. Weed species richness was higher in the organic crop rotation, but did not differ between CD and CS crop rotations. Weed control treatment reduced species richness in both conventional rotations, but not in the organic one. Redundancy analyses revealed that crop rotation intensity accounted for the largest part of the explained variation in weed species composition. Results from the study indicate that the maintenance of weed species richness and conservation of species with important ecological functions requires not only temporal diversification of crop species in the rotation, but also an adjustment of weed control strategies.
Standard criteria donor pancreas donation status is associated with improved kidney transplant outcomes
Authors: Weiss Andrew S. , Smits Gerard , Wiseman Alexander C. 
Published: September 2009

Abstract:  Background:  Organ donor characteristics can be used to predict outcomes in kidney transplantation. We hypothesized that pancreas donation status could reflect organ quality and be predictive of kidney graft outcomes following Standard Criteria Donor (SCD) kidney transplantation.Methods:  We performed a retrospective analysis of deceased donor kidney alone (DD KA) transplants reported to SRTR from 1992 to 2005. Group 1 = kidney alone recipients from pancreas donors (KA, P+) and Group 2 = kidney alone recipients from non‐pancreas donors (KA, P−). We compared patient and graft survival between groups at 10‐yr post‐transplant.Results:  Group 1 (KA, P+) comprised 19 633 (20%) recipients and Group 2 (KA, P−) comprised 78 737 (80%) recipients. Ten‐yr graft survival for Group 1 vs. Group 2 was 42.6% and 36.9% (p < 0.0001), respectively. Pancreas donation status (non‐pancreas donor) was associated with a hazard ratio for graft loss of 1.23 on univariate analysis (p < 0.0001), and KA, P‐remained an independent risk factor for graft failure at 10 yr, HR 1.09 (p < 0.0001).Conclusion:  Donor pancreas donation status is an independent predictor of improved outcomes of SCD kidney recipients. Further study of the pancreas organ donor pre‐procurement is warranted to optimize not only pancreas utilization but also kidney graft outcomes.
Social Environment and Feeding State Influence Movement Decisions in a Web‐building Spider
Authors: Salomon Maxence 
Published: September 2009

AbstractIt is well recognized that feeding rate has a major influence on the amount of movement between microhabitats for many animals. However, the role of other extrinsic and intrinsic factors, and particularly how these factors may interact, is not well understood. This three‐part study examines the movement decisions of a web‐building spider, Latrodectus hesperus, by assessing microhabitat tenacity in established spiders and by testing how the presence of conspecific neighbours and the combined influence of individual feeding state (determined by prior feeding experience) and neighbour presence influence microhabitat residence time in unestablished spiders. The results show that naturally established spiders did not leave their microhabitats readily, emphasizing the importance of choosing a profitable location. Unestablished spiders stayed longer in microhabitats occupied by conspecifics than in unoccupied ones, and there was practically no cannibalism even though neighbours shared webs. Furthermore, feeding state and neighbour presence showed an interactive effect on microhabitat residence time. When spiders were housed alone, microhabitat residence time increased with feeding state. However, in the presence of conspecifics, spiders had a low propensity to move, regardless of feeding state. Together, these results demonstrate the combined importance of grouping dynamics and feeding state in shaping movement decisions.
The Round‐Eared Sengi and the Evolution of Social Monogamy: Factors that Constrain Males to Live with a Single Female
Authors: Schubert Melanie , Pillay Neville , Ribble David O. , Schradin Carsten 
Published: September 2009

AbstractAnimal dispersion in space and time results from environmental pressures, and affects the outcome of a species’ social organization. When females are solitary, males may either roam or be pair‐living. We studied possible environmental influences affecting the social organization of the round‐eared sengi (Macroscelides proboscideus) in a semi‐desert in South Africa, using trapping and radio‐tracking across 2.5 yr. Adult sex ratios did not deviate from 1:1 and we found no indication of sexual dimorphism in body mass. Females maintained exclusive areas, which had little overlap (<4%) with neighbouring females (NF), and males overlapped predominately only with the home range of single females. Generally, inter‐ and intra‐sexual overlap with neighbouring individuals was low (3–6%) for both sexes, indicating territoriality and pair‐living. Pairs were perennial and territories were maintained year‐round. However, males generally maintained much larger areas than females, which were sensitive to population density. Male space use appeared to be primarily limited by the presence of neighbouring males. Female home ranges were smaller‐sized despite changes in population density, possibly for energetic efficiency. Some paired males attempted to take over widowed females, but shifted back to their original home range following the intrusion of an un‐paired male. We conclude that social monogamy is the predominant social organization in round‐eared sengis in a semi‐desert that may have resulted from females living solitarily in small exclusive territories, balanced sex ratios, and from a low variation of body mass between males.
Understanding the use of Bayes factor for testing candidate genes
Authors: Varona Luis 
Published: September 2009

SummaryAfter quantitative trait loci (QTL) detection, one of the main objectives of research is to identify the causal mutation explaining phenotypic differences. Candidate genes are usually selected according to the physiological mechanism of the trait and their location within the same region of the QTL. After detection of any polymorphism at the candidate gene sequence, it is important to determine whether the detected mutation is the one that causes the phenotypic variation. This is not, however, an easy task, because of the linkage disequilibrium between the genes located in the same region. Several methods have been proposed that consider the neutral marker information in validating the involvement of candidate genes. However, some statistical information may be lost because of the presence of both the QTL and candidate gene effects in the model of analysis. Here, the Bayes factor is suggested as an alternative and a procedure for its calculation between candidate gene and QTL models is presented. The procedure is illustrated with a simulation study and with an example consisting of three SNPs detected at the leptin receptor (LEPR) in an experimental intercross between Iberian and Landrace pigs. The results indicate that the Bayes factor procedure is more powerful than the classical approach.
Congenital cystic adenomatoid malformation of the lung: Hazards of delayed diagnosis
Authors: COLLINS Anne M. , RIDGWAY Paul F. , KILLEEN Ronan P. , DODD Jonathan D. , TOLAN Michael 
Published: September 2009

ABSTRACTCongenital cystic adenomatoid malformation is a rare pulmonary developmental anomaly, which typically manifests in neonates and infants. Presentation in adulthood is uncommon, with <60 cases reported in the literature. The majority of cases involve one lobe only. We report a case of type 1 congenital cystic adenomatoid malformation in an adult presenting with a respiratory tract infection and haemoptysis. At thoracotomy, complex cystic masses were noted in the right upper and lower lobes. Lung‐sparing surgery, in the form of two segmentectomies and a non‐anatomical resection, was performed in order to avoid pneumonectomy. Such presentations may be problematic as potentially incomplete resections may increase the risk of complications and malignant transformation. This suggests the importance of appropriate clinical and radiological follow up.
Resistance and reactance in oscillation lung function reflect basal lung function and bronchial hyperresponsiveness respectively
Authors: KIM Hyeong Yoon , SHIN Yun Ho , JUNG Da Woon , JEE Hye Mi , PARK Hye Won , HAN Man Yong 
Published: September 2009

ABSTRACTBackground and objective:  Currently there are few data available regarding the use of impulse oscillometry parameters to assess airflow obstruction during standardized methacholine challenge testing.Methods:  Methacholine challenge tests were performed using impulse oscillometry and conventional spirometry in 64 healthy and 39 asthmatic children, in order to determine airway resistance (R) and reactance (X) at frequencies of 5–35 Hz, as well as FEV1.Results:  Baseline R and X were significantly different between the healthy and asthmatic children, with the most discriminating parameter being resistance at 5 Hz (R5). In asthmatic children BHR was well demonstrated by FEV1, X5 and X10, but not by R5. However, when the actual R5 values obtained in this study were compared with the predicted values, there appeared to be differences in the lung function measures that corresponded to varying methacholine concentrations. In addition, the PC20_FEV1 and PC70_X5 were significantly more sensitive than other parameters for methacholine challenge testing.Conclusions:  Measuring resistance at 5 Hz using impulse oscillometry facilitates significant differentiation of baseline lung function between asthmatic and healthy children. Additionally, X may be a suitable replacement for PC20 in methacholine challenge testing.
Rolipram attenuates bleomycin A5‐induced pulmonary fibrosis in rats
Authors: PAN Jin Bing , HOU Yu Hong , ZHANG Guo Jun 
Published: September 2009

ABSTRACTBackground and objective: Pulmonary fibrosis has a poor prognosis. The pathogenesis of fibrotic disorders is unclear, but the extent of lung damage due to persistent inflammation is regarded as a critical factor. Rolipram inhibits inflammation induced by various stimuli, as well as the chemotaxis of fibroblasts. In this study rolipram was used to treat pulmonary fibrosis induced by bleomycin A5 in rats, and the possible mechanisms were investigated.Methods: Rolipram (0.25 mg/kg) was administered intraperitoneally daily, following intratracheal instillation of bleomycin A5 (5 mg/kg). Animals were killed at 7 or 28 days after bleomycin A5 instillation, and indices of lung damage and fibrosis were evaluated.Results: Bleomycin A5 induced pulmonary inflammation and fibrosis, increased the levels of malondialdehyde and tumour necrosis factor‐α and enhanced accumulation of collagen in the lungs. Rolipram administration significantly attenuated these effects.Conclusions: Rolipram ameliorated pulmonary inflammation and fibrosis induced by bleomycin A5 in rats. The effects of rolipram may be associated with its antioxidant activity and inhibition of tumour necrosis factor‐α production.
Correlation between serum biomarkers and BODE index in patients with stable COPD
Authors: LIU Shih‐Feng , CHIN Chien‐Hung , WANG Chin‐Chou , LIN Meng‐Chih 
Published: September 2009

ABSTRACTBackground and objective:  The BODE index, based on BMI, obstructive ventilatory impairment, dyspnoea scale and exercise capacity, has been used to evaluate the severity of patients with COPD. However, the correlations between serum biomarkers and the BODE index in patients with stable COPD are not widely studied. This study evaluated potential serum biomarkers for their ability to identify smokers with COPD and reflect disease severity.Methods:  A comparative study was conducted of 100 clinically stable COPD patients and 50 matched healthy smokers and the difference in levels of biomarkers between the COPD patients and healthy smokers was measured. Serum inflammatory mediators measured were growth‐related oncogene‐α (GRO‐α), IL‐8, tumour necrosis factor‐α (TNF‐α), matrix metalloproteinase‐9 (MMP‐9) and monocyte chemoattractant protein‐1 (MCP‐1). Variables included age, pack‐years, current or ex‐smoker status, inhaler or oral steroid use and BODE index components, including airflow obstruction, the distance walked in 6MWD, modified Medical Research Council (MMRC) dyspnoea scale and BMI. The association between serum biomarkers and the components of the BODE index was assessed in the COPD patients.Results:  The level of serum MCP‐1 was significantly different between the COPD group and the healthy smoker group (P = 0.003). Significant results in univariate and multivariate analysis of the association between biomarkers and BODE components were: serum MCP‐1 correlated with FEV1% and 6MWD; serum IL‐8 and GRO‐α correlated with steroid use; serum TNF‐α correlated with steroid use and FEV1%; and serum MMP‐9 correlated with MMRC dyspnoea scale.Conclusions:  No single specific serum inflammatory mediator was completely correlated with BODE variable parameters in patients with stable COPD. Serum MCP‐1 may be an important biomarker for identifying COPD subjects from healthy smokers and classifying COPD severity.
Endobronchial extension of granulomatous lymphadenitis in an HIV‐positive man with immune reconstitution syndrome
Authors: STEINFORT Daniel P. , SMALLWOOD David , ANTIPPA Phillip , IRVING Louis B. 
Published: September 2009

ABSTRACTEndobronchial granuloma is a rare manifestation of endobronchial tuberculosis (TB). This case report describes a patient with endobronchial granuloma due to contiguous extension of granulomatous mediastinal lymph node inflammation, occurring following commencement of highly active anti‐retroviral therapy in an HIV‐positive man. Bronchoscopic findings mirrored CT imaging of endobronchial involvement of sub‐carinal lymphadenopathy. Microbiologic studies were negative for acid‐fast bacilli, fungal elements and malignancy. Mycobacterial and fungal culture as well as PCR for TB were all negative. Empiric anti‐tuberculous therapy was commenced with complete resolution of symptoms. Immune reconstitution syndrome with development of active TB is common in patients commencing highly active retroviral therapy. Lymphadenitis is the commonest manifestation of this, and 20% of patients are culture negative for mycobacteria. Endobronchial granulomata due to TB are rare and no specific endobronchial therapy is required in such disease.
Management of complications from diagnostic and interventional bronchoscopy
Authors: LEE Pyng , MEHTA Atul C. , MATHUR Praveen N. 
Published: September 2009

ABSTRACTFrom the humble beginnings as a mere curiosity, the art of bronchoscopy has progressed at a rapid pace. The millennium ushers in new technologies and refinements in established techniques to facilitate early detection of cancer, precise targeting of pulmonary nodules and infiltrates, near‐total staging of the mediastinum with combined endoscopic modalities and more effective palliation of inoperable tumours. Bronchoscopists are faced with an increasing myriad of tools and equipment, each promising to carry out better than the previous. It is opportune to review the complications of established bronchoscopic techiques and how to manage them as well as new complications associated with novel technologies. In this article, we provide a concise overview of diagnostic and therapeutic bronchoscopic modalities, discussion of associated complications and their management strategies.
Determinants of initiation and progression of idiopathic pulmonary fibrosis
Authors: KOTTMANN Robert Matthew , HOGAN Christopher M. , PHIPPS Richard P. , SIME Patricia J. 
Published: September 2009

ABSTRACTIPF is a devastating disease with few therapeutic options. The precise aetiology of IPF remains elusive. However, our understanding of the pathologic processes involved in the initiation and progression of this disease is improving. Data on the mechanisms underlying IPF have been generated from epidemiologic investigations as well as cellular and molecular studies of human tissues. Although no perfect animal model of human IPF exists, pre‐clinical animal studies have helped define pathways which are likely important in human disease. Epithelial injury, fibroblast activation and repetitive cycles of injury and abnormal repair are almost certainly key events. Factors which have been associated with initiation and/or progression of IPF include viral infections, abnormal cytokine, chemokine and growth factor production, oxidant stress, autoimmunity, inhalational of toxicants and gastro‐oesophageal reflux disease. Furthermore, recent evidence identifies a role for a variety of genetic and epigenetic abnormalities ranging from mutations in surfactant protein C to abnormalities in telomere length and telomerase activity. The challenge remains to identify additional inciting agents and key dysregulated pathways that lead to disease progression so that we can develop targeted therapies to treat or prevent this serious disease.