bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative Assessment of Limb Position Sense Following Stroke
Authors: Dukelow Sean P. , Herter Troy M. , Moore Kimberly D. , Demers Mary Jo , Glasgow Janice I. , Bagg Stephen D. , Norman Kathleen E. , Scott Stephen H.
Published: October 2009

Background. Impairment of position sense of the upper extremity (UE) may impede activities of daily living and limit motor gains after stroke. Most clinical assessments of position sense rely on categorical or ordinal ratings by clinicians that lack sensitivity to change or the ability to discriminate subtle deficits. Objective. Use robotic technology to develop a reliable, quantitative technique with a continuous scale to assess UE position sense following stroke. Methods. Forty-five patients recruited from an inpatient stroke rehabilitation service and 65 age-matched healthy controls performed an arm position matching task. Each UE was fitted in the exoskeleton of a KINARM device. One UE was passively placed in one of 9 positions, and the subject was told to match his or her position with the other UE. Patients were compared with statistical distributions of control data to identify those with deficits in UE position sense. Test—retest sessions using 2 raters established interrater reliability. Results. Two thirds of left hemiparetic and one third of right hemiparetic patients had deficits in limb position sense. Left-affected stroke subjects demonstrated significantly more trial-to-trial variability than right-affected or control subjects. The robotic assessment technique demonstrated good interrater reliability but limited agreement with the clinical thumb localizing test. Conclusions. Robotic technology can provide a reliable quantitative means to assess deficits in limb position sense following stroke.
Olfactory Mucosal Autografts and Rehabilitation for Chronic Traumatic Spinal Cord Injury
Authors: Lima Carlos , Escada Pedro , Pratas-Vital José , Branco Catarina , Arcangeli Carlo Alberto , Lazzeri Giovanna , Santana Maia Carlos Alberto , Capucho Clara , Hasse-Ferreira Armando , Peduzzi Jean D.
Published: October 2009

Background/objective . Basic science advances in spinal cord injury (SCI) are leading to novel clinical approaches. The authors report a prospective, uncontrolled pilot study of the safety and outcomes of implanting olfactory mucosal autografts (OMA) in 20 patients with chronic, sensorimotor complete or motor complete SCI. Methods. Seven paraplegic and 13 tetraplegic subjects (17 men and 3 women; 19-37 years old) who sustained a traumatic SCI 18 to 189 months previously (mean = 49 months) were enrolled. Preoperative rehabilitation that emphasized lower extremity stepping using either overground walking training or a robotic weight-supported treadmill training was provided for 25 to 39 hours per week for a median of 4 months at 3 sites. No change in ASIA Impairment Scale (AIS) motor scores for the lower extremities or AIS grades of completeness was found. OMAs were transplanted into 1.3- to 4-cm lesions at C4-T12 neurological levels after partial scar removal. Therapy was continued postoperatively. Preoperative and postoperative assessments included AIS scores and classification, electromyography (EMG) of attempted voluntary contractions, somatosensory evoked potentials (SSEP), urodynamic studies with sphincter EMG, spinal cord magnetic resonance imaging (MRI), and otolaryngology and psychology evaluations. The Functional Independence Measure (FIM) and Walking Index for Spinal Cord Injury (WISCI) were obtained in 13 patients. Results. All patients survived and recovered olfaction. One patient was rehospitalized for aseptic meningitis. Minor adverse events occurred in 4 others. The mean duration of follow-up was 27.7 months (range = 12-45 months). By MRI, the lesion site was filled in all patients with no neoplastic overgrowth or syringomyelia. AIS grades improved in 11 of 20 patients, 6 (A → C), 3 (B → C), and 2 (A → B), and declined in 1 (B → A). Improvements included new voluntary EMG responses (15 patients) and SSEPs (4 patients). Scores improved in the FIM and WISCI (13/13 tested), and urodynamic responses improved in 5 patients. Conclusion. OMA is feasible, relatively safe, and possibly beneficial in people with chronic SCI when combined with postoperative rehabilitation. Future controlled trials may need to include a lengthy and intensive rehabilitation arm as a control.
Patient Counseling for Unintentional Injury Prevention
Authors: Ballesteros Michael F. , Gielen Andrea C.
Published: October 2009

Injury prevention counseling (IPC) by health care providers is one strategy to reduce injury risk by encouraging people to modify their environment or their personal behaviors to protect themselves or their loved ones. National surveys indicate that few patients are receiving IPC. The evidence of IPC being effective at increasing safety practices is inconsistent. This may be explained partially because counseling recommendations for some injury issues may involve more effort, cost, or inconvenience by the patient. IPC that is based on behavior change theories is more likely to be effective. Physicians and other health care providers can play a critical role in efforts to prevent injuries, but barriers for delivering IPC need to be overcome.
A role for thrombin in the initiation of the immune response to therapeutic factor VIII
Authors: Skupsky Jonathan , Zhang Ai-Hong , Su Yan , Scott David W.
Published: October 2009

Administration of human factor VIII (FVIII) to FVIII knockout hemophilia mice is a useful small animal model to study the physiologic response in patients iatrogenically immunized to this therapeutic protein. These mice manifest a robust, T cell–dependent, antibody response to exogenous FVIII treatment, even when encountered through traditionally tolerogenic routes. Thus, FVIII given via these routes elicits both T- and B-cell responses, whereas a control, foreign protein, such as ovalbumin (OVA), is poorly immunogenic. When FVIII is heat inactivated, it loses function and much of its immunogenicity. This suggests that FVIII's immunogenicity is principally tied to its function and not its structure. If mice are treated with the anticoagulant warfarin, which depletes other coagulation factors including thrombin, there is a reduced immune response to FVIII. Furthermore, when mice are treated with the direct thrombin inhibitor, hirudin, the T-cell responses and the serum anti-FVIII antibody concentrations are again significantly reduced. Notably, when FVIII is mixed with OVA, it acts to increase the immune response to OVA. Finally, administration of thrombin with OVA is sufficient to induce immune responses to OVA. Overall, these data support the hypothesis that formation of thrombin through the procoagulant activity of FVIII is necessary to induce costimulation for the immune response to FVIII treatment.
In vivo delivery of a microRNA-regulated transgene induces antigen-specific regulatory T cells and promotes immunologic tolerance
Authors: Annoni Andrea , Brown Brian D. , Cantore Alessio , Sergi Lucia Sergi , Naldini Luigi , Roncarolo Maria-Grazia
Published: October 2009

We previously showed that incorporating target sequences for the hematopoietic-specific microRNA miR-142 into an antigen-encoding transgene prevents antigen expression in antigen-presenting cells (APCs). To determine whether this approach induces immunologic tolerance, we treated mice with a miR-142–regulated lentiviral vector encoding green fluorescent protein (GFP), and subsequently vaccinated the mice against GFP. In contrast to control mice, no anti-GFP response was observed, indicating that robust tolerance to the transgene-encoded antigen was achieved. Furthermore, injection of the miR-142–regulated vector induced a population of GFP-specific regulatory T cells. Interestingly, an anti-GFP response was observed when microRNA miR-122a was inserted into the vector and antigen expression was detargeted from hepatocytes as well as APCs. This demonstrates that, in the context of lentiviral vector-mediated gene transfer, detargeting antigen expression from professional APCs, coupled with expression in hepatocytes, can induce antigen-specific immunologic tolerance.
Contributions of extravascular and intravascular cells to fibrin network formation, structure, and stability
Authors: Campbell Robert A. , Overmyer Katherine A. , Selzman Craig H. , Sheridan Brett C. , Wolberg Alisa S.
Published: October 2009

Fibrin is essential for hemostasis; however, abnormal fibrin formation is hypothesized to increase thrombotic risk. We previously showed that in situ thrombin generation on a cell's surface modulates the 3-dimensional structure and stability of the fibrin network. Currently, we compared the abilities of extravascular and intravascular cells to support fibrin formation, structure, and stability. Extravascular cells (fibroblasts, smooth muscle) supported formation of dense fibrin networks that resisted fibrinolysis, whereas unstimulated intravascular (endothelial) cells produced coarse networks that were susceptible to fibrinolysis. All 3 cell types produced a fibrin structural gradient, with a denser network near, versus distal to, the cell surface. Although fibrin structure depended on cellular procoagulant activity, it did not reflect interactions between integrins and fibrin. These findings contrasted with those on platelets, which influenced fibrin structure via interactions between β3 integrins and fibrin. Inflammatory cytokines that induced prothrombotic activity on endothelial cells caused the production of abnormally dense fibrin networks that resisted fibrinolysis. Blocking tissue factor activity significantly reduced the density and stability of fibrin networks produced by cytokine-stimulated endothelial cells. Together, these findings indicate fibrin structure and stability reflect the procoagulant phenotype of the endogenous cells, and suggest abnormal fibrin structure is a novel link between inflammation and thrombosis.
Endocrinological derangements in COPD
Authors: Laghi F. , Adiguzel N. , Tobin M. J.
Published: October 2009

Chronic obstructive pulmonary disease (COPD) is no longer considered to affect only the lungs and airways but also the rest of the body. The systemic manifestations of COPD include a number of endocrine disorders, such as those involving the pituitary, the thyroid, the gonads, the adrenals and the pancreas.

The mechanisms by which COPD alters endocrine function are incompletely understood but likely involve hypoxaemia, hypercapnia, systemic inflammation and glucocorticoid administration. Altered endocrine function can worsen the clinical manifestations of COPD through several mechanisms, including decreased protein anabolism, increased protein catabolism, nonenzymatic glycosylation and activation of the rennin–angiotensin–aldosterone system.

Systemic effects of endocrine disorders include abnormalities in control of breathing, decreases in respiratory and limb-muscle mass and function, worsening of respiratory mechanics, impairment of cardiac function and disorders of fluid balance.

Research on endocrine manifestations of COPD embraces techniques of molecular biology, integrative physiology and controlled clinical trials. A sound understanding of the various disorders of endocrine function associated with COPD is prudent for every physician who practices pulmonary medicine.
Simvastatin and sildenafil combine to attenuate pulmonary hypertension
Authors: Zhao L. , Sebkhi A. , Ali O. , Wojciak-Stothard B. , Mamanova L. , Yang Q. , Wharton J. , Wilkins M. R.
Published: October 2009

Statins have been proposed to be a potential treatment for pulmonary arterial hypertension. If introduced into clinical practice, the statin would have to be used in conjunction with established therapy. We investigated the effects of combining simvastatin with a phosphodiesterase type-5 inhibitor, sildenafil, in the rat model of hypoxia-induced pulmonary hypertension.

Rats were allocated to either: 1) a prevention protocol, to receive simvastatin 20 mg·kg−1·day−1by intraperitoneal injection or sildenafil 75 mg·kg−1·day−1orally or the combination (or vehicle) for 2 weeks beginning at the start of exposure to hypoxia (10% inspired oxygen); or 2) a treatment protocol, where the same agents were administered in the last 2 weeks of a 4-week period of hypoxia.

In both protocols, the combination of sildenafil and simvastatin lowered pulmonary artery pressure and produced a significantly greater reduction in right ventricular hypertrophy and pulmonary vascular muscularisation than either drug alone. Moreover, the combination augmented significantly endothelial nitric oxide synthase expression and cGMP levels in the lung and right ventricle above that produced by either drug independently and resulted in greater inhibition of RhoA activity.

These data suggest that simvastatin can be usefully combined with sildenafil in the treatment of pulmonary arterial hypertension to achieve greater therapeutic benefit.
Risk of mortality associated with formoterol: a systematic review and meta-analysis
Authors: Wijesinghe M. , Weatherall M. , Perrin K. , Harwood M. , Beasley R.
Published: October 2009

There is concern long-acting β-agonist (LABA) drugs may increase the risk of asthma mortality.

We undertook a systematic review which included the AstraZeneca Formoterol Clinical Trial Safety Database and Novartis Food and Drug Aministration Formoterol Briefing Document. Randomised controlled clinical trials of duration ≥4 weeks that compared formoterol with a non-LABA comparator treatment in asthma were included in a meta-analysis of the risk of all-cause mortality and asthma death. Simple contingency tables, Peto's one-step method and a Bayesian analysis were used.

There were 42 deaths (nine from asthma) recorded in 62 studies with 49,327 subjects. The simple contingency table odds ratio for risk of all-cause mortality with formoterol was 1.1 (95% CI 0.6–2.2) and for asthma death was 2.7 (95% CI 0.5–26.7). Analyses by the other methods using both “as randomised” and “as exposed” classifications of treatment gave similar risk estimates with wide confidence and credible intervals.

We conclude that there was insufficient power to determine whether formoterol increases the risk of mortality. However, the point estimates of a 2.0- to 3.2-fold increased risk of asthma death are not reassuring and add weight to evidence that LABA use in certain circumstances may increase the risk of asthma mortality.
OGO: an ontological approach for integrating knowledge about orthology
Authors: Miñarro-Gimenez Jose Antonio , Madrid Marisa , Fernandez-Breis Jesualdo Tomas
Published: October 2009

Background

There exist several information resources about orthology of genes and proteins, and there are also systems for querying those resources in an integrated way. However, caveats with current approaches include lack of integration, since results are shown sequentially by resource, meaning that there is redundant information and the users are required to combine the results obtained manually.

Results

In this paper we have applied the Ontological Gene Orthology approach, which makes use of a domain ontology to integrate the information output from selected orthology resources. The integrated information is stored in a knowledge base, which can be queried through semantic languages. A friendly user interface has been developed to facilitate the search; consequently, users do not need to have knowledge on ontologies or ontological languages to obtain the relevant information.

Conclusion

The development and application of our approach allows users to retrieve integrated results when querying orthology information, providing a gene product-oriented output instead of a traditional information resource-oriented one. Besides this benefit for users, it also allows a better exploitation and management of orthology information and knowledge.
KA-SB: from data integration to large scale reasoning
Authors: Roldán-García María del Mar , Navas-Delgado Ismael , Kerzazi Amine , Chniber Othmane , Molina-Castro Joaquín , Aldana-Montes José F
Published: October 2009

Background

The analysis of information in the biological domain is usually focused on the analysis of data from single on-line data sources. Unfortunately, studying a biological process requires having access to disperse, heterogeneous, autonomous data sources. In this context, an analysis of the information is not possible without the integration of such data.

Methods

KA-SB is a querying and analysis system for final users based on combining a data integration solution with a reasoner. Thus, the tool has been created with a process divided into two steps: 1) KOMF, the Khaos Ontology-based Mediator Framework, is used to retrieve information from heterogeneous and distributed databases; 2) the integrated information is crystallized in a (persistent and high performance) reasoner (DBOWL). This information could be further analyzed later (by means of querying and reasoning).

Results

In this paper we present a novel system that combines the use of a mediation system with the reasoning capabilities of a large scale reasoner to provide a way of finding new knowledge and of analyzing the integrated information from different databases, which is retrieved as a set of ontology instances. This tool uses a graphical query interface to build user queries easily, which shows a graphical representation of the ontology and allows users o build queries by clicking on the ontology concepts.

Conclusion

These kinds of systems (based on KOMF) will provide users with very large amounts of information (interpreted as ontology instances once retrieved), which cannot be managed using traditional main memory-based reasoners. We propose a process for creating persistent and scalable knowledgebases from sets of OWL instances obtained by integrating heterogeneous data sources with KOMF. This process has been applied to develop a demo tool http://khaos.uma.es/KA-SB, which uses the BioPax Level 3 ontology as the integration schema, and integrates UNIPROT, KEGG, CHEBI, BRENDA and SABIORK databases.
Effects of a fibre-enriched milk drink on insulin and glucose levels in healthy subjects
Authors: Lummela Netta , Kekkonen Riina A , Jauhiainen Tiina , Pilvi Taru K , Tuure Tuula , Järvenpää Salme , Eriksson Johan G , Korpela Riitta
Published: October 2009

Background

The glycaemic response to foods is dependent on the quality and content of carbohydrates. Carbohydrates in the form of dietary fibre have favourable effects on insulin and glucose metabolism and may help to control energy intake. Dairy products have a relatively low carbohydrate content, and most of the carbohydrate is in the form of lactose which causes gastrointestinal symptoms in part of the population. In order to avoid these symptoms, dairy products can be replaced with lactose-free dairy products which are on the market in many parts of the world. However, the effects of lactose-free products on insulin and glucose metabolism have not been studied.

Methods

In the present study, we investigated the effects of 1) a lactose-free milk drink, 2) a novel fibre-enriched, fat- and lactose-free milk drink and 3) normal fat-free milk on serum glucose and insulin levels and satiety using a randomized block design. Following an overnight fast, 26 healthy volunteers ingested 200 ml of one of these drinks on three non-consecutive days. Insulin and glucose levels and subjective satiety ratings were measured before the ingestion of the milk product and 20, 40, 60, 120 and 180 minutes after ingestion. The responses were calculated as the area under the curve subtracted by the baseline value (AUC minus baseline).

Results

The insulin response was significantly lower for the fibre-enriched milk drink than it was for the other milk products (AUC, P = 0.007). There were no differences in the response for glucose or in the AUC for the subjective satiety ratings between the studied milk products.

Conclusion

The present results suggest that this novel milk drink could have positive effects on insulin response.
Preliminary spatiotemporal analysis of the association between socio-environmental factors and suicide
Authors: Qi Xin , Tong Shilu , Hu Wenbiao
Published: October 2009

Background

The seasonality of suicide has long been recognised. However, little is known about the relative importance of socio-environmental factors in the occurrence of suicide in different geographical areas. This study examined the association of climate, socioeconomic and demographic factors with suicide in Queensland, Australia, using a spatiotemporal approach.

Methods

Seasonal data on suicide, demographic variables and socioeconomic indexes for areas in each Local Government Area (LGA) between 1999 and 2003 were acquired from the Australian Bureau of Statistics. Climate data were supplied by the Australian Bureau of Meteorology. A multivariable generalized estimating equation model was used to examine the impact of socio-environmental factors on suicide.

Results

The preliminary data analyses show that far north Queensland had the highest suicide incidence (e.g., Cook and Mornington Shires), while the south-western areas had the lowest incidence (e.g., Barcoo and Bauhinia Shires) in all the seasons. Maximum temperature, unemployment rate, the proportion of Indigenous population and the proportion of population with low individual income were statistically significantly and positively associated with suicide. There were weaker but not significant associations for other variables.

Conclusion

Maximum temperature, the proportion of Indigenous population and unemployment rate appeared to be major determinants of suicide at a LGA level in Queensland.
Suppression of growth, migration and invasion of highly-metastatic human breast cancer cells by berbamine and its molecular mechanisms of action
Authors: Wang Shan , Liu Qian , Zhang Ying , Liu Ke , Yu Pengfei , Liu Kun , Luan Jinling , Duan Huiying , Lu Zhaoqiao , Wang Fengfei , Wu Erxi , Yagasaki Kazumi , Zhang Guoying
Published: October 2009

Background

Breast cancer is the second leading cause of cancer related deaths among females worldwide. Berbamine (BER), a kind of bis-benzylisoquinoline alkaloid, has been used to treat clinical patients with inflammation and cancer for many years in China. The purpose of this study is to investigate the activity of BER against highly-metastatic human breast cancer and its molecular mechanisms of action.

Results

In our study, we found that BER inhibits growth of highly-metastatic human breast cancer cell lines MDA-MB-231 and MDA-MB-435S cells dose-dependently and time-dependently. The sera from BER-treated rats suppress the growth of MDA-MB-231 cells. BER shows synergistic effects with some existing anticancer agents such as trichostatin A (TSA, the histone deacetylase inhibitor), celecoxib (the inhibitor of COX-2), and carmofur against the growth of MDA-MB-231 cells. BER also displays the strong activity of inducing apoptosis in both estrogen receptor-negative MDA-MB-231 cells and estrogen receptor-alpha-positive MCF-7 breast cancer cells, but not in normal human mammary epithelial cell line MCF10A. BER down-regulates anti-apoptotic protein Bcl-2 levels and up-regulates pro-apoptotic protein Bax expressions in MDA-MB-231 and MDA-MB-435S cells. BER also has synergistic effects with anticancer agents trichostatin A, celecoxib and/or carmofur on reducing Bcl-2/Bax ratios and VEGF secretions in MDA-MB-231 cells. In addition, BER significantly suppresses cell migration and invasion, as well as decreases pro-MMP-9/pro-MMP-2 activation in breast cancer cells. Furthermore, BER suppresses Akt and nuclear factor κ B signaling by reducing the phosphorylation of c-Met and Akt, and inhibiting their downstream targets such as nuclear factor κ B p-65, Bcl-2/Bax, osteopontin, VEGF, MMP-9 and MMP-2 on protein and/or mRNA levels in breast cancer cells.

Conclusion

Our findings have showed that BER suppresses the growth, migration and invasion in highly-metastatic human breast cancer cells by possibly inhibiting Akt and NF-κ B signaling with their upstream target c-Met and downstream targets Bcl-2/Bax, osteopontin, VEGF, MMP-9 and MMP-2. BER has synergistic effects with anticancer agents trichostatin A, celecoxib and carmofur on inhibiting the growth of MDA-MB-231 cells and reducing the ratio of Bcl-2/Bax and/or VEGF expressions in the cancer cells. These findings suggest that BER may have the wide therapeutic and/or adjuvant therapeutic application in the treatment of human breast cancer and other cancers.
Audit of short term outcomes of surgical and medical second trimester termination of pregnancy
Authors: Mauelshagen Annamarie , Sadler Lynn C , Roberts Helen , Harilall Mahesh , Farquhar Cynthia M
Published: October 2009

Background

As comparisons of modern medical and surgical second trimester termination of pregnancy (TOP) are limited, and the optimum method of termination is still debated, an audit of second trimester TOP was undertaken, with the objective of comparing the outcomes of modern medical and surgical methods.

Methods

All cases of medical and surgical TOP between the gestations of 13 and 20 weeks from 1st January 2007 to 30th June 2008, among women residing in the local health board district, a tertiary teaching hospital in an urban setting, were identified by a search of ICD-10 procedure codes (surgical terminations) and from a ward database (medical terminations). Retrospective review of case notes was undertaken. A total of 184 cases, 51 medical and 133 surgical TOP, were identified. Frequency data were compared using Chi-squared or Fischer's Exact tests as appropriate and continuous data are presented as mean and standard deviation if normally distributed or median and interquartile range if non-parametric.

Results

Eighty-one percent of surgical terminations occurred between 13 to 16 weeks gestation, while 74% of medical terminations were performed between 17 to 20 weeks gestation. The earlier surgical TOP occurred in younger women and were more often indicated for maternal mental health. Sixteen percent of medical TOP required surgical delivery of the placenta. Evacuation of retained products was required more often after medical TOP (10%) than after surgical TOP (1%). Other serious complications were rare.

Conclusion

Both medical and surgical TOP are safe and effective for second trimester termination. Medical TOP tend to be performed at later gestations and are associated with a greater likelihood of manual removal of the placenta and delayed return to theatre for retained products. This case series does not address long term complications.
The third Symptom Management Research Trial in Oncology (SMaRT Oncology-3): a randomised trial to determine the efficacy of adding a complex intervention for major depressive disorder (Depression Care for People with Lung Cancer) to usual care, compared to usual care alone in patients with lung cancer
Authors: Walker Jane , Cassidy Jim , Sharpe Michael ,   SMaRT Oncology-3 Trialists
Published: October 2009

Background

Depression Care for People with Lung Cancer is a complex intervention delivered by specially trained cancer nurses, under the supervision of a psychiatrist. It is given as a supplement to the usual care for depression, which patients receive from their general practitioner and cancer service. The third Symptom Management Research Trial in Oncology (SMaRT Oncology-3 Trial) will test its efficacy when compared to usual care alone.

Design

A two arm parallel group multi-centre randomised controlled trial. 200 patients will be recruited through established systematic Symptom Monitoring Services, which screen patients for depression. Patients will have: a diagnosis of lung cancer; an estimated life expectancy of three months or more and a diagnosis of Major Depressive Disorder. Patients will be randomised to usual care or usual care plus Depression Care for People with Lung Cancer. Randomisation will be carried out by telephoning a secure computerised central randomisation system or by using a secure web interface. The primary outcome measure is average depression severity. This will be assessed using scores on the 20-item Symptom Hopkins Checklist (SCL-20D), collected every four weeks over 32 weeks. Secondary outcomes include severity of anxiety, pain and fatigue; self-rated improvement of depression; quality of life and satisfaction with depression care.

Trial Registration

Current controlled trials ISRCTN75905964
Enzymatic hydrolyzing performance of Acremonium cellulolyticus and Trichoderma reesei against three lignocellulosic materials
Authors: Fujii Tatsuya , Fang Xu , Inoue Hiroyuki , Murakami Katsuji , Sawayama Shigeki
Published: October 2009

Background

Bioethanol isolated from lignocellulosic biomass represents one of the most promising renewable and carbon neutral alternative liquid fuel sources. Enzymatic saccharification using cellulase has proven to be a useful method in the production of bioethanol. The filamentous fungi Acremonium cellulolyticus and Trichoderma reesei are known to be potential cellulase producers. In this study, we aimed to reveal the advantages and disadvantages of the cellulase enzymes derived from these fungi.

Results

We compared A. cellulolyticus and T. reesei cellulase activity against the three lignocellulosic materials: eucalyptus, Douglas fir and rice straw. Saccharification analysis using the supernatant from each culture demonstrated that the enzyme mixture derived from A. cellulolyticus exhibited 2-fold and 16-fold increases in Filter Paper enzyme and β-glucosidase specific activities, respectively, compared with that derived from T. reesei. In addition, culture supernatant from A. cellulolyticus produced glucose more rapidly from the lignocellulosic materials. Meanwhile, culture supernatant derived from T. reesei exhibited a 2-fold higher xylan-hydrolyzing activity and produced more xylose from eucalyptus (72% yield) and rice straw (43% yield). Although the commercial enzymes Acremonium cellulase (derived from A. cellulolyticus, Meiji Seika Co.) demonstrated a slightly lower cellulase specific activity than Accellerase 1000 (derived from T. reesei, Genencor), the glucose yield (over 65%) from lignocellulosic materials by Acremonium cellulase was higher than that of Accellerase 1000 (less than 60%). In addition, the mannan-hydrolyzing activity of Acremonium cellulase was 16-fold higher than that of Accellerase 1000, and the conversion of mannan to mannobiose and mannose by Acremonium cellulase was more efficient.

Conclusion

We investigated the hydrolysis of lignocellulosic materials by cellulase derived from two types of filamentous fungi. We found that glucan-hydrolyzing activity of the culture supernatant from A. cellulolyticus was superior to that from T. reesei, while the xylan-hydrolyzing activity was superior for the cellulase from T. reesei. Moreover, Acremonium cellulase exhibited a greater glucan and mannan-hydrolyzing activity than Accellerase 1000.
ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
Authors: MacCallum Iain , Przybylski Dariusz , Gnerre Sante , Burton Joshua , Shlyakhter Ilya , Gnirke Andreas , Malek Joel , McKernan Kevin , Ranade Swati , Shea Terrance P , Williams Louise , Young Sarah , Nusbaum Chad , Jaffe David B
Published: October 2009

We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds. Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1% (EULER-SR).
Coordinated activation of the secretory pathway during notochord formation in theXenopusembryo
Authors: Tanegashima Kosuke , Zhao Hui , Rebbert Martha L. , Dawid Igor B.
Published: October 2009

We compared the transcriptome in the developing notochord of Xenopus laevis embryos with that of other embryonic regions. A coordinated and intense activation of a large set of secretory pathway genes was observed in the notochord, but not in notochord precursors in the axial mesoderm at early gastrula stage. The genes encoding Xbp1 and Creb3l2 were also activated in the notochord. These two transcription factors are implicated in the activation of secretory pathway genes during the unfolded protein response, where cells react to the stress of a build-up of unfolded proteins in their endoplasmic reticulum. Xbp1 and Creb3l2 are differentially expressed but not differentially activated in the notochord. Reduction of expression of Xbp1 or Creb3l2 by injection of antisense morpholinos led to strong deficits in notochord but not somitic muscle development. In addition, the expression of some, but not all, genes encoding secretory proteins was inhibited by injection of xbp1 morpholinos. Furthermore, expression of activated forms of Xbp1 or Creb3l2 in animal explants could activate a similar subset of secretory pathway genes. We conclude that coordinated activation of a battery of secretory pathway genes mediated by Xbp1 and Creb/ATF factors is a characteristic and necessary feature of notochord formation.
The glypican Dally is required in the niche for the maintenance of germline stem cells and short-range BMP signaling in theDrosophilaovary
Authors: Guo Zheng , Wang Zhaohui
Published: October 2009

The Drosophila ovary is an excellent system with which to study germline stem cell (GSC) biology. Two or three female GSCs are maintained in a structure called a niche at the anterior tip of the ovary. The somatic niche cells surrounding the GSCs include terminal filament cells, cap cells and escort stem cells. Mounting evidence has demonstrated that BMP-like morphogens are the immediate upstream signals to promote GSC fate by preventing the expression of Bam, a key differentiation factor. In contrast to their morphogenic long-range action in imaginal epithelia, BMP molecules in the ovarian niche specify GSC fate at single-cell resolution. How this steep gradient of BMP response is achieved remains elusive. In this study, we found that the glypican Dally is essential for maintaining GSC identity. Dally is highly expressed in cap cells. Cell-specific Dally-RNAi, mutant clonal analysis and cell-specific rescue of the GSC-loss phenotype suggest that Dally acts in the cap cells adjacent to the GSCs. We confirmed that Dally facilitated BMP signaling in GSCs by examining its downstream targets in various dally mutants. Conversely, when we overexpressed Dally in somatic cells outside the niche, we increased the number of GSC-like cells apparently by expanding the pro-GSC microenvironment. Furthermore, in a genetic setting we revealed a BMP-sensitivity distinction between germline and somatic cells, namely that Dally is required for short-range BMP signaling in germline but not in somatic cells. We propose that Dally ensures high-level BMP signaling in the ovarian niche and thus female GSC determination.
Self-renewing epiblast stem cells exhibit continual delineation of germ cells with epigenetic reprogramming in vitro
Authors: Hayashi Katsuhiko , Surani M. Azim
Published: October 2009

Pluripotent epiblast stem cells (EpiSCs) derived from postimplantation embryos exhibit properties that are characteristically different when compared with pluripotent embryonic stem cells (ESCs) derived from mouse blastocysts. However, EpiSCs are relatively less well characterised compared with ESCs. In particular, the relationship between EpiSCs and primordial germ cells (PGCs)is unknown, and is worthy of investigation because PGCs originate from postimplantation epiblast cells in vivo. We show that EpiSCs have an infinite capacity for generating PGCs, under conditions that sustain their pluripotency and self-renewal. These PGCs generated in vitro show appropriate transcriptional and epigenetic reprogramming events and are able to develop further into late germ cells. Notably, the PGCs can, in turn, be induced to undergo dedifferentiation into pluripotent embryonic germ cells (EGCs), which resemble ESCs and not the EpiSC from which they are derived. Our observations demonstrate intrinsic reprogramming during specification of PGCs that results in the erasure of epigenetic memory of EpiSCs following reactivation of the X-chromosome, DNA demethylation and re-expression of key pluripotency genes. This study provides novel insights into the nature and properties of EpiSCs,and introduces an in vitro model system that will be useful for investigations on PGC specification and on mechanisms regulating epigenetic reprogramming in germ cells.
BMP signaling regulates sympathetic nervous system development through Smad4-dependent and -independent pathways
Authors: Morikawa Yuka , Zehir Ahmet , Maska Emily , Deng Chuxia , Schneider Michael D. , Mishina Yuji , Cserjesi Peter
Published: October 2009

Induction of the sympathetic nervous system (SNS) from its neural crest(NC) precursors is dependent on BMP signaling from the dorsal aorta. To determine the roles of BMP signaling and the pathways involved in SNS development, we conditionally knocked out components of the BMP pathways. To determine if BMP signaling is a cell-autonomous requirement of SNS development, the Alk3 (BMP receptor IA) was deleted in the NC lineage. The loss of Alk3 does not prevent NC cell migration, but the cells die immediately after reaching the dorsal aorta. The paired homeodomain factor Phox2b, known to be essential for survival of SNS precursors, is downregulated, suggesting that Phox2b is a target of BMP signaling. To determine if Alk3 signals through the canonical BMP pathway, Smad4was deleted in the NC lineage. Loss of Smad4 does not affect neurogenesis and ganglia formation; however, proliferation and noradrenergic differentiation are reduced. Analysis of transcription factors regulating SNS development shows that the basic helix-loop-helix factor Ascl1 is downregulated by loss of Smad4 and that Ascl1 regulates SNS proliferation but not noradrenergic differentiation. To determine if the BMP-activated Tak1 (Map3k7) pathway plays a role in SNS development, Tak1 was deleted in the NC lineage. We show that Tak1 is not involved in SNS development. Taken together, our results suggest multiple roles for BMP signaling during SNS development. The Smad4-independent pathway acts through the activation of Phox2b to regulate survival of SNS precursors, whereas the Smad4-dependent pathway controls noradrenergic differentiation and regulates proliferation by maintaining Ascl1 expression.
Pancreatic neurogenin 3-expressing cells are unipotent islet precursors
Authors: Desgraz Renaud , Herrera Pedro L.
Published: October 2009

Pancreatic islet endocrine cells arise during development from precursors expressing neurogenin 3 (Ngn3). As a population, Ngn3+ cells produce all islet cell types, but the potential of individual Ngn3+cells, an issue central to organogenesis in general and to in vitro differentiation towards cell-based therapies, has not been addressed. We performed in vivo clonal analyses in mice to study the proliferation and differentiation of very large numbers of single Ngn3+ cells using MADM, a genetic system in which a Cre-dependent chromosomal translocation labels, at extremely low mosaic efficiency, a small number of Ngn3+cells. We scored large numbers of progeny arising from single Ngn3+cells. In newborns, labeled islets frequently contained just a single tagged endocrine cell, indicating for the first time that each Ngn3+ cell is the precursor of a single endocrine cell. In adults, small clusters of two to three Ngn3+ progeny were detected, but all expressed the same hormone, indicating a low rate of replication from birth to adult stages. We propose a model whereby Ngn3+ cells are monotypic (i.e. unipotent)precursors, and use this paradigm to refocus ideas on how cell number and type must be regulated in building complete islets of Langerhans.
LRT, a tendon-specific leucine-rich repeat protein, promotes muscle-tendon targeting through its interaction with Robo
Authors: Wayburn Bess , Volk Talila
Published: October 2009

Correct muscle migration towards tendon cells, and the adhesion of these two cell types, form the basis for contractile tissue assembly in the Drosophila embryo. While molecules promoting the attraction of muscles towards tendon cells have been described, signals involved in the arrest of muscle migration following the arrival of myotubes at their corresponding tendon cells have yet to be elucidated. Here, we describe a novel tendon-specific transmembrane protein, which we named LRT due to the presence of a leucine-rich repeat domain (LRR) in its extracellular region. Our analysis suggests that LRT acts non-autonomously to better target the muscle and/or arrest its migration upon arrival at its corresponding tendon cell. Muscles in embryos lacking LRT exhibited continuous formation of membrane extensions despite arrival at their corresponding tendon cells, and a partial failure of muscles to target their correct tendon cells. In addition,overexpression of LRT in tendon cells often stalled muscles located close to the tendon cells. LRT formed a protein complex with Robo, and we detected a functional genetic interaction between Robo and LRT at the level of muscle migration behavior. Taken together, our data suggest a novel mechanism by which muscles are targeted towards tendon cells as a result of LRT-Robo interactions. This mechanism may apply to the Robo-dependent migration of a wide variety of cell types.
Epidemiology and disease burden from allergic disease in Scotland: analyses of national databases
Authors: Anandan C , Gupta R , Simpson CR , Fischbacher C , Sheikh A
Published: October 2009

Summary

Background

There are ongoing concerns about the quality of care provided to patients with allergic disorders in Scotland, but there are relatively few reliable data on the overall disease burden. We sought to: (1) describe the incidence, prevalence and outcome of allergic disorders; (2) estimate healthcare burden and costs; and (3) investigate ethnic variations in the epidemiology and outcomes from allergic disorders in Scotland.

Methods

Data sources: national surveys; primary care data; prescribing and medication data; hospital admissions data and mortality data.

Results

Allergic disorders are extremely common in Scotland, affecting about one in three of the population at some time in their lives. Incidence was highest for eczema (10.2 per 1000 registered patients). Over 4% of all GP consultations and 1.5% of hospital admissions were for allergic disorders. There were 100 asthma deaths in 2005 (20 per million people). Direct healthcare costs for allergic disorders were an estimated £130 million per year, the majority of these being incurred in primary care and related to asthma.

Conclusions

Allergic disorders are common in Scotland and given the very high proportion of children now affected, the high disease burden associated with these conditions is likely to persist for many decades.
Examination performance of graduate entry medical students compared with mainstream students
Authors: Calvert Melanie J , Ross Nick M , Freemantle Nick , Xu Yong , Zvauya Remigio , Parle Jim V
Published: October 2009

Summary

Objectives

To assess whether medical students on graduate entry/fast- track programmes perform as well as students on standard courses.

Design

Retrospective cohort study.

Setting

University of Birmingham Medical School.

Participants

Medical students on graduate entry/fast-track course and standard (5-year) course (‘mainstream’).

Main outcome measures

Examination marks from all assessments taken simultaneously by graduate entry course (GEC) and mainstream course students once the cohorts have combined: i.e. for the final three years of the programme. Honours awards for 2007 and 2008 graduates.

Results

In total 19,263 examination results were analysed from 1547 students. Of these 161 were GEC students and 1386 were mainstream medical students. On average mainstream students, male students, overseas students and students of South Asian ethnicity obtained lower examination marks than graduate entry students, female students, home or EU students and students of non-South Asian ethnicity, respectively. Graduate entry students were significantly more likely to achieve honours degrees than mainstream students.

Conclusion

On average the academic performance of Graduate Entry medical students at the University of Birmingham is better than mainstream medical students.
Testing and modelling non‐normality within the one‐factor model
Authors: Molenaar Dylan , Dolan Conor V. , Verhelst Norman D.
Published: October 2009

Maximum likelihood estimation in the one‐factor model is based on the assumption of multivariate normality for the observed data. This general distributional assumption implies three specific assumptions for the parameters in the one‐factor model: the common factor has a normal distribution; the residuals are homoscedastic; and the factor loadings do not vary across the common factor scale. When any of these assumptions is violated, non‐normality arises in the observed data. In this paper, a model is presented based on marginal maximum likelihood to enable explicit tests of these assumptions. In addition, the model is suitable to incorporate the detected violations, to enable statistical modelling of these effects. Two simulation studies are reported in which the viability of the model is investigated. Finally, the model is applied to IQ data to demonstrate its practical utility as a means to investigate ability differentiation.
Simultaneous Screening and Quantification of 29 Drugs of Abuse in Oral Fluid by Solid-Phase Extraction and Ultraperformance LC-MS/MS
Authors: Badawi Nora , Simonsen Kirsten Wiese , Steentoft Anni , Bernhoft Inger Marie , Linnet Kristian
Published: October 2009

Background: The European DRUID (Driving under the Influence of Drugs, Alcohol And Medicines) project calls for analysis of oral fluid (OF) samples, collected randomly and anonymously at the roadside from drivers in Denmark throughout 2008–2009. To analyze these samples we developed an ultra performance liquid chromatography–tandem mass spectrometry (UPLC-MS/MS) method for detection of 29 drugs and illicit compounds in OF. The drugs detected were opioids, amphetamines, cocaine, benzodiazepines, and Δ-9-tetrahydrocannabinol.

Method: Solid-phase extraction was performed with a Gilson ASPEC XL4 system equipped with Bond Elut Certify sample cartridges. OF samples (200 mg) diluted with 5 mL of ammonium acetate/methanol (vol/vol 90:10) buffer were applied to the columns and eluted with 3 mL of acetonitrile with aqueous ammonium hydroxide. Target drugs were quantified by use of a Waters ACQUITY UPLC system coupled to a Waters Quattro Premier XE triple quadrupole (positive electrospray ionization mode, multiple reaction monitoring mode).

Results: Extraction recoveries were 36%–114% for all analytes, including Δ-9-tetrahydrocannabinol and benzoylecgonine. The lower limit of quantification was 0.5 μg/kg for all analytes. Total imprecision (CV) was 5.9%–19.4%. With the use of deuterated internal standards for most compounds, the performance of the method was not influenced by matrix effects. A preliminary account of OF samples collected at the roadside showed the presence of amphetamine, cocaine, codeine, Δ-9-tetrahydrocannabinol, tramadol, and zopiclone.

Conclusions: The UPLC-MS/MS method makes it possible to detect all 29 analytes in 1 chromatographic run (15 min), including Δ-9-tetrahydrocannabinol and benzoylecgonine, which previously have been difficult to incorporate into multicomponent methods.