bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA-seq analyses of gene expression in the microsclerotia of Verticillium dahliae
Authors: Duressa Dechassa , Anchieta Amy , Chen Dongquan , Klimes Anna , Garcia-Pedrajas Maria D , Dobinson Katherine F , Klosterman Steven J 
Published: September 2013

Abstract

Background
The soilborne fungus, Verticillium dahliae, causes Verticillium wilt disease in plants. Verticillium wilt is difficult to control since V. dahliae is capable of persisting in the soil for 10 to 15 years as melanized microsclerotia, rendering crop rotation strategies for disease control ineffective. Microsclerotia of V. dahliae overwinter and germinate to produce infectious hyphae that give rise to primary infections. Consequently, microsclerotia formation, maintenance, and germination are critically important processes in the disease cycle of V. dahliae.

Results
To shed additional light on the molecular processes that contribute to microsclerotia biogenesis and melanin synthesis in V. dahliae, three replicate RNA-seq libraries were prepared from 10 day-old microsclerotia (MS)-producing cultures of V. dahliae, strain VdLs.17 (average = 52.23 million reads), and those not producing microsclerotia (NoMS, average = 50.58 million reads). Analyses of these libraries for differential gene expression revealed over 200 differentially expressed genes, including up-regulation of melanogenesis-associated genes tetrahydroxynaphthalene reductase (344-fold increase) and scytalone dehydratase (231-fold increase), and additional genes located in a 48.8 kilobase melanin biosynthetic gene cluster of strain VdLs.17. Nearly 50% of the genes identified as differentially expressed in the MS library encode hypothetical proteins. Additional comparative analyses of gene expression in V. dahliae, under growth conditions that promote or preclude microsclerotial development, were conducted using a microarray approach with RNA derived from V. dahliae strain Dvd-T5, and from the amicrosclerotial vdh1 strain. Differential expression of selected genes observed by RNA-seq or microarray analysis was confirmed using RT-qPCR or Northern hybridizations.

Conclusion
Collectively, the data acquired from these investigations provide additional insight into gene expression and molecular processes that occur during MS biogenesis and maturation in V. dahliae. The identified gene products could therefore potentially represent new targets for disease control through prevention of survival structure development.
The effect of intravenous iron on postoperative transfusion requirements in hip fracture patients: study protocol for a randomized controlled trial
Authors: Rowlands Martin , Forward Daren P , Sahota Opinder , Moppett Iain K 
Published: September 2013

Abstract

Background
Anaemia following hip fracture is common. Approximately 30 to 45% of patients have haemoglobin concentrations below population norms on admission, and around 10% are severely anaemic. Anaemia on admission, and in the postoperative period, is associated with poor outcomes with regard to mobility, postoperative mortality and readmission. There is currently no clear consensus on the optimal method of managing perioperative anaemia in this group of frail patients with frequent comorbidity. Liberal red cell transfusion in the postoperative period does not appear to improve outcome, whereas tranexamic acid appears to reduce transfusion rate at the expense of increased cardiovascular morbidity. There are encouraging results from one centre with the use of agents to stimulate red cell production, including intravenous iron and erythropoietin. UK practice differs significantly from these patients and these studies, and it is not clear whether these promising results will translate to the UK population.

Methods/Design
This is a single-centre randomized controlled parallel group trial, in a British university hospital.Randomization is achieved using a website and computer-generated concealed tables. Participants are 80 patients 70 years or over with acute hip fracture undergoing operative repair. The intervention group receive three daily infusions of 200 mg iron sucrose, starting within 24 hours of admission. The control group receive standard hospital care at the discretion of the clinical team. Red cell transfusions for each group are given in accordance with standard clinical triggers. The primary outcome is an increase in mean reticulocyte count in the intervention group at day 7. Secondary outcome measures include haemoglobin concentrations, early and late transfusion rates, infectious and cardiovascular complications, mobility and 30-day mortality.

Discussion
This is a pilot study to demonstrate haematopoietic efficacy of intravenous iron in this setting. Hence, we have chosen to measure change in reticulocyte count rather than the more clinically relevant differences in haemoglobin concentration or transfusion rate. If our results are positive, the study will provide the necessary information for development of a full-scale trial of intravenous iron.

Trial registration
Current Controlled Trials ISRCTN76424792; UK Medicines and Healthcare products Regulatory Authority (EuDRACT: 2011-003233-34).
Haploidentical stem cell transplantation in two children with mucopolysaccharidosis VI: clinical and biochemical outcome
Authors: Jester Sandra , Larsson Julia , Eklund Erik A , Papadopoulou Domniki , Månsson Jan-Eric , Békássy Albert N , Turkiewicz Dominik , Toporski Jacek , Øra Ingrid 
Published: September 2013

Abstract

Background
Mucopolysaccharidosis VI (MPS VI) is an autosomal recessive progressive multiorgan disorder due to mutation in the gene encoding the enzyme Arylsulfatase B (ARSB). Dysfunctional ARSB causes lysosomal accumulation of glycosaminoglycans (GAG). Currently, enzyme replacement therapy (ERT) is preferred to hematopoietic stem cell transplantation (SCT) due to the treatment-related risks of the latter. However, ERT constitutes an expensive life-long treatment. Increased experience and safety of SCT-procedures in recent years suggest that SCT should be further explored as a treatment option.
This is the first report on haploidentical SCT in patients with MPS VI. The primary objective was to assess the treatment safety and clinical and biochemical outcome.

Patients and methods
Two siblings diagnosed with MPS VI at 10 months of age and at birth with genotype p.C192R, reported as mild to intermediate phenotype, underwent unrelated umbilical cord blood transplantation pre-symptomatic. Due to graft failure, both patients were urgently re-transplantated with haploidentical SCT with the father as donor. Continuous clinical and biochemical status was monitored and concluded 3.8 and 4.6 years after the haploidentical SCT.

Results
Haploidentical SCT resulted in prompt and sustained engraftment. Complete donor chimerism was achieved in both patients, apart from mixed B cells chimerism in patient 2. ARSB activity in leukocytes post transplant increased from 0.0 to 19.0 μkat/kg protein (patient 1) and from 3.6 to 17.9 μkat/kg protein (patient 2) (ref. 17–40). Total urinary GAG normalized in both patients, although patient 2’s values slightly exceed normal range since 6 months. However, dermatan sulfaturia was substantially normalized since 16 months and 12 months post-SCT, respectively. Height was -1.85 SD and -1.27 SD at follow-up. Patient 1 had impaired visual acuity and discrete hepatomegaly. Patient 2 had elevated intraocular pressure and X-ray revealed steep acetabular angles and slightly flattened lumbar vertebrae.

Conclusion
This study demonstrates that young children with MPS VI tolerate haploidentical SCT. Normalization of enzyme production and dermatan sulfaturia indicates correction of the inborn error of metabolism and coincide with no obvious symptoms of progressive MPS VI up to 4.6 years post-SCT.
Factors influencing the cell adhesion and invasion capacity of Mycoplasma gallisepticum
Authors: Fürnkranz Ursula , Siebert-Gulle Karin , Rosengarten Renate , Szostak Michael P 
Published: September 2013

Abstract

Background
The cell invasiveness of Mycoplasma gallisepticum, the causative agent of respiratory disease in chickens and infectious sinusitis in turkeys, may be a substantial factor in the well-known chronicity of these diseases and in the systemic spread of infection. To date, not much is known about the host factors and mechanisms involved in promotion or obstruction of M. gallisepticum adherence and/or cell invasion.
In the current study, the influence of extracellular matrix (ECM) proteins such as fibronectin, collagen type IV and heparin, as well as plasminogen/plasmin, on the adhesion and cell invasion levels of M. gallisepticum to chicken erythrocytes and HeLa cells was investigated in vitro. Two strains, Rhigh and Rlow, which differ in their adhesion and invasion capacity, were analyzed by applying a modified gentamicin invasion assay. Binding of selected ECM molecules to M. gallisepticum was proven by Western blot analysis.

Results
Collagen type IV, fibronectin, and plasminogen exerted positive effects on adhesion and cell invasion of M. gallisepticum, with varying degrees, depending on the strain used. Especially strain Rhigh, with its highly reduced cell adhesion and invasion capabilities seemed to profit from the addition of plasminogen. Western and dot blot analyses showed that Rhigh as well as Rlow are able to adsorb horse fibronectin and plasminogen present in the growth medium. Depletion of HeLa cell membranes from cholesterol resulted in increased adhesion, but decreased cell invasion.

Conclusion
ECM molecules seem to play a supportive role in the adhesion/cell invasion process of M. gallisepticum. Cholesterol depletion known to affect lipid rafts on the host cell surface had contrary effects on cell adherence and cell invasion of M. gallisepticum.
Comparative analysis of the Trichoderma reeseitranscriptome during growth on the cellulase inducing substrates wheat straw and lactose
Authors: Bischof Robert , Fourtis Lukas , Limbeck Andreas , Gamauf Christian , Seiboth Bernhard , Kubicek Christian P 
Published: September 2013

Abstract

Background
Renewable lignocellulosic biomass is an advantageous resource for the production of second generation biofuels and other biorefinery products. In Middle Europe, wheat straw is one of the most abundant low-cost sources of lignocellulosic biomass. For its efficient use, an efficient mix of cellulases and hemicellulases is required. In this paper, we investigated how cellulase production by T. reesei on wheat straw compares to that on lactose, the only soluble and also cheap inducing carbon source for enzyme production.

Results
We have examined and compared the transcriptome of T. reesei growing on wheat straw and lactose as carbon sources under otherwise similar conditions. Gene expression on wheat straw exceeded that on lactose, and 1619 genes were found to be only induced on wheat straw but not on lactose. They comprised 30% of the CAZome, but were also enriched in genes associated with phospholipid metabolism, DNA synthesis and repair, iron homeostatis and autophagy. Two thirds of the CAZome was expressed both on wheat straw as well as on lactose, but 60% of it at least >2-fold higher on the former. Major wheat straw specific genes comprised xylanases, chitinases and mannosidases. Interestingly, the latter two CAZyme families were significantly higher expressed in a strain in which xyr1 encoding the major regulator of cellulase and hemicellulase biosynthesis is non-functional.

Conclusions
Our data reveal several major differences in the transcriptome between wheat straw and lactose which may be related to the higher enzyme formation on the former and their further investigation could lead to the development of methods for increasing enzyme production on lactose.
Metabolism modifications and apoptosis induction after Cellfood™ administration to leukemia cell lines
Authors: Catalani Simona , Carbonaro Valentina , Palma Francesco , Arshakyan Marselina , Galati Rossella , Nuvoli Barbara , Battistelli Serafina , Canestrari Franco , Benedetti Serena 
Published: September 2013

Abstract

Background
Cellfood™ (CF) is a nutritional supplement containing deuterium sulphate, minerals, amino acids, and enzymes, with well documented antioxidant properties. Its organic and inorganic components are extracted from the red algae Lithothamnion calcareum, whose mineral extract has shown growth-inhibitory effect both on in vitro and in vivo models. The purpose of this study was to evaluate the antiproliferative effects of CF on leukemic cells. In fact, according to its capacity to modulate O2 availability and to improve mitochondrial respiratory metabolism, we wondered if CF could affect cancer cell metabolism making cells susceptible to apoptosis.

Methods
Three leukemic cell lines, Jurkat, U937, and K562, were treated with CF 5 μl/ml up to 72 hours. Cell viability, apoptosis (i.e. caspase-3 activity and DNA fragmentation), hypoxia inducible factor 1 alpha (HIF-1α) concentration, glucose transporter 1 (GLUT-1) expression, lactate dehydrogenase (LDH) activity and lactate release in the culture medium were detected and compared with untreated cells.

Results
CF significantly inhibited leukemic cell viability by promoting cell apoptosis, as revealed by caspase-3 activation and DNA laddering. In particular, CF treated cells showed lower HIF-1α levels and lower GLUT-1 expression as compared to untreated cells. At the same time, CF was able to reduce LDH activity and, consequently, the amount of lactate released in the extracellular environment.

Conclusions
We supplied evidence for an antiproliferative effect of CF on leukemia cell lines by inducing cell death through an apoptotic mechanism and by altering cancer cell metabolism through HIF-1α and GLUT-1 regulation. Thanks to its antioxidative and proapoptotic properties, CF might be a good candidate for cancer prevention.
Understanding the physical activity promotion behaviours of podiatrists: a qualitative study
Authors: Crisford Paul , Winzenberg Tania , Venn Alison , Cleland Verity 
Published: September 2013

AbstractBackgroundHealth professionals are encouraged to play a part in reducing the health risks of physical inactivity. Little is known of the physical activity promotion practice behaviours of podiatrists.MethodsWe performed 20 semi‐structured interviews with purposefully selected podiatrists to explore their physical activity promotion attitudes, beliefs, knowledge and practice. Transcribed interviews were coded using an iterative thematic approach to identify major themes and salient beliefs.ResultsOverall, the participants had a positive attitude to physical activity promotion, considering it a normal part of their role. They saw their role as giving information, encouraging activity and making recommendations, however in practice they were less inclined to follow up on recommendations, monitor activity levels or document the process. Their approach was generally opportunistic, informal and unstructured and the content of assessment and promotion dependent upon the presenting patient's condition. Advice tended to be tailored to the patient's capabilities and interests. They considered there are opportunities to promote physical activity during regular consultations, however, were more likely to do so in patients with chronic diseases such as diabetes. Main barriers to physical activity promotion included unreceptive and unmotivated patients as well as a lack of time, skills and resources.ConclusionsPhysical activity promotion appears feasible in podiatry practice in terms of opportunity and acceptability to practitioners, but there is scope for improvement. Strategies to improve promotion need to consider the major issues, barriers and opportunities as well as provide a more structured approach to physical activity promotion by podiatrists.
Novel perspectives for evolving enzyme cocktails for lignocellulose hydrolysis in biorefineries
Authors: Mohanram Saritha , Amat Dolamani , Choudhary Jairam , Arora Anju , Nain Lata 
Published: September 2013

Abstract
The unstable and uncertain availability of petroleum sources as well as rising cost of fuels have shifted global efforts to utilize renewable resources for the production of greener energy and a replacement which can also meet the high energy demand of the world. Bioenergy routes suggest that atmospheric carbon can be cycled through biofuels in carefully designed systems for sustainability. Significant potential exists for bioconversion of biomass, the most abundant and also the most renewable biomaterial on our planet. However, the requirements of enzyme complexes which act synergistically to unlock and saccharify polysaccharides from the lignocellulose complex to fermentable sugars incur major costs in the overall process and present a great challenge. Currently available cellulase preparations are subject to tight induction and regulation systems and also suffer inhibition from various end products. Therefore, more potent and efficient enzyme preparations need to be developed for the enzymatic saccharification process to be more economical. Approaches like enzyme engineering, reconstitution of enzyme mixtures and bioprospecting for superior enzymes are gaining importance. The current scenario, however, also warrants the need for research and development of integrated biomass production and conversion systems.
Divisor class groups and graded canonical modules of multisection rings
Authors: Kurano Kazuhiko 
Published: September 2013

AbstractWe describe the divisor class group and the graded canonical module of the multisection ring T (X;D1,…, Ds) for a normal projective variety X and Weil divisors D1,…, Ds on X under a mild condition. In the proof, we use the theory of Krull domain and the equivariant twisted inverse functor.
Critical Mediations: Haewŏn Chinhon Kut, a Shamanic Ritual for Korean “Comfort Women”
Authors: Kim David J. 
Published: September 2013

On July 13, 1990, a group of shamans innovated and performed a ritual they refer to as the haewŏn chinhon to appease the deceased spirits of Japanese military “comfort women.” Caught unprepared for the large number of spirits who appeared, as well as the accompanying spiritual and emotional toil, they made a promise to the spirits that they would perform the ritual in all eight provinces of Korea — three in the North and five in the South — keeping in mind, of course, the obvious geo-political problems in that regard. Eventually in 2003, the shamans began their fulfillment of that promise with another series of haewŏn chinhon rituals, this time better prepared and stronger in numbers.
This article analyzes one of these rituals in detail, not only focusing on its structural aspects but also considering it as a site to reexamine Gayatiri Spivak's conceptualizations of the subaltern, as they relate to both comfort women and shamanic activity. Drawing on the work of Jacques Derrida, Spivak theorizes the subaltern as both stemming from and producing what she refers to as a “blank space” in text, and consequently speech, which opens a fissure for the potential constitution of the other. This productive space — unscripted and undifferentiated — I argue, is likewise a potential site for what Walter Benjamin referred to as the emergence of “historical materialism,” which reveals itself in flashes, or unexpected moments of danger. Within the structured mechanics of ritual there is space for chance and contingency. The unforeseen accident lurks as a break in the action, which takes place outside ritual structure and goes beyond representation and repetition. During the performance that I detail, there was one such moment — completely unexpected — that reveals more about the mimetic possibilities of shamanism than a ritual that goes entirely as planned. This article examines this incident, when a shaman, unable to control the possessing spirits, collapses to the ground, as well as the events that follow. The article also contextualizes this ritual in relation to debates surrounding the “comfort women” issue, and how it is both situated within and outside of what C. Sarah Soh refers to as the “paradigmatic” narrative of victimization, in addition to the larger problem of representation as it relates to both presence and discursive claims to factual truths.
Acetabular component migration in total HIP arthroplasty using CT and a semiautomated program for volume merging
Authors: Olivecrona L. , Crafoord J. , Olivecrona H. , Noz M. E. , Maguire G. Q. , Zeleznik M. P. , Svensson L. , Weidenhielm L. 
Published: September 2013

Purpose: To develop a non-invasive method for detection of acetabular cup migration after total hip arthroplasty (THA) with a higher degree of accuracy than routine plain radiography. Material and Methods: Two CT examinations, 10 min apart, were obtained from each of 10 patients that had undergone THA. Using an in-house developed semiautomated program for volume merging, the pelves in the two examinations were fused and the acetabular cup was visually and numerically evaluated to test the method's accuracy in detecting migration. Results: In the visual evaluation of the best match a 1-mm translation of the cup was detectable. The numerical evaluation, comparing landmarks placed in the images of the acetabular cup and the head of the femur component in the two examinations, showed the mean difference in orientation of acetabular axes to be 2.5°, the mean distance between centre of cup face to be 2.5 mm and the mean distance between centre of the head of the prosthetic femoral component to be 1 mm. Conclusion: This method has a significantly higher accuracy than routine plain radiography in detecting acetabular cup migration and could be used in clinical practice. It gives both a visual and a numerical correlate to migration.
Semiautomatic core biopsy: A modified biopsy technique in breast diseases
Authors: Abdsaleh S. , Azavedo E. , Lindgren P. G. 
Published: September 2013

Purpose: To evaluate a semiautomatic gun to retrieve diagnostic core specimens of lesions in the breast and the axillary region. Material and Methods: In a series of 180 consecutive core biopsies (2.1 mm), 145 (142 breasts and 3 axillae) were performed with a semiautomatic gun (18 stereotaxic and 127 US-guided) from lesions presenting mammographically as microcalcifications (n = 15) and opacities (n = 130). The gun did not work satisfactorily in 34 lesions, which were tumors with a very hard consistency. One additional patient was excluded because of technical failure. Biopsy diagnoses in the 145 patients were correlated to surgical histopathology, follow-up mammograms and/or clinical findings. Results: Histologic examination of the specimens resulted in correct diagnoses in 89% (129/145) of the total material and in 87% (108/124) of cancers. In 107 cases, in which only 1 specimen was obtained, 83 of 89 cancers (87%) were detected. Length of specimens ranged from 3 mm (n = 2) to 17 mm (n = 31). Among patients with a 17-mm-long specimen, there was only 1 false-negative diagnosis. Conclusion: The semiautomatic gun provided diagnostic specimens in a majority of cases and could be used as an alternative to the automatic guns when size or location of the lesions necessitates a high precision. It was not suitable for use in very hard tumors.
Functional Genetics in the Post-genomics Era: Building a Better Roadmap in Drosophila
Authors: Kulathinal Rob J 
Published: September 2013

Abstract
In this commentary, Rob Kulathinal describes two papers from the Perrimon laboratory, each describing a new online resource that can assist geneticists with the design of their RNAi experiments. Hu et al.’s “UP-TORR: online tool for accurate and up-to-date annotation of RNAi reagents” and “FlyPrimerBank: An online database for Drosophila melanogaster gene expression analysis and knockdown evaluation of RNAi reagents” are published, respectively, in this month’s issue of GENETICS and G3: Genes|Genomes|Genetics.