bluuebunny/crossref_metadata_2025_split huggingface dataset:
Development of human limbs.
Authors: Ermolenko Alexander 
Published: January 2011

AbstractThis work offers a new view on the developmental history of tetrapods. It proposes an original evolution model of human limbs based on metameric formation of osteogenic buds in accordance to primary segmentation and biplanar symmetry. While going through evolution, osteogenic buds initially identical to each other were changing their sizes, realigning, regressing, uniting while keeping the direction of the formation in accordance to the following formula (taking into account sesamoid bones):2; 1; 2; 3; 2; 3; 5; 5; 8; 8 (in the upper limb together with the upper limb girdle); 3; 2; 3; 2; 1; 2; 8; 8; 5; 5 (in the lower limb together with the pelvic bones).
Anti-HIV therapy: pipeline approaches and future directions
Authors: Dwivedi Lavkush , Shrivastava Mansi 
Published: January 2011

AbstractHuman immunodeficiency virus (HIV), with about 30 million deaths and double infections (in developing countries), is an open challenge today for global scientists. Developing safe and effective measurements against it has become the prime need of hour. Though, putting it at health priority, various efforts like chemotherapy, vaccines and others are attempted globally over last decade. Consequently, highly active antiretroviral therapy was introduced but fails to completely block the viral replication due to drug resistance and various other severe side effects. The antigenic variability and lack of appropriate experimental models is the major obstacle in the development of an ever effective treatment against HIV. However, to overcome the present hurdles and to emerge a preventive HIV vaccine efforts at various platforms are done. A renewed, coordinated research, preclinical studies, clinical trials together with sufficient long term scientific and commercial commitments are made. Few of the therapeutic efforts viz. RNA interference (RNAi) based replication arrest of HIV, viral enzymes’ inhibitors, nanotechnology based HIV control and various preclinically trialed vaccines are reviewed in this paper. Also, the observed toxicity of existing therapeutic regimen, key challenges and future prospects for the development of better tolerated prophylactic HIV-1 vaccine are discussed.
GPU accelerated biochemical network simulation
Authors: Zhou Yanxiang , Liepe Juliane , Sheng Xia , Stumpf Michael P. H. , Barnes Chris 
Published: January 2011

Abstract
Motivation: Mathematical modelling is central to systems and synthetic biology. Using simulations to calculate statistics or to explore parameter space is a common means for analysing these models and can be computationally intensive. However, in many cases, the simulations are easily parallelizable. Graphics processing units (GPUs) are capable of efficiently running highly parallel programs and outperform CPUs in terms of raw computing power. Despite their computational advantages, their adoption by the systems biology community is relatively slow, since differences in hardware architecture between GPUs and CPUs complicate the porting of existing code.
Results: We present a Python package, cuda-sim, that provides highly parallelized algorithms for the repeated simulation of biochemical network models on NVIDIA CUDA GPUs. Algorithms are implemented for the three popular types of model formalisms: the LSODA algorithm for ODE integration, the Euler–Maruyama algorithm for SDE simulation and the Gillespie algorithm for MJP simulation. No knowledge of GPU computing is required from the user. Models can be specified in SBML format or provided as CUDA code. For running a large number of simulations in parallel, up to 360-fold decrease in simulation runtime is attained when compared to single CPU implementations.
Availability: http://cuda-sim.sourceforge.net/
Contact: christopher.barnes@imperial.ac.uk; m.stumpf@imperial.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
A k-mer scheme to predict piRNAs and characterize locust piRNAs
Authors: Zhang Yi , Wang Xianhui , Kang Le 
Published: January 2011

Abstract
Motivation: Identifying piwi-interacting RNAs (piRNAs) of non-model organisms is a difficult and unsolved problem because piRNAs lack conservative secondary structure motifs and sequence homology in different species.
Results: In this article, a k-mer scheme is proposed to identify piRNA sequences, relying on the training sets from non-piRNA and piRNA sequences of five model species sequenced: rat, mouse, human, fruit fly and nematode. Compared with the existing ‘static’ scheme based on the position-specific base usage, our novel ‘dynamic’ algorithm performs much better with a precision of over 90% and a sensitivity of over 60%, and the precision is verified by 5-fold cross-validation in these species. To test its validity, we use the algorithm to identify piRNAs of the migratory locust based on 603 607 deep-sequenced small RNA sequences. Totally, 87 536 piRNAs of the locust are predicted, and 4426 of them matched with existing locust transposons. The transcriptional difference between solitary and gregarious locusts was described. We also revisit the position-specific base usage of piRNAs and find the conservation in the end of piRNAs. Therefore, the method we developed can be used to identify piRNAs of non-model organisms without complete genome sequences.
Availability: The web server for implementing the algorithm and the software code are freely available to the academic community at http://59.79.168.90/piRNA/index.php.
Contact: lkang@ioz.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
Aerosol optical thickness and spatial variability along coastal and offshore waters of the eastern Arabian Sea
Authors: Menon Harilal B. , Sangekar Nutan , Lotliker Aneesh , Krishna Moorthy Krishnaswamy , Vethamony Ponnumani 
Published: January 2011

AbstractMenon, H. B., Sangekar, N., Lotliker, A., Krishna Moorthy, K., and Vethamony, P. 2011. Aerosol optical thickness and spatial variability along coastal and offshore waters of the eastern Arabian Sea. – ICES Journal of Marine Science, 68: 745–750. Data from the ocean-colour monitor (OCM) on board the Indian Remote Sensing Satellite P4 were used to analyse the spatial and temporal distribution of aerosol optical thickness (AOT) over the coastal and offshore waters of the eastern Arabian Sea. Zero water-leaving radiance from the near infrared (NIR) region was assumed for oceanic (open ocean) waters, because of the absorption of long-wave radiation by water molecules. As this assumption fails in coastal waters, it was necessary to correct for water-leaving radiance and sun glint to the NIR bands. The aerosol size-distribution parameter (α) was derived from a relationship between two NIR bands. The Ångström turbidity parameter (β) was obtained using an algorithm relating in situ hand-held, sun-photometer measurements and aerosol radiance (La) at 490 nm. The relationship between β and La (490) was derived with a sensitivity analysis, using a calibrated radiative transfer model. AOTs were retrieved for each pixel of 500 nm. The algorithm's performance was tested by comparing OCM-derived AOT values with in situ AOT and MODIS-derived values. Aerosol maps thus generated from January to December 2005 demonstrate the potential of this new retrieval method for producing AOT climatology from OCM data over coastal waters.
A Three-Dimensional Multiscale Model for Gas Exchange in Fruit
Authors: Ho Quang Tri , Verboven Pieter , Verlinden Bert E. , Herremans Els , Wevers Martine , Carmeliet Jan , Nicolaï Bart M. 
Published: January 2011

Abstract
Respiration of bulky plant organs such as roots, tubers, stems, seeds, and fruit depends very much on oxygen (O2) availability and often follows a Michaelis-Menten-like response. A multiscale model is presented to calculate gas exchange in plants using the microscale geometry of the tissue, or vice versa, local concentrations in the cells from macroscopic gas concentration profiles. This approach provides a computationally feasible and accurate analysis of cell metabolism in any plant organ during hypoxia and anoxia. The predicted O2 and carbon dioxide (CO2) partial pressure profiles compared very well with experimental data, thereby validating the multiscale model. The important microscale geometrical features are the shape, size, and three-dimensional connectivity of cells and air spaces. It was demonstrated that the gas-exchange properties of the cell wall and cell membrane have little effect on the cellular gas exchange of apple (Malus × domestica) parenchyma tissue. The analysis clearly confirmed that cells are an additional route for CO2 transport, while for O2 the intercellular spaces are the main diffusion route. The simulation results also showed that the local gas concentration gradients were steeper in the cells than in the surrounding air spaces. Therefore, to analyze the cellular metabolism under hypoxic and anoxic conditions, the microscale model is required to calculate the correct intracellular concentrations. Understanding the O2 response of plants and plant organs thus not only requires knowledge of external conditions, dimensions, gas-exchange properties of the tissues, and cellular respiration kinetics but also of microstructure.
Three-Dimensional Architecture of Grana and Stroma Thylakoids of Higher Plants as Determined by Electron Tomography
Authors: Austin Jotham R. , Staehelin L. Andrew 
Published: January 2011

Abstract
We have investigated the three-dimensional (3D) architecture of the thylakoid membranes of Arabidopsis (Arabidopsis thaliana), tobacco (Nicotiana tabacum), and spinach (Spinacia oleracea) with a resolution of approximately 7 nm by electron tomography of high-pressure-frozen/freeze-substituted intact chloroplasts. Higher-plant thylakoids are differentiated into two interconnected and functionally distinct domains, the photosystem II/light-harvesting complex II-enriched stacked grana thylakoids and the photosystem I/ATP synthase-enriched, nonstacked stroma thylakoids. The grana thylakoids are organized in the form of cylindrical stacks and are connected to the stroma thylakoids via tubular junctions. Our data confirm that the stroma thylakoids are wound around the grana stacks in the form of multiple, right-handed helices at an angle of 20° to 25° as postulated by a helical thylakoid model. The junctional connections between the grana and stroma thylakoids all have a slit-like architecture, but their size varies tremendously from approximately 15 × 30 nm to approximately 15 × 435 nm, which is approximately 5 times larger than seen in chemically fixed thylakoids. The variable slit length results in less periodicity in grana/stroma thylakoid organization than proposed in the original helical model. The stroma thylakoids also exhibit considerable architectural variability, which is dependent, in part, on the number and the orientation of adjacent grana stacks to which they are connected. Whereas some stroma thylakoids form solid, sheet-like bridges between adjacent grana, others exhibit a branching geometry with small, more tubular sheet domains also connecting adjacent, parallel stroma thylakoids. We postulate that the tremendous variability in size of the junctional slits may reflect a novel, active role of junctional slits in the regulation of photosynthetic function. In particular, by controlling the size of junctional slits, plants could regulate the flow of ions and membrane molecules between grana and stroma thylakoid membrane domains.
Cytokinin Regulates the Activity of Reproductive Meristems, Flower Organ Size, Ovule Formation, and Thus Seed Yield inArabidopsis thaliana
Authors: Bartrina Isabel , Otto Elisabeth , Strnad Miroslav , Werner Tomáš , Schmülling Thomas 
Published: January 2011

AbstractThe size and activity of the shoot apical meristem is regulated by transcription factors and low molecular mass signals, including the plant hormone cytokinin. The cytokinin status of the meristem depends on different factors, including metabolic degradation of the hormone, which is catalyzed by cytokinin oxidase/dehydrogenase (CKX) enzymes. Here, we show that CKX3 and CKX5 regulate the activity of the reproductive meristems of Arabidopsis thaliana. CKX3 is expressed in the central WUSCHEL (WUS) domain, while CKX5 shows a broader meristematic expression. ckx3 ckx5 double mutants form larger inflorescence and floral meristems. An increased size of the WUS domain and enhanced primordia formation indicate a dual function for cytokinin in defining the stem cell niche and delaying cellular differentiation. Consistent with this, mutation of a negative regulator gene of cytokinin signaling, ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6, which is expressed at the meristem flanks, caused a further delay of differentiation. Terminal cellular differentiation was also retarded in ckx3 ckx5 flowers, which formed more cells and became larger, corroborating the role of cytokinin in regulating flower organ size. Furthermore, higher activity of the ckx3 ckx5 placenta tissue established supernumerary ovules leading to an increased seed set per silique. Together, the results underpin the important role of cytokinin in reproductive development. The increased cytokinin content caused an ~55% increase in seed yield, highlighting the relevance of sink strength as a yield factor.
Molecular and cellular effects of multi‐targeted cyclin‐dependent kinase inhibition in myeloma: biological and clinical implications
Authors: McMillin Douglas W. , Delmore Jake , Negri Joseph , Buon Leutz , Jacobs Hannah M. , Laubach Jacob , Jakubikova Jana , Ooi Melissa , Hayden Patrick , Schlossman Robert , Munshi Nikhil C. , Lengauer Christoph , Richardson Paul G. , Anderson Kenneth C. , Mitsiades Constantine S. 
Published: January 2011

SummaryCell cycle regulators, such as cyclin‐dependent kinases (CDKs), are appealing targets for multiple myeloma (MM) therapy given the increased proliferative rates of tumour cells in advanced versus early stages of MM. We hypothesized that a multi‐targeted CDK inhibitor with a different spectrum of activity compared to existing CDK inhibitors could trigger distinct molecular sequelae with therapeutic implications for MM. We therefore studied the small molecule heterocyclic compound NVP‐LCQ195/AT9311 (LCQ195), which inhibits CDK1, CDK2 and CDK5, as well as CDK3 and CDK9. LCQ195 induced cell cycle arrest and eventual apoptotic cell death of MM cells, even at sub‐μmol/l concentrations, spared non‐malignant cells, and overcame the protection conferred to MM cells by stroma or cytokines of the bone marrow milieu. In MM cells, LCQ195 triggered decreased amplitude of transcriptional signatures associated with oncogenesis, drug resistance and stem cell renewal, including signatures of activation of key transcription factors for MM cells e.g. myc, HIF‐1α, IRF4. Bortezomib‐treated MM patients whose tumours had high baseline expression of genes suppressed by LCQ195 had significantly shorter progression‐free and overall survival than those with low levels of these transcripts in their MM cells. These observations provide insight into the biological relevance of multi‐targeted CDK inhibition in MM.
Impact of reduced chemotherapy treatment for good risk childhood acute lymphoblastic leukaemia on infectious morbidity*
Authors: van Tilburg Cornelis M. , Sanders Elisabeth A.M. , Nibbelke Elisabeth E. , Pieters Rob , Revesz Tom , Westers Paul , Wolfs Tom F.W. , Bierings Marc B. 
Published: January 2011

SummaryReducing infectious morbidity is an important goal to improve childhood acute lymphoblastic leukaemia (ALL) survival. To explore the impact of chemotherapy reduction on infectious morbidity, we compared outpatient and inpatient infectious morbidity of reduced versus intensive (conventional) chemotherapy. One hundred and seventy‐one children newly diagnosed with ALL between 2004 and 2007 and treated according to the Dutch Childhood Oncology Group ALL 10 protocol were prospectively followed during the 2‐year treatment course. Stratified by minimal residual disease, 54 patients received reduced (standard risk; SR) and 117 patients received intensive (medium risk; MR) intensification/maintenance treatment. SR outpatients had a median of 1 febrile episode versus 4 in MR outpatients (P = 0·002). SR patients had fewer hospitalizations for fever. They were admitted a median of 0 times, with a median of 0 days of hospitalization, median 0 days of fever, median 0 times chemotherapy interruption and median 0 times intravenous antibiotics. MR patients were admitted for fever median 2 times (P < 0·001) with 10 days of hospitalization (P < 0·001), 2 days of fever (P < 0·001), one chemotherapy interruption (P < 0·001) and two intravenous antibiotics administration (P < 0·001). These data indicate that reduced intensification/maintenance compared to conventional intensive intensification/maintenance chemotherapy for good risk childhood ALL resulted in major decrease of infectious morbidity.
Erythropoiesis failure due to RPS19 deficiency is independent of an activated Tp53 response in a zebrafish model of Diamond–Blackfan anaemia
Authors: Torihara Hidetsugu , Uechi Tamayo , Chakraborty Anirban , Shinya Minori , Sakai Noriyoshi , Kenmochi Naoya 
Published: January 2011

SummaryDiamond–Blackfan anaemia (DBA) is a cancer‐prone genetic disorder characterized by pure red‐cell aplasia and associated physical deformities. The ribosomal protein S19 gene (RPS19) is the most frequently mutated gene in DBA (∼ 25%). TP53‐mediated cell cycle arrest and/or apoptosis in erythroid cells have been suggested to be major factors for DBA development, but it is not clear why mutations in the ubiquitously expressed RPS19 gene specifically affect erythropoiesis. Previously, we showed that RPS19 deficiency in zebrafish recapitulates the erythropoietic and developmental phenotypes of DBA, including defective erythropoiesis with severe anaemia. In this study, we analysed the simultaneous loss‐of‐function of RPS19 and Tp53 in zebrafish to investigate the role of Tp53 in the erythroid and morphological defects associated with RPS19 deficiency. Co‐inhibition of Tp53 activity rescued the morphological abnormalities, but did not alleviate erythroid aplasia in RPS19‐deficient zebrafish. In addition, knockdown of two other RP genes, rps3a and rpl36a, which result in severe morphological abnormalities but only mild erythroid defects, also elicited an activated Tp53 response. These results suggest that a Tp53‐independent but RPS19‐dependent pathway could be responsible for defective erythropoiesis in RPS19‐deficient zebrafish.
Enhanced ex vivo inhibition of platelet function following addition of dipyridamole to aspirin after transient ischaemic attack or ischaemic stroke: First results from the TRinity AntiPlatelet responsiveness (TrAP) study
Authors: Tobin William Oliver , Kinsella Justin A. , Collins Daniel Ronan , Coughlan Tara , O’Neill Desmond , Egan Bridget , Tierney Sean , Feeley Thomas Martin , Murphy Raymond P. , McCabe Dominick J. H. 
Published: January 2011

Summary Ex vivo dipyridamole ‘non‐responsiveness’ has not been extensively studied in ischaemic cerebrovascular disease. Platelet surface marker expression, leucocyte‐platelet complex formation and inhibition of platelet function at high shear stress as detected by the PFA‐100® Collagen‐Adenosine‐diphosphate (C‐ADP) and Collagen‐Epinephrine cartridges was assessed in 52 patients within 4 weeks of transient ischaemic attack (TIA) or ischaemic stroke on aspirin, and then 14 d (14 d) and >90 d (90 d) after adding dipyridamole. A novel definition of ‘Dipyridamole non‐responsiveness’ was used. The median C‐ADP closure time increased following addition of dipyridamole, remained elevated at 90 d (P ≤ 0·03), and was unaffected by aspirin dose. 59% at 14 d and 56% at 90 d were ‘dipyridamole non‐responders’ on the PFA‐100. The proportion of non‐responders at 14 and 90 d was similar (P = 0·9). Compared with baseline (4·6%), median monocyte‐platelet complexes increased at 14 d (5·0%, P = 0·03) and 90 d (4·9%, P = 0·04). Low C‐ADP closure times were associated with increased monocyte‐platelet complexes at 14 d (r = −0·32, P = 0·02) and 90 d (r = −0·33, P = 0·02). Monocyte‐platelet complexes increased in the subgroup of dipyridamole non‐responders on the PFA‐100 (P ≤ 0·045), but not in responders (P ≥ 0·5), at 14 and 90 d versus baseline. Additional inhibition of platelet function has been detected with the PFA‐100 when dipyridamole is added to aspirin. Elevated monocyte‐platelet complexes may contribute to ex vivo dipyridamole non‐responsiveness.
The non‐relapse mortality rate for patients with diffuse large B‐cell lymphoma is greater than relapse mortality 8 years after autologous stem cell transplantation and is significantly higher than mortality rates of population controls
Authors: Hill Brian T. , Rybicki Lisa , Bolwell Brian J. , Smith Stephen , Dean Robert , Kalaycio Matt , Pohlman Brad , Tench Shawnda , Sobecks Ronald , Andresen Steven , Copelan Edward , Sweetenham John 
Published: January 2011

SummaryHigh dose chemotherapy followed by autologous stem cell transplantation (ASCT) is the preferred treatment modality for patients with relapsed or refractory diffuse large B‐cell lymphoma (DLBCL). To assess long‐term outcomes of these patients, we retrospectively analysed data from 309 consecutive patients who underwent ASCT for DLBCL between 1994 and 2006. We found that non‐relapse mortality (NRM) became the major cause of death beginning approximately 8 years after ASCT. The most common causes of NRM during the study period were respiratory failure (31%), infection (13%), cardiac toxicity (15%) and secondary malignancy (15%). The strongest predictor of relapse mortality (RM) was disease status at transplant: patients who were in second or greater complete or partial remission had a higher risk of RM than those in first complete or partial remission [hazard ratio (HR) 3·7, P < 0·001], as did those who were relapsed or refractory (HR 4·9, P < 0·001). We describe the longest reported follow‐up of a large cohort of DLBCL patients uniformly‐treated with ASCT. Although relapse was initially the more likely cause of death, NRM exceeded RM after 8 years. After ASCT, surviving patients have significantly increased risk mortality rates relative to the general population and this excess risk persists over time.
The effects of the combination of freezing and the use of natural antioxidant technology on the quality of frozen sardine fillets (Sardinella aurita)
Authors: Ozogul Yesim , Durmuş Mustafa , Balıkcı Esra , Ozogul Fatih , Ayas Deniz , Yazgan Hatice 
Published: January 2011

SummaryThe effects of combination of freezing and the use of antioxidant technology on the quality of frozen sardine fillets were investigated in terms of sensory, biochemical [thiobarbituric acid (TBA), total volatile basic nitrogen (TVB‐N), peroxide value (PV) and free fatty acids (FFA)] and microbiological analyses [total viable count (TVC)]. Fish were filleted and divided into three groups. The first group was used as the control (C) without rosemary extract, the second group was treated with 1% rosemary extracts for 2 min (R1) and the third was treated with 2% rosemary extracts for 2 min (R2). All groups were frozen at −18 °C over the storage period of 6 months. The results obtained from this study showed that the combination of antioxidant and frozen storage resulted in significant reduction of bacterial growth and stabilised the biochemical characteristics, especially for R2. However, the use of antioxidant at the level of 2% (R2) gave a bitter taste according to sensory assessment whereas the panellists mostly preferred R1.