bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population size effects on germination, growth and symbiotic nitrogen fixation in an actinorhizal plant at the edge of its range
Authors: Markham John H. 
Published: April 2008

Populations at the edge of their range are known to have decreased fitness. However, the factors that cause this and the specific plant characters involved are not well understood. To determine whether symbiotic interactions play a role in altering fitness, I examined population age, seed viability, and nodulation in relation to population size of Ceanothus herbaceous Raf. at the northern limit of its range. Tap roots from three populations were grown in each of the three population’s soils to examine the specificity between C. herbaceous and Frankia . Population size ranged from 14 to 7300 individuals. There was a positive exponential relationship between population size, seed germination, and the proportion of plants forming nodules in the field. Populations varied in age by 26 years and age was not related to size. Recruitment into these populations was episodic and was positively correlated to growing season temperatures. Nodulation rates in the growth experiment were similar to those in the field, and plants showed much greater growth when nodulated. Plants from the largest population showed the greatest growth when infected with Frankia from their own soil. These plants also had significantly higher nitrogen-fixing activity per total plant mass than all other plant–soil combinations, suggesting that the plants from this population show some degree of specificity to the Frankia they are normally found with. Plants from the largest population grown in soil from other populations showed lower nitrogen-fixing activity per nodule mass than any other plant–soil combination. There was a positive relationship between nodule mass allocation and plant growth, a trend not seen in other nitrogen-fixing symbioses where nodule allocation is much higher. These results illustrate the importance of considering both the regeneration and growth phases when evaluating the effects of small population size on plant performance
Genetic and morphological analysis of floral homeotic mutantstepal-like bractandfagopyrum apetalaofFagopyrum esculentum
Authors: Logacheva Maria D. , Fesenko Ivan N. , Fesenko Aleksey N. , Penin Aleksey A. 
Published: April 2008

The studies on floral homeotic mutants of the model plant species Arabidopsis thaliana (L.) Heynh. and Antirrhinum majus L. have clarified many important aspects of the genetic control of flower development. However, the details of this process can vary in species representing different lineages of flowering plants. The studies on floral homeotic mutants of nonmodel plant species may significantly improve the understanding of the mechanisms of morphological evolution of flowers. We report here the results of the genetic and morphological analysis of two floral homeotic mutants of common buckwheat ( Fagopyrum esculentum Moench.). The mutant, tepal-like bract (tlb), is characterized by the transformation of bracts into petaloid organs, whereas fagopyrum apetala (fap), has a carpelloid perianth. Both mutant phenotypes are caused by a single recessive nuclear mutation. The double mutant fap tlb combines the features of tlb and fap. Our results show that single gene mutations are sufficient to convert the buckwheat bract into a tepal and to confer carpel identity on first whorl organs. These results are consistent with the premise that variations on the ABC model can be used to explain a wide range of floral architectures.
The Role of Constraints in Hebbian Learning
Authors: Miller Kenneth D. , MacKay David J. C. 
Published: April 2008

Models of unsupervised, correlation-based (Hebbian) synaptic plasticity are typically unstable: either all synapses grow until each reaches the maximum allowed strength, or all synapses decay to zero strength. A common method of avoiding these outcomes is to use a constraint that conserves or limits the total synaptic strength over a cell. We study the dynamic effects of such constraints. Two methods of enforcing a constraint are distinguished, multiplicative and subtractive. For otherwise linear learning rules, multiplicative enforcement of a constraint results in dynamics that converge to the principal eigenvector of the operator determining unconstrained synaptic development. Subtractive enforcement, in contrast, typically leads to a final state in which almost all synaptic strengths reach either the maximum or minimum allowed value. This final state is often dominated by weight configurations other than the principal eigenvector of the unconstrained operator. Multiplicative enforcement yields a “graded” receptive field in which most mutually correlated inputs are represented, whereas subtractive enforcement yields a receptive field that is “sharpened” to a subset of maximally correlated inputs. If two equivalent input populations (e.g., two eyes) innervate a common target, multiplicative enforcement prevents their segregation (ocular dominance segregation) when the two populations are weakly correlated; whereas subtractive enforcement allows segregation under these circumstances. These results may be used to understand constraints both over output cells and over input cells. A variety of rules that can implement constrained dynamics are discussed.
A Smoothing Regularizer for Feedforward and Recurrent Neural Networks
Authors: Wu Lizhong , Moody John 
Published: April 2008

We derive a smoothing regularizer for dynamic network models by requiring robustness in prediction performance to perturbations of the training data. The regularizer can be viewed as a generalization of the first-order Tikhonov stabilizer to dynamic models. For two layer networks with recurrent connections described by the training criterion with the regularizer is where Φ = {U, V, W} is the network parameter set, Z(t) are the targets, I(t) = {X(s), s = 1,2, …, t} represents the current and all historical input information, N is the size of the training data set, [Formula: see text] is the regularizer, and λ is a regularization parameter. The closed-form expression for the regularizer for time-lagged recurrent networks is where ‖ ‖ is the Euclidean matrix norm and γ is a factor that depends upon the maximal value of the first derivatives of the internal unit activations f(). Simplifications of the regularizer are obtained for simultaneous recurrent nets (τ ↦ 0), two-layer feedforward nets, and one layer linear nets. We have successfully tested this regularizer in a number of case studies and found that it performs better than standard quadratic weight decay.
Hebbian Learning of Context in Recurrent Neural Networks
Authors: Brunel Nicolas 
Published: April 2008

Single electrode recordings in the inferotemporal cortex of monkeys during delayed visual memory tasks provide evidence for attractor dynamics in the observed region. The persistent elevated delay activities could be internal representations of features of the learned visual stimuli shown to the monkey during training. When uncorrelated stimuli are presented during training in a fixed sequence, these experiments display significant correlations between the internal representations. Recently a simple model of attractor neural network has reproduced quantitatively the measured correlations. An underlying assumption of the model is that the synaptic matrix formed during the training phase contains in its efficacies information about the contiguity of persistent stimuli in the training sequence. We present here a simple unsupervised learning dynamics that produces such a synaptic matrix if sequences of stimuli are repeatedly presented to the network at fixed order. The resulting matrix is then shown to convert temporal correlations during training into spatial correlations between attractors. The scenario is that, in the presence of selective delay activity, at the presentation of each stimulus, the activity distribution in the neural assembly contains information of both the current stimulus and the previous one (carried by the attractor). Thus the recurrent synaptic matrix can code not only for each of the stimuli presented to the network but also for their context. We combine the idea that for learning to be effective, synaptic modification should be stochastic, with the fact that attractors provide learnable information about two consecutive stimuli. We calculate explicitly the probability distribution of synaptic efficacies as a function of training protocol, that is, the order in which stimuli are presented to the network. We then solve for the dynamics of a network composed of integrate-and-fire excitatory and inhibitory neurons with a matrix of synaptic collaterals resulting from the learning dynamics. The network has a stable spontaneous activity, and stable delay activity develops after a critical learning stage. The availability of a learning dynamics makes possible a number of experimental predictions for the dependence of the delay activity distributions and the correlations between them, on the learning stage and the learning protocol. In particular it makes specific predictions for pair-associates delay experiments.
Ceruloplasmin is a Better Predictor of the Long-Term Prognosis Compared with Fibrinogen, CRP, and IL-6 in Patients with Severe Unstable Angina
Authors: Ziakas Antonios , Gavrilidis Stavros , Souliou Efthimia , Giannoglou George , Stiliadis Ioannis , Karvounis Haralambos , Efthimiadis George , Mochlas Sotirios , Vayona M. Arvanitidou , Hatzitolios Apostolos , Savopoulos Christos , Pidonia Ifigenia , Parharidis George 
Published: April 2008

Background. We investigated the time course and prognostic value of fibrinogen (Fib), C-reactive protein (CRP), interleukin-6 (IL-6), and ceruloplasmin (CP) in patients with severe unstable angina. Methods. All 4 substances were measured on admission and after 6, 12, 24, 48, and 72 hours, and after 7 days and 6 months in 40 patients with Braunwald's classification class IIIB unstable angina. Results. All recorded substances increased significantly; 15 patients had cardiovascular events during hospitalization and 11 patients during follow-up. The time course and the mean values of Fib, CRP, and IL-6 were similar in patients with and without complications both during hospitalization and follow-up. However, CP levels from 6 hours until 6 months were significantly higher in patients with complications during follow-up ( P < .05). Conclusions. Fib, CRP, IL-6, and CP levels alter in patients with severe unstable angina. However, only CP levels were related to 12-month follow-up prognosis.
Flow-Mediated Arterial Dilation in Primary Antiphospholipid Syndrome
Authors: Bilora Franca , Sartori Maria Teresa , Zanon Ezio , Campagnolo Enrico , Arzenton Marianna , Rossato Alberto 
Published: April 2008

Objective. To investigate precocious alterations in the artery wall of patients with primary antiphospholipid syndrome (APS). Methods. We evaluated flow-mediated dilation (FMD) of the brachial artery and intima-media thickness (IMT) of carotid arteries in 16 patients and 16 healthy controls matched for age, gender, and other cardiovascular risk factors. Results. FMD of the brachial artery was significantly lower in patients than in controls (6.3 ± 5.2% vs 18.2 ± 2.7; P < .005). IMT was similar in the 2 groups. FMD was significantly reduced in patients with anticardiolipin antibodies IgM. Conclusions. APS correlates closely with precocious atherosclerosis, and the correlation with a type of anticardiolipin antibody may be predictive of more accelerated atherosclerosis.
Efficient transduction of pigtailed macaque hematopoietic repopulating cells with HIV-based lentiviral vectors
Authors: Trobridge Grant D. , Beard Brian C. , Gooch Christina , Wohlfahrt Martin , Olsen Philip , Fletcher James , Malik Punam , Kiem Hans-Peter 
Published: April 2008

AbstractLentiviral vectors are attractive for hematopoietic stem cell (HSC) gene therapy because they do not require mitosis for nuclear entry, they efficiently transduce hematopoietic repopulating cells, and self-inactivating (SIN) designs can be produced at high titer. Experiments to evaluate HIV-derived lentiviral vectors in nonhuman primates prior to clinical trials have been hampered by low transduction frequencies due in part to host restriction by TRIM5α. We have established conditions for efficient transduction of pigtailed macaque (Macaca nemestrina) long-term repopulating cells using VSV-G–pseudotyped HIV-based lentiviral vectors. Stable, long-term, high-level gene marking was observed in 3 macaques using relatively low MOIs (5-10) in a 48-hour ex vivo transduction protocol. All animals studied had rapid neutrophil engraftment with a median of 10.3 days to a count greater than 0.5 × 109/L (500/μL). Expression was detected in all lineages, with long-term marking levels in granulocytes at approximately 20% to 30%, and in lymphocytes at approximately 12% to 23%. All animals had polyclonal engraftment as determined by analysis of vector integration sites. These data suggest that lentiviral vectors should be highly effective for HSC gene therapy, particularly for diseases in which maintaining the engraftment potential of stem cells using short-term ex vivo transduction protocols is critical.
Generation of functional platelets from human embryonic stem cells in vitro via ES-sacs, VEGF-promoted structures that concentrate hematopoietic progenitors
Authors: Takayama Naoya , Nishikii Hidekazu , Usui Joichi , Tsukui Hiroko , Sawaguchi Akira , Hiroyama Takashi , Eto Koji , Nakauchi Hiromitsu 
Published: April 2008

AbstractHuman embryonic stem cells (hESCs) could potentially represent an alternative source for blood transfusion therapies and a promising tool for studying the ontogeny of hematopoiesis. When we cultured hESCs on either C3H10T1/2 or OP-9 cells to facilitate hematopoiesis, we found that exogenous administration of vascular endothelial growth factor promoted the emergence of sac-like structures, which we named embryonic stem cell–derived sacs (ES-sacs). These ES-sacs consisted of multiple cysts demarcated by cellular monolayers that retained some of the properties of endothelial cells. The spherical cells inside ES-sacs expressed primarily CD34, along with VE-cadherin, CD31, CD41a, and CD45, and were able to form hematopoietic colonies in semisolid culture and to differentiate into mature megakaryocytes by day 24 in the presence of thrombopoietin. Apparently, ES-sacs provide a suitable environment for hematopoietic progenitors. Relatively large numbers of mature megakaryocytes could be induced from the hematopoietic progenitors within ES-sacs, which were then able to release platelets that displayed integrin αIIbβ3 activation and spreading in response to ADP or thrombin. This novel protocol thus provides a means of generating platelets from hESCs, which could serve as the basis for efficient production of platelets for clinical transfusion and studies of thrombopoiesis.
First clinical use of ofatumumab, a novel fully human anti-CD20 monoclonal antibody in relapsed or refractory follicular lymphoma: results of a phase 1/2 trial
Authors: Hagenbeek Anton , Gadeberg Ole , Johnson Peter , Møller Pedersen Lars , Walewski Jan , Hellmann Andrzej , Link Brian K. , Robak Tadeusz , Wojtukiewicz Marek , Pfreundschuh Michael , Kneba Michael , Engert Andreas , Sonneveld Pieter , Flensburg Mimi , Petersen Jørgen , Losic Nedjad , Radford John 
Published: April 2008

Abstract
Ofatumumab is a unique monoclonal antibody that targets a distinct small loop epitope on the CD20 molecule. Preclinical data show that ofatumumab is active against B-cell lymphoma/chronic lymphocytic leukemia cells with low CD20-antigen density and high expression of complement inhibitory molecules. In a phase 1/2 trial evaluating safety and efficacy of ofatumumab in relapsed or refractory follicular non-Hodgkin lymphoma (FL) grade 1 or 2, 4 dose groups of 10 patients received 4 weekly infusions of 300, 500, 700, or 1000 mg. Patients had a median of 2 prior FL therapies and 13% had elevated lactate dehydrogenase. No safety concerns or maximum tolerated dose was identified. A total of 274 adverse events were reported; 190 were judged related to ofatumumab, most occurring on the first infusion day with Common Terminology Criteria grade 1 or 2. Eight related events were grade 3. Treatment caused immediate and profound B-cell depletion, and 65% of patients reverted to negative BCL2 status. Clinical response rates ranged from 20% to 63%. Median time to progression for all patients/responders was 8.8/32.6 months, and median duration of response was 29.9 months at a median/maximum follow-up of 9.2/38.6 months. Ofatumumab is currently being evaluated in patients with rituximab-refractory FL. This trial was registered at www.clinicaltrials.gov as #NCT00092274.
Clinical significance of minimal residual disease in childhood acute lymphoblastic leukemia and its relationship to other prognostic factors: a Children's Oncology Group study
Authors: Borowitz Michael J. , Devidas Meenakshi , Hunger Stephen P. , Bowman W. Paul , Carroll Andrew J. , Carroll William L. , Linda Stephen , Martin Paul L. , Pullen D. Jeanette , Viswanatha David , Willman Cheryl L. , Winick Naomi , Camitta Bruce M. 
Published: April 2008

Abstract
Minimal residual disease (MRD) is an important predictor of relapse in acute lymphoblastic leukemia (ALL), but its relationship to other prognostic variables has not been fully assessed. The Children's Oncology Group studied the prognostic impact of MRD measured by flow cytometry in the peripheral blood at day 8, and in end-induction (day 29) and end-consolidation marrows in 2143 children with precursor B-cell ALL (B-ALL). The presence of MRD in day-8 blood and day-29 marrow MRD was associated with shorter event-free survival (EFS) in all risk groups; even patients with 0.01% to 0.1% day-29 MRD had poor outcome compared with patients negative for MRD patients (59% ± 5% vs 88% ± 1% 5-year EFS). Presence of good prognostic markers TEL-AML1 or trisomies of chromosomes 4 and 10 still provided additional prognostic information, but not in National Cancer Insitute high-risk (NCI HR) patients who were MRD+. The few patients with detectable MRD at end of consolidation fared especially poorly, with only a 43% plus or minus 7% 5-year EFS. Day-29 marrow MRD was the most important prognostic variable in multi-variate analysis. The 12% of patients with all favorable risk factors, including NCI risk group, genetics, and absence of days 8 and 29 MRD, had a 97% plus or minus 1% 5-year EFS with nonintensive therapy. These studies are registered at www.clinicaltrials.gov as NCT00005585, NCT00005596, and NCT00005603.
Multidimensional scaling for large genomic data sets
Authors: Tzeng Jengnan , Lu Henry Horng-Shing , Li Wen-Hsiung 
Published: April 2008

Abstract

Background
Multi-dimensional scaling (MDS) is aimed to represent high dimensional data in a low dimensional space with preservation of the similarities between data points. This reduction in dimensionality is crucial for analyzing and revealing the genuine structure hidden in the data. For noisy data, dimension reduction can effectively reduce the effect of noise on the embedded structure. For large data set, dimension reduction can effectively reduce information retrieval complexity. Thus, MDS techniques are used in many applications of data mining and gene network research. However, although there have been a number of studies that applied MDS techniques to genomics research, the number of analyzed data points was restricted by the high computational complexity of MDS. In general, a non-metric MDS method is faster than a metric MDS, but it does not preserve the true relationships. The computational complexity of most metric MDS methods is over O(N
2
), so that it is difficult to process a data set of a large number of genes N, such as in the case of whole genome microarray data.

Results
We developed a new rapid metric MDS method with a low computational complexity, making metric MDS applicable for large data sets. Computer simulation showed that the new method of split-and-combine MDS (SC-MDS) is fast, accurate and efficient. Our empirical studies using microarray data on the yeast cell cycle showed that the performance of K-means in the reduced dimensional space is similar to or slightly better than that of K-means in the original space, but about three times faster to obtain the clustering results. Our clustering results using SC-MDS are more stable than those in the original space. Hence, the proposed SC-MDS is useful for analyzing whole genome data.

Conclusion
Our new method reduces the computational complexity from O(N
3) to O(N) when the dimension of the feature space is far less than the number of genes N, and it successfully reconstructs the low dimensional representation as does the classical MDS. Its performance depends on the grouping method and the minimal number of the intersection points between groups. Feasible methods for grouping methods are suggested; each group must contain both neighboring and far apart data points. Our method can represent high dimensional large data set in a low dimensional space not only efficiently but also effectively.
Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes
Authors: Zweers Jessica C , Barák Imrich , Becher Dörte , Driessen Arnold JM , Hecker Michael , Kontinen Vesa P , Saller Manfred J , Vavrová L'udmila , van Dijl Jan Maarten 
Published: April 2008

Abstract

Background
The Gram-positive bacterium Bacillus subtilis is an important producer of high quality industrial enzymes and a few eukaryotic proteins. Most of these proteins are secreted into the growth medium, but successful examples of cytoplasmic protein production are also known. Therefore, one may anticipate that the high protein production potential of B. subtilis can be exploited for protein complexes and membrane proteins to facilitate their functional and structural analysis. The high quality of proteins produced with B. subtilis results from the action of cellular quality control systems that efficiently remove misfolded or incompletely synthesized proteins. Paradoxically, cellular quality control systems also represent bottlenecks for the production of various heterologous proteins at significant concentrations.

Conclusion
While inactivation of quality control systems has the potential to improve protein production yields, this could be achieved at the expense of product quality. Mechanisms underlying degradation of secretory proteins are nowadays well understood and often controllable. It will therefore be a major challenge for future research to identify and modulate quality control systems of B. subtilis that limit the production of high quality protein complexes and membrane proteins, and to enhance those systems that facilitate assembly of these proteins.