bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving accuracy of cell and chromophore concentration measurements using optical density
Authors: Myers John A , Curtis Brandon S , Curtis Wayne R 
Published: May 2013

Abstract

Background
UV–vis spectrophotometric optical density (OD) is the most commonly-used technique for estimating chromophore formation and cell concentration in liquid culture. OD wavelength is often chosen with little thought given to its effect on the quality of the measurement. Analysis of the contributions of absorption and scattering to the measured optical density provides a basis for understanding variability among spectrophotometers and enables a quantitative evaluation of the applicability of the Beer-Lambert law. This provides a rational approach for improving the accuracy of OD measurements used as a proxy for direct dry weight (DW), cell count, and pigment levels.

Results
For pigmented organisms, the choice of OD wavelength presents a tradeoff between the robustness and the sensitivity of the measurement. The OD at a robust wavelength is primarily the result of light scattering and does not vary with culture conditions; whereas, the OD at a sensitive wavelength is additionally dependent on light absorption by the organism’s pigments. Suitably robust and sensitive wavelengths are identified for a wide range of organisms by comparing their spectra to the true absorption spectra of dyes. The relative scattering contribution can be reduced either by measurement at higher OD, or by the addition of bovine serum albumin. Reduction of scattering or correlation with off-peak light attenuation provides for more accurate assessment of chromophore levels within cells. Conversion factors between DW, OD, and colony-forming unit density are tabulated for 17 diverse organisms to illustrate the scope of variability of these correlations. Finally, an inexpensive short pathlength LED-based flow cell is demonstrated for the online monitoring of growth in a bioreactor at culture concentrations greater than 5 grams dry weight per liter which would otherwise require off-line dilutions to obtain non-saturated OD measurements.

Conclusions
OD is most accurate as a time-saving proxy measurement for biomass concentration when light attenuation is dominated by scattering. However, the applicability of OD-based correlations is highly dependent on the measurement specifications (spectrophotometer model and wavelength) and culture conditions (media type; growth stage; culture stress; cell/colony geometry; presence and concentration of secreted compounds). These variations highlight the importance of treating literature conversion factors as rough approximations as opposed to concrete constants. There is an opportunity to optimize measurements of cell pigment levels by considering scattering and absorption-dependent wavelengths of the OD spectrum.
Co-cultivation of Lactobacillus zeae and Veillonella criceti for the production of propionic acid
Authors: Dietz David , Sabra Wael , Zeng An-Ping 
Published: May 2013

Abstract

Abstract
In this work a defined co-culture of the lactic acid bacterium Lactobacillus zeae and the propionate producer Veillonella criceti has been studied in continuous stirred tank reactor (CSTR) and in a dialysis membrane reactor. It is the first time that this reactor type is used for a defined co-culture fermentation. This reactor allows high mixing rates and working with high cell densities, making it ideal for co-culture investigations. In CSTR experiments the co-culture showed over a broad concentration range an almost linear correlation in consumption and production rates to the supply with complex nutrients. In CSTR and dialysis cultures a strong growth stimulation of L. zeae by V. criceti was shown. In dialysis cultures very high propionate production rates (0.61 g L-1h-1) with final titers up to 28 g L-1 have been realized. This reactor allows an individual, intracellular investigation of the co-culture partners by omic-technologies to provide a better understanding of microbial communities.
Prediction of lung tumor types based on protein attributes by machine learning algorithms
Authors: Hosseinzadeh Faezeh , KayvanJoo Amir Hossein , Ebrahimi Mansuor , Goliaei Bahram 
Published: May 2013

Abstract
Early diagnosis of lung cancers and distinction between the tumor types (Small Cell Lung Cancer (SCLC) and Non-Small Cell Lung Cancer (NSCLC) are very important to increase the survival rate of patients. Herein, we propose a diagnostic system based on sequence-derived structural and physicochemical attributes of proteins that involved in both types of tumors via feature extraction, feature selection and prediction models. 1497 proteins attributes computed and important features selected by 12 attribute weighting models and finally machine learning models consist of seven SVM models, three ANN models and two NB models applied on original database and newly created ones from attribute weighting models; models accuracies calculated through 10-fold cross and wrapper validation (just for SVM algorithms). In line with our previous findings, dipeptide composition, autocorrelation and distribution descriptor were the most important protein features selected by bioinformatics tools. The algorithms performances in lung cancer tumor type prediction increased when they applied on datasets created by attribute weighting models rather than original dataset. Wrapper-Validation performed better than X-Validation; the best cancer type prediction resulted from SVM and SVM Linear models (82%). The best accuracy of ANN gained when Neural Net model applied on SVM dataset (88%). This is the first report suggesting that the combination of protein features and attribute weighting models with machine learning algorithms can be effectively used to predict the type of lung cancer tumors (SCLC and NSCLC).
Black tea, green tea and risk of breast cancer: an update
Authors: Wu Yili , Zhang Dongfeng , Kang Shan 
Published: May 2013

AbstractPrevious meta-analysis indicated conflicting results in case–control versus cohort studies on the association of green tea with breast cancer risk, and conflicting results were also found in case–control versus cohort studies in another meta-analysis on the association of black tea with breast cancer risk. Many studies were published after the previous meta-analysis. Besides, the dose-response relationship of tea consumption with breast cancer risk is unclear. Thus the association of tea consumption with breast cancer risk was assessed incorporating new publications. Summary relative risk (RR) for highest versus lowest level of tea consumption was calculated based on fixed or random effect models. Dose-response relationship was assessed by restricted cubic spline model and multivariate random-effect meta-regression. The combined results from 9 studies suggested no significant association between green tea consumption and breast cancer risk (RR = 0.82, 95% CI = 0.64-1.04). No significant association was found among cohort studies and case-control studies after sensitivity analysis, respectively. A linear but not significant dose-response association was found between green tea consumption and breast cancer risk. The combined results from 25 studies demonstrated no significant association between black tea consumption and breast cancer risk (RR = 0.98, 95% CI = 0.93-1.03), and no significant association was found in subgroup analysis. A linear but not significant dose-response association was found between black tea consumption and breast cancer risk. Based on the current evidence, black tea and green tea might not contribute significantly to breast cancer risk, respectively.
Hydrothermal synthesis and characterization of straw bundle-like lithium sodium disilicate (silinaite) micro-rods
Authors: Alemi Abdolali , Joo Sang Woo , Khademinia Shahin , Dolatyari Mahboubeh , Bakhtiari Akbar , Moradi Hossein , Saeidi Sorayya 
Published: May 2013

Abstract
Highly mono-shaped straw bundle-like silinaite micro-rods have been synthesized using an aqueous mixture of silicic acid, lithium sulfate, and sodium hydroxide under hydrothermal conditions at 180°C. The synthesized materials were characterized by powder X-ray diffraction technique and Fourier transform infrared spectroscopy. The morphologies of the synthesized materials were studied by field emission scanning electron microscopy technique. The synthesized micro-rods are composed of long, fine nanosheets. Electronic absorption and photoluminescence spectra of the synthesized materials were also studied. With increasing reaction time, a blueshift was observed in the UV–vis electronic absorption and emission spectra of the synthesized materials.
Preconditioning diabetic mesenchymal stem cells with myogenic medium increases their ability to repair diabetic heart
Authors: Khan Mohsin , Ali Fatima , Mohsin Sadia , Akhtar Shoaib , Mehmood Azra , Choudhery Mahmood S , Khan Shaheen N , Riazuddin Sheikh 
Published: May 2013

Abstract
Introduction
Mesenchymal stem cells (MSCs) have the potential for treatment of diabetic cardiomyopathy; however, the repair capability of MSCs declines with age and disease. MSCs from diabetic animals exhibit impaired survival, proliferation, and differentiation and therefore require a strategy to improve their function. The aim of the study was to develop a preconditioning strategy to augment the ability of MSCs from diabetes patients to repair the diabetic heart.

Methods
Diabetes was induced in C57BL/6 mice (6 to 8 weeks) with streptozotocin injections (55 mg/kg) for 5 consecutive days. MSCs isolated from diabetic animals were preconditioned with medium from cardiomyocytes exposed to oxidative stress and high glucose (HG/H-CCM).

Results
Gene expression of VEGF, ANG-1, GATA-4, NKx2.5 MEF2c, PCNA, and eNOS was upregulated after preconditioning with HG/H-CCM, as evidenced by reverse transcriptase/polymerase chain reaction (RT-PCR). Concurrently, increased AKT phosphorylation, proliferation, angiogenic ability, and reduced levels of apoptosis were observed in HG/H-CCM-preconditioned diabetic MSCs compared with nontreated controls. HG/H-CCM-preconditioned diabetic-mouse-derived MSCs (dmMSCs) were transplanted in diabetic animals and demonstrated increased homing concomitant with augmented heart function. Gene expression of angiogenic and cardiac markers was significantly upregulated in conjunction with paracrine factors (IGF-1, HGF, SDF-1, FGF-2) and, in addition, reduced fibrosis, apoptosis, and increased angiogenesis was observed in diabetic hearts 4 weeks after transplantation of preconditioned dmMSCs compared with hearts with nontreated diabetic MSCs.

Conclusions
Preconditioning with HG/H-CCM enhances survival, proliferation, and the angiogenic ability of dmMSCs, augmenting their ability to improve function in a diabetic heart.
Global sensitivity analysis for crosswell seismic and neutron-capture measurements in CO2 storage projects
Authors: Chugunov Nikita , Altundas Yusuf Bilgin , Ramakrishnan T. S. , Senel Ozgur 
Published: May 2013

Quantification of reservoir uncertainty is an essential part of a monitoring design. A systematic approach that quantitatively links predicted uncertainties in a monitoring program to the underlying reservoir variability is, however, needed. We developed a methodology for quantifying uncertainty in crosswell seismic monitoring combined with neutron-capture logging and applied global sensitivity analysis (GSA) to compute and rank contributions of uncertain reservoir parameters to the predicted uncertainty of the measurements. The workflow is illustrated by a numerical study using a simplified model of a [Formula: see text] storage site where crosswell measurements have not actually been taken. Synthetic seismic responses are computed through the integration of multiphase flow, a new thermodynamically consistent fluid substitution model, and a fast marching eikonal solver. We quantified uncertainty in first-arrival times to illustrate the potential utility of crosswell seismic surveys and their limitation. Consistent with these calculations, uncertainties in neutron capture cross-section logs are also computed and related to predicted [Formula: see text] migration. The predicted uncertainty range for neutron-capture measurements indicated significant sensitivity to the uncertainty of the reservoir properties (standard deviations [STDs] of up to 6 c.u. in the injector and up to 3.5 c.u. in the monitoring well). However, the STD of predicted time-lapse crosswell seismic responses for two different source locations did not exceed 0.75 ms during the life of the project, suggesting limited value of first-arrival measurements for reservoir-parameter inversion in this case. With the time-dependent uncertainty of the predicted measurements, calculated GSA indices provided a quantitative basis for the monitoring program design. Practical implications of GSA results for model reduction and subsequent inversion were also evaluated.
The upside of uncertainty: Identification of lithology contact zones from airborne geophysics and satellite data using random forests and support vector machines
Authors: Cracknell Matthew J. , Reading Anya M. 
Published: May 2013

Inductive machine learning algorithms attempt to recognize patterns in, and generalize from empirical data. They provide a practical means of predicting lithology, or other spatially varying physical features, from multidimensional geophysical data sets. It is for this reason machine learning approaches are increasing in popularity for geophysical data inference. A key motivation for their use is the ease with which uncertainty measures can be estimated for nonprobabilistic algorithms. We have compared and evaluated the abilities of two nonprobabilistic machine learning algorithms, random forests (RF) and support vector machines (SVM), to recognize ambiguous supervised classification predictions using uncertainty calculated from estimates of class membership probabilities. We formulated a method to establish optimal uncertainty threshold values to identify and isolate the maximum number of incorrect predictions while preserving most of the correct classifications. This is illustrated using a case example of the supervised classification of surface lithologies in a folded, structurally complex, metamorphic terrain. We found that (1) the use of optimal uncertainty thresholds significantly improves overall classification accuracy of RF predictions, but not those of SVM, by eliminating the maximum number of incorrectly classified samples while preserving the maximum number of correctly classified samples; (2) RF, unlike SVM, was able to exploit dependencies and structures contained within spatially varying input data; and (3) high RF prediction uncertainty is spatially coincident with transitions in lithology and associated contact zones, and regions of intense deformation. Uncertainty has its upside in the identification of areas of key geologic interest and has wide application across the geosciences, where transition zones are important classes in their own right. The techniques used in this study are of practical value in prioritizing subsequent geologic field activities, which, with the aid of this analysis, may be focused on key lithology contacts and problematic localities.
pRB, p107 and the regulation of the E2F transcription factor
Authors: Dyson Nicholas 
Published: May 2013

Small DNA tumor viruses, such as adenovirus, encode proteins that deregulate the cell cycle. These proteins are potent transforming agents when tested in standard oncogenic assays. For adenovirus the best characterized viral oncoproteins are the early region IA (E1A) products. Mutational studies have shown that ElA’s oncogenic ability is determined primarily by its ability to bind to certain cellular proteins and interfere with their function. One of these cellular targets for E1A is the product of the retinoblastoma tumor suppressor gene, pRB. pRB is a negative regulator of cell proliferation, and its inactivation has been shown to be an important oncogenic step in the development of many human cancers. In adenovirus-mediated transformation, E1A binds to pRB and inacti-vates it, thus functionally mimicking the loss of pRB often seen in human tumors.
There is now compelling evidence to suggest that pRB regulates transcription at specific phases of the cell cycle by physically associating with key transcription factors. The best characterized target of pRB is the transcription factor E2F. The interaction of pRB and E2F leads to the inhibition of E2F-mediated transactivation. Most of the genes that are known to be controlled by E2F have key roles in the regulation of cell proliferation. During cell cycle pro-gression, phosphorylation of pRB appears to change its conformation and E2F is released. In pathogenic settings E2F transactivation is not regulated by pRB binding. In human tumors with mutations in the retinoblastoma gene, functional pRB is absent and hence can no longer inhibit E2F activity. During adenovirus transformation, E1A binds to pRB and displaces E2F. In both these cases, E2F is released from pRB-mediated regulation at inappropriate times. The activation of these E2F-responsive genes may lead to the stimulation of cell proliferation. While we do not know whether E2F is the only target for pRB action, this work has formed a general picture of how tumor suppres-sor gene products such as pRB can control specific tran-scriptional events and act as negative regulators of cell growth.
Recent experiments have shown that E2F represents the combined activity of an extensive series of protein complexes. There are at least five genes that encode E2F polypeptides, and probably several more have yet to be identified. The E2F transcription factor is a heterodimer composed of two related polypeptides, one encoded by a member of the E2F gene family and the other by a member of the DP family. Intriguingly DP and E2F genes are also found in Drosophila and these may provide alternative approaches to the investigation of E2F function. In mammalian cells E2F/DP heterodimers are regulated, at least in part, by the formation of many larger complexes. E2F is found in separate complexes with pRB, p107/cyclin A/cdk2 or p107/cyclin E/cdk2, and additional complexes exist that have yet to be fully characterized. These E2F complexes are detected at specific points of the cell cycle and appear to provide different elements of E2F regulation.
Regulation and function of the MAP kinase cascade in Xenopus oocytes
Authors: Kosako Hidetaka , Gotoh Yukiko , Nishida Eisuke 
Published: May 2013

ABSTRACT
In Xenopus oocytes, activation of MAP kinase occurs during meiotic maturation through a protein kinase cascade (the MAP kinase cascade), which is utilized commonly in various intracellular signaling pathways in eukaryotes. Studies with a neutralizing antibody against Xenopus MAP kinase kinase (MAPKK), a direct upstream activator for MAP kinase, have shown that the MAP kinase cascade plays a crucial role in both initiating oocyte matu- ration and inducing metaphase arrest.
Specificity in recognition of phosphopeptides by src-homology 2 domains
Authors: Cantley Lewis C. , Songyang Zhou 
Published: May 2013

ABSTRACT
SH2 domains and SH3 domains, found in a number of protein-tyrosine kinases and substrates of protein-tyrosine kinases, provide specificity in downstream signaling. Both of these domains bind to relatively short linear sequences of peptides to provide specific interactions between proteins. The SH2 domains directly bind to phosphotyro- sine residues of proteins in a specific sequence context. We have devised a phosphopeptide library technique that allows us to rapidly determine the sequence specificity of individual SH2 domains on the basis of amino acids selected at position +1, +2 and +3 C-terminal of the phos- photyrosine. The optimal motif for 22 distinct SH2 domains has been determined and used to predict likely sites of in vivo interaction. A second phosphopeptide library was devised in which the amino acids N-terminal of the phos- photyrosine were also varied. The residues N-terminal of phosphotyrosine had little influence on binding to the N- SH2 domain of the 85 kDa subunit of phosphoinositide 3- kinase. These results indicate that for this SH2 domain, specificity is determined by sequences carboxy-terminal of the phosphotyrosine moiety. Knowledge of the specificity of SH2 domains allows predictions about likely downstream targets on the basis of primary sequence of proteins. Some of these predictions will be discussed.
Signal transduction through the GTP-binding proteins Rac and Rho
Authors: Ridley Anne J. 
Published: May 2013

ABSTRACT
Actin reorganization is an early response to many extra- cellular factors. In Swiss 3T3 fibroblasts, the Ras-related GTP-binding proteins Rho and Rac act as key signal trans- ducers in these responses: Rho is required for growth factor-induced formation of stress fibres and focal adhesions, whereas membrane ruffling is regulated by Rac proteins. Several proteins that act as GTPase activating proteins (GAPs) for Rho-related proteins have been iden- tified, and these could act either as targets or down-regu- lators of Rho or Rac in cells. In vitro, the GAP domain of pl90 has a striking preference for Rho as a substrate, and when microinjected into Swiss 3T3 cells it inhibits stress fibre formation but not membrane ruffling induced by growth factors. BcrGAP acts on Rac but not Rho in vitro, and specifically inhibits membrane ruffling in vivo. Finally, RhoGAP acts preferentially on the Rho-related protein G25K/Cdc42Hs in vitro, but can inhibit Rho-mediated responses in vivo. These results suggest that p!90, Bcr and RhoGAP play specific roles in signalling pathways through different Rho family members.
The mechanisms underlying Rho-regulated stress fibre formation have been investigated further by analysing the role of other signals known to be activated by lysophos- phatidic acid (LPA). Neither activation of PK-C, increased intracellular Ca2+, decreased cAMP levels or Ras activa- tion appear to mediate stress fibre formation. However, LPA stimulates tyrosine phosphorylation of a number of proteins, including the focal adhesion kinase, pp125FAK, and genistein, a tyrosine kinase inhibitor, prevents this increase in tyrosine phosphorylation. Genistein also inhibits LPA- and Rho-induced stress fibre formation, implying that a tyrosine kinase lies downstream of Rho in this signal transduction pathway.
A developmental context for multiple genetic alterations in Wilms’ tumor
Authors: Feinberg Andrew P. 
Published: May 2013

ABSTRACT
Wilms’ tumor has served as an example of Knudson’s two- hit hypothesis of recessive tumor genes, but the genetics has proven to be surprisingly complex. WTI, a tumor sup- pressor gene on llpl3, is mutated in only a small fraction of Wilms’ tumors, and a second chromosomal region, 11p15, harbors a second Wilms’ tumor gene also involved in other cancers. In addition, loss of genomic imprinting, or parental origin-specific gene expression of at least two genes, appears to be an early step in Wilms’ tumorigenesis and common cancers. Finally, genes on other chromosomes also play a role. I propose a model of Wilms’ tumori- genesis in which multiple genetic alterations act within a specific developmental context, accounting for the epi- demiological and pathological heterogeneity of Wilms’ tumor, as well as the tissue specificity of the tumor types arising from alterations in these genes.
Pax genes in development
Authors: Mansouri Ahmed , Stoykova Anastassia , Gruss Peter 
Published: May 2013

SUMMARY
The Pax gene family consists of nine members encoding nuclear transcription factors. Their temporally and spatially restricted expression pattern during embryogenesis suggests that they may play a key role during embryogenesis.
Direct evidence for the important role of the Pax genes during embryonic development has been demonstrated by the correlation of mouse developmental mutants and human syndromes with mutations in some Pax genes. To date three Pax genes have been shown to be mutated in undulated, Splotch and small eye, respectively. In man, Pax-3 is mutated in the Waardenburg syndrome, while in aniridia Pax-6 is mutated.