bluuebunny/crossref_metadata_2025_split huggingface dataset:
Continuous approximations for optimizing allele trajectories
Authors: LIU A. Y. H. , WOOLLIAMS J. A. 
Published: June 2010

SummaryThe incorporation of genetic information such as quantitative trait loci (QTL) data into breeding schemes has become feasible as DNA technologies have advanced. Such strategies allow the frequency of desirable QTL to be controlled over a predefined time frame, allowing the allele trajectory for QTL to be manipulated. A continuous approximation to changes in allele frequency was developed to approximate the selection procedure as a continuous rather than a discrete process, and analytical solutions were obtained, which shed light on how allele trajectories behave under different objective functions. Three different objectives were considered: (1) minimizing the total selection intensity, (2) minimizing the sum of squared selection intensities and (3) equalizing the selection intensity applied over time. Simulations and genetic algorithms were performed to test the accuracy and robustness of the continuous approximation. Theory shows firstly that the total selection intensity required for moving an allele from a starting frequency to another frequency point can be predicted independent of its trajectory, and secondly that objectives (2) and (3) are equivalent as the number of selection opportunities (T) becomes large. The prediction of total selection intensity provides a good fit for these two objectives, with the accuracy of prediction improving asTincreases. However, for (1) the continuous approximation does not fit due to the existence of a discontinuous solution in which the continuous approximation is applied before the frequency of the selected allele reaches 0·5 followed by rapid fixation.
Correlations between bed occupancy rates andClostridium difficileinfections: a time-series analysis
Authors: KAIER K. , LUFT D. , DETTENKOFER M. , KIST M. , FRANK U. 
Published: June 2010

SUMMARYA time-series analysis was performed to identify the impact of bed occupancy rates and length of hospital stay on the incidence ofClostridium difficileinfections (CDI). Between January 2003 and July 2008, a mean incidence of 0·5 CDI cases/1000 patient days was recorded. Application of a multivariate model (R2=0·50) showed that bed occupancy rates on general wards (P<0·01) and length of stay in intensive care units (ICUs) (P<0·01) influenced the incidence of CDI. Overcrowding on general wards and long periods in ICUs were identified as being positively associated with the incidence of CDI.
Explaining the 25-year decline of serum cholesterol by dietary changes and use of lipid-lowering medication in Finland
Authors: Valsta Liisa M , Tapanainen Heli , Sundvall Jouko , Laatikainen Tiina , Männistö Satu , Pietinen Pirjo , Vartiainen Erkki 
Published: June 2010

AbstractObjectiveTo assess to what extent the observed dietary changes and increased use of lipid-lowering medication can explain the almost 20 % decline in serum cholesterol (referring to serum total cholesterol) level observed from 1982 to 2007 in Finland.DesignPredicted changes of serum cholesterol were calculated by the Keys’ equation assuming the effect of trans fatty acids to be similar to SFA and using the dietary intake data of the national dietary surveys between 1982 and 2007. The effect of medication was estimated based on the information on use of lipid-lowering medication among survey participants. The predicted serum cholesterol levels were compared with observed changes in analysed serum cholesterol levels.SettingFour cross-sectional population surveys, in 1982, 1992, 2002 and 2007, in the provinces of North Karelia, Northern Savo and Southwestern Finland.SubjectsA total of 2325 men and 2638 women aged 26–64 years selected randomly from the national population register for the four surveys.ResultsChanges in dietary fat quality and cholesterol intake explain 0·70 mmol/l (65 %) of the decrease in men and 0·65 mmol/l (60 %) of the decrease in women in all subjects. Decline in dietary SFA intake is the main explanatory factor (47 % in men and 41 % in women) for the changes. The impact of lipid-lowering medication on observed cholesterol levels was found to be 16 % among men and 7 % among women.ConclusionsThe decrease in serum cholesterol levels in Finland can be explained mainly by dietary changes, especially changes in fat quality. The effect of lipid-lowering medication is less significant.
Diet composition of pregnant Finnish women: changes over time and across seasons
Authors: Prasad Marianne , Lumia Mirka , Erkkola Maijaliisa , Tapanainen Heli , Kronberg-Kippilä Carina , Tuokkola Jetta , Uusitalo Ulla , Simell Olli , Veijola Riitta , Knip Mikael , Ovaskainen Marja-Leena , Virtanen Suvi M 
Published: June 2010

AbstractObjectiveTo describe the diet of a population of pregnant Finnish women over a period of 7 years, with special attention paid to seasonal fluctuations in food consumption and nutrient intake.DesignA validated 181-item FFQ was applied retrospectively, after delivery, to assess the maternal diet during the 8th month of pregnancy.SettingType 1 Diabetes Prediction and Prevention Nutrition Study Cohort.SubjectsThe cohort comprised a total of 4880 women who had newly delivered during the years 1997–2004, with the offspring carrying increased genetic risk for type 1 diabetes mellitus.ResultsOver the study period, the proportion of energy derived from fat decreased while the intake from protein and carbohydrate increased. The intake of vitamin D increased from food sources. Seasonal variation was observed in the mean daily consumption of vegetables, fruits and berries and cereals. Intake of dietary fibre, total fat, MUFA, vitamins A, D, E and C, folate and iron also showed seasonal fluctuation.ConclusionsThese results show an overall positive trend in the diet of pregnant Finnish women through the study years. However, there is still room for improvement, particularly in the types of dietary fats. Although food fortification with vitamin D since 2003 was reflected in the increased intake of vitamin D from foods, the mean intake levels still fell below the recommendations. Seasonal changes in food consumption were observed and related to corresponding fluctuations in nutrient intakes. The mean folate intake fell below the recommendation throughout the year.
Dietary habits and nutrient intake of Finnish adolescents
Authors: Hoppu Ulla , Lehtisalo Jenni , Tapanainen Heli , Pietinen Pirjo 
Published: June 2010

AbstractObjectiveTo evaluate food and nutrient intake and especially eating during the school day among Finnish secondary-school pupils.DesignCross-sectional study. Data were collected using a structured questionnaire mailed to home and by 48 h dietary recall interviews performed at schools in 2007.SettingTwelve schools in three cities in Finland.SubjectsThe seventh grade pupils (a total of 1469 at the mean age of 13·8 years). Questionnaire data were available from 726 pupils and dietary data from a subgroup of 40 % (n 306).ResultsAccording to the questionnaire data, 40 % of the girls and 28 % of the boys reported eating fresh vegetables daily and the respective figures for fruit were 32 % and 23 %. Altogether, 71 % of the adolescents reported having school lunch every day. The average intake of sucrose was higher and the average intakes of fibre, iron, folate and vitamin D were lower than recommended. School lunch provided around 20 % of daily energy intake, while the recommended daily energy intake level is one-third. However, the school lunch as consumed was nutritionally superior to the other daily meals. Snacks provided 41 % of the daily energy. The most common sources of sucrose were sugary drinks.ConclusionsLow consumption of fruit and vegetables and abundant consumption of sucrose-rich drinks and snacks are the main problems in the diet of Finnish adolescents. The nutritional quality of the school lunch is good, but the supply of healthy snacks must be improved in schools. Schools can promote healthy eating habits by making healthy choices easy during the school day.
Traumatic Brain Injury: An Overview of Pathobiology with Emphasis on Military Populations
Authors: Cernak Ibolja , Noble-Haeusslein Linda J 
Published: June 2010

Correction to: Journal of Cerebral Blood Flow & Metabolism (2010) 30, 255–266; doi:10.1038/jcbfm.2009.203 Following the publication of this article, the authors noted that the definition for TBI in the footnote to Table 2, ‘TBI, total body irradiation’, was incorrect. It should have read ‘TBI, traumatic brain injury’. The typesetters would like to apologize for this error.
Deficiency of PAR4 Attenuates Cerebral Ischemia–Reperfusion Injury in Mice
Authors: Mao Yingying , Zhang Ming , Tuma Ronald F , Kunapuli Satya P 
Published: June 2010

Correction to: Journal of Cerebral Blood Flow & Metabolism (2010) 30, 1044–1052; doi: 10.1038/jcbfm.2009.283 Following the online publication of this article, the authors noticed that one of the names in the Acknowledgements section was misspelled. The correct spelling is Ms Varshana Gurusamy.
(Corrected) Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress.
Authors: Maloney Andy , Herskowitz Lawrence , Koch Steven 
Published: June 2010

AbstractThe molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to transport various cargos inside cells.During the stepping process, the kinesin motor domains bind and unbind from their binding sites on the microtubules. Binding and unbinding rates of biomolecules are highly dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding and unbinding rates for kinesin and thus offers a tool to specifically probe those steps. We will report the effects of different osmolytes on microtubule speed and other observables in the gliding motility assay.Kinesin’s kinetic core cycle hydrolyzes ATP with the help of a water molecule. Any modification to the water molecules the kinesin is in will change how ATP hydrolyzes and will ultimately affect how kinesin moves along microtubules. We will report preliminary results showing how kinesin is affected when the solvent it is in is changed from light water to heavy water.When used in a surface assay or in devices, the kinesin and microtubule system is also dependent on substrate passivation. Kinesin motor domains do not transport microtubules in the gliding motility assay if kinesin is added to a glass microscope slide that has not been functionalized. Functionalization of the glass slides and slips is typically performed with bovine milk proteins called caseins. Bovine casein is a globular protein that can be broken up into four constituents: αs1, αs2, β, and κ. Each casein constituent affects how kinesin adheres to the glass and ultimately the speed at which microtubules are observed to glide at. Building on the work of Verma et.al., we have found that each constituent individually produces different outcomes in gliding assays. We will present these findings and discuss implications they have for use of gliding assays to study kinesin and use of kinesin-microtubule system in microdevices.[1] Chaen, S, N Yamamoto, I Shirakawa, and H Sugi. 2001. Effect of deuterium oxide on actomyosin motility in vitro. Biochimica et biophysica acta 1506, no. 3: 218-23.[2] Vivek Verma, William O Hancock, Jeffrey M Catchmark, "The role of casein in supporting the operation of surface bound kinesin," J. Biol. Eng. 2008; 2: 14.
Acknowledgements:
This work was supported by the DTRA CB Basic Research Program under Grant No. HDTRA1-09-1-008.CORRECTIONS: At the workshop, Erik Schaffer pointed out to us that some of our speed differences (casein data) were surely due to microscope increasing in temperature. I've edited the poster to correct for this. Thanks, Erik!
Autoantibodies against cardiac troponin I in patients with congestive heart failure
Authors: Düngen Hans‐Dirk , Platzeck Maria , Vollert Jörn , Searle Julia , Müller Christian , Reiche Janett , Mehrhof Felix , Müller Reinhold , Möckel Martin 
Published: June 2010

AimsIn this randomized, double‐blind clinical study, we investigated the relationship between autoantibodies against cardiac troponin I (cTnI) and disease severity in elderly congestive heart failure (CHF) patients before and after titration of beta‐blocker therapy.Methods and resultsAnti‐cTnI, cTnI, and N‐terminal pro‐brain natriuretic peptide (NT‐proBNP) levels in blood from 138 patients (73 ± 5.6 years, 48% male) with CHF in American Heart Association stages A–C were measured at baseline and after titration of beta‐blockers to maximal tolerated dose. Median follow‐up period was 85 days. Anti‐cTnI was measured using an experimental assay (Abbott Diagnostics) and is expressed as a relative value unit (RVU) in relation to the mean value of a low‐level control sample. Anti‐cTnI values in CHF patients were also compared with measurements taken in a normal reference population of 300 healthy individuals (50% male). Cardiac troponin I and NT‐proBNP levels were measured using routine assays (Architect® Abbott Diagnostics and Roche Diagnostics®). Median anti‐cTnI was 0.53 and 0.56 RVU in healthy and CHF subjects, respectively (P = n.s.), and increased significantly to 0.67 RVU (P < 0.001) after beta‐blocker titration. Mean cTnI values were 0.021 µg/L at baseline and fell significantly to 0.0046 µg/L at follow‐up (P < 0.001). Median NT‐proBNP values were 352 ng/L at baseline and 414 ng/L after titration (P = n.s.). In contrast to NT‐proBNP and cTnI, anti‐cTnI was not associated with the severity of CHF at baseline or follow‐up.ConclusionLevels of anti‐cTnI tend to increase in elderly patients with CHF following titration of beta‐blocker therapy but do not correlate with disease severity. Anti‐cTnI is not a useful biomarker for heart failure diagnosis, prognosis, or monitoring. In contrast, levels of cTnI decreased following therapy and did correlate with disease severity.
Generation of Retroviral Particles for the Spleen Necrosis Virus (SNV)-Based Vector System and Their Use in Transduction of Various Cell Types: Figure 1.
Authors: Parveen Zahida , Mukhtar Muhammad , Pomerantz Roger J. 
Published: June 2010

INTRODUCTIONGenetically engineered retroviruses are widely used for gene delivery into human cells. A number of investigators have studied spleen necrosis virus (SNV) as a vehicle for gene delivery. Vectors developed from SNV and its closely associated avian reticuloendotheliosis virus strain A (REV-A) can be used for gene transfer into a variety of cells, including primary hematopoietic cells and human brain and post-mitotic neuronal cells that are difficult to transduce with other vector systems. SNV-based vector systems have the advantage of being quite safe, because wild-type SNV is unable to infect human cells and has less preference for integration into transcriptionally active sites or genes. However, the generation of retroviral vectors requires cotransfection of more than one plasmid into a packaging cell line, which is a tedious process. The development of stable packaging cell lines expressing envelope (Env) proteins and the structural proteins Gag-Pol will enhance mass production of retroviral vectors for future gene therapy experiments both in vitro and in vivo. This protocol describes the generation of retroviral particles for the SNV-based vector system. These particles can then be used for transduction of various cell types; as an example, a technique for transduction of post-mitotic neurons is also presented.
Production of SV40-Derived Vectors
Authors: Strayer David S. , Mitchell Christine , Maier Dawn A. , Nichols Carmen N. 
Published: June 2010

INTRODUCTIONRecombinant simian virus 40 (rSV40)-derived vectors are particularly useful for gene delivery to bone marrow progenitor cells and their differentiated derivatives, certain types of epithelial cells (e.g., hepatocytes), and central nervous system neurons and microglia. They integrate rapidly into cellular DNA to provide long-term gene expression in vitro and in vivo in both resting and dividing cells. Here we describe a protocol for production and purification of these vectors. These procedures require only packaging cells (e.g., COS-7) and circular vector genome DNA. Amplification involves repeated infection of packaging cells with vector produced by transfection. Cotransfection is not required in any step. Viruses are purified by centrifugation using discontinuous sucrose or cesium chloride (CsCl) gradients and resulting vectors are replication-incompetent and contain no detectable wild-type SV40 revertants. These approaches are simple, give reproducible results, and may be used to generate vectors that are deleted only for large T antigen (Tag), or for all SV40-coding sequences capable of carrying up to 5 kb of foreign DNA. These vectors are best applied to long-term expression of proteins normally encoded by mammalian cells or by viruses that infect mammalian cells, or of untranslated RNAs (e.g., RNA interference). The preparative approaches described facilitate application of these vectors and allow almost any laboratory to exploit their strengths for diverse gene delivery applications.
Titering Replication-Defective rSV40 Vectors
Authors: Strayer David S. , Mitchell Christine , Maier Dawn A. , Nichols Carmen N. 
Published: June 2010

INTRODUCTIONRecombinant simian virus 40 (rSV40)-derived vectors are particularly useful for gene delivery to bone marrow progenitor cells and their differentiated derivatives, certain types of epithelial cells (e.g., hepatocytes), and central nervous system neurons and microglia. They integrate rapidly into cellular DNA to provide long-term gene expression in vitro and in vivo in both resting and dividing cells. Techniques used to produce, purify, and quantitate these vectors are simple, give reproducible results, and may be used to generate vectors that are deleted only for large T antigen (Tag), or for all SV40-coding sequences capable of carrying up to 5 kb of foreign DNA. Viruses are purified by centrifugation using discontinuous sucrose or cesium chloride (CsCl) gradients. Resulting vectors are replication-incompetent and contain no detectable wild-type SV40 revertants. Viruses are titered by quantitative polymerase chain reaction (qPCR), described here. qPCR measures the number of rSV40 genomes in purified viral stocks using primers specific for the rSV40, coupled with SYBR Green detection of PCR products. Sample purity is assessed using qPCR via melt (dissociation) curve analysis. The only specialized equipment necessary is a quantitative real-time PCR machine.
Purification of RNA Using TRIzol (TRI Reagent)
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W. 
Published: June 2010

INTRODUCTIONTRIzol solubilization and extraction is a relatively recently developed general method for deproteinizing RNA. This method is particularly advantageous in situations where cells or tissues are enriched for endogenous RNases or when separation of cytoplasmic RNA from nuclear RNA is impractical. TRIzol (or TRI Reagent) is a monophasic solution of phenol and guanidinium isothiocyanate that simultaneously solubilizes biological material and denatures protein. After solubilization, the addition of chloroform causes phase separation (much like extraction with phenol:chloroform:isoamyl alcohol), where protein is extracted to the organic phase, DNA resolves at the interface, and RNA remains in the aqueous phase. Therefore, RNA, DNA, and protein can be purified from a single sample (hence, the name TRIzol). TRIzol extraction is also an effective method for isolating small RNAs, such as microRNAs, piwi-associated RNAs, or endogeneous, small interfering RNAs. However, TRIzol is expensive and RNA pellets can be difficult to resuspend. Thus, the use of TRIzol is not recommend when regular phenol extraction is practical.
Ethanol Precipitation of RNA and the Use of Carriers
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W. 
Published: June 2010

INTRODUCTIONRecovery of deproteinized RNA almost always is performed via precipitation with ethanol. If the RNA is free of contaminants (i.e., it is well extracted) as determined by spectrophotometry, it will resuspend easily and be ready for any subsequent manipulation. Ethanol precipitation is quite useful because it provides quantitative recovery of any-sized RNA, from several kilobases to 20 nucleotides (nt). Major considerations in this protocol are RNA concentration, pellet identification, and resuspension.
Polyacrylamide Gel Electrophoresis of RNA: Figure 1.
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W. 
Published: June 2010

INTRODUCTIONPerhaps the most important and certainly the most often used technique in RNA analysis is gel electrophoresis. This technique is generally applicable for RNA detection, quantification, purification by size, and quality assessment. Because RNAs are negatively charged, they migrate toward the anode in the presence of electric current. The gel acts as a sieve to selectively impede the migration of the RNA in proportion to its mass, given that its mass is generally proportional to its charge. Because mass is approximately related to chain length, the length of an RNA is more generally determined by its migration. In addition, topology (i.e., circularity) can affect migration, making RNAs appear longer on the gel than they actually are. Gels are used in a wide variety of techniques, including Northern blotting, primer extension, footprinting, and analyzing processing reactions. They are invaluable as preparative and fractionating tools. There are two common types of gel: polyacrylamide and agarose. For most applications, denaturing acrylamide gels are most appropriate. These gels are extremely versatile and can resolve RNAs from ~600 to ≤20 nucleotides (nt). In certain circumstances, e.g., resolving different conformers of RNAs or RNA-protein complexes, native gels are appropriate. The only disadvantage to acrylamide gels is that they are not suitable for analyzing large RNAs (≥600 nt); for such applications, agarose gels are preferred. This protocol describes how to prepare, load, and run polyacrylamide gels for RNA analysis.
Nondenaturing Agarose Gel Electrophoresis of RNA
Authors: Rio Donald C. , Ares Manuel , Hannon Gregory J. , Nilsen Timothy W. 
Published: June 2010

INTRODUCTIONPerhaps the most important and certainly the most often used technique in RNA analysis is gel electrophoresis. Because RNAs are negatively charged, they migrate toward the anode in the presence of electric current. The gel acts as a sieve to selectively impede the migration of the RNA in proportion to its mass, given that its mass is generally proportional to its charge. Because mass is approximately related to chain length, the length of an RNA is more generally determined by its migration. In addition, topology (i.e., circularity) can affect migration, making RNAs appear longer on the gel than they actually are. There are two common types of gel: polyacrylamide and agarose. For most applications involving RNAs of ≤600 nucleotides, denaturing acrylamide gels are most appropriate. In contrast, agarose gels are generally used to analyze RNAs of ≥600 nucleotides, and are especially useful for analysis of mRNAs (e.g., by Northern blotting). RNA analysis on agarose gels is essentially identical to DNA analysis (except that the gel boxes used must be dedicated to RNA work or to other ribonuclease-free work). Here we describe the use of straightforward Tris borate, EDTA (TBE) gels for routine analysis. These gels are appropriate for determining the quantity and integrity of RNA before using it for other applications. This procedure should not be used to determine size with accuracy, because the RNA will not remain in its extended state throughout the run.