A new database program installed at the SUERC radiocarbon laboratory

The SUERC Radiocarbon Dating Laboratory has recently replaced its spreadsheet-based record keeping with a new database program, custom designed to help laboratory staff manage the high throughput of nearly 5000 cathodes in the past year. The system can accept data from a variety of sources in addition to manual entry; experimental results can be uploaded from spreadsheets, while integration with graphitisation lines means that graphite yields are automatically recorded. The system is able to pass radiocarbon results directly to OxCal 4 for calibration, with the resulting plots incorporated into the dating certificates issued to submitters. There are also benefits to submitters, with electronic sample submission both eliminating transcription errors and speeding up the logging-in process which keeps turnaround times down. For bone samples, data on collagen yields are now stored electronically and are more readily obtainable from the laboratory. The new SUERC Radiocarbon Dating Laboratory database will make a significant contribution to maintaining the high quality of results produced by the laboratory, aiding staff in tracking sample progress and monitoring quality assurance (QA) samples going through the laboratory, eliminating transcription errors and making communication easier between laboratory staff and sample submitters

Letter Written by Katherine Trickey to Her Folks Dated November 26, 1944

[Transcription begins] 26 Nov 44 Sun. 8.30. A.M. Dear Folks, I’m glad you received my box O.K. I thought it would be something for you for Thanksgiving. Isn’t the news about the boys being home grand; I wish that I could get home at the same time but I guess that is out of the question unless they stay as long as Xmas which doesn’t seem possible. Let me know when you know any exact dates on which they will be at home so that I may at least write them there. I’ll get home Thursday not Friday evening; I miscalculated. Perhaps it would be better to go to Bangor Tuesday so that I would have Tuesday, Wed & Thursday evening there and come back to Lewiston Friday evening so as to have all day Sat there with Dot & Beverley. Do you suppose Mother that would be too close to Xmas for you to get ready to go. If so, we can go Wed really just as well. Did the weather hold good so that you really could all be together at Aunt Grace’s for Thanksgiving? We had a very nice meal here. And the afternoon off as I mentioned in my last letter I believe. I had a cold and laryngitis so stayed in and went to bed. I was much better in the morning and it is practically well now. Friday we had another orientation class, going out to the Village Fighting Course to observe the boys practicing out there. It is very realistic with plenty of live ammunition so that the boys have to learn to do it correctly and they do. The safety factor is of course very carefully planned and the boys very rarely get hurt. It is certainly interesting to have a chance to watch the various types of training even if it is difficult to lose that much time at the office. Ida and I had to work in the evening to make up for it. We are slightly swamped this week as Minnie and Pope are both on furlough and Wise had an emergency furlough which left us all alone. We have one of the new girls now which helps. I am working today also to catch up. So with all the responsibility in the barracks and her, I am keeping plenty busy these days. It will get established soon and I’ll know what I’m doing and it won’t be much extra work. I am really going to enjoy having a room again instead of being out in the barracks. It will be a good change. Olga is going to be very nice to room with. The only thing will be that there is a great temptation to stay there and read instead of mingling with anyone and thus becoming very unsocial ...We will have to spend some money on it – curtains, rugs, lamp, hot plate maybe, card table etc. And then of course after we get it fixed up, the army will decide to change us someway probably!! 24 days before I start! Love Kay [Transcription ends

Information content based model for the topological properties of the gene regulatory network of Escherichia coli

Gene regulatory networks (GRN) are being studied with increasingly precise quantitative tools and can provide a testing ground for ideas regarding the emergence and evolution of complex biological networks. We analyze the global statistical properties of the transcriptional regulatory network of the prokaryote Escherichia coli, identifying each operon with a node of the network. We propose a null model for this network using the content-based approach applied earlier to the eukaryote Saccharomyces cerevisiae. (Balcan et al., 2007) Random sequences that represent promoter regions and binding sequences are associated with the nodes. The length distributions of these sequences are extracted from the relevant databases. The network is constructed by testing for the occurrence of binding sequences within the promoter regions. The ensemble of emergent networks yields an exponentially decaying in-degree distribution and a putative power law dependence for the out-degree distribution with a flat tail, in agreement with the data. The clustering coefficient, degree-degree correlation, rich club coefficient and k-core visualization all agree qualitatively with the empirical network to an extent not yet achieved by any other computational model, to our knowledge. The significant statistical differences can point the way to further research into non-adaptive and adaptive processes in the evolution of the E. coli GRN.Comment: 58 pages, 3 tables, 22 figures. In press, Journal of Theoretical Biology (2009)

Community Perceptions of the Environmental Remediation Effort in the Milwaukee River Estuary

The Environmental Protection Agency (EPA), Wisconsin Department of Natural Resources (DNR), and Milwaukee County Parks Department have been working on an environmental remediation project that seeks to remove chemical contaminants and pollution from the Milwaukee River. The purpose of this research is to discover community member’s perceptions on the quality and safety of the Milwaukee River, and determine whether their perspectives on safe and desirable uses of the river differ from those of the organizations overseeing the Great Lake Legacy Act (GLLA) project. The results from this study show that the communities in the project area believe that the quality of the river has improved but it is still unsafe in some ways. This study shows that understanding the perceptions about quality, safety and uses of the river can improve the relationship between remediation organizations and the affected community.Ope

Letter written by Patricia O\u27Brien Aiken to Lieutenant Albert Shelton Aiken Postmarked March 30, 1942

Hi Sugar – I got quite a kick out of your letter. The letterhead was censored and also the place you arrived at and then what has been fairly good so that you got in a lot of flying time. It looked so ridiculous, I just had to laugh. However if you’re where I think you are, I think the Alaskan mainland would be better even if it doesn’t have any inner-spring mattresses..

A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions

Transcription is the central process of gene regulation. In higher eukaryotes, the transcription of a gene is usually regulated by multiple cis-regulatory regions (CRRs). In different tissues, different transcription factors bind to their cis-regulatory motifs in these CRRs to drive tissue-specific expression patterns of their target genes. By combining the genome-wide gene expression data with the genomic sequence data, we proposed multiple-instance scoring (MIS) method to predict the tissue-specific motifs and the corresponding CRRs. The method is mainly based on the assumption that only a subset of CRRs of the expressed gene should function in the studied tissue. By testing on the simulated datasets and the fly muscle dataset, MIS can identify true motifs when noise is high and shows higher specificity for predicting the tissue-specific functions of CRRs

Comparing non-verbal vocalisations in conversational speech corpora

Conversations do not only consist of spoken words but they also consist of non-verbal vocalisations. Since there is no standard to define and to classify (possible) non-speech sounds the annotations for these vocalisations differ very much for various corpora of conversational speech. There seems to be agreement in the six inspected corpora that hesitation sounds and feedback vocalisations are considered as words (without a standard orthography). The most frequent non-verbal vocalisation are laughter on the one hand and, if considered a vocal sound, breathing noises on the other

Roles of transcription factors, RBPA and SIGF, in the mycobacterium tuberculosis

The mechanism of prokaryotic transcription has been characterized primarily in the classic system, Escherichia coli, and cannot be confidently extended to include other prokaryotic species, such as those of the Actinobacteria phylum. Actinobacteria represents a diverse group of Gram-positive species that range from soil dwellers to obligate pathogens, such as Mycobacterium tuberculosis (Tb). These species encode RNA polymerase (RNAP) binding proteins that are not present in model organisms, and therefore present a unique lens through which the basic mechanism of transcription can be further explored outside of model systems. In addition, these mechanisms of transcriptional regulation can be studied in the context of M. Tuberculosis pathogenesis. The model we use for tuberculosis is Mycobacterium Smegmatis, a homologue, which has a faster doubling time and is only Biosafety level 1. Within Actinobacteria, notable conserved RNAP binding proteins include RNA polymerase binding protein A (RbpA) and CarD. RbpA is specific to Actinobacteria, binding the β subunit of RNAP and primary σ factors. CarD binds to the β subunit and associates with DNA. Both proteins are upregulated upon exposure to stress, and have implications in the initiation of rRNA transcription. Each is proposed to stimulate the formation of transcriptionally competent RNAP-holoenzyme open promoter complexes, and CarD is thought to act as a global transcriptional regulator. RbpA and CarD are believed to be essential in M. Tuberculosis and M. Smegmatis. Recent structural analyses of RbpA and CarD suggest the two proteins may share a region of similarity that could compete for binding to the β subunit, and brings into question whether the two proteins are capable of coordinately modulating transcription or antagonize each other's activity. This was investigated through purification of CarD and RbpA and in vitro studies performed with [α-32P] Uridine triphosphate used to measure the level of transcription. These experiments led to the conclusion that RbpA and CarD are able to associate with the same RNAP and have an additive stabilizing action on the polymerase. Whether or not RbpA is an essential protein was also investigated genetically, and by using a Tetracycline on/off system. Sigma factors play an important role in transcription due to their ability to recognize promoter regions and initiate transcription. One connection that we have preliminary data for, through DNA pull downs, is that sigF binds rRNA promoters, and CarD and RbpA are both studied in the context of rRNA transcription. Therefore sigF is another factor that could be regulating rRNA transcription, possibly during stress. SigF is also the sigma factor that responds to oxidative stress, and CarD is involved in oxidative stress. Sigma F is a member of a family of 13 different sigma factors that are preset in M. Tuberculosis. There are two different types of sigma factors: primary, which are essential for normal growth, and alternative, which are typically expressed during differing environmental conditions. Sigma F has been shown to be upregulated during oxidative stress, which is why it was of particular interest to us. To investigate the roles of sig F, we exposed sig F deletion mutants and wild type strains to oxidative stress and measured ribosomal RNA production by reverse transcription quantitative real time PCR. It was concluded that sigF is a probable suppressor of rRNA when exposed to oxidative stress

Intracellular Regulatory Networks are close to Monotone Systems

Several meso-scale biological intracellular regulatory networks that have specified directionality of interactions have been recently assembled from experimental literature. Directed networks where links are characterized as positive or negative can be converted to systems of differential equations and analyzed as dynamical systems. Such analyses have shown that networks containing only sign-consistent loops, such as positive feed-forward and feedback loops function as monotone systems that display well-ordered behavior. Perturbations to monotone systems have unambiguous global effects and a predictability characteristic that confers advantages for robustness and adaptability. We find that three intracellular regulatory networks: bacterial and yeast transcriptional networks and a mammalian signaling network contain far more sign-consistent feedback and feed-forward loops than expected for shuffled networks. Inconsistent loops with negative links can be more easily removed from real regulatory networks as compared to shuffled networks. This topological feature in real networks emerges from the presence of hubs that are enriched for either negative or positive links, and is not due to a preference for double negative links in paths. These observations indicate that intracellular regulatory networks may be close to monotone systems and that this network topology contributes to the dynamic stability