A “plant gene vector cassette” to be used in combination with various Escherichia coli gene-cloning vectors was constructed. This cassette contains a replication and mobilization unit which allows it to be maintained and to be transferred back and forth between E. coli and Agrobacterium tumefaciens hosts provided these hosts contain plasmid RK2 replication and mobilization helper functions. The cassette also harbors a transferable DNA unit with plant selectable marker genes and cloning sites which can be combined with different bacterial replicons, thus facilitating the reisolation of transferred DNA from transformed plants in E. coli. The vector cassette contains two different promoters derived from the T-DNA-encoded genes 5 and nopaline synthase (NOS). By comparing the levels of expression of the marker enzymes linked to each of these promoter sequences, it was found that the gene 5 promoter is active in a tissue-specific fashion whereas this is not the case for the NOS promoter. This observation provides the first documented instance of a gene derived from a procaryotic host the expression of which is apparently regulated by plant growth factors.

https://link.springer.com/content/pdf/10.1007/BF00331014.pdf

The promoter of TL-DNA gene 5 controls the tissue-specific expression of chimaeric genes carried by a novel type of Agrobacterium binary vector

Cours d'economie politique

Bioinformatics — The Machine Learning Approach

2012 [AS13b, Wal12a]. 2013 [Alv13, Bar13, Cam13, Car13, CCS13, Cut13, Edi14, Swe13]. 2014 [CDS13, DN14, ND14, Rod14, Tym14a]. 2015 [DeL14a, DeL14b, She15b]. 2016 [AT16a, CCV16, CCV17, MR15, SDCT16a, SDCT16c, She16a]. 2017 [DG17, EC17, Fit18b, MJ18, TCSM17, TCM17]. 2018 [BG18b, DD17, Dec19b, Gol18, JI18, MKMP18, MMK18, PQH17, She18]. 2019 [Cut19, FI19, HPQ19, MP19a, MPRM19, MP19b, MS19, Rod18, She19a]. 2020 [DH19].

/pdf/a-complete-bibliography-of-publications-in-sigcse-bulletin-1aolnsl5m4.pdf

A Complete Bibliography of Publications in SIGCSE Bulletin: 2000{2009

/pdf/the-evaluation-of-forensic-dna-evidence-by-committee-on-dna-9gjpzg3wn7.pdf

The Evaluation of Forensic DNA Evidence. By Committee on DNA Forensic Science: an Update, National Research Council. National Academy Press, 1996. 254 pages. Price £30.95, hard cover. ISBN 0 309 05395 1.

J Forensic Sci, July 2015, Vol. 60, No. 4 doi: 10.1111/1556-4029.12805 Available online at: onlinelibrary.wiley.com Letter to the Editor— Context Management Toolbox: A Linear Sequential Unmasking (LSU) Approach for Minimizing Cognitive Bias in Forensic Decision Making Sir, The 2009 NAS report (1) criticized forensic scientists for making insufficient efforts to reduce their vulnerability to cogni- tive and contextual bias. Over the past few years, however, the field has begun to take steps to address this issue. There have been major workshops on cognitive bias, and the Organization of Scientific Area Committees (OSAC), 1 as well as the National Commission on Forensic Science, have created committees on Human Factors that are specifically charged with examining this issue. 2 A number of tools and methods for minimizing bias are under consideration. Some of these tools have already been imple- mented in a few forensic laboratories. In general, these tools are designed to protect and enhance the independence of mind of forensic examiners, particularly those who rely on subjective judgment to make their decisions. Several types of contextual information are of concern, as illus- trated in Fig. 1. We organize them into a taxonomy of five levels (based on a four-level taxonomy suggested by Stoel et al. [2]). The five-level taxonomy differentiates task-irrelevant information that may be conveyed to an analyst by the trace evidence itself (Level 1), the reference samples (Level 2), the case information (Level 3), examiners’ base rate expectations that arise from their experience (e.g., when the examiner expects a particular result— Level 4), and organizational and cultural factors (Level 5). A variety of tools are available for addressing cognitive bias. Different tools are useful for managing exposure to each level of task-irrelevant information. For example, case managers (3,4) is a straightforward tool for dealing with bias from case informa- tion (Level 3). In general, these procedures are designed to pre- vent contextual bias by protecting the examiner from exposure to task-irrelevant information. However, it is important to note that some types of information, while potentially biasing, may also be task relevant (5). These types of biasing information are more difficult to deal with. For example, in some instances, evidence that analysts must examine to perform their duties may contain information that is potentially biasing. This can pertain to cases in which Level 1 information, the trace evidence being evaluated, contains contextual informa- tion (e.g., blood spatter patterns that contain information about the nature of the crime, or handwriting and voice samples in which the meaning of the words is potentially biasing). Reference samples are another example of relevant material that is also potentially biasing (Level 2). These samples are clearly relevant because the analyst must compare them to trace evidence samples to determine whether they are similar enough to conclude that they come from the same source. But it is pos- sible that an analyst’s interpretation of the trace evidence might inadvertently be influenced by knowing the characteristics of the See: http://www.nist.gov/forensics/osac/hfc.cfm. The authors of this letter are comprised primarily from members of the OSAC Human Factors Committee, the Human Factors Subcommittee of the National Commission on Forensic Science, and authors of the original Sequential Unmasking. © 2015 American Academy of Forensic Sciences Fig. 1––A taxonomy of the different levels at which task-irrelevant and potentially biasing contextual information may reach a forensic scientist. reference samples—a form of bias arising from circular reason- ing. To manage this type of bias, one must look to other tools in the context management toolbox. The most widely discussed tool for this purpose is sequential unmasking (6). In contrast to other context management tools (3,5), the sequential unmasking approach does not prevent exposure to biasing relevant information. However, it does mandate that this information be presented as late as possible in the exami- nation process and only when it is necessary. A critical ele- ment of sequential unmasking is that the forensic examiner must first examine and document the trace evidence from the crime scene (Level 1), before being exposed to the known reference material (Level 2). This approach is linear in the sense that one must begin with the trace evidence before being exposed to and working with the reference material, thus working from the evidence to the sus- pect, rather than from the suspect to the evidence. The trace evi- dence should be interpreted the same in this initial step, regardless of any suspect who is considered as a possible (or even likely) source of the trace evidence. However, according to sequential unmasking (6), examiners are permitted to revisit, as well as change, their initial analysis of the trace evidence once they have reviewed the reference material, provided that they document these changes. Sequential unmasking allows unlimited and unrestricted changes to the evidence once exposed to the reference material. We believe it is important to impose limits and restrictions for when examiners are permitted to revisit and alter their initial analysis of trace evidence. The analysis of traces is most objec- tive when the examination is “context free”—that is, prior to exposure to the known reference samples. However, seeing the reference samples could alert the examiner to a possible over- sight, error, or misjudgment in the analysis of the trace evidence. Here, we seek to strike a balance between restrictive proce- dures that forbid analysts from changing their opinion and those that allow unlimited and unrestricted changes. The requirement that changes be documented does not eliminate the possibility that such changes arose from bias—it only makes that possibility more transparent.

/pdf/letter-to-the-editor-context-management-toolbox-a-linear-3qvxylpqqy.pdf

Letter to the Editor- Context Management Toolbox: A Linear Sequential Unmasking (LSU) Approach for Minimizing Cognitive Bias in Forensic Decision Making.

Bioinformatics is a new and rapidly evolving discipline that has emerged from the fields of experimental molecular biology and biochemistry, and from the artificial intelligence, database, pattern recognition, and algorithms disciplines of computer science Largely because of the inherently interdisciplinary nature of bioinformatics research, academia has been slow to respond to strong industry and government demands for trained scientists to develop and apply novel bioinformatic techniques to the rapidly growing freely available repositories of genetic and proteomic data While some institutions are responding to this demand by establishing graduate programs in bioinformatics, the entrance barriers for these programs are high, largely because of the significant amount of prerequisite knowledge in the disparate fields of biochemistry and computer science required for sophisticated new approaches to the analysis and interpretation of bioinformatics data The authors present an undergraduate-level bioinformatics curriculum in computer science designed for the baccalaureate student This program is designed to be tailored easily to the needs and resources of a variety of institutions

Crossing the interdisciplinary barrier: a baccalaureate computer science option in bioinformatics

Bioinformatics is a new and rapidly evolving discipline that has emerged from the fields of experimental molecular biology and biochemistry, and from the the artificial intelligence, database, and algorithms disciplines of computer science. Largely because of the inherently interdisciplinary nature of bioinformatics research, academia has been slow to respond to strong industry and government demands for trained scientists to develop and apply novel bioinformatics techniques to the rapidly-growing, freely-available repositories of genetic and proteomic data. While some institutions are responding to this demand by establishing graduate programs in bioinformatics, the entrance barriers for these programs are high, largely due to the significant amount of prerequisite knowledge in the disparate fields of biochemistry and computer science required to author sophisticated new approaches to the analysis of bioinformatics data. We present a proposal for an undergraduate-level bioinformatics curriculum in computer science that lowers these barriers.

/pdf/a-proposed-undergraduate-bioinformatics-curriculum-for-4kr3kq8yia.pdf

A proposed undergraduate bioinformatics curriculum for computer scientists

Current biological sequence comparison tools utilize full database searches to find approximate matches between a database and a query. A new approach to sequence comparisons can be performed by indexing the database using a novel indexing scheme. An indexed scheme can immediately eliminate highly mismatched sequences thereby improving performance and accuracy. iBlast is proposed as an indexed version of BLAST. In its initial implementation, iBlast uses a sequence-based index to catalog genomic databases in an NCR Teradata RDBMS. Several types of indexes and querying methods are explored to determine the most efficient solution utilizing the parallel nature of the Teradata system. Significant speedups were obtained and are explained in further detail in this paper. Future indexing methods based on prokaryotic and eukaryotic genome structures are also proposed.

/pdf/indexing-genomic-databases-1adccvxmq1.pdf

Indexing genomic databases

Dear Sir,A challenge to the reliability of low copy number (LCN)DNA profiling in the trial of Sean Hoey in Belfast CrownCourt in Northern Ireland (R v Hoey [2007] NICC 49, 20December, 2007) prompted the UK’s new Forensic ScienceRegulator (Andrew Rennison) to commission a review oflow template DNA profiling techniques. That review [2],conducted by Professor Brian Caddy (with the assistance ofDr. Adrian Linacre and Dr. Graham Taylor) was released on12 April, 2008 and concluded that LCN DNA profiling is“robust” and “fit for purpose.” Yet, the review accepts thatthe evidence presented in Sean Hoey’s trial was insufficientto establish the validity of the technique. It also enumerates21 recommendations for specific improvements that shouldbe undertaken to improve the methodology, including suchbasic steps as the development of a consensus on theinterpretation of test results and efforts to establish “bestpractices” for interpretation.We believe the conclusions of the review are inconsistentwith its recommendations in a number of respects. Forexample, it is difficult to see how a forensic techniquecould be deemed adequately validated for use in thecourtroom when there is not yet a consensus on how itsresults should be interpreted. The review thus raisesimportant issues about what it means for a forensic sciencetechnique to be validated. It also establishes grounds forconcern about the way that LCN DNA test results havebeen interpreted in earlier cases.We are concerned that the review team relied only oninput regarding the merits of LCN approaches fromorganizations that are dedicated to promoting its use bylaw enforcement. Consultation with known critics of thetechnique (or even a review of their published works)would have provided the reviewers with a broaderperspective of what work remains to be done before theapproach can become generally accepted within theinternational scientific community. There are in fact thingsabout LCN approaches upon which the reviewers andcritics do agree. For instance, caution that “[p]ublicizing thepotential of the application of LCN typing withoutdescribing its limitations may cause misunderstanding” [1]which is consistent with the review’s recommendations 1,3, and 13. But given the conclusion that “[t]he methodcannot be used for exculpatory purposes” [1], the review’sultimate conclusion that LCN testing is “fit for purpose”leaves the important but unanswered question of “what isthat purpose?”

/pdf/comments-on-the-review-of-low-copy-number-testing-4ysf3ae5km.pdf

Dan E. Krane

Papers

Letter to the Editor- Context Management Toolbox: A Linear Sequential Unmasking (LSU) Approach for Minimizing Cognitive Bias in Forensic Decision Making.

Crossing the interdisciplinary barrier: a baccalaureate computer science option in bioinformatics

A proposed undergraduate bioinformatics curriculum for computer scientists

Indexing genomic databases

Comments on the review of low copy number testing.