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At least 649 records · Page 36Linked to original sources

Resistance to change in surgical residency: an ethnographic study of work hours reform.

BACKGROUND: Although the practical challenges to work hour restrictions have been the focus of much discussion, cultural resistance to such change has received less attention. Surgical residency has its own unique social structure, and we hypothesized that challenges to this would provide impediments to successful implementation of duty hours reform. STUDY DESIGN: We used ethnographic research methods to study the efforts at work hour restriction over a 15-month period before the introduction of the Accreditation Council for Graduate Medical Education regulations. These methods, validated for studying institutional change, build on intense periods of observation. Records of observations are then analyzed and coded to uncover cultural and political challenges. The frequency of successful hand-offs in sign-out situations between day and night float residents was measured as an objective index of success. RESULTS: Practical issues were addressed initially by scheduling adjustments including creating a night float system. The hand-offs that this system required, however, were successful only 14% of the time. Subsequent steps to address the challenge to resident identity by top-down support of a new definition of professionalism increased the number of successful hand-offs to 39%. Finally, a reduction in a noted hierarchy violation led to successful hand-offs 79% of the time. CONCLUSIONS: These results demonstrate that practical solutions alone may not be a sufficient basis for change in surgical residency. While we face other challenges to the traditional surgical culture, attention to social and political issues may enhance the success of our efforts.

Boston↗

Phylogeny of finescale shiners of the genus Lythrurus (Cypriniformes: Cyprinidae) inferred from four mitochondrial genes.

We infer the phylogenetic relationships of finescale shiners of the genus Lythrurus, a group of 11 species of freshwater minnows widely distributed in eastern North America, using DNA sequences from the ND2 (1047 bp), ATPase8 and 6 (823 bp), and ND3 (421 bp) mitochondrial protein-coding genes. The topologies resulting from maximum parsimony, Bayesian, and maximum likelihood tree building methods are broadly congruent, with two distinct clades within the genus: the L. umbratilis clade (L. umbratilis + L. lirus + (L. fasciolaris + (L. ardens, L. matutinus))) and the L. bellus clade (L. fumeus + L. snelsoni + (L. roseipinnis + (L. atrapiculus + (L. bellus, L. algenotus)))). Support is weak at the base of several clades, but strongly supported nodes differ significantly from prior investigations. In particular, our results confirm and extend earlier studies recovering two clades within Lythrurus corresponding to groups with largely "northern" and "southern" geographic distributions. Several species in this genus are listed in the United States as threatened or of special concern due to habitat degradation or limited geographic ranges. In this study, populations assigned to L. roseipinnis show significant genetic divergence suggesting that there is greater genetic diversity within this species than its current taxonomy reflects. A full accounting of the biodiversity of the genus awaits further study.

Animals↗

MedlineR: an open source library in R for Medline literature data mining.

SUMMARY: We describe an open source library written in the R programming language for Medline literature data mining. This MedlineR library includes programs to query Medline through the NCBI PubMed database; to construct the co-occurrence matrix; and to visualize the network topology of query terms. The open source nature of this library allows users to extend it freely in the statistical programming language of R. To demonstrate its utility, we have built an application to analyze term-association by using only 10 lines of code. We provide MedlineR as a library foundation for bioinformaticians and statisticians to build more sophisticated literature data mining applications. AVAILABILITY: The library is available from http://dbsr.duke.edu/pub/MedlineR.

Abstracting and Indexing↗

8-Hydroxyguanine (7,8-dihydro-8-oxoguanine) in hot spots of the c-Ha-ras gene: effects of sequence contexts on mutation spectra.

We previously reported that 8-hydroxyguanine (7,8-dihydro-8-oxoguanine) at the second position of codon 12 of the c-Ha-ras gene induces many types of mutations in NIH3T3 cells. In this study we incorporated the modified base into the first and second positions of codon 12 in the coding strand and into the first position of codon 61 in the non-coding strand of the gene using a new 8-hydroxyguanine phosphoramidite as a building block during oligonucleotide synthesis. The ras genes with 8-hydroxyguanine were transfected into NIH3T3 cells and the mutations induced were analyzed. 8-Hydroxyguanine residues at the first positions of codons 12 and 61 induced mutations to T at the modified sites almost exclusively. On the other hand, the DNA lesion at the second position of codon 12 induced a G-->A transition in addition to a G-->T transversion, confirming our previous results. Mutations in 5'-flanking sites were observed with 8-hydroxyguanine at the second position of codon 12 or the first position of codon 61. These results indicate that 8-hydroxyguanine in mammalian cells mainly induces a G-->T transversion at the modified site, but that other types of mutations are also elicited.

3T3 Cells↗

Integrated power controllers and RF data transmitters for totally implantable telemetry.

Data transmitters and power/source controllers are common elements in all totally implantable instrumentation systems. Two custom-designed integrated circuits have been developed for these elements and have significant impact on the realization of compact reliable telemetry packages. The first is an elapsed-time power switch that can remotely turn on implanted battery-powered systems with a short RF burst; to prevent accidental battery drainage, it will automatically turn off after a preprogrammed time (1-5 min). The second is a precision RF transmitter capable of operation up to 125 MHz in either FM or pulse-coded format and requires only two nonintegrated inductors. These IC systems are basic building blocks for a large number of totally implantable telemetry applications.

Electric Power Supplies↗

[Perception in space. Visual aspects of space perception].

The ability to apprehend and appropriate space is based on a series of perceptive and cognitive processes, in which vision plays a leading part. Preliminary, elementary operations first allow a subject to achieve the elaboration of a visually structured percept. Both experiences on healthy subjects, and pathological data have provided evidence for a right hemisphere superiority in tasks such as localization of stimuli and discrimination of line orientation. Depth perception rests both on indirect cues (e.g. relative size of objects, perspective and movement parallax) and on two types of specific stereoscopic processes: the so-called local and global stereoscopies, which depend respectively on the integrity of visual cortices and of inferior occipito-temporal areas (with a right-hemisphere dominance). Movement perception is integrated at the level of area V5, at the lateral occipito-temporal junction on both sides. The accuracy of reaching movements and displacements within space require the elaboration of a system of coordinates in which the position of the egocentric reference will then be taken into account. This is achieved by successive coding of eye and head position relative to the body axis, and by building the body reference from proprioceptive and vestibular afferences to the parietal cortex. Finally, attention must be both diffusely scattered throughout the whole space and voluntarily allocated as needed on a given object. Simultanagnosia and unilateral spatial neglect (USN) are examples of disruption of these attentional processes. Simultanagnosia illustrates the loss of the ability to shift attention from one point to another, but both shrinking of the attentional field and poorly sustained fixation are also possible mechanisms of this syndrome. USN probably has several components. Unilateral brain damage causes interhemispheric attentional imbalance that explains the attentional preference for the ipsilesional side of space. The predominance of neglect following right-sided lesions might be the consequence of hemispheric specialization regarding directed attention, with the left hemisphere preferentially allocating attention to objects and the right one being able to attend to the whole space. The anatomical basis of such a functional differentiation is still unclear.

Animals↗

Absorbed fractions in a voxel-based phantom calculated with the MCNP-4B code.

A new approach for calculating internal dose estimates was developed through the use of a more realistic computational model of the human body. The present technique shows the capability to build a patient-specific phantom with tomography data (a voxel-based phantom) for the simulation of radiation transport and energy deposition using Monte Carlo methods such as in the MCNP-4B code. MCNP-4B absorbed fractions for photons in the mathematical phantom of Snyder et al. agreed well with reference values. Results obtained through radiation transport simulation in the voxel-based phantom, in general, agreed well with reference values. Considerable discrepancies, however, were found in some cases due to two major causes: differences in the organ masses between the phantoms and the occurrence of organ overlap in the voxel-based phantom, which is not considered in the mathematical phantom.

Algorithms↗

Artificial neural network method for discriminating coding regions of eukaryotic genes.

This paper describes the application of artificial neural networks to discriminating the coding system of eukaryotic genes. We choose > 300 genes from eight eukaryotic organisms: human, mouse, rat, horse, ox, sheep, soybean and rabbit, from which we build up different discrimination models relevant to their promoter regions, poly(A) signals, splice site locations of introns and noose structures. The results shows that as long as the coding length is definite, the only correct coding region can be chosen from the large number of possible solutions discriminated by neural networks.

Animals↗

Noncoded residues as building blocks in the design of specific secondary structures: symmetrically disubstituted glycines and beta-alanine.

Structural changes can be induced in a peptide by selective substitution of coded alpha-amino acid residues by noncoded alpha-amino acid residues and the consequent production of analogues with modified structure and conformational preferences. In this review article we summarize the solid state structural results and the conformational preferences of two classes of "building blocks": (a) the linear and cyclic symmetrically alpha, alpha-disubstituted glycines in which either two identical n-alkyl groups replace the hydrogen atoms of the glycine residue or a cyclic aliphatic side-chain system is formed by linking the two alpha-carbon side chains, respectively; and (b) the beta-alanine residue. Examples, whenever possible, of the use of these residues for the elucidation of the bioactive conformation in the appropriate biological systems will be given.

Amino Acid Sequence↗

Prognosis of stage II colon cancer by non-neoplastic mucosa gene expression profiling.

We have assessed the possibility to build a prognosis predictor (PP), based on non-neoplastic mucosa microarray gene expression measures, for stage II colon cancer patients. Non-neoplastic colonic mucosa mRNA samples from 24 patients (10 with a metachronous metastasis, 14 with no recurrence) were profiled using the Affymetrix HGU133A GeneChip. Patients were repeatedly and randomly divided into 1000 training sets (TSs) of size 16 and validation sets (VS) of size 8. For each TS/VS split, a 70-gene PP, identified on the TS by selecting the 70 most differentially expressed genes and applying diagonal linear discriminant analysis, was used to predict the prognoses of VS patients. Mean prognosis prediction performances of the 70-gene PP were 81.8% for accuracy, 73.0% for sensitivity and 87.1% for specificity. Informative genes suggested branching signal-transduction pathways with possible extensive networks between individual pathways. They also included genes coding for proteins involved in immune surveillance. In conclusion, our study suggests that one can build an accurate PP for stage II colon cancer patients, based on non-neoplastic mucosa microarray gene expression measures.

Adenocarcinoma↗

Genetic code, hamming distance and stochastic matrices.

In this paper we use the Gray code representation of the genetic code C=00, U=10, G=11 and A=01 (C pairs with G, A pairs with U) to generate a sequence of genetic code-based matrices. In connection with these code-based matrices, we use the Hamming distance to generate a sequence of numerical matrices. We then further investigate the properties of the numerical matrices and show that they are doubly stochastic and symmetric. We determine the frequency distributions of the Hamming distances, building blocks of the matrices, decomposition and iterations of matrices. We present an explicit decomposition formula for the genetic code-based matrix in terms of permutation matrices, which provides a hypercube representation of the genetic code. It is also observed that there is a Hamiltonian cycle in a genetic code-based hypercube.

Amino Acids↗

Atoms-in-molecules study of the genetically encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding.

This article presents a study of the molecular charge distributions of the genetically encoded amino acids (AA), one that builds on the previous determination of their equilibrium geometries and the demonstrated transferability of their common geometrical parameters. The properties of the charge distributions are characterized and given quantitative expression in terms of the bond and atomic properties determined within the quantum theory of atoms-in-molecules (QTAIM) that defines atoms and bonds in terms of the observable charge density. The properties so defined are demonstrated to be remarkably transferable, a reflection of the underlying transferability of the charge distributions of the main chain and other groups common to the AA. The use of the atomic properties in obtaining an understanding of the biological functions of the AA, whether free or bound in a polypeptide, is demonstrated by the excellent statistical correlations they yield with experimental physicochemical properties. A property of the AA side chains of particular importance is the charge separation index (CSI), a quantity previously defined as the sum of the magnitudes of the atomic charges and which measures the degree of separation of positive and negative charges in the side chain of interest. The CSI values provide a correlation with the measured free energies of transfer of capped side chain analogues, from the vapor phase to aqueous solution, yielding a linear regression equation with r2 = 0.94. The atomic volume is defined by the van der Waals isodensity surface and it, together with the CSI, which accounts for the electrostriction of the solvent, yield a linear regression (r2 = 0.98) with the measured partial molar volumes of the AAs. The changes in free energies of transfer from octanol to water upon interchanging 153 pairs of AAs and from cyclohexane to water upon interchanging 190 pairs of AAs, were modeled using only three calculated parameters (representing electrostatic and volume contributions) yielding linear regressions with r2 values of 0.78 and 0.89, respectively. These results are a prelude to the single-site mutation-induced changes in the stabilities of two typical proteins: ubiquitin and staphylococcal nuclease. Strong quadratic correlations (r2 approximately 0.9) were obtained between DeltaCSI upon mutation and each of the two terms DeltaDeltaH and TDeltaDeltaS taken from recent and accurate differential scanning calorimetry experiments on ubiquitin. When the two terms are summed to yield DeltaDeltaG, the quadratic terms nearly cancel, and the result is a simple linear fit between DeltaDeltaG and DeltaCSI with r2 = 0.88. As another example, the change in the stability of staphylococcal nuclease upon mutation has been fitted linearly (r2 = 0.83) to the sum of a DeltaCSI term and a term representing the change in the van der Waals volume of the side chains upon mutation. The suggested correlation of the polarity of the side chain with the second letter of the AA triplet genetic codon is given concrete expression in a classification of the side chains in terms of their CSI values and their group dipole moments. For example, all amino acids with a pyrimidine base as their second letter in mRNA possess side-chain CSI < or = 2.8 (with the exception of Cys), whereas all those with CSI > 2.8 possess an purine base. The article concludes with two proposals for measuring and predicting molecular complementarity: van der Waals complementarity expressed in terms of the van der Waals isodensity surface and Lewis complementarity expressed in terms of the local charge concentrations and depletions defined by the topology of the Laplacian of the electron density. A display of the experimentally accessible Laplacian distribution for a folded protein would offer a clear picture of the operation of the "stereochemical code" proposed as the determinant in the folding process.

Amino Acids↗

Simplified primer design for PCR-based gene targeting and microarray primer database: two web tools for fission yeast.

PCR-based gene targeting is a popular method for manipulating yeast genes in their normal chromosomal locations. The manual design of primers, however, can be cumbersome and error-prone. We have developed a straightforward web-based tool that applies user-specified inputs to automate and simplify the task of primer selection for deletion, tagging and/or regulated expression of genes in Schizosaccharomyces pombe. This tool, named PPPP (for Pombe PCR Primer Programs), is available at http://www.sanger.ac.uk/PostGenomics/S_pombe/software/. We also present a searchable Microarray Primer Database to retrieve the sequences and accompanying information for primers and PCR products used to build our in-house Sz. pombe microarrays. This database contains information on both coding and intergenic regions to provide context for the microarray data, and it should be useful also for other applications, such as quantitative PCR. The database can be accessed at http://www.sanger.ac.uk/PostGenomics/S_pombe/microarray/.

DNA Primers↗

Microcomputer system for automatic identification of the Cryptococcus neoformans and its clinical application.

In this study, microcomputer image processing and pattern recognition technology, and the knowledge of morphology and optical characteristics of Cryptococcus neoformans were used for identification of Cryptococcus neoformans. Four groups of mice were lethally infected with standard strain, Wuhan strain, American B-2643 strain and Var. Shanghainesis of the Cryptococcus neoformans. The samples collected included mice brain, lung, kidney, liver, small intestine tissue and were observed under a light microscope. More than 600 images of the fungus were input into a microcomputer. A system of computer for automatic identification of the Cryptococcus neoformans was developed. The technique involved image preprocessing, image segmenting, coding of line-length on the edge, curve fitting, extracting of image feature, building of image library and feature data bank etc.. And then, 768 images of the clinical samples and other fungus samples whose morphological features tend to be confused with Cryptococcus neoformans were input into microcomputer and subjected to automatic identification. The Cryptococcus neoformans was accurately identified within 15 min, and the consistency rate with results of routine culture was 98%.

Animals↗

Characterization of the horse (Equus caballus) IGHA gene.

Nucleotide sequences of the immunoglobulin constant heavy chain genes of the horse have been described for IGHM, IGHG and IGHE genes, but not for IGHA. Here, we provide the nucleotide sequence of the genomic IGHA gene of the horse ( Equus caballus), including its secretion region and the transmembrane exon. The equine IGHA gene shows the typical structure of a mammalian IGHA gene, with only three exons, separated by two introns of similar size. The hinge exon is located at the 5' end of the CH2 exon and encodes a hinge region of 11 amino acids, which contains five proline residues. The coding nucleotide sequence of the secreted form of the equine IGHA gene shares around 72% identity with the human IGHA1 and IGHA2 genes, as well as the bovine, ovine, porcine and canine IGHA genes, without distinct preference for any of these species. The same species also cluster together in a phylogenetic tree of the IGHA coding regions of various mammals, whereas rodent, rabbit, marsupial and monotreme IGHA genes each build a separate cluster.

Amino Acid Sequence↗

Evil intent and design responsibility.

Mass casualty attacks in recent years have demonstrated the need to include "evil intent" as a design consideration. Three recent actual or potential weapons of mass destruction (WMD) attacks did not involve nuclear bombs or other devices designed as weapons, but rather benign objects used with evil intent. Just as unplanned events such as hurricanes, earthquakes, fires, and user misuse have been codified into design requirements based on the likelihood and potential impact of the event, "evil intent" has to become part of the design process for buildings, vehicles, equipment, and other items. The endstate should be reasonable additions to existing codes and standards such that it is clear what is and is not designed for. In the absence of specific design guidance, professionals with appropriate expertise can assess potential for "evil intent" and provide recommendations to design out or warn against this potential harm to public safety, particularly when codified requirements are not present.

Facility Design and Construction↗

Detection of temporal patterns in dog-human interaction.

A new time structure model and pattern detection procedures developed by (Magnusson, M.S., 1996. Hidden real-time patterns in intra- and inter-individual behaviour description and detection. Eur. J. Psychol. Assess. 12, 112-123; Magnusson, M.S., 2000. Discovering hidden time patterns in behaviour: T-patterns and their detection. Behav. Res. Methods, Instrum. Comput. 32, 93-110) enables us to detect complex temporal patterns in behaviour. This method has been used successfully in studying human and neuronal interactions (Anolli, L., Duncan, S. Magnusson, M.S., Riva G. (Eds.), 2005. The Hidden Structure of Interaction, IOS Press, Amsterdam). We assume that similarly to interactions between humans, cooperative and communicative interaction between dogs and humans also consist of patterns in time. We coded and analyzed a cooperative situation when the owner instructs the dog to help build a tower and complete the task. In this situation, a cooperative interaction developed spontaneously, and occurrences of hidden time patterns in behaviour can be expected. We have found such complex temporal patterns (T-patterns) in each pair during the task that cannot be detected by "standard" behaviour analysis. During cooperative interactions the dogs' and humans' behaviour becomes organized into interactive temporal patterns and that dog-human interaction is much more regular than yet has been thought. We have found that communicative behaviour units and action units can be detected in the same T-pattern during cooperative interactions. Comparing the T-patterns detected in the dog-human dyads, we have found a typical sequence emerging during the task, which was the outline of the successfully completed task. Such temporal patterns were conspicuously missing from the "randomized data" that gives additional support to the claim that interactive T-patterns do not occur by chance or arbitrarily but play a functional role during the task.

Animals↗

Sharkmer: repurposing PCR primers for targeted genome assembly using in silico PCR.

SUMMARY: We introduce an in silico PCR (sPCR) method for the assembly of specific genomic regions spanned by PCR primers using raw sequence reads. This allows a user to quickly isolate the exact regions that are abundant in public archives of gene sequences, leveraging the decades of work that have gone into optimizing primer sequences for benchtop PCR. We implement sPCR in sharkmer as a targeted de Bruijn graph assembler seeded with the forward primer sequence and terminated with the reverse primer sequence. This is useful for a variety of routine tasks, including validating the species identity of a dataset, identifying contaminants, and quickly building phylogenies from raw sequence data. AVAILABILITY AND IMPLEMENTATION: sharkmer is written in Rust. Code, instructions for installation and use, tests, and other resources are available in the GitHub repository at https://github.com/caseywdunn/sharkmer and at Zenodo with DOI 10.5281/zenodo.19020708. It can also be installed via bioconda.

Software↗