Chaos game representation for comparison of whole genomes

BACKGROUND: Chaos game representation of genome sequences has been used for visual representation of genome sequence patterns as well as alignment-free comparisons of sequences based on oligonucleotide frequencies. However the potential of this representation for making alignment-based comparisons of whole genome sequences has not been exploited. RESULTS: We present here a fast algorithm for identifying all local alignments between two long DNA sequences using the sequence information contained in CGR points. The local alignments can be depicted graphically in a dot-matrix plot or in text form, and the significant similarities and differences between the two sequences can be identified. We demonstrate the method through comparison of whole genomes of several microbial species. Given two closely related genomes we generate information on mismatches, insertions, deletions and shuffles that differentiate the two genomes. CONCLUSION: Addition of the possibility of large scale sequence alignment to the repertoire of alignment-free sequence analysis applications of chaos game representation, positions CGR as a powerful sequence analysis tool

Introduction: Examined Live – An Epistemological Exchange Between Philosophy and Cultural Psychology on Reflection

Besides the general agreement about the human capability of reflection, there is a large area of disagreement and debate about the nature and value of “reflective scrutiny” and the role of “second-order states” in everyday life. This problem has been discussed in a vast and heterogeneous literature about topics such as epistemic injustice, epistemic norms, agency, understanding, meta-cognition etc. However, there is not yet any extensive and interdisciplinary work, specifically focused on the topic of the epistemic value of reflection. This volume is one of the first attempts aimed at providing an innovative contribution, an exchange between philosophy, epistemology and psychology about the place and value of reflection in everyday life. Our goal in the next sections is not to offer an exhaustive overview of recent work on epistemic reflection, nor to mimic all of the contributions made by the chapters in this volume. We will try to highlight some topics that have motivated a new resumption of this field and, with that, drawing on chapters from this volume where relevant. Two elements defined the scope and content of this volume, on the one hand, the crucial contribution of Ernest Sosa, whose works provide original and thought-provoking contributions to contemporary epistemology in setting a new direction for old dilemmas about the nature and value of knowledge, giving a central place to reflection. On the other hand, the recent developments of cultural psychology, in the version of the “Aalborg approach”, reconsider the object and scope of psychological sciences, stressing that “[h]uman conduct is purposeful”

Associations between subspecialty fellowship interest and knowledge of internal medicine: A hypothesis-generating study of internal medicine residents

<p>Abstract</p> <p>Background</p> <p>Little is known about whether and how medical knowledge relates to interest in subspecialty fellowship training. The purpose of this study was to examine the relationships between residents' interest in subspecialty fellowship training and their knowledge of internal medicine (IM).</p> <p>Methods</p> <p>A questionnaire was emailed to 48 categorical postgraduate-year (PGY) two and three residents at a New York university-affiliated IM residency program in 2007 using the Survey Monkey online survey instrument. Overall and content area-specific percentile scores from the IM in-training examination (IM-ITE) for the same year was used to determine objective knowledge.</p> <p>Results</p> <p>Forty-five of 48 residents (response rate was 93.8%) completed the survey. Twenty-two (49%) were PG2 residents and 23(51%) were PGY3 residents. Sixty percent of respondents were male. Six (13%) residents were graduates of U.S. medical schools. Eight (18%) reported formal clinical training prior to starting internal medicine residency in the U.S. Of this latter group, 6 (75%) had training in IM and 6 (75) % reported a training length of 3 years or less. Thirty-seven of 45 (82%) residents had a subspecialty fellowship interest. Residents with a fellowship interest had a greater mean overall objective knowledge percentile score (56.44 vs. 31.67; p = 0.04) as well as greater mean percentile scores in all content areas of IM. The adjusted mean difference was statistically significant (p < 0.02) across three content areas.</p> <p>Conclusions</p> <p>More than half of surveyed residents indicated interest in pursuing a subspecialty fellowship. Fellowship interest appears positively associated with general medical knowledge in this study population. Further work is needed to explore motivation and study patterns among internal medicine residents.</p

Acute appendicitis secondary to Enterobius vermicularis infection in a middle-aged man: a case report

<p>Abstract</p> <p>Introduction</p> <p>Acute appendicitis due to <it>Enterobius vermicularis </it>is very rare, affecting mostly children. Whether pinworms cause inflammation of the appendix or just appendiceal colic has been a matter of controversy.</p> <p>Case presentation</p> <p>A Caucasian 52-year-old man was referred to our Emergency Department with acute abdominal pain in his right lower quadrant. The physical and laboratory examination revealed right iliac fossa tenderness and leukocytosis with neutrophilia. An open appendectomy was performed. The pathological examination showed the lumen containing pinworms. Two oral doses of mebendazole were administered postoperatively. The follow-up to date was without incident and he was free of symptoms one year after the operation.</p> <p>Conclusion</p> <p>The finding of <it>E. vermicularis </it>in appendectomy pathological specimens is infrequent. Parasitic infections rarely cause acute appendicitis, especially in adults.</p> <p>One should keep in mind that the clinical signs of intestinal parasite infection may mimic acute appendicitis, although rare. A careful evaluation of symptoms such as pruritus ani, or eosinophilia on laboratory examination, could prevent unnecessary appendectomies.</p

Characterization of a New Mouse Model for Peripheral T Cell Lymphoma in Humans

Peripheral T cell lymphomas (PTCLs) are associated with a poor prognosis due to often advanced disease at the time of diagnosis and due to a lack of efficient therapeutic options. Therefore, appropriate animal models of PTCL are vital to improve clinical management of this disease. Here, we describe a monoclonal CD8+ CD4− αβ T cell receptor Vβ2+ CD28+ T cell lymphoma line, termed T8-28. T8-28 cells were isolated from an un-manipulated adult BALB/c mouse housed under standard pathogen-free conditions. T8-28 cells induced terminal malignancy upon adoptive transfer into syngeneic BALB/c mice. Despite intracellular expression of the cytotoxic T cell differentiation marker granzyme B, T8-28 cells appeared to be defective with respect to cytotoxic activity as read-out in vitro. Among the protocols tested, only addition of interleukin 2 in vitro could partially compensate for the in vivo micro-milieu in promoting growth of the T8-28 lymphoma cells

Contrasting prefrontal cortex contributions to episodic memory dysfunction in behavioural variant frontotemporal dementia and alzheimer's disease

Recent evidence has questioned the integrity of episodic memory in behavioural variant frontotemporal dementia (bvFTD), where recall performance is impaired to the same extent as in Alzheimer's disease (AD). While these deficits appear to be mediated by divergent patterns of brain atrophy, there is evidence to suggest that certain prefrontal regions are implicated across both patient groups. In this study we sought to further elucidate the dorsolateral (DLPFC) and ventromedial (VMPFC) prefrontal contributions to episodic memory impairment in bvFTD and AD. Performance on episodic memory tasks and neuropsychological measures typically tapping into either DLPFC or VMPFC functions was assessed in 22 bvFTD, 32 AD patients and 35 age- and education-matched controls. Behaviourally, patient groups did not differ on measures of episodic memory recall or DLPFC-mediated executive functions. BvFTD patients were significantly more impaired on measures of VMPFC-mediated executive functions. Composite measures of the recall, DLPFC and VMPFC task scores were covaried against the T1 MRI scans of all participants to identify regions of atrophy correlating with performance on these tasks. Imaging analysis showed that impaired recall performance is associated with divergent patterns of PFC atrophy in bvFTD and AD. Whereas in bvFTD, PFC atrophy covariates for recall encompassed both DLPFC and VMPFC regions, only the DLPFC was implicated in AD. Our results suggest that episodic memory deficits in bvFTD and AD are underpinned by divergent prefrontal mechanisms. Moreover, we argue that these differences are not adequately captured by existing neuropsychological measures

Multidetector CT cystography for imaging colovesical fistulas and iatrogenic bladder leaks

Multidetector computed tomography (MDCT) cystography currently represents the modality of choice to image the urinary bladder in traumatized patients. In this review we present our experience with MDCT cystography applications outside the trauma setting, particularly for diagnosing bladder fistulas and leaks. A detailed explanation is provided concerning exam preparation, acquisition technique, image reconstruction and interpretation. Colovesical fistulas most commonly occur as a complication of sigmoid diverticular disease, and often remain occult after extensive diagnostic work-up including cystoscopy and contrast-enhanced CT. We consistently achieved accurate preoperative visualization of colovesical fistulas using MDCT cystography. Urinary leaks and injuries represent a non-negligible occurrence after pelvic surgery, particularly obstetric and gynaecological procedures: in our experience MDCT cystography is useful to investigate iatrogenic bladder leaks or fistulas. In our opinion, MDCT cystography should be recommended as the first line modality for direct visualization or otherwise confident exclusion of both spontaneous enterovesical fistulas and bladder injuries following instrumentation procedures, obstetric or surgical interventions

Dopaminergic modulation of appetitive trace conditioning: the role of D1 receptors in medial prefrontal cortex

Rationale: Trace conditioning may provide a behavioural model suitable to examine the maintenance of ‘on line’ information and its underlying neural substrates. Objectives: Experiment la was run to establish trace conditioning in a shortened procedure which would be suitable to test the effects of dopamine (DA) D1 receptor agents administered by microinjection directly into the brain. Experiment lb examined the effects of the DA D1 agonist SKF81297 and the DA D1 antagonist SCH23390 following systemic administration in pre-trained animals. Experiment 2 went on to test the effects of systemically administered SKF81297 on the acquisition of trace conditioning. In experiment 3, SKF81297 was administered directly in prelimbic (PL) and infralimbic (IL) sub-regions of medial prefrontal cortex (mPFC) to compare the role of different mPFC sub-regions. Results: Whilst treatment with SCH23390 impaired motor responding and/or motivation, SKF81297 had relatively little effect in the pre-trained animals tested in experiment 1b. However, systemic SKF81297 depressed the acquisition function at the 2-s trace interval in experiment 2. Similarly, in experiment 3, SKF81297 (0.1 μg in 1.0 μl) microinjected into either PL or IL mPFC impaired appetitive conditioning at the 2-s trace interval. Conclusions: Impaired trace conditioning under SKF81297 is likely to be mediated in part (but not exclusively) within the IL and PL mPFC sub-regions. The finding that trace conditioning was impaired rather than enhanced under SKF81297 provides further evidence for the inverse U-function which has been suggested to be characteristic of mPFC DA function