SRCP: a comprehensive pipeline for accurate annotation and quantification of circRNAs

Here we describe a new integrative approach for accurate annotation and quantification of circRNAs named Short Read circRNA Pipeline (SRCP). Our strategy involves two steps: annotation of validated circRNAs followed by a quantification step. We show that SRCP is more sensitive than other individual pipelines and allows for more comprehensive quantification of a larger number of differentially expressed circRNAs. To facilitate the use of SRCP, we generate a comprehensive collection of validated circRNAs in five different organisms, including humans. We then utilize our approach and identify a subset of circRNAs bound to the miRNA-effector protein AGO2 in human brain samples.

Publisher Correction: Evolution of chalcone isomerase from a noncatalytic ancestor

In the version of this article originally published, the number for the equal contributions footnote was missing for Miriam Kaltenbach and Jason R. Burke in the author list. The error has been corrected in the PDF and print versions of this article.

Evolution of chalcone isomerase from a noncatalytic ancestor

The emergence of catalysis in a noncatalytic protein scaffold is a rare, unexplored event. Chalcone isomerase (CHI), a key enzyme in plant flavonoid biosynthesis, is presumed to have evolved from a nonenzymatic ancestor related to the widely distributed fatty-acid binding proteins (FAPs) and a plant protein family with no isomerase activity (CHILs). Ancestral inference supported the evolution of CHI from a protein lacking isomerase activity. Further, we identified four alternative founder mutations, i.e., mutations that individually instated activity, including a mutation that is not phylogenetically traceable. Despite strong epistasis in other cases of protein evolution, CHI's laboratory reconstructed mutational trajectory shows weak epistasis. Thus, enantioselective CHI activity could readily emerge despite a catalytically inactive starting point. Accordingly, X-ray crystallography, NMR, and molecular dynamics simulations reveal reshaping of the active site toward a productive substrate-binding mode and repositioning of the catalytic arginine that was inherited from the ancestral fatty-acid binding proteins.

Functional Proteins from Short Peptides: Dayhoff's Hypothesis Turns 50

First and foremost: Margaret Dayhoff's 1966 hypothesis on the origin of proteins is now an accepted model for the emergence of large, globular, functional proteins from short, simple peptides. However, the fundamental question of how the first protein(s) emerged still stands. The tools and hypotheses pioneered by Dayhoff, and the over 65 million protein sequences and 12 000 structures known today, enable those who follow in her footsteps to address this question.

Inferring Indel Parameters using a Simulation-based Approach

In this study, we present a novel methodology to infer indel parameters from multiple sequence alignments (MSAs) based on simulations. Our algorithm searches for the set of evolutionary parameters describing indel dynamics which best fits a given input MSA. In each step of the search, we use parametric bootstraps and the Mahalanobis distance to estimate how well a proposed set of parameters fits input data. Using simulations, we demonstrate that our methodology can accurately infer the indel parameters for a large variety of plausible settings. Moreover, using our methodology, we show that indel parameters substantially vary between three genomic data sets: Mammals, bacteria, and retroviruses. Finally, we demonstrate how our methodology can be used to simulate MSAs based on indel parameters inferred from real data sets.

Unenhanced spiral CT for the assessment of renal colic. How does limiting the referral base affect the discovery of additional findings not related to urinary tract calculi?

The value of unenhanced spiral CT (UESCT) for investigating acute flank pain suggestive of urinary tract calculi is increasingly appreciated in the last few years. Recent studies have identified the advantages of UESCT in recognizing alternative findings within or outside the urinary tract. We sought to determine how narrowing the referral base for the UESCT would affect the discovery of potentially significant alternative findings in patients with acute flank pain suggestive of renal colic. Between January 1999 and December 1999, 425 patients, 271 (63.8%) men and 154 (36.2%) women who were 1-90 years old (mean 45.7 years old) with acute flank pain were studied with UESCT. CT studies were solely ordered by urologists, and only patients with intractable renal colic or patients that returned more than once to the emergency room with the complaint of acute flank pain were studied. A calculus within the ureter was diagnostic of an obstructive stone. Any other abnormality within the abdomen and pelvis was reported. A ureteral calculus was detected on 251 (59%) CT scans. Nineteen (4.5%) CT scans were consistent with recent excretion of a stone. In 112 (26.3%) CT scans, the cause for the patient's acute flank pain could not be explained. Forty-three (10.1%) alternative significant diagnoses that explain the patient's complaints were found. Nineteen (44%) were findings related to the urinary tract, and 24 (56%) were not related to the urinary tract. Ninety-seven (22.3%) additional findings not significant to the patient's current complaint were also reported. Even when narrowing the indications for the UESCT, about 10% of significant alternative findings to urinary stones were encountered. The variety of diagnoses found unexpectedly on the UESCT that alter a patient's management demonstrates the pivotal role of UESCT in triaging these patients rapidly towards optimal therapy. The UESCT can be used as a useful screening tool, sometimes revealing the exact pathology and sometimes directing the radiologist to the modality by which to continue.

Absence of neuropsychologic deficits in patients receiving long-term treatment with alprazolam-XR for panic disorder

Studies to date on the effects of benzodiazepines on neuropsychologic function have yielded conflicting data with respect to the type, severity, and duration of deficits that may be induced by these agents. As part of a placebo-controlled trial of alprazolam-XR (extended release) administered in combination with cognitive-behavioral therapy in patients with panic disorder, a battery of tests was used to measure neuropsychologic function. Thirty-eight outpatients were randomly assigned to receive either alprazolam-XR or placebo. Dosages were titrated up so that the alprazolam group (N = 18) received a mean dose of 4 mg/day (reduced in two patients because of sedative side effects). Neuropsychologic function after 6 weeks of therapy at the target dosage was compared with baseline assessments in each group. Both groups showed a statistically significant improvement from baseline to repeated assessments on measures of attention, executive functioning, psychomotor speed, and visual memory (p < 0.001); these gains were attributed to a practice effect. No significant changes were noted in measures of learning, verbal memory, or reaction time, and neither group showed any deterioration from baseline to retesting in any aspect of neuropsychologic function. These findings call into question the assumption that long-term benzodiazepine therapy produces significant neuropsychologic deficit in patients with diagnosed anxiety disorders.

Quality of well being in panic disorder: the assessment of psychiatric and general disability

BACKGROUND

Panic disorder is a common and debilitating anxiety disorder which significantly disrupts the lives of patients and their family members. Recent epidemiological studies and analyses of data from clinical trials suggest that patients with panic disorder suffer significant work and social dysfunction. The authors hypothesized that this dysfunction could be characterized using both a well-validated, generalized scale of functioning and a specifically designed scale for assessing function in psychiatric patients and that these findings would correlate with symptomatology.

METHOD

Fifty-six patients with panic disorder were characterized using the Sheehan Disability Scale, the Anxiety Sensitivity Index, and the Spielberger State Trait Anxiety Scale. Measures of health related quality of life from the Quality of Well Being Scale were compared with ratings for matched, historical, and population controls.

RESULTS

Patients with panic disorder lost 39 quality-adjusted days for each year that they lived with the disorder. This decrease in quality of life is similar to what is observed in patients with non-insulin dependent diabetes. Diminished quality of life is correlated with the number of panic attacks, state anxiety, and depressive symptoms. These patients also demonstrated significant dysfunction in Sheehan total disability and subscale scores, including work-related functioning.

CONCLUSIONS

This study demonstrates that the specific disabilities inherent in panic disorder can be linked to declines in quality of life as measured by the Quality of Well Being Scale and by measures of work-related dysfunction. Such an association between disease specific measures and a generalized measure of health related quality of life may offer clinicians a new tool to understand panic disorder and to conceptualize it within the broader context of disease and disability.

Distribution of cerebral flow using retrograde versus antegrade cerebral perfusion

BACKGROUND

This study compared flow to the brain with retrograde and antegrade cerebral perfusion during circulatory arrest.

METHODS

Twenty-four rabbits were injected with 5 mCi of technetium-99 macroaggregated albumin, a tracer trapped in the capillaries. Group I (n = 6) were maintained normothermic, and the tracer was injected into the ascending aorta. Group II (n = 6) were maintained normothermic, and underwent cannulation of the superior vena cava (SVC), exsanguination through the aorta, and injection of the tracer into the SVC, which was proximally occluded. In group III (n = 6), the animal was cooled to 25 degrees C. The animal was exsanguinated through the aorta and tracer was injected into the ascending aorta. In group IV (n = 6), animals were cooled to 25 degrees C. The animal was exsanguinated through the ascending aorta and tracer was injected into the SVC. Three animals (group V) were exsanguinated through the ascending aorta and a retrograde venogram of the SVC was performed. Scintigraphy of groups I to IV was carried out on a digital gamma camera. Brain trapping of tracer was graded from 0 to 5, with 0 being no tracer in the brain and 5 being dominant tracer trapping in the brain.

RESULTS

Tracer trapping in the brain showed group I, 3.67+/-0.82; group II, 0; group III, 4.67+/-0.41; group IV, 0.17+/-0.41 (p<0.0001). Retrograde venogram of the SVC showed flow into the cerebral veins.

CONCLUSIONS

Retrograde flow through the SVC reaches the cerebral venous system. Flow arriving in retrograde fashion does not go through the capillary system.

CT diagnosis of non-traumatic subarachnoid haemorrhage in patients with brain edema

The aim of the study is to prove, retrospectively, that it is unlikely that the computerized tomography (CT) diagnosis of subarachnoid haemorrhage (SH) accompanies the CT diagnosis of generalized brain edema. A total of 100 comatose patients underwent CT of the brain. Of this number, 42 underwent an enhanced CT scan. In 26 patients, lumbar puncture was also performed. A control group of ten patients diagnosed with headache and having a normal CT scan underwent NECT and ECT. Measurements of the white and gray matter density in Hounsfield units (HU) were performed in all 110 cases, including the controls. The brain tissue density and the difference between the densities of the white and gray matter were lower in the cases with brain edema than in the controls. The data values were statistically significant. Small cerebral ventricles, sulci and cisterns and small differences between white and gray matter measurements were observed in the CT scans of the brain edema cases. All 100 patients had CT diagnosis of brain edema and SH. There was no bloody or xanthochromic CSF in any of the 26 lumbar punctures performed. In the enhanced CT scans, there was poor or no filling of the lateral sinuses. The compression of the lateral sinuses by the edematous brain tissue most probably results in their stenosis or obstruction due to disturbed brain venous drainage which can mimic CT findings of SH.

A neuropsychological study of panic disorder: negative findings

BACKGROUND

Gray (1982) proposed that the septo-hippocampal system, which plays an important role in learning and memory, may partially mediate anxiety. Thus, patients with anxiety disorders may manifest neurocognitive performance deficits. We hypothesized that patients with panic disorder would demonstrate learning and memory deficits relative to normal comparison subjects.

METHOD

Comprehensive neuropsychological batteries were administered to 69 panic disorder subjects and 19 normal volunteers.

RESULTS

There were no significant group differences in any neuropsychological performance domain including learning, memory, attention, visuospatial functioning, and psychomotor speed. Multiple regression conducted to evaluate the contribution of clinical symptoms to neuropsychological impairment within the panic disorder sample revealed that anxiety severity did not affect neuropsychological test performance.

LIMITATIONS

Most patients had mild or moderate, rather than severe, panic disorder.

CONCLUSION

Neuropsychological dysfunction was not associated with panic disorder.

Unilateral medial dislocation of the temporomandibular joint

We present our experience of the rare condition of unilateral medial dislocation of the temporomandibular joint (TMJ) in 11 patients with head trauma who had received a direct lateral blow on the chin. The diagnosis was made by direct coronal CT of the TMJ performed from 6 h to 7 days following the injury. In 6 patients, subcondylar fracture of the ipsilateral mandibular ramus was also demonstrated. A second CT performed 11-16 months following the first one demonstrated pseudoarthrosis of the fractured ramus in these 6 patients. The second CT was identical to the first in the remaining 5 patients with pure dislocation of the condyle. All patients suffered from severe disability of the TMJ. The maximal vertical distance between the upper and lower incisors in patients with uncomplicated dislocation ranged between 8 and 12 mm. In cases with complicated medial condylar dislocation with fracture and pseudoarthrosis of the mandibular ramus, this distance ranged between 16 and 25 mm, probably because of additional movement in the area of the pseudoarthrosis. The maximal vertical distance between the incisors was compared with a control group of 20 normal adults who had values from 40 to 52 mm. Medial unilateral dislocation of the TMJ can appear in two forms: uncomplicated or complicated, with pseudoarthrosis of the ipsilateral mandibular ramus.

The effect of restricting the indications for lumbosacral spine radiography in patients with acute back symptoms

A prospective study was performed to evaluate the effect of using a special requisition form on the utilization of lumbosacral spine radiography for patients presenting in the emergency room with acute lower back complaints. Over a 1-year period, emergency room house officers were encouraged to complete a special form that listed only three acceptable indications for lumbosacral spine radiographs: history of trauma, evidence of focal neurologic abnormality, and "other." Neurologic abnormalities included hypesthesia, hyperesthesia or anesthesia of lumbar or sacral dermatomes, weakness or hyporeflexia of the lower extremities, and bladder or bowel incontinence. If the indication "other" was chosen, radiographs were done only if the form contained both a one- to two-sentence history and the signed approval of a supervising attending physician. The number and results of lumbosacral spine examinations were compared with those from the previous year, which served as a control. In the control year 1443 examinations were performed, and in the experimental year only 759 were done (a decrease of 47%). The percentage of patients with vertebral fractures increased from 5.1% to 5.8% in the experimental year if only the detection of new fractures was considered positive, and from 9.1% to 13.4% if the detection of fractures of all ages was regarded as significant. The use of the special requisition form appears to be a simple and effective means of reducing unnecessary lumbosacral radiography in the emergency room setting.

[Benign fibrolipomyomatous tumor of the perinephric capsule. A report on one case]

The authors describe a case of perinephric capsule tumor and emphasize the difficult in establishing diagnosis by radiological and especially angiographic investigations. The exact nature of the tumor can be determined only by histological examination. They review the published literature which demonstrates the rare nature of capsular fibrolipomyomata having clinical manifestations, the difficulty in making a differential diagnosis from hamartoma, and the possibility of malignant changes occurring in the tumor.

[Angiomyolipomas (hamartomas) of the kidney. Radiological study apropos of 2 cases. Review of the literature]

Two patients with renal angiomyolipomas studied angiographically are reported:--A case of tuberous sclerosis with bilateral multiple lesions, renal, hepatic and adrenal;--An isolated lesion whose preoperative diagnosis allowed the excision of the tumor. A review of the literature from 1965 to 1977 identified 242 cases of which 177 were isolated angiomyolipomas. There were 54 cases associated with tuberous sclerosis and one with von Hippel-Lindau disease. The radiologic and especially the angiographic signs are illustrated, the hemorrhagic risks are stressed, and the diagnostic features of fetal renal hamartoma are described.

[Voluminous hypernephroma of intermittent development. Diagnostic difficulties (author's transl)]

The authors report a case of cancer of the kidney of intermittent development for which nephro-urotomography was negative. They stress the interest of: --preliminary echotomography in patients with palpable masses in the left hypochondrium; --pharmaco-angiography for improved visualization of masses that are only weakly opaque; --a rapid infusion technique, proposed by various authors, which appears to be the most appropriate for the study of this type of mass which is mainly intermittent in its development.

A family study of gender identification

Self-reports about 70 masculine and feminine behaviors were collected from 177 undergraduates and their families. These self-report scores were correlated within family pairs to assess family resemblances in masculine or feminine preferences. The obtained family correlations were compared with those predicted by a simple additive-genetic theory, an X- linkage model, and a same-sex identification theory of gender-identity acquisition. The obtained pattern of correlations (mother x daughter=.26, sister x sister=.28, father x son=.33, and brother x brother=.23, all other family correlations near 0) strongly rejects the X-linkage and simple additive-genetic models of gender-identity acquisition. On the other hand, the obtained family correlations are quite consistent with a same-sex theory of gender identification, although, of course, within-family correlations only suggest causal relations, they do not prove them. Other factors such as social class could affect sex role identification as well.

[Contribution of arteriography to diagnosis of secondary arterio-digestive fistulas. Intestinal haemorrhage due to ilio-ileal fistula, a complication in vascular reconstruction (author's transl)]

The authors describe a case of secondary ilio-ileal fistula revealed by an intestinal haemorrhage which occurred ten years after vascular reconstruction. They stress the importance of arteriography which shows up the pseudo-aneurysm causing the fistularisation and vascular contrast material escaping into the digestive lumen. A complete review of the literature on arterio-colonic fistulas, and more particularly, ileo-ileal fistulas, shows that they usually express themselves clinically in the form of digestive haemorrhages occurring generally after vascular graft and after a variable lapse of time. The association of digestive haemorrhage and a previous vascular reconstruction should suggest the diagnosis of arterio-digestive fistula and should lead to early angiography to enable coherent surgical strategy to be put into operation.

Labyrinthine and vestibulospinal effects on spinal motoneurons in the pigeon

Experiments were performed on pigeons to investigate the effects of labyrinthine stimulation on motoneurons innervating neck and limb muscles. Intracellular recordings from the ventral horn of the spinal cord in the neck revealed that stimulation of the ipsilateral labyrinth with only a single shock evokes prominent EPSPs and/or IPSPs in the majority of neck motoneurons at thresholds less than 3--4 times the threshold for the labyrinth-evoked N1 potential recorded in the ipsilateral vestibular nuclei. In many neck motoneurons, the latencies of the PSPs were short enough so that no more than two synapses could be involved in their transmission. Recordings were also obtained from identified motoneurons which innervate muscles of the wing or the leg. Stimulation of the labyrinth, even with multiple stimuli, failed to elicit any observable PSPs in limb motoneurons. These data were consistent with other observations that in awake pigeons stimulation of the labyrinth with weak shocks evoked a pronounced turning of the head to the contralateral side, while even strong or multiple stimuli failed to produce any observable movement of wings or legs. Thus in the pigeon the association of the labyrinth with limb muscles is insignificant when compared to the association of the labyrinth with neck muscles. In addition, supraspinal descending fibers in the pigeon may make monosynaptic excitatory and inhibitory contact with spinal motoneurons.

[Radiology of tumours of the region of the ampulla of Vater (author's transl)]

On the basis of 18 personal cases, the authors discuss the different radiological appearances of tumours of the ampulla of Vater region. After a review of the histopathological aspects, they attempt to separate the respective indications for the various endoscopic and radiological studies possible, stressing the importance of duodenoscopy. They give an illustrated classification of the different appearances seen.