String Matching and 1d Lattice Gases

We calculate the probability distributions for the number of occurrences $n$ of a given $l$ letter word in a random string of $k$ letters. Analytical expressions for the distribution are known for the asymptotic regimes (i) $k \gg r^l \gg 1$ (Gaussian) and $k,l \to \infty$ such that $k/r^l$ is finite (Compound Poisson). However, it is known that these distributions do now work well in the intermediate regime $k \gtrsim r^l \gtrsim 1$. We show that the problem of calculating the string matching probability can be cast into a determining the configurational partition function of a 1d lattice gas with interacting particles so that the matching probability becomes the grand-partition sum of the lattice gas, with the number of particles corresponding to the number of matches. We perform a virial expansion of the effective equation of state and obtain the probability distribution. Our result reproduces the behavior of the distribution in all regimes. We are also able to show analytically how the limiting distributions arise. Our analysis builds on the fact that the effective interactions between the particles consist of a relatively strong core of size $l$, the word length, followed by a weak, exponentially decaying tail. We find that the asymptotic regimes correspond to the case where the tail of the interactions can be neglected, while in the intermediate regime they need to be kept in the analysis. Our results are readily generalized to the case where the random strings are generated by more complicated stochastic processes such as a non-uniform letter probability distribution or Markov chains. We show that in these cases the tails of the effective interactions can be made even more dominant rendering thus the asymptotic approximations less accurate in such a regime.Comment: 44 pages and 8 figures. Major revision of previous version. The lattice gas analogy has been worked out in full, including virial expansion and equation of state. This constitutes the main part of the paper now. Connections with existing work is made and references should be up to date now. To be submitted for publicatio

Mutations in RAD21 disrupt regulation of apob in patients with chronic intestinal pseudo-obstruction

Background Aims Chronic intestinal pseudo-obstruction (CIPO) is characterized by severe intestinal dysmotility that mimics a mechanical subocclusion with no evidence of gut obstruction. We searched for genetic variants associated with CIPO to increase our understanding of its pathogenesis and to identify potential biomarkers. Methods We performed whole-exome sequencing of genomic DNA from patients with familial CIPO syndrome. Blood and lymphoblastoid cells were collected from patients and controls (individuals without CIPO); levels of messenger RNA (mRNA) and proteins were analyzed by quantitative reverse-transcription polymerase chain reaction, immunoblot, and mobility shift assays. Complementary DNAs were transfected into HEK293 cells. Expression of rad21 was suppressed in zebrafish embryos using a splice-blocking morpholino (rad21a). Gut tissues were collected and analyzed. Results We identified a homozygous mutation (p.622, encodes Ala>Thr) in RAD21 in patients from a consanguineous family with CIPO. Expression of RUNX1, a target of RAD21, was reduced in cells from patients with CIPO compared with controls. In zebrafish, suppression of rad21a reduced expression of runx1; this phenotype was corrected by injection of human RAD21 mRNA, but not with the mRNA from the mutated p.622 allele. rad21a Morpholino zebrafish had delayed intestinal transit and greatly reduced numbers of enteric neurons, similar to patients with CIPO. This defect was greater in zebrafish with suppressed expression of ret and rad21, indicating their interaction in the regulation of gut neurogenesis. The promoter region of APOB bound RAD21 but not RAD21 p.622 Ala>Thr; expression of wild-type RAD21 in HEK293 cells repressed expression of APOB, compared with control vector. The gut-specific isoform of APOB (APOB48) is overexpressed in sera from patients with CIPO who carry the RAD21 mutation. APOB48 also is overexpressed in sporadic CIPO in sera and gut biopsy specimens. Conclusions Some patients with CIPO carry mutations in RAD21 that disrupt the ability of its product to regulate genes such as RUNX1 and APOB. Reduced expression of rad21 in zebrafish, and dysregulation of these target genes, disrupts intestinal transit and the development of enteric neurons. © 2015 by the AGA Institute

EXTRACORPOREAL ELECTROMAGNETIC SHOCK-WAVE LITHOTRIPSY OF URETERAL STONES INSITU

Between June 1989 and June 1990, 277 patients with ureteric stones were treated by the Siemens Lithostar Plus in situ. In 113 patients, the stones were in the upper third of ureter, in 51 in the midureter, and in another 113 in the lower ureter. After a mean follow-up of 32 weeks, 79 % of the patients were stone free. While this figure was 85 % for upper ureteric stones, it was 71 % and 76 % for mid and lower ureteric stones, respectively. There was complete fragment clearance in 86 % of the stones with a diameter of 1 to 10 mm (n = 140), 78 % of those 11 to 20 mm (n = 118), and 32 % of those larger than 21 mm (n = 19). We believe that, despite the fact that some of the stones in the present series were impacted, such high success rates justify in situ extracorporeal lithotripsy as the initial treatment of ureteric stones

Vertebral fracture associated with shockwave lithotripsy in a patient with granulomatous spondylitis.

Extracorporeal shockwave lithotripsy (SWL) is an accepted treatment modality in the treatment of urinary stone disease. Many complications have been reported secondary to high-energy shockwaves, but the effects of SWL on the skeletal system have rarely been investigated. We represent the first case of a burst-type vertebral fracture after SWL in an elderly osteoporotic patient with granulomatous spondylitis

Prognostic factors for renal cell carcinoma

An elementary phenomenological consideration is presented regarding the longwavelength quantum dynamics in cuprate superconductors. The emphasis is on theinterplay of the charge- and spin order associated with the stripe phenomenonon the one hand, and superconductivity on the other hand

Effectiveness of extracorporeal shockwave lithotripsy in the management of stone-bearing horseshoe kidneys

Although extracorporeal shockwave lithotripsy (SWL) has dramatically changed the management of urinary tract stone disease, the anatomic abnormalities of horseshoe kidneys cause some difficulties in the use of SWL in this disorder. In this study, 18 patients with stone-bearing horseshoe kidneys were investigated retrospectively in order to determine the effectiveness of SWL, Patients received an average of 11,437 +/- 3062 shocks at an average of 18.8 kV with the Siemens Lithostar, Ten patients were treated in the supine position; stones could be localized in the prone position in eight. Catheterization with a double-J stent was the only adjunctive procedure; it was used in four patients prior to SWL. Adequate stone fragmentation (smaller than 5 mm) was achieved in 14 of the 18 patients (78%), Although 5 of them (28%) became stone free within 6 months after the treatment, residual fragments persisted in 9 patients (50%) during the mean follow-up of 55 months, Stones of 4 patients (22%) were not fragmented adequately, We concluded that although adequate fragmentation can be achieved in stone-bearing horseshoe kidneys, the anatomic abnormalities prevent fragment passage in a substantial number of patients