A rare case of hepatic duct injury from blunt abdominal trauma

Background: A 25 year-old male was brought to the emergency room following an apparent suicide attempt by jumping from the fourth floor. Case Report: Patient had a large abdominal laceration in the right upper quadrant (RUQ). CT scan showed a sub-scapular hematoma of the liver. Due to the repeated episodes of hypotension, a laporotomy was performed and the left hepatic artery was ligated while the ductal injury was managed with a Roux-en-Y left hepatic jejunostomy and stent. Bile leakage was resolved post-operatively by day 5 and the patient was discharged home on day 13 after clearance from psychiatry. Conclusions: While non-iatrogenic extrahepatic biliary trauma is rare, a high degree of suspicion is essential, especially in cases like the one discussed in this report. Diagnosis can be difficult in patients undergoing observation

A multiple testing procedure for multi-dimensional pairwise comparisons with application to gene expression studies

Figure S1. A graphical display of various hypotheses of interest. (TIFF 149 kb

Thermodynamics of quantum gases for the entire range of temperature

We have analytically explored thermodynamics of free Bose and Fermi gases for the entire range of temperature, and have extended the same for harmonically trapped cases. We have obtained approximate chemical potentials of the quantum gases in closed forms of temperature so that the thermodynamic properties of the quantum gases become plausible specially in the intermediate regime between the classical and quantum limits.Comment: 5 pages, 3 figures. Teaching Articl

Anisotropy in the helicity modulus of a quantum 3D XY-model: application to YBCO

We present a variational study of the helicity moduli of an anisotropic quantum three-dimensional (3D) XY-model of YBCO in superconducting state. It is found that both the ab-plane and the c-axis helicity moduli, which are proportional to the inverse square of the corresponding magnetic field penetration depth, vary with temperature T as T to the fourth power in the zero temperature limit. Moreover, the c-axis helicity modulus drops with temperature much faster than the ab-plane helicity modulus because of the weaker Josephson couplings along the c-axis compared to those along the ab-plane. These findings are in disagreement with the experiments on high quality samples of YBCO.Comment: 9 pages, 1 figur

Anisotropy in the helicity modulus of a 3D XY-model: application to YBCO

We present a Monte Carlo study of the helicity moduli of an anisotropic classical three-dimensional (3D) XY-model of YBCO in superconducting state. It is found that both the ab-plane and the c-axis helicity moduli, which are proportional to the inverse square of the corresponding magnetic field penetration depth, vary linearly with temperature at low temperatures. The result for the c-axis helicity modulus is in disagreement with the experiments on high quality samples of YBCO. Thus we conclude that purely classical phase fluctuations of the superconducting order parameter cannot account for the observed c-axis electrodynamics of YBCO.Comment: 7 pages, 1 figur

A Minimal Set of Tissue-Specific Hypomethylated CpGs Constitute Epigenetic Signatures of Developmental Programming

Background: Cell specific states of the chromatin are programmed during mammalian development. Dynamic DNA methylation across the developing embryo guides a program of repression, switching off genes in most cell types. Thus, the majority of the tissue specific differentially methylated sites (TS-DMS) must be un-methylated CpGs. Methodology and Principal Findings Comparison of expanded Methyl Sensitive Cut Counting data (eMSCC) among four tissues (liver, testes, brain and kidney) from three C57BL/6J mice, identified 138,052 differentially methylated sites of which 23,270 contain CpGs un-methylated in only one tissue (TS-DMS). Most of these CpGs were located in intergenic regions, outside of promoters, CpG islands or their shores, and up to 20% of them overlapped reported active enhancers. Indeed, tissue-specific enhancers were up to 30 fold enriched in TS-DMS. Testis showed the highest number of TS-DMS, but paradoxically their associated genes do not appear to be specific to the germ cell functions, but rather are involved in organism development. In the other tissues the differentially methylated genes are associated with tissue-specific physiological or anatomical functions. The identified sets of TS-DMS quantify epigenetic distances between tissues, generated during development. We applied this concept to measure the extent of reprogramming in the liver of mice exposed to in utero or early postnatal nutritional stress. Different protocols of food restriction reprogrammed the liver methylome in different but reproducible ways. Conclusion and Significance Thus, each identified set of differentially methylated sites constituted an epigenetic signature that traced the developmental programing or the early nutritional reprogramming of each exposed mouse. We propose that our approach has the potential to outline a number of disease-associated epigenetic states. The composition of differentially methylated CpGs may vary with each situation, behaving as a composite variable, which can be used as a pre-symptomatic marker for disease

Paradigm of tunable clustering using binarization of consensus partition matrices (Bi-CoPaM) for gene discovery

Copyright @ 2013 Abu-Jamous et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.Clustering analysis has a growing role in the study of co-expressed genes for gene discovery. Conventional binary and fuzzy clustering do not embrace the biological reality that some genes may be irrelevant for a problem and not be assigned to a cluster, while other genes may participate in several biological functions and should simultaneously belong to multiple clusters. Also, these algorithms cannot generate tight clusters that focus on their cores or wide clusters that overlap and contain all possibly relevant genes. In this paper, a new clustering paradigm is proposed. In this paradigm, all three eventualities of a gene being exclusively assigned to a single cluster, being assigned to multiple clusters, and being not assigned to any cluster are possible. These possibilities are realised through the primary novelty of the introduction of tunable binarization techniques. Results from multiple clustering experiments are aggregated to generate one fuzzy consensus partition matrix (CoPaM), which is then binarized to obtain the final binary partitions. This is referred to as Binarization of Consensus Partition Matrices (Bi-CoPaM). The method has been tested with a set of synthetic datasets and a set of five real yeast cell-cycle datasets. The results demonstrate its validity in generating relevant tight, wide, and complementary clusters that can meet requirements of different gene discovery studies.National Institute for Health Researc

Casimir force on interacting Bose-Einstein condensate

We have presented an analytic theory for the Casimir force on a Bose-Einstein condensate (BEC) which is confined between two parallel plates. We have considered Dirichlet boundary conditions for the condensate wave function as well as for the phonon field. We have shown that, the condensate wave function (which obeys the Gross-Pitaevskii equation) is responsible for the mean field part of Casimir force, which usually dominates over the quantum (fluctuations) part of the Casimir force.Comment: Accepted in Journal of Physics B: Atomic, Molecular and Optical Physic

CLME: An R Package for Linear Mixed Effects Models under Inequality Constraints

In many applications researchers are typically interested in testing for inequality constraints in the context of linear fixed effects and mixed effects models. Although there exists a large body of literature for performing statistical inference under inequality constraints, user friendly statistical software implementing such methods is lacking, especially in the context of linear fixed and mixed effects models. In this article we introduce CLME, a package in the R language that can be used for testing a broad collection of inequality constraints. It uses residual bootstrap based methodology which is reasonably robust to non-normality as well as heteroscedasticity. The package is illustrated using two data sets. The package also contains a graphical user interface built using the shiny package