Client Applications and Server-Side Docker for Management of RNASeq and/or VariantSeq Workflows and Pipelines of the GPRO Suite.

The GPRO suite is an in-progress bioinformatic project for -omics data analysis. As part of the continued growth of this project, we introduce a client- and server-side solution for comparative transcriptomics and analysis of variants. The client-side consists of two Java applications called "" and "" to manage pipelines and workflows based on the most common command line interface tools for RNA-seq and Variant-seq analysis, respectively.

SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files.

Motivation: Sequence analyses oriented to investigate specific features, patterns and functions of protein and DNA/RNA sequences usually require tools based on graphic interfaces whose main characteristic is their intuitiveness and interactivity with the user's expertise, especially when curation or primer design tasks are required. However, interface-based tools usually pose certain computational limitations when managing large sequences or complex datasets, such as genome and transcriptome assemblies. Having these requirments in mind we have developed SeqEditor an interactive software tool for nucleotide and protein sequences' analysis.

Simulating Multilevel Dynamics of Antimicrobial Resistance in a Membrane Computing Model.

Membrane computing is a bio-inspired computing paradigm whose devices are the so-called membrane systems or P systems. The P system designed in this work reproduces complex biological landscapes in the computer world. It uses nested "membrane-surrounded entities" able to divide, propagate, and die; to be transferred into other membranes; to exchange informative material according to flexible rules; and to mutate and be selected by external agents.

Functional insights into the infective larval stage of Anisakis simplex s.s., Anisakis pegreffii and their hybrids based on gene expression patterns.

Background: Anisakis simplex sensu stricto and Anisakis pegreffii are sibling species of nematodes parasitic on marine mammals. Zoonotic human infection with third stage infective larvae causes anisakiasis, a debilitating and potentially fatal disease. These 2 species show evidence of hybridisation in geographical areas where they are sympatric.

A membrane computing simulator of trans-hierarchical antibiotic resistance evolution dynamics in nested ecological compartments (ARES).

Background: Antibiotic resistance is a major biomedical problem upon which public health systems demand solutions to construe the dynamics and epidemiological risk of resistant bacteria in anthropogenically-altered environments. The implementation of computable models with reciprocity within and between levels of biological organization (i.e.

GyDB mobilomics: LTR retroelements and integrase-related transposons of the pea aphid Acyrthosiphon pisum genome.

The Gypsy Database concerning Mobile Genetic Elements (release 2.0) is a wiki-style project devoted to the phylogenetic classification of LTR retroelements and their viral and host gene relatives characterized from distinct organisms. Furthermore, GyDB 2.

The Gypsy Database (GyDB) of mobile genetic elements: release 2.0.

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages.

Increases in soluble tumor necrosis factor receptors coincide with increases in interleukin-6 and proteinases after major surgery.

Background/aims: To determine whether increases in soluble tumor necrosis factor receptors (sTNFRs) are associated with the levels of cytokines and proteinases in patients undergoing major surgery.

Methodology: Eleven patients who underwent esophagectomy for squamous cell carcinoma of the thoracic esophagus were studied. The circulating blood concentrations of interleukin-6 (IL-6), IL-8, sTNF-R55, sTNF-R75, elastase/al-proteinase inhibitor complex (elastase) and matrix metalloproteinase-9 (MMP-9) were measured by ELISA or EIA before surgery, just after surgery, and on postoperative days (POD) 1 and 3.

Bioinformatic flowchart and database to investigate the origins and diversity of clan AA peptidases.

Background: Clan AA of aspartic peptidases relates the family of pepsin monomers evolutionarily with all dimeric peptidases encoded by eukaryotic LTR retroelements. Recent findings describing various pools of single-domain nonviral host peptidases, in prokaryotes and eukaryotes, indicate that the diversity of clan AA is larger than previously thought. The ensuing approach to investigate this enzyme group is by studying its phylogeny.

The Gypsy Database (GyDB) of mobile genetic elements.

In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) retroelements. Phylogenetic analyses based on the gag-pro-pol internal region commonly presented by these two groups strongly support a certain number of previously described Ty3/Gypsy lineages originally reported from reverse-transcriptase (RT) analyses.

Recurrence of colonic cancer twice at the site of stapled colorectal anastomosis.

Recurrence at the site of a stapled anastomosis is generally believed to result from the luminal implantation of viable cancer cells during stapling. We report a case in which colon cancer recurred twice at the site of a stapled anastomosis, despite povidone iodine (PVP-I) lavage consisting of an enema with 5% PVP-I solution before the operation and intraoperative lavage of the rectal remnant and the descending colon with a 10% PVP-I solution. Three months after sigmoidectomy to resect a carcinoma of the sigmoid colon, a circular anastomotic recurrence was found at the suture line after anastomosis with a stapler.

Increased serum vascular endothelial growth factor following major surgical injury.

Objectives: Vascular endothelial growth factor (VEGF) plays an important role in angiogenesis. We evaluated the changes in serum levels of VEGF following major surgical trauma and postoperative inflammatory complications.

Materials And Methods: The serum concentration of VEGF was measured with enzyme-linked immunosorbent assay in 41 patients with esophageal cancer who underwent right transthoracic esophagectomy with extensive lymphadenectomy and in 13 patients with gallstones who underwent less-invasive laparoscopic cholecystectomy for comparison.

Serum p53 antibody as a predictor of early recurrence in patients with postoperative esophageal squamous cell carcinoma.

It is reported that surveillance of serum p53 antibody (Ab) is a useful marker in detecting esophageal squamous cell carcinoma (ESCC). But there is little reported about prognostic significance of serum p53-Ab in postoperative patients with ESCC. The aim of this study is to evaluate the significance of preoperative serum p53-Ab as a marker of early recurrence after curative resection for ESCC.

Temporal resolution of the skin impedance measurement in frequency-domain method.

The temporal-resolution of the frequency-domain method for the identification of the impedance locus depends on the basis frequency used in the current waveform construction, i.e., the higher basis frequency provides the better temporal resolution.

Characteristics of human luminance discrimination and modeling a neural network based on the response properties of the visual cortex.

Reaction time (RT) and error rate that depend on stimulus duration were measured in a luminance-discrimination reaction time task. Two patches of light with different luminance were presented to participants for 'short' (150 ms) or 'long' (1 s) period on each trial. When the stimulus duration was 'short', the participants responded more rapidly with poorer discrimination performance than they did in the longer duration.

Joint angle control by FES using a feedback error learning controller.

The feedback error learning (FEL) scheme was studied for a functional electrical stimulation (FES) controller. This FEL controller was a hybrid regulator with a feedforward and a feedback controller. The feedforward controller learned the inverse dynamics of a controlled object from feedback controller outputs while control.

A case of cardiac tamponade following esophageal resection.

We report a rare case of cardiac tamponade after esophageal resection for esophageal cancer. A 69-year-old man underwent subtotal esophagectomy and reconstruction of the gastric tube with cervical anastomosis via the poststernal route and three-field lymphadectomy via a median sternotomy. On postoperative day 4, the patient developed dyspnea, chest oppression, and hemodynamic instability due to cardiac tamponade.

Sensory supported FES control in gait training of incomplete spinal cord injury persons.

Sensory supported electrical stimulation of the peroneal nerve during treadmill walking is proposed as a gait-training modality in incomplete spinal cord injury (SCI) patients. A multisensor device provides information on the tilt of the shank during gait. The information provided significantly improves the triggering instant of the electrical stimulation.

Sequential grouping of tone sequence as reflected by the mismatch negativity.

The human sequential grouping that organizes parts of tones into a group was examined by the mismatch negativity (MMN), a component of event-related potentials that reveals the sensory memory process. The sequential grouping is accomplished by the combinations of some factors, e.g.

Wearable data collection system for online gait stability analysis.

We had shown in our previous research that the stability assessment and control are essential for generation of faster and more energy efficient functional electrical stimulation (FES) and/or crutch-assisted gait. The objective of our recent research work has been to design a wearable and portable system for gait stability analysis with online capabilities that is also applicable to crutch-assisted gait modes. The developed wearable stability assessment system for as yet only biped gait consists of foot switches and goniometers attached to the leg joints.

Response to preoperative chemotherapy affects prognosis in esophageal cancer.

The effect of preoperative chemotherapy on prognosis is still controversial. We have investigated the relationship between responses to preoperative chemotherapy and prognosis after curative operations in patients with esophageal squamous cell carcinoma. Thirty-nine patients received preoperative chemotherapy with continuous infusion of 500 mg/m2 of 5-fluorouracil (5-FU) and intravenous injection of 20 mg/m2 of leucovorin every 12 hours for 5 days.

[Effect of nedaplatin, 5-FU, and leucovorin combined with radiation therapy in unresectable esophageal carcinoma].

A 51-year-old male was assessed as having esophageal squamous cell carcinoma with trachea invasion and cervical lymph node metastasis. After one course of chemotherapy using cisplatin (CDDP), 5-fluorouracil (5-FU) and Leucovorin (LV), the patient had progressive disease (PD) of the primary lesion and metastatic lymph nodes, and a side effect of severe nausea. One course of nedaplatin, 5-FU and LV combined with radiation was performed alternatively.

Infected hepatic cyst.

We describe an unusual case involving an infected hepatic cyst. An 88-year-old woman presented with acute onset of right upper quadrant abdominal pain, mild left lower abdominal pain, diarrhea, and fever. On admission, computed tomography revealed multiple hepatic cysts including an 8-cm cyst located in the left medial segment of the liver, which demonstrated a thickened wall enhanced with contrast media.

Serum levels of vascular endothelial growth factor, basic fibroblast growth factor and endostatin in human metastatic liver tumors.

Background/aims: Angiogenic factors are related to the malignant potential of tumors. This study aimed to investigate the relationship of serum angiogenic factors to liver metastasis.

Methodology: The serum levels of vascular endothelial growth factor, basic fibroblast growth factor and endostatin were measured using EIA in 25 patients with metastatic liver tumors and were compared with those of 12 cancer patients without metastasis and 15 controls.