The ParTriCluster Algorithm for Gene Expression Analysis

Analyzing gene expression patterns is becoming a highly relevant task in the Bioinformatics area. This analysis makes it possible to determine the behavior patterns of genes under various conditions, a fundamental information for treating diseases, among other applications. A recent advance in this area is the Tricluster algorithm, which is the first algorithm capable of determining 3D clusters (genes × samples × timestamps), that is, groups of genes that behave similarly across samples and timestamps. However, even though biological experiments collect an increasing amount of data to be analyzed and correlated, the triclustering problem remains a bottleneck due to its NP-Completeness, so its parallelization seems to be an essential step towards obtaining feasible solutions. In this work we propose and evaluate the implementation of a parallel version of the Tricluster algorithm using the filter-labeled-stream paradigm supported by the Anthill parallel programming environment. The results show that our parallelization scales well with the data size, being able to handle severe load imbalances that are inherent to the problem. Further more, the parallelization strategy is applicable to any depth-first searches.     

Fatal Campylobacter jejuni infection in a patient splenectomised for thalassaemia

A 35 year old man with a fatal Campylobacter jejuni infection is described. He had HbE/beta zero thalassaemia and had undergone splenectomy nine months previously for hypersplenism; he also had chronic hepatitis C infection. He presented with high grade fever but no gastrointestinal symptoms and rapidly progressed to septicaemic shock and hepatic encephalopathy despite treatment with penicillin, gentamicin, and, later, chloramphenicol and ceftazidime. Only one case of Campylobacter jejuni septicaemia occurring post-splenectomy has been reported previously, also in an iron overloaded thalassaemia patient. Unusual Gram negative bacilli must be covered by the chosen antibiotic regimen when splenectomised thalassaemic patients present with high grade fever.     

Analysis of Radio Resource Allocation in LTE Uplink

Long term evolution (LTE) uses orthogonal frequency division multiple access (OFDMA) and single carrier frequency division multiple access (SC-FDMA) as the downlink and uplink transmission schemes respectively. The Quality of Service (QoS) provision to users is one of the key objectives of the wireless network operators. This paper analyses an uplink LTE radio scheduler, called bandwidth and QoS aware (BQA) scheduler and evaluates its QoS performance. The BQA uplink scheduler is designed to provide efficient and fair allocation of the radio resources to users according to: the QoS of various traffic classes and the instantaneous channel conditions. The scheduler functionality is divided into time domain packet scheduling (TDPS) and frequency domain packet scheduling (FDPS). In this paper, an innovative feature, that is user QoS provisioning with dynamic QoS weights, is employed for the BQA scheduler along with multi-bearer users support. The QoS performance of the BQA scheduler is analyzed in several simulation scenarios using heterogeneous traffic environment. The results show that the BQA scheduler guarantees provision of QoS to users.     

A Multifunctional Nanoplatform for Imaging,Radiotherapy, and the Prediction of Therapeutic Response

Gold nanoparticles have garnered interest as both radiosensitzers and computed tomography (CT) contrast agents. However, the extremely high concentrations of gold required to generate CT contrast is far beyond that needed for meaningful radiosensitization, which limits their use as combined therapeutic–diagnostic (theranostic) agents. To establish a theranostic nanoplatform with well‐aligned radiotherapeutic and diagnostic properties for better integration into standard radiation therapy practice, a gold‐ and superparamagnetic iron oxide nanoparticle (SPION)‐loaded micelle (GSM) is developed. Intravenous injection of GSMs into tumor‐bearing mice led to selective tumoral accumulation, enabling magnetic resonance (MR) imaging of tumor margins. Subsequent irradiation leads to a 90‐day survival of 71% in GSM‐treated mice, compared with 25% for irradiation‐only mice. Furthermore, measurements of the GSM‐enhanced MR contrast are highly predictive of tumor response. Therefore, GSMs may not only guide and enhance the efficacy of radiation therapy, but may allow patients to be managed more effectively.     

Pharmacophore Synergism in Diverse Scaffold Clinches in Aurora Kinase B

Aurora kinase B (AKB) is a crucial signaling kinase with an important role in cell division. Therefore, inhibition of AKB is an attractive approach to the treatment of cancer. In the present work, extensive quantitative structure–activity relationships (QSAR) analysis has been performed using a set of 561 structurally diverse aurora kinase B inhibitors. The Organization for Economic Cooperation and Development (OECD) guidelines were used to develop a QSAR model that has high statistical performance (R²_tr = 0.815, Q²_LMO = 0.808, R²_ex = 0.814, CCC_ex = 0.899). The seven-variable-based newly developed QSAR model has an excellent balance of external predictive ability (Predictive QSAR) and mechanistic interpretation (Mechanistic QSAR). The QSAR analysis successfully identifies not only the visible pharmacophoric features but also the hidden features. The analysis indicates that the lipophilic and polar groups—especially the H-bond capable groups—must be present at a specific distance from each other. Moreover, the ring nitrogen and ring carbon atoms play important roles in determining the inhibitory activity for AKB. The analysis effectively captures reported as well as unreported pharmacophoric features. The results of the present analysis are also supported by the reported crystal structures of inhibitors bound to AKB.     

Closure versus non-closure of peritoneum at cesarean section--evaluation of pain. A randomized study

OBJECTIVE: To evaluate the effects of leaving the parietal peritoneum open at lower segment cesarean section (LSCS) measured by postoperative pain. DESIGN: A randomized, prospective and double-blind study. SETTING: Department of Obstetrics and Gynecology, Aarhus University Hospital, Denmark. POPULATION: Forty women referred for an elective cesarean section were assigned to one of two groups: peritoneum open (n=21) or peritoneum closed (n=19). METHODS: Pain was evaluated twice a day from the first to the fifth postoperative day by Visual Analog Scales. MAIN OUTCOME MEASURES: Postoperative pain. Other outcomes include usage of analgesics, bowel function, postoperative complications, and hospital stay. RESULTS: We found no overall difference in postoperative pain. A tendency to less pain was found in the non-closure group from the third postoperative day to the fifth postoperative day. No differences were found either in the incidence of postoperative complications, or the time to return of bowel function. Concerning opiate analgesics the non-closure group had a significantly higher use in the second postoperative 24-hour period, but in the remains of the registration period it was significantly lower. For oral analgesics no difference was found in the first 24-hour period, but in the remains of the period the non-closure group had a significantly lower use. CONCLUSIONS: The VAS-scales showed no difference in postoperative pain comparing closure to non-closure of the parietal peritoneum. However, the use of analgesics is lower in the non-closure group. We suggest leaving the parietal peritoneum open when performing LSCS.     

Allogeneic cell therapy for a murine mammary carcinoma

The effect of allogeneic cell therapy on tumor growth was studied in a murine model of mammary carcinoma (4T1) as an experimental model of solid tumors in humans. i.v. inoculation of 4T1 (H-2d) cells into syngeneic mice [BALB/c or (BALB/cXC57BL/6)F1] (F1) carrying the H-2d histocompatible antigens results in tumor colonies in the lungs that finally cause the death of all of the mice. Sublethally irradiated F1 mice were inoculated with 4T1 cells to simulate minimal residual disease and with immunocompetent splenocytes derived from naive donors of F1 (syngeneic), BALB/c (syngeneic to the tumor but semiallogeneic to the host), or C57BL/6 (allogeneic to the tumor and semiallogeneic to the host) mice. The survival of F1 tumor-bearing mice that were treated with allogeneic C57BL/6 splenocytes was significantly prolonged (P < 0.02) compared with hosts given F1 or BALB/c-derived splenocytes that are syngeneic to 4T1 tumor cells. Adoptive transfer of lung cells that were isolated from F1 primary mice inoculated with 4T1 cells and syngeneic BALB/c or F1 splenocytes led to local tumor growth and death in secondary recipients. In contrast, only 1 of 22 secondary recipients developed tumors when inoculated with lung cells derived from F1 mice given allogeneic C57BL/6 splenocytes. All of the 21 secondary hosts survived disease-free for a follow-up time of >200 days. These results indicate that immunocompetent cells allogeneic to the mammary carcinoma cells were able to inhibit tumor development in the primary hosts and to prevent tumor growth in the adoptive recipients, which suggests that allogeneic cell therapy may be an efficient antitumor tool to eradicate minimal residual disease in human solid tumors.     

Immunohistochemical diagnosis of typhus rickettsioses using an anti-lipopolysaccharide monoclonal antibody

A monoclonal antibody directed against an epitope on the lipopolysaccharide of typhus-group rickettsiae was developed for the purpose of detecting this heat-stable, proteinase-resistant antigen in formalin-fixed, paraffin-embedded tissues. Rickettsia prowazekii organisms were identified in endothelium and macrophages in sections of the brains of three Egyptian men who died of epidemic louse-borne typhus in Cairo during World War II and in the brain from a recent case of typhus fever acquired in Burundi. R. typhi organisms were identified in endothelial cells from a fatal case of murine typhus and in experimentally infected mice. This approach is applicable not only to the study of archival tissues and experimental animal models but also could be used to establish a timely diagnosis of typhus-group rickettsiosis by immunohistochemical examination of cutaneous biopsies of rash lesions during the acute stage of illness.     

Novel transition between different configurations of planartransmission lines

New designs of coplanar waveguide (CPW)-microstrip, CPW-stripline, conductor backed CPW (CBCPW)-microstrip, and CBCPW-stripline transitions are presented. Simulation using the high frequency structures simulator (HFSS) shows that the return loss of the CPW-microstrip transition is less than -25 dB up to 11 GHz. Similarly is the CPW-stripline transition. In the case of two back to back CBCPW-stripline transitions, the return loss is less than -22 dB up to 9 GHz. Experimentally, the S ₁₁ of two back to back CBCPW-microstrip transitions on an alumina substrate is less than -15 dB up to 25 GHz     

Computer-aided design of microstrip filters by iterated analysis

An iterative method for the design of microstrip low-pass elliptic function filters is described. The method, which is a direct extension of the work of H.J. Orchard (IEEE Trans. Circuit Syst., vol.CAS-32, no.11, p.1089-96, 1985), determines the microstrip line parameters that produce the same locations of the frequencies of transmission zeros and reflection zeros of an equivalent lumped-element prototype. Effects of the discontinuities at the junction are easily accounted for in the iteration. A design example is included, and an experimental seventh-order filter designed and constructed using the procedure gives measured results that agree closely with theory