Construction a RBS library with different translational activity

The first step in programming and controlling cell behavior is to establish a library of well-defined components, a.k.a. "biobricks", that serve as the building blocks of artificial gene networks. The main challenge in genetic circuit design lies in selecting well-matched genetic components that when coupled, reliably and consistently act in a desired behavior. Although the parameter values are calculated by model equations, it is hard to select the biobricks that reliably implements a desired cellular function with quantitative values. To overcome this problem, the RBSs were designed to control the expression of downstream genes when necessary. This protocol will describe how to generate a RBS library with different ribosome binding affinities. The degenerated primers designed for PCR are used to generate mutations in RBS regions, while the mutated RBS activity are assayed using green fluorescence protein on a low copy number plasmid. In addition, a library of RBS's with different transcriptional strength can be built to fit the specific parameter values derived from model equations. Because the reporter protein activity has a positive correlation to RBS translational activity, we can design customizable RBS translational strengths for application

The Problem of Embeddedness: Knowledge Transfer, Situated Practice, and the Role of Information Systems

This study examines the problems associated with the use of knowledge management systems designed for transferring internal best practices. The field research explores the nature of engineers’ tacit knowledge in a dynamic context maintaining semiconductor fabrication machines. It illustrates the problem underlying the codification of tacit knowledge embedded in situated practice. Three problems of such embeddedness are explained with reference to task complexity, the collaboration mode, and industrial context. The study analyzes knowledge in actual practice in a high-velocity industry via a situated practice perspective, and suggests how it might affect the use of information systems

A systematic approach to detecting transcription factors in response to environmental stresses

Abstract Background Eukaryotic cells have developed mechanisms to respond to external environmental or physiological changes (stresses). In order to increase the activities of stress-protection functions in response to an environmental change, the internal cell mechanisms need to induce certain specific gene expression patterns and pathways by changing the expression levels of specific transcription factors (TFs). The conventional methods to find these specific TFs and their interactivities are slow and laborious. In this study, a novel efficient method is proposed to detect the TFs and their interactivities that regulate yeast genes that respond to any specific environment change. Results For each gene expressed in a specific environmental condition, a dynamic regulatory model is constructed in which the coefficients of the model represent the transcriptional activities and interactivities of the corresponding TFs. The proposed method requires only microarray data and information of all TFs that bind to the gene but it has superior resolution than the current methods. Our method not only can find stress-specific TFs but also can predict their regulatory strengths and interactivities. Moreover, TFs can be ranked, so that we can identify the major TFs to a stress. Similarly, it can rank the interactions between TFs and identify the major cooperative TF pairs. In addition, the cross-talks and interactivities among different stress-induced pathways are specified by the proposed scheme to gain much insight into protective mechanisms of yeast under different environmental stresses. Conclusion In this study, we find significant stress-specific and cell cycle-controlled TFs via constructing a transcriptional dynamic model to regulate the expression profiles of genes under different environmental conditions through microarray data. We have applied this TF activity and interactivity detection method to many stress conditions, including hyper- and hypo- osmotic shock, heat shock, hydrogen peroxide and cell cycle, because the available expression time profiles for these conditions are long enough. Especially, we find significant TFs and cooperative TFs responding to environmental changes. Our method may also be applicable to other stresses if the gene expression profiles have been examined for a sufficiently long time.</p

Oxaliplatin-induced acquired long QT syndrome with torsades de pointes and myocardial injury in a patient with dilated cardiomyopathy and rectal cancer

AbstractA 67-year-old woman presented with a history of dilated cardiomyopathy with congestive heart failure since 2003, who subsequently developed lower rectal cancer (adenocarcinoma) with liver, bone, and lymph node metastasis. Abdominoperineal resection and hepatectomy were performed. The patient received two rounds of intravenous chemotherapy, including 12 and six courses of FOLFOX4 (5-fluorouracil, leucovorin, and oxaliplatin; 85 mg/m2 per cycle). She underwent a third round of intravenous FOLFOX4 because of tumor progression. During the 21st course of FOLFOX4 regimen, the patient developed ST segment depression in lead II and prolongation of QT interval with polymorphic ventricular tachycardia, torsades de pointes right after the start of oxaliplatin infusion. Immediate defibrillation and cardiopulmonary resuscitation were administered, and the patient regained spontaneous circulation and consciousness. Twelve-lead electrocardiogram showed ST segment elevation in III, aVF, and ST segment depression in V4–6 after resuscitation. To our knowledge, prolongation of QT interval with torsades de pointes and coronary spasm with myocardial injury that were stabilized in one patient following oxaliplatin infusion has not been reported. We present a patient with these rare complications

Etiology and Treatment of Childhood Peptic Ulcer Disease in Taiwan: A Single Center 9-Year Experience

Background/PurposePeptic ulcer disease (PUD) in children is relatively rare as compared with adults. This study aimed to assess the etiology, clinical and histological characteristics, and treatment of PUD in children.MethodsAll children aged < 18 years with an endoscopic diagnosis of PUD were enrolled in a tertiary referral center. The demographic data, clinical, endoscopic, and histological findings were compared between patients with different causes of PUD.ResultsFrom 1234 endoscopic examinations, 67 (5.4%) children (median age, 11.4 years) with gastric ulcer (GU; n = 27) or duodenal ulcer (DU; n = 40) were included. Thirty-two (47.7%) of them had Helicobacter pylori infection and 11 (16.5%) had previous use of non-steroidal anti-inflammatory drugs (NSAIDs). Non-H. pylori, non-NSAID PUD was found in 24 (35.8%) patients. Children with H. pylori-related PUD had a significantly higher mean age, antral chronic inflammatory score, rate of familial PUD, and presence of DU and nodular gastritis than those with NSAID-related and non-H. pylori, non-NSAID PUD (p < 0.01). In contrast, children with NSAID-related PUD had a higher rate of upper gastrointestinal bleeding, associated with acute febrile disease, than those with H. pylori-related and non-H. pylori, non-NSAID PUD (p < 0.05). All but two patients with non-H. pylori, non-NSAID PUD were disease free after H. pylori eradication and proton pump inhibitor treatment for 1–2 months.ConclusionIn children, H. pylori-related PUD is associated with familial peptic ulcer and the presence of DU. However, short-term NSAID use is correlated highly with GU. The outcome of childhood PUD is good

Miniature RT–PCR system for diagnosis of RNA-based viruses

This paper presents an innovative portable chip-based RT–PCR system for amplification of specific nucleic acid and detection of RNA-based viruses. The miniature RT–PCR chip is fabricated using MEMS (Micro-electro-mechanical-system) techniques, and comprises a micro temperature control module and a PDMS (polydimethylsiloxane)-based microfluidic control module. The heating and sensing elements of temperature control module are both made of platinum and are located within the reaction chambers in order to generate a rapid and uniform thermal cycling. The microfluidic control module is capable of automating testing process with minimum human intervention. In this paper, the proposed miniature RT–PCR system is used to amplify and detect two RNA-based viruses, namely dengue virus type-2 and enterovirus 71 (EV 71). The experimental data confirm the ability of the system to perform a two-step RT–PCR process. The developed miniature system provides a crucial tool for the diagnosis of RNA-based viruses

Temperature Field Analysis for PZT Pyroelectric Cells for Thermal Energy Harvesting

This paper proposes the idea of etching PZT to improve the temperature variation rate of a thicker PZT sheet in order to enhance the energy conversion efficiency when used as pyroelectric cells. A partially covered electrode was proven to display a higher output response than a fully covered electrode did. A mesh top electrode monitored the temperature variation rate and the electrode area. The mesh electrode width affected the distribution of the temperature variation rate in a thinner pyroelectric material. However, a pyroelectric cell with a thicker pyroelectric material was beneficial in generating electricity pyroelectrically. The PZT sheet was further etched to produce deeper cavities and a smaller electrode width to induce lateral temperature gradients on the sidewalls of cavities under homogeneous heat irradiation, enhancing the temperature variation rate

Clinical application of tumor volume in advanced nasopharyngeal carcinoma to predict outcome

<p>Abstract</p> <p>Background</p> <p>Current staging systems have limited ability to adjust optimal therapy in advanced nasopharyngeal carcinoma (NPC). This study aimed to delineate the correlation between tumor volume, treatment outcome and chemotherapy cycles in advanced NPC.</p> <p>Methods</p> <p>A retrospective review of 110 patients with stage III-IV NPC was performed. All patients were treated first with neoadjuvant chemotherapy, then concurrent chemoradiation, and followed by adjuvant chemotherapy as being the definitive therapy. Gross tumor volume of primary tumor plus retropharyngeal nodes (GTVprn) was calculated to be an index of treatment outcome.</p> <p>Results</p> <p>GTVprn had a close relationship with survival and recurrence in advanced NPC. Large GTVprn (≧13 ml) was associated with a significantly poorer local control, lower distant metastasis-free rate, and poorer survival. In patients with GTVprn ≧ 13 ml, overall survival was better after ≧4 cycles of chemotherapy than after less than 4 cycles.</p> <p>Conclusions</p> <p>The incorporation of GTVprn can provide more information to adjust treatment strategy.</p

First- and Second-trimester Down Syndrome Screening: Current Strategies and Clinical Guidelines

SummaryDown syndrome (DS) is the most common human disease caused by a structural chromosome defect. The original screening test for DS was maternal age or a history of a previously affected infant. Maternal serum screening has been incorporated into routine prenatal checkup in Taiwan since 1994. We used free β-human chorionic gonadotropin and α-fetoprotein (double test) as the serum markers, and this was carried out between the 15 to 20th week of gestation. The overall detection rate was 56% and was compatible with studies of Caucasian populations. The impact of double tests in Taiwan has shown itself by a dramatic lowering of the rate of DS live birth from 0.63 before screening to 0.16 per 1,000 live births at present. However, because of its relatively low detection rate and poor cost-effectiveness, the double test is not justified as a routine screening tool currently. First-trimester combined test is now becoming more widely available and provides increased sensitivity when detecting DS; it has a detection rate of approximately 85% with a false-positive rate of 5%. Nuchal translucency measurement requires ongoing quality control and sufficient certificated obstetricians; therefore, first-trimester ultrasound is limited only in designated centers. The quadruple test, having comparable detection rate, should be considered for incorporation into second-trimester screening in Taiwan in the near future. Other screening approaches and combinations have also been utilized in the Western countries. In this review, we outline the various options with respect to DS screening and hope that this will provide practical information for physicians offering such screenings. [Taiwan J Obstet Cynecol 2008;47(2):157-1 62