PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (1597113)

Clipboard (0)
None

Related Articles

1.  Automatic interactive optimization for volumetric modulated arc therapy planning 
Background
Intensity modulated radiotherapy treatment planning for sites with many different organs-at-risk (OAR) is complex and labor-intensive, making it hard to obtain consistent plan quality. With the aim of addressing this, we developed a program (automatic interactive optimizer, AIO) designed to automate the manual interactive process for the Eclipse treatment planning system. We describe AIO and present initial evaluation data.
Methods
Our current institutional volumetric modulated arc therapy (RapidArc) planning approach for head and neck tumors places 3-4 adjustable OAR optimization objectives along the dose-volume histogram (DVH) curve that is displayed in the optimization window. AIO scans this window and uses color-coding to differentiate between the DVH-lines, allowing it to automatically adjust the location of the optimization objectives frequently and in a more consistent fashion. We compared RapidArc AIO plans (using 9 optimization objectives per OAR) with the clinical plans of 10 patients, and evaluated optimal AIO settings. AIO consistency was tested by replanning a single patient 5 times.
Results
Average V95&V107 of the boost planning target volume (PTV) and V95 of the elective PTV differed by ≤0.5%, while average elective PTV V107 improved by 1.5%. Averaged over all patients, AIO reduced mean doses to individual salivary structures by 0.9-1.6Gy and provided mean dose reductions of 5.6Gy and 3.9Gy to the composite swallowing structures and oral cavity, respectively. Re-running AIO five times, resulted in the aforementioned parameters differing by less than 3%.
Conclusions
Using the same planning strategy as manually optimized head and neck plans, AIO can automate the interactive Eclipse treatment planning process and deliver dosimetric improvements over existing clinical plans.
doi:10.1186/s13014-015-0388-6
PMCID: PMC4394415  PMID: 25885689
Automatic treatment planning; Volumetric modulated arc therapy; OAR sparing
2.  The Respiratory Arsenite Oxidase: Structure and the Role of Residues Surrounding the Rieske Cluster 
PLoS ONE  2013;8(8):e72535.
The arsenite oxidase (Aio) from the facultative autotrophic Alphaproteobacterium Rhizobium sp. NT-26 is a bioenergetic enzyme involved in the oxidation of arsenite to arsenate. The enzyme from the distantly related heterotroph, Alcaligenes faecalis, which is thought to oxidise arsenite for detoxification, consists of a large α subunit (AioA) with bis-molybdopterin guanine dinucleotide at its active site and a 3Fe-4S cluster, and a small β subunit (AioB) which contains a Rieske 2Fe-2S cluster. The successful heterologous expression of the NT-26 Aio in Escherichia coli has resulted in the solution of its crystal structure. The NT-26 Aio, a heterotetramer, shares high overall similarity to the heterodimeric arsenite oxidase from A. faecalis but there are striking differences in the structure surrounding the Rieske 2Fe-2S cluster which we demonstrate explains the difference in the observed redox potentials (+225 mV vs. +130/160 mV, respectively). A combination of site-directed mutagenesis and electron paramagnetic resonance was used to explore the differences observed in the structure and redox properties of the Rieske cluster. In the NT-26 AioB the substitution of a serine (S126 in NT-26) for a threonine as in the A. faecalis AioB explains a −20 mV decrease in redox potential. The disulphide bridge in the A. faecalis AioB which is conserved in other betaproteobacterial AioB subunits and the Rieske subunit of the cytochrome bc1 complex is absent in the NT-26 AioB subunit. The introduction of a disulphide bridge had no effect on Aio activity or protein stability but resulted in a decrease in the redox potential of the cluster. These results are in conflict with previous data on the betaproteobacterial AioB subunit and the Rieske of the bc1 complex where removal of the disulphide bridge had no effect on the redox potential of the former but a decrease in cluster stability was observed in the latter.
doi:10.1371/journal.pone.0072535
PMCID: PMC3758308  PMID: 24023621
3.  Development and validation of a new global well-being outcomes rating scale for integrative medicine research 
Background
Researchers are finding limitations of currently available disease-focused questionnaire tools for outcome studies in complementary and alternative medicine/integrative medicine (CAM/IM).
Methods
Three substudies investigated the new one-item visual analogue Arizona Integrative Outcomes Scale (AIOS), which assesses self-rated global sense of spiritual, social, mental, emotional, and physical well-being over the past 24 hours and the past month. The first study tested the scale's ability to discriminate unhealthy individuals (n = 50) from healthy individuals (n = 50) in a rehabilitation outpatient clinic sample. The second study examined the concurrent validity of the AIOS by comparing ratings of global well-being to degree of psychological distress as measured by the Brief Symptom Inventory (BSI) in undergraduate college students (N = 458). The third study evaluated the relationships between the AIOS and positively- and negatively-valenced tools (Positive and Negative Affect Scale and the Positive States of Mind Scale) in a different sample of undergraduate students (N = 62).
Results
Substudy (i) Rehabilitation patients scored significantly lower than the healthy controls on both forms of the AIOS and a current global health rating. The AIOS 24-hours correlated moderately and significantly with global health (patients r = 0.50; controls r = 0.45). AIOS 1-month correlations with global health were stronger within the controls (patients r = 0.36; controls r = 0.50). Controls (r = 0.64) had a higher correlation between the AIOS 24-hour and 1-month forms than did the patients (r = 0.33), which is consistent with the presumptive improvement in the patients' condition over the previous 30 days in rehabilitation. Substudy (ii) In undergraduate students, AIOS scores were inversely related to distress ratings, as measured by the global severity index on the BSI (rAIOS24h = -0.42, rAIOS1month = -0.40). Substudy (iii) AIOS scores were significantly correlated with positive affect (rAIOS24h = 0.56, rAIOS1month = 0.57) and positive states of mind (rAIOS24h = 0.42, rAIOS1month = 0.45), and inversely correlated with negative affect (rAIOS24h = -0.41, rAIOS1month = -0.59).
Conclusions
The AIOS is able to distinguish relatively sicker from relatively healthier individuals; and correlates in expected directions with a measure of distress and indicators of positive and negative affect and positive states of mind. The AIOS offers a tool for CAM/IM research that extends beyond a disease emphasis.
doi:10.1186/1472-6882-4-1
PMCID: PMC343287  PMID: 14725717
complementary and alternative medicine; well-being; global outcomes; questionnaire; validation; rehabilitation
4.  SMALL INTESTINAL OBSTRUCTION FROM PERITONEAL ADHESIONS IN CHILDREN SMALL INTESTINAL OBSTRUCTION FROM PERITONEAL ADHESIONS IN CHILDREN  
Abstract
Purpose: The purpose of this study was to assess the incidence of peritoneal adhesions leading to small intestinal obstruction after laparotomy in children in a tertiary paediatric surgical centre.
Methods: A retrospective review of 430 children aged <15 years who had trans-abdominal procedures over a 7 year period.
Results: Four hundred and fifty nine abdominal procedures were performed in 430 children during the study period. The follow up period ranged from 4 months – 7 years (Median 33 months). 22 (4.8%) had intra-operative confirmation of small intestinal obstruction. Their ages ranged from 21 days – 14 years (median 7 years). Postoperative adhesions due to laparotomy for typhoid perforation were the commonest, occurring in 10 (45%). Children undergoing emergency laparotomy were more likely to develop post operative small intestinal obstruction compared to elective laparotomy (p<0.025). Six (27.3%) children had bowel gangrene at laparotomy requiring bowel resection and anastomosis. Post-operative small intestinal obstruction developed in 6 (27.3%). One child died due to sepsis from intestinal gangrene. Conclusion: Small bowel obstruction due to adhesions requiring operative intervention in children in our setting is not un-common. Bowel gangrene is a common complication of postoperative small intestinal obstruction in children in our setting and should be suspected to avoid serious postoperative mortality and morbidity.
PMCID: PMC4170251  PMID: 25452942
Adhesions; Intestinal obstruction; children
5.  Neoadjuvant chemoradiotherapy for locally advanced rectal cancer: The debate continues 
Rectal carcinoma represents the 30% of all colorectal cancers, with about 40000 new cases/years. In the past two decades, the management of rectal cancer has made important progress, highlighting the main role of a multimodality strategy approach, combining surgery, radiation therapy and chemotherapy. Nowadays, surgery remains the primary treatment and neo-adjuvant chemoradiotherapy, based on fluoropyrimidine (5-FU) continuous infusion, is considered the standard in locally advanced rectal carcinoma. The aim is to reduce the incidence of local recurrence and to perform a conservative surgery. To improve these purposes different drugs combination have been tested in the neo-adjuvant setting. At American Society of Clinical Oncology 2014 an important abstract was presented focusing on the role of adding oxaliplatin to concomitant treatment, in patients with locally advanced rectal carcinoma. Rodel et al reported on the CAO/ARO/AIO-04 randomized phase III trial that compared standard treatment with 5-FU and radiation therapy, to oxaliplatin plus 5-FU in association with radiation therapy. The addition of oxaliplatin to the neo-adjuvant treatment has been shown to improve disease-free survival from 71.2% to 75.9% (P = 0.03). This editorial was planned to clarify the optimal treatment in patients with locally advanced rectal cancer, considering the results from CAO/ARO/AIO-04 study.
doi:10.4251/wjgo.v6.i12.438
PMCID: PMC4266815  PMID: 25516776
Chemoradiotherapy; Rectal cancer; Locally advanced disease; Neoadjuvant; Debate
6.  Evaluation of Innotrac Aio! Second-Generation Cardiac Troponin I Assay: The Main Characteristics for Routine Clinical Use 
The availability of a simple, sensitive, and rapid test using whole blood to facilitate processing and to reduce the turnaround time could improve the management of patients presenting with chest pain. The aim of this study was an evaluation of the Innotrac Aio! second-generation cardiac troponin I (cTnI) assay. The Innotrac Aio! second-generation cTnI assay was compared with the Abbott AxSYM first-generation cTnI, Beckman Access AccuTnI, and Innotrac Aio! first-generation cTnI assays. We studied serum samples from 15 patients with positive rheumatoid factor but with no indication of myocardial infarction (MI). Additionally, the stability of the sample with different matrices and the influence of hemodialysis on the cTnI concentration were evaluated. Within-assay CVs were 3.2%–10.9%, and between-assay precision ranged from 4.0% to 17.2% for cTnI. The functional sensitivity (CV = 20 %) and the concentration giving CV of 10% were approximated to be 0.02 and 0.04, respectively. The assay was found to be linear within the tested range of 0.063–111.6 μ g/L. The correlations between the second-generation Innotrac Aio!, Access, and AxSYM cTnI assays were good (r coefficients 0.947–0.966), but involved differences in the measured concentrations, and the biases were highest with cTnI at low concentrations. The second-generation Innotrac Aio! cTnI assay was found to be superior to the first-generation assay with regard to precision in the low concentration range. The stability of the cTnI level was best in the serum, lithium-heparin plasma, and lithium-heparin whole blood samples (n = 10 , decrease < 10 % in 24 hours at +20°C and at +4°C. There was no remarkable influence of hemodialysis on the cTnI release. False-positive cTnI values occurred in the presence of very high rheumatoid factor values, that is, over 3000 U/L. The 99th percentile of the apparently healthy reference group was ≤ 0.03   μ g/L. The results demonstrate the very good analytical performance of the second-generation Innotrac Aio! cTnI assay.
doi:10.1155/JAMMC/2006/39325
PMCID: PMC1903460  PMID: 17671616
7.  An ArsR/SmtB Family Member Is Involved in the Regulation by Arsenic of the Arsenite Oxidase Operon in Thiomonas arsenitoxydans 
Applied and Environmental Microbiology  2014;80(20):6413-6426.
The genetic organization of the aioBA operon, encoding the arsenite oxidase of the moderately acidophilic and facultative chemoautotrophic bacterium Thiomonas arsenitoxydans, is different from that of the aioBA operon in the other arsenite oxidizers, in that it encodes AioF, a metalloprotein belonging to the ArsR/SmtB family. AioF is stabilized by arsenite, arsenate, or antimonite but not molybdate. Arsenic is tightly attached to AioF, likely by cysteine residues. When loaded with arsenite or arsenate, AioF is able to bind specifically to the regulatory region of the aio operon at two distinct positions. In Thiomonas arsenitoxydans, the promoters of aioX and aioB are convergent, suggesting that transcriptional interference occurs. These results indicate that the regulation of the aioBA operon is more complex in Thiomonas arsenitoxydans than in the other aioBA containing arsenite oxidizers and that the arsenic binding protein AioF is involved in this regulation. On the basis of these data, a model to explain the tight control of aioBA expression by arsenic in Thiomonas arsenitoxydans is proposed.
doi:10.1128/AEM.01771-14
PMCID: PMC4178639  PMID: 25107975
8.  Profound systemic inflammatory response syndrome following non-emergent intestinal surgery in children☆ 
Journal of pediatric surgery  2013;48(9):1936-1940.
Purpose
Systemic inflammatory response syndrome (SIRS) is an uncommon but severe complication in surgical patients. While SIRS is well known, it is poorly described in the pediatric population. The goal of this study was to describe the incidence of profound SIRS following non-emergent intestinal surgery in children and to identify potential risk factors.
Methods
A retrospective review was conducted for patients 0–19 years of age following intestinal surgery and/or lysis of adhesions from 01/01/1999-02/28/2012. Children were excluded for preoperative instability or frank bowel perforation. Patients were then placed in a post-operative SIRS or non-SIRS group as defined by the 2005 International Pediatric Sepsis Consensus Conference Guidelines (6. B. Goldstein, B. Giroir, A. Randolph, and Sepsis International Consensus Conference on Pediatric, ‘International Pediatric Sepsis Consensus Conference: Definitions for Sepsis and Organ Dysfunction in Pediatrics’, Pediatr Crit Care Med, 6 (2005), 2–8.).
Results
SIRS was identified in 17 of the 381 patients. Logistic regression analysis was performed and showed heart disease, kidney disease, PN dependence, and intestinal obstruction to be predictive of post-operative SIRS.
Conclusion
This study represents one of the first reports to identify a previously poorly described process of significant SIRS after intestinal surgery in children. Both systemic organ failure and intestinal dysfunction are strong risk factors for post-operative SIRS in children. Potentially, these pre-existing conditions may lead to disruption of normal intestinal flora or barrier function, which in turn may predispose these children for dramatic SIRS after intestinal surgery. Understanding how these factors lead to SIRS will be critical to developing prevention strategies.
doi:10.1016/j.jpedsurg.2013.05.065
PMCID: PMC3787315  PMID: 24074671
Systemic inflammatory response syndrome; SIRS; Intestinal surgery; Parenteral nutrition
9.  Palliative first-line therapy with weekly high-dose 5-fluorouracil and sodium folinic acid as a 24-hour infusion (AIO regimen) combined with weekly irinotecan in patients with metastatic adenocarcinoma of the stomach or esophagogastric junction followed by secondary metastatic resection after downsizing 
Summary
Background
The aim of this retrospective study was to evaluate the efficacy and safety of weekly high-dose 5-fluorouracil (5-FU)/folinic acid (FA) as 24-h infusion (AIO regimen) plus irinotecan in patients with histologically proven metastatic gastroesophageal adenocarcinoma (UICC stage IV).
Material/Methods
From 08/1999 to 12/2008, 76 registered, previously untreated patients were evaluable. Treatment regimen: irinotecan (80 mg/m2) as 1-h infusion followed by 5-FU (2000 mg/m2) combined with FA (500 mg/m2) as 24-h infusion (d1, 8, 15, 22, 29, 36, qd 57).
Results
Median age: 59 years; male/female: 74%/26%; ECOG ≤1: 83%; response: CR: 1%, PR: 16%, SD: 61%, PD: 17%, not evaluable in terms of response: 5%; tumor control: 78%; median OS: 11.2 months; median time-to-progression: 5.3 months; 1-year survival rate: 49%; 2-year survival rate: 17%; no evidence of disease: 6.6%; higher grade toxicities (grade 3/4): anemia: 7%, leucopenia: 1%, ascites: 3%, nausea: 3%, infections: 12%, vomiting: 9%, GI bleeding of the primary tumor: 4%, diarrhea: 17%, thromboembolic events: 4%; secondary metastatic resection after downsizing: 16 patients (21%), R-classification of secondary resections: R0/R1/R2: 81%/6%/13%, median survival of the 16 patients with secondary resection: 23.7 months.
Conclusions
Combined 5-FU/FA as 24-h infusion plus irinotecan may be considered as an active palliative first-line treatment accompanied by tolerable toxicity; thus offering an alternative to cisplatin-based treatment regimens. Thanks to efficient interdisciplinary teamwork, secondary metastatic resections could be performed in 16 patients. In total, the patients who had undergone secondary resection had a median survival of 23.7 months, whereas the median survival of patients without secondary resection was 10.1 months (p≤0.001).
doi:10.12659/MSM.881764
PMCID: PMC3539586  PMID: 21525806
gastroesophageal cancer; palliative chemotherapy; irinotecan; 5-fluorouracil
10.  Single Stage Transanal Pull-Through for Hirschsprung’s Disease in Neonates: Our Early Experience 
Objective:
Hirschsprung’s disease is one of the common causes of intestinal obstruction in neonates. Transanal endorectal pull-through represents the latest development in the concept of the minimally invasive surgery for Hirschsprung’s disease. In this study, we present our early experience with single stage transanal pull through in neonates.
Design: Retrospective study of neonates with single stage transanal pull-through done for Hirschsprung’s disease in our institute from January 2011 to January 2013.
Material and Method:
Five newborn boys who presented with Hirschsprung’s disease were studied. The selection criteria included radiological transition zone at rectosigmoid or mid-sigmoid region, weight more than 2 kg, no evidence of enterocolitis or sepsis and no associated major anomaly. Single stage transanal endorectal pull-through was done in these patients. The follow-up period ranged from 6 months to 2 years.
Results:
Five patients with a mean age of 26.4 days (range 15-45 days) and a mean weight of 2.6 Kg (range 2.2 to 3.7 Kg) underwent transanal endorectal pull through. The mean operating time was 68 min (range 60 to 120 min). The average intra-operative blood loss was 20 ml (range – 10 to 30 ml) and the average length of bowel resected was 12.8 cm (range – 10 to 18 cm). Post-operatively patients passed first stool between 2nd and 3rd day. Oral feeding was resumed on 5th to 6th post-operative day. The average post-operative duration of stay in hospital was 10 days. None of the patients had post-operative bleeding, urethral injury, anastomotic leak or retraction of anastomotic site. Three patients developed perianal excoriation and one patient had post-operative enterocolitis. No mortality occurred in the series.
Conclusion:
Advancement in pediatric anaesthesia, availability of pediatric surgical expertise, improvement in pre-operative and post-operative management and nursing care has made single stage transanal pull-through in neonates a feasible option. The early results are comparable to single stage or multistage surgery in older children.
PMCID: PMC4420292  PMID: 26023459
Hirschsprung’s disease; Transanal pull through; Single stage surgery
11.  MicroRNA-21 Knockout Improve the Survival Rate in DSS Induced Fatal Colitis through Protecting against Inflammation and Tissue Injury 
PLoS ONE  2013;8(6):e66814.
Background
MicroRNA-21 (miR-21) is overexpressed in most inflammatory diseases, but its physiological role in gut inflammation and tissue injury is poorly understood. The goal of this work is to understand the role of miR-21 in colitis and damage progression of intestine in a genetically modified murine model.
Methods
Experimental colitis was induced in miR-21 KO and wild-type (WT) mice by 3.5% dextran sulphate sodium (DSS) administration for 7 days. Disease activity index(DAI), blood parameters, intestinal permeability, histopathologic injury, cytokine and chemokine production, and epithelial cells apoptosis were examined in colons of miR-21 KO and WT mice.
Results
miR-21 was overexpressed in intestine of inflammatory bowel diseases (IBD) and acute intestinal obstruction (AIO) patients when compared with normal intestinal tissues. Likewise, miR-21 was up-regulated in colon of IL-10 KO mice when compared with control mice. WT mice rapidly lost weight and were moribund 5 days after treatment with 3.5% DSS, while miR-21 KO mice survived for at least 6 days. Elevated leukocytes and more severe histopathology were observed in WT mice when compared with miR-21 KO mice. Elevated levels of TNF-α and macrophage inflammatory protein-2(MIP-2) in colon culture supernatants from WT mice exhibited significant higher than miR-21 KO mice. Furthermore, CD3 and CD68 positive cells, intestinal permeability and apoptosis of epithelial cells were significantly increased in WT mice when compared with miR-21 KO mice. Finally, we found that miR-21 regulated the intestinal barrier function through modulating the expression of RhoB and CDC42.
Conclusion
Our results suggest that miR-21 is overexpressed in intestinal inflammation and tissue injury, while knockout of miR-21 in mice improve the survival rate in DSS-induced fatal colitis through protecting against inflammation and tissue injury. Therefore, attenuated expression of miR-21 in gut may prevent the onset or progression of inflammatory bowel disease in patients.
doi:10.1371/journal.pone.0066814
PMCID: PMC3691313  PMID: 23826144
12.  Detectable signals of episodic risk effects on acute HIV transmission: Strategies for analyzing transmission systems using genetic data 
Epidemics  2012;5(1):44-55.
Episodic high-risk sexual behavior is common and can have a profound effect on HIV transmission. In a model of HIV transmission among men who have sex with men (MSM), changing the frequency, duration and contact rates of high-risk episodes can take endemic prevalence from zero to 50% and more than double transmissions during acute HIV infection (AHI). Undirected test and treat could be inefficient in the presence of strong episodic risk effects. Partner services approaches that use a variety of control options will be likely to have better effects under these conditions, but the question remains: What data will reveal if a population is experiencing episodic risk effects? HIV sequence data from Montreal reveals genetic clusters whose size distribution stabilizes over time and reflects the size distribution of acute infection outbreaks (AIOs). Surveillance provides complementary behavioral data. In order to use both types of data efficiently, it is essential to examine aspects of models that affect both the episodic risk effects and the shape of transmission trees. As a demonstration, we use a deterministic compartmental model of episodic risk to explore the determinants of the fraction of transmissions during acute HIV infection (AHI) at the endemic equilibrium. We use a corresponding individual-based model to observe AIO size distributions and patterns of transmission within AIO. Episodic risk parameters determining whether AHI transmission trees had longer chains, more clustered transmissions from single individuals, or different mixes of these were explored. Encouragingly for parameter estimation, AIO size distributions reflected the frequency of transmissions from acute infection across divergent parameter sets. Our results show that episodic risk dynamics influence both the size and duration of acute infection outbreaks, thus providing a possible link between genetic cluster size distributions and episodic risk dynamics.
doi:10.1016/j.epidem.2012.11.003
PMCID: PMC3748724  PMID: 23438430
Episodic risk; Individual-based model; Acute infection clusters; Identifiability
13.  Involvement of RpoN in Regulating Bacterial Arsenite Oxidation 
Applied and Environmental Microbiology  2012;78(16):5638-5645.
In this study with the model organism Agrobacterium tumefaciens, we used a combination of lacZ gene fusions, reverse transcriptase PCR (RT-PCR), and deletion and insertional inactivation mutations to show unambiguously that the alternative sigma factor RpoN participates in the regulation of AsIII oxidation. A deletion mutation that removed the RpoN binding site from the aioBA promoter and an aacC3 (gentamicin resistance) cassette insertional inactivation of the rpoN coding region eliminated aioBA expression and AsIII oxidation, although rpoN expression was not related to cell exposure to AsIII. Putative RpoN binding sites were identified throughout the genome and, as examples, included promoters for aioB, phoB1, pstS1, dctA, glnA, glnB, and flgB that were examined by using qualitative RT-PCR and lacZ reporter fusions to assess the relative contribution of RpoN to their transcription. The expressions of aioB and dctA in the wild-type strain were considerably enhanced in cells exposed to AsIII, and both genes were silent in the rpoN::aacC3 mutant regardless of AsIII. The expression level of glnA was not influenced by AsIII but was reduced (but not silent) in the rpoN::aacC3 mutant and further reduced in the mutant under N starvation conditions. The rpoN::aacC3 mutation had no obvious effect on the expression of glnB, pstS1, phoB1, or flgB. These experiments provide definitive evidence to document the requirement of RpoN for AsIII oxidation but also illustrate that the presence of a consensus RpoN binding site does not necessarily link the associated gene with regulation by AsIII or by this sigma factor.
doi:10.1128/AEM.00238-12
PMCID: PMC3406167  PMID: 22660703
14.  Measuring changes in self-concept: a qualitative evaluation of outcome questionnaires in people having acupuncture for their chronic health problems 
Background
Changes in self-concept are an important potential outcome for many interventions for people with long-term conditions. This study sought to identify and evaluate outcome questionnaires suitable for quantifying changes in self-concept in people with long-term conditions, in the context of treatment with acupuncture and Chinese medicine.
Methods
A literature search was followed by an evaluation of three questionnaires: The Wellbeing Questionnaire W-BQ12, the Patient Enablement Instrument (PEI), and the Arizona Integrative Outcome Scale (AIOS). A convenience sample of 23 people completed the questionnaires on two occasions and were interviewed about their experience and their questionnaire responses. All acupuncturists were interviewed.
Results
Changes in self-concept were common and emerged over time. The three questionnaires had different strengths and weaknesses in relation to measuring changes in self-concept. The generic AIOS had face validity and was sensitive to changes in self-concept over time, but it lacked specificity. The PEI was sensitive and specific in measuring these changes but had lower acceptability. The sensitivity of the W-BQ12 was affected by initial high scores (ceiling effect) and a shorter timescale but was acceptable and is suitable for repeated administration. The PEI and W-BQ12 questionnaires worked well in combination.
Conclusion
Changes in self-concept are important outcomes of complex interventions for people with long-term illness and their measurement requires carefully evaluated tools and long-term follow-up. The literature review and the analysis of the strengths and weaknesses of the questionnaires is a resource for other researchers. The W-BQ12 and the PEI both proved useful for this population and a larger quantitative study is planned.
doi:10.1186/1472-6882-6-7
PMCID: PMC1434784  PMID: 16539737
15.  A randomized, phase III trial of capecitabine plus bevacizumab (Cape-Bev) versus capecitabine plus irinotecan plus bevacizumab (CAPIRI-Bev) in first-line treatment of metastatic colorectal cancer: The AIO KRK 0110 Trial/ML22011 Trial 
BMC Cancer  2011;11:367.
Background
Several randomized trials have indicated that combination chemotherapy applied in metastatic colorectal cancer (mCRC) does not significantly improve overall survival when compared to the sequential use of cytotoxic agents (CAIRO, MRC Focus, FFCD 2000-05). The present study investigates the question whether this statement holds true also for bevacizumab-based first-line treatment including escalation- and de-escalation strategies.
Methods/Design
The AIO KRK 0110/ML22011 trial is a two-arm, multicenter, open-label randomized phase III trial comparing the efficacy and safety of capecitabine plus bevacizumab (Cape-Bev) versus capecitabine plus irinotecan plus bevacizumab (CAPIRI-Bev) in the first-line treatment of metastatic colorectal cancer. Patients with unresectable metastatic colorectal cancer, Eastern Cooperative Oncology Group (ECOG) performance status 0-1, will be assigned in a 1:1 ratio to receive either capecitabine 1250 mg/m2 bid for 14d (d1-14) plus bevacizumab 7.5 mg/kg (d1) q3w (Arm A) or capecitabine 800 mg/m2 BID for 14d (d1-14), irinotecan 200 mg/m2 (d1) and bevacizumab 7.5 mg/kg (d1) q3w (Arm B). Patients included into this trial are required to consent to the analysis of tumour tissue and blood for translational investigations. In Arm A, treatment escalation from Cape-Bev to CAPIRI-Bev is recommended in case of progressive disease (PD). In Arm B, de-escalation from CAPIRI-Bev to Cape-Bev is possible after 6 months of treatment or in case of irinotecan-associated toxicity. Re-escalation to CAPIRI-Bev after PD is possible. The primary endpoint is time to failure of strategy (TFS). Secondary endpoints are overall response rate (ORR), overall survival, progression-free survival, safety and quality of life.
Conclusion
The AIO KRK 0110 trial is designed for patients with disseminated, but asymptomatic mCRC who are not potential candidates for surgical resection of metastasis. Two bevacizumab-based strategies are compared: one starting as single-agent chemotherapy (Cape-Bev) allowing escalation to CAPIRI-Bev and another starting with combination chemotherapy (CAPIRI-Bev) and allowing de-escalation to Cape-Bev and subsequent re-escalation if necessary.
Trial Registration
ClinicalTrials.gov Identifier NCT01249638
EudraCT-No.: 2009-013099-38
doi:10.1186/1471-2407-11-367
PMCID: PMC3173448  PMID: 21861888
16.  Distribution of Microbial Arsenic Reduction, Oxidation and Extrusion Genes along a Wide Range of Environmental Arsenic Concentrations 
PLoS ONE  2013;8(10):e78890.
The presence of the arsenic oxidation, reduction, and extrusion genes arsC, arrA, aioA, and acr3 was explored in a range of natural environments in northern Chile, with arsenic concentrations spanning six orders of magnitude. A combination of primers from the literature and newly designed primers were used to explore the presence of the arsC gene, coding for the reduction of As (V) to As (III) in one of the most common detoxification mechanisms. Enterobacterial related arsC genes appeared only in the environments with the lowest As concentration, while Firmicutes-like genes were present throughout the range of As concentrations. The arrA gene, involved in anaerobic respiration using As (V) as electron acceptor, was found in all the systems studied. The As (III) oxidation gene aioA and the As (III) transport gene acr3 were tracked with two primer sets each and they were also found to be spread through the As concentration gradient. Sediment samples had a higher number of arsenic related genes than water samples. Considering the results of the bacterial community composition available for these samples, the higher microbial phylogenetic diversity of microbes inhabiting the sediments may explain the increased number of genetic resources found to cope with arsenic. Overall, the environmental distribution of arsenic related genes suggests that the occurrence of different ArsC families provides different degrees of protection against arsenic as previously described in laboratory strains, and that the glutaredoxin (Grx)-linked arsenate reductases related to Enterobacteria do not confer enough arsenic resistance to live above certain levels of As concentrations.
doi:10.1371/journal.pone.0078890
PMCID: PMC3815024  PMID: 24205341
17.  EGFR pathway biomarkers in erlotinib-treated patients with advanced pancreatic cancer: translational results from the randomised, crossover phase 3 trial AIO-PK0104 
British Journal of Cancer  2012;108(2):469-476.
Background:
We aimed to identify molecular epidermal growth factor receptor (EGFR) tissue biomarkers in pancreatic cancer (PC) patients treated with the anti-EGFR agent erlotinib within the phase 3 randomised AIO-PK0104 study.
Methods:
AIO-PK0104 was a multicenter trial comparing gemcitabine/erlotinib followed by capecitabine with capecitabine/erlotinib followed by gemcitabine in advanced PC; primary study end point was the time-to-treatment failure after first- and second-line therapy (TTF2). Translational analyses were performed for KRAS exon 2 mutations, EGFR expression, PTEN expression, the EGFR intron 1 and exon 13 R497K polymorphism (PM). Biomarker data were correlated with TTF, overall survival (OS) and skin rash.
Results:
Archival tumour tissue was available from 208 (74%) of the randomised patients. The KRAS mutations were found in 70% (121 out of 173) of patients and exclusively occurred in codon 12. The EGFR overexpression was detected in 89 out of 181 patients (49%) by immunohistochemistry (IHC), and 77 out of 166 patients (46%) had an EGFR gene amplification by fluorescence in-situ hybridisation (FISH); 30 out of 171 patients (18%) had a loss of PTEN expression, which was associated with an inferior TTF1 (first-line therapy; HR 0.61, P=0.02) and TTF2 (HR 0.66, P=0.04). The KRAS wild-type status was associated with improved OS (HR 1.68, P=0.005); no significant OS correlation was found for EGFR–IHC (HR 0.96), EGFR–FISH (HR 1.22), PTEN–IHC (HR 0.77), intron 1 (HR 0.91) or exon 13 R497K PM (HR 0.83). None of the six biomarkers correlated with the occurrence of skin rash.
Conclusion:
The KRAS wild-type was associated with an improved OS in erlotinib-treated PC patients in this phase 3 study; it remains to be defined whether this association is prognostic or predictive.
doi:10.1038/bjc.2012.495
PMCID: PMC3566829  PMID: 23169292
EGFR; erlotinib; capecitabine; gemcitabine; pancreatic cancer
18.  Conservative treatment of adhesive small bowel obstruction in children: a systematic review 
BMJ Open  2014;4(9):e005789.
Objective
To assess the effectiveness of conservative treatment for adhesive small bowel obstruction (ASBO) in children.
Design
Systematic review of studies involved children with ASBO who received initial conservative/non-operative treatment.
Setting
The search was performed in April 2013 using PubMed (see online supplementary file 1), current contents, and the Cochrane database.
Participants
Children with ASBO.
Interventions
Conservative treatment included nasogastric decompression, parenteral fluids and correction of electrolyte and fluid imbalance.
Primary outcome
Treatment success.
Secondary outcomes
Length of hospital stay and the time to first feeding after hospital admission.
Results
7 studies (six retrospective, one prospective), involving 8–109 patients (age: 1 month to 16 years) treated conservatively, were included in the review. The nature of conservative treatment was generally consistent between studies (nasogastric decompression, parenteral fluids and correction of electrolyte and fluid imbalance), although patients in one study also received Gastrografin. The rate of conservative treatment success ranged from 16% to 75% among the five studies, but one trial showed 0% successful rate. The hospital length of stay ranged from 3 to 6.5 days for conservative treatment (vs 10.2–13 days for operative treatment). The time to first feeding ranged from 31 to 84 h for conservative treatment.
Conclusions
In conclusion, in the majority of cases, conservative treatment is an effective means of managing ASBO in children.
doi:10.1136/bmjopen-2014-005789
PMCID: PMC4166136  PMID: 25223569
QUALITATIVE RESEARCH
19.  Bond Strength and Interfacial Morphology of Different Dentin Adhesives in Primary Teeth 
Objective:
To evaluate the interfacial morphology and the bond strength produced by the three-step, two-step and single-step bonding systems in primary teeth.
Materials and Methods:
Occlusal surfaces of 72 extracted human deciduous teeth were ground to expose the dentin. The teeth were divided into four groups: (a) Scotchbond Multipurpose (3M, ESPE), (b) Adh Se (Vivadent), (d) OptiBond All-in-One (Kerr) and (e)Futurabond NR (VOCO, Cuxhaven, Germany). The adhesives were applied to each group following the manufacturer’s instructions. Then, teeth from each group were divided into two groups: (A) For viewing interfacial morphology (32 teeth), with 8 teeth in each group, and (B) For measurement of bond strength (40 teeth), with 10 teeth in each group. All the samples were prepared for viewing under SEM. The statistical analysis was done using SPSS version 15.0 software.
Results:
Observational measurement of tag length in different adhesives revealed that Scotchbond had the most widely spread values with a range from 12.20 to 89.10μm while OptiBond AIO had the narrowest range (0 to 22.50). The bond strength of Scotchbond Multipurpose was significantly higher (7.4744±1.88763) (p<0.001) as compared to Futurabond NR (3.8070±1.61345), Adhe SE (4.4478 ± 1.3820) and OptiBond-all-in-one (4.4856±1.07925).
Conclusion:
The three-step bonding system showed better results as compared to simplified studied bonding systems
PMCID: PMC4043550  PMID: 24910694
Bond strength; SEM, Bonding systems; Primary teeth
20.  HIV-1 Drug Resistance Emergence among Breastfeeding Infants Born to HIV-Infected Mothers during a Single-Arm Trial of Triple-Antiretroviral Prophylaxis for Prevention of Mother-To-Child Transmission: A Secondary Analysis 
PLoS Medicine  2011;8(3):e1000430.
Analysis of a substudy of the Kisumu breastfeeding trial by Clement Zeh and colleagues reveals the emergence of HIV drug resistance in HIV-positive infants born to HIV-infected mothers treated with antiretroviral drugs.
Background
Nevirapine and lamivudine given to mothers are transmitted to infants via breastfeeding in quantities sufficient to have biologic effects on the virus; this may lead to an increased risk of a breastfed infant's development of resistance to maternal antiretrovirals. The Kisumu Breastfeeding Study (KiBS), a single-arm open-label prevention of mother-to-child HIV transmission (PMTCT) trial, assessed the safety and efficacy of zidovudine, lamivudine, and either nevirapine or nelfinavir given to HIV-infected women from 34 wk gestation through 6 mo of breastfeeding. Here, we present findings from a KiBS trial secondary analysis that evaluated the emergence of maternal ARV-associated resistance among 32 HIV-infected breastfed infants.
Methods and Findings
All infants in the cohort were tested for HIV infection using DNA PCR at multiple study visits during the 24 mo of the study, and plasma RNA viral load for all HIV-PCR–positive infants was evaluated retrospectively. Specimens from mothers and infants with viral load >1,000 copies/ml were tested for HIV drug resistance mutations. Overall, 32 infants were HIV infected by 24 mo of age, and of this group, 24 (75%) infants were HIV infected by 6 mo of age. Of the 24 infants infected by 6 mo, nine were born to mothers on a nelfinavir-based regimen, whereas the remaining 15 were born to mothers on a nevirapine-based regimen. All infants were also given single-dose nevirapine within 48 hours of birth. We detected genotypic resistance mutations in none of eight infants who were HIV-PCR positive by 2 wk of age (specimens from six infants were not amplifiable), for 30% (6/20) at 6 wk, 63% (14/22) positive at 14 wk, and 67% (16/24) at 6 mo post partum. Among the 16 infants with resistance mutations by 6 mo post partum, the common mutations were M184V and K103N, conferring resistance to lamivudine and nevirapine, respectively. Genotypic resistance was detected among 9/9 (100%) and 7/15 (47%) infected infants whose mothers were on nelfinavir and nevirapine, respectively. No mutations were detected among the eight infants infected after the breastfeeding period (age 6 mo).
Conclusions
Emergence of HIV drug resistance mutations in HIV-infected infants occurred between 2 wk and 6 mo post partum, most likely because of exposure to maternal ARV drugs through breast milk. Our findings may impact the choice of regimen for ARV treatment of HIV-infected breastfeeding mothers and their infected infants.
Trial Registration
ClinicalTrials.gov NCT00146380
Please see later in the article for the Editors' Summary
Editors' Summary
Background
Globally, more than 2 million children are infected with the human immunodeficiency virus (HIV) that causes acquired immunodeficiency syndrome (AIDS), and half a million children are newly infected every year. These infections are mainly the result of mother-to-child transmission (MTCT) of HIV during pregnancy, labor and delivery, or through breastfeeding. MTCT can be greatly reduced by treating HIV-positive mothers and their babies with antiretroviral drugs (ARVs). Without ARVs, up to half of babies born to HIV-positive mothers become infected with HIV. This rate of transmission falls to below 5% if a combination of three ARVs is given to the mother throughout pregnancy. Unfortunately, this triple-ARV therapy is too expensive for use in the resource-limited countries where most MTCT occurs. Instead, many such countries have introduced simpler, shorter ARV regimens such as a daily dose of zidovudine (a nucleoside reverse transcriptase inhibitor or NRTI) given to HIV-positive women during late pregnancy coupled with single-dose nevirapine (a non-nucleoside reverse transcriptase inhibitor or NNRTI) at the onset of labor, zidovudine and lamivudine (another NRTI) during labor and delivery, and single-dose nevirapine given to the baby at birth.
Why Was This Study Done?
More than 95% of HIV-exposed children are born in resource-limited settings where breastfeeding is the norm and is crucial for child survival even though it poses a risk of HIV transmission. Consequently, several recent studies have investigated whether MTCT can be further reduced by giving the mother ARVs while she is breastfeeding. In the Kisumu Breastfeeding Study (KiBS), for example, researchers assessed the effects of giving zidovudine, lamivudine, and either nevirapine or nelfinavir (a protease inhibitor) to HIV-infected women from 34 weeks of pregnancy through 6 months of breastfeeding. The results of KiBS indicate that this approach might be a safe, feasible way to reduce MTCT (see the accompanying paper by Thomas and colleagues). However, low amounts of nevirapine and lamivudine are transferred from mother to infant in breast milk and this exposure to ARVs could induce the development of resistance to ARVs among HIV-infected infants. In this KiBS substudy, the researchers investigate whether HIV drug resistance emerged in any of the HIV-positive infants in the parent study.
What Did the Researchers Do and Find?
In KiBS, 32 infants were HIV-positive at 24 months old; 24 were HIV-positive at 6 months old when their mothers stopped taking ARVs and when breastfeeding was supposed to stop. The researchers analyzed blood samples taken from these infants at various ages and from their mothers for the presence of HIV drug resistance mutations (DNA changes that make HIV resistant to killing by ARVs). They detected no resistance mutations in samples taken from 2-week old HIV-positive infants or from the infants who became infected after the age of 6 months. However, they found resistance mutations in a third and two-thirds of samples taken from 6-week and 6-month old HIV-positive infants, respectively. The commonest mutations conferred resistance to lamivudine and nevirapine. Moreover, resistance mutations were present in samples taken from all the HIV-positive infants whose mothers who had received nelfinavir but in only half those taken from infants whose mothers who had received nevirapine. Finally, most of the mothers of HIV-positive infants had no HIV drug resistance mutations, and only one mother-infant pair had an overlapping pattern of HIV drug resistance mutations.
What Do These Findings Mean?
These findings indicate that, in this KiBS substudy, the emergence of HIV drug resistance mutations in HIV-infected infants whose mothers were receiving ARVs occurred between 2 weeks and 6 months after birth. The pattern of mutations suggests that drug resistance most likely arose through exposure of the infants to low levels of ARVs in breast milk rather than through MTCT of drug-resistant virus. These findings need confirming but suggest that infants exposed to ARVs through breast milk—a situation that may become increasingly common given the reduction in MTCT seen in KiBS and other similar trials—should be carefully monitored for HIV infection. Providers should consider the mothers' regimen when choosing treatment for infants who are found to be HIV-infected despite maternal triple drug prophylaxis. Infants exposed to a maternal regimen with NNRTI drugs should receive first-line therapy with lopinavir/ritonavir, a protease inhibitor. The significance of the NRTI mutations such as M184V with regard to response to therapy needs further evaluation. The M184V mutation may result in hypersensitization to other NRTI drugs and delay or reverse zidovudine resistance. Given the limited availability of alternative drugs for infants in resource-limited settings, provision of the standard WHO-recommended first-line NRTI backbone, which includes 3TC, with enhanced monitoring of the infant to ensure virologic suppression, could be considered. Such an approach should reduce both illness and morbidity among infants who become HIV positive through breastfeeding.
Additional Information
Please access these Web sites via the online version of this summary at http://dx.doi.org/ 10.1371/journal.pmed.1000430.
The accompanying PLoS Medicine Research article by Thomas and colleagues describes the primary findings of the Kisumu Breastfeeding Study
Information is available from the US National Institute of Allergy and Infectious Diseases on HIV infection and AIDS
HIV InSite has comprehensive information on HIV/AIDS
Information is available from Avert, an international AIDS charity, on many aspects of HIV/AIDS, including information on children, HIV, and AIDS and on preventing mother-to-child transmission of HIV (in English and Spanish)
UNICEF also has information about children and HIV and AIDS (in several languages)
The World Health organization has information on mother-to-child transmission of HIV (in several languages), and guidance on the use of ARVs for preventing MTCT
doi:10.1371/journal.pmed.1000430
PMCID: PMC3066134  PMID: 21468304
21.  Developing and Implementing All-in-One Standard Paediatric Parenteral Nutrition 
Nutrients  2013;5(6):2006-2018.
Parenteral nutrition (PN) is a feeding mode suitable for children that do not achieve requirements via the enteral route. For this intervention to be successful, healthcare professionals require: knowledge on nutrient requirements; access to an aseptic compounding facility; and a system that ensures adequate and safe delivery of PN. Previously, it was thought that individualised PN was the “gold standard” for delivering nutrients to children; however, studies have highlighted concerns regarding inadequate delivery of nutrients, prescribing and compounding errors. We, therefore, set out to develop and implement all-in-one (AIO) paediatric PN solutions. Through a systematic approach, four AIO PN solutions were developed: birth–two months of age (Ped 1); two months–10 kg (Ped 2); 11–15 kg (Ped 3); and 16–30 kg (Ped 4). We implemented them with the help of a teaching pack, over a one month time period, and reviewed usage at six months. At that time, five children initially received standard PN without electrolyte changes; but after a few days, electrolytes needed amendments, and three required individualised PN. A change to AIO PN is feasible and safe; however, some may require electrolyte changes, and there will always be those that will require individualised PN.
doi:10.3390/nu5062006
PMCID: PMC3725489  PMID: 23739142
parenteral nutrition; all-in-one parenteral nutrition; paediatrics; development; implementation
22.  Etiology and Outcome of Acute Intestinal Obstruction: A Review of 367 Patients in Eastern India 
Background/Aim:
The etiology of acute intestinal obstruction, which is one of the commonest surgical emergencies, varies between countries and has also changed over the decades. We aimed to provide a complete epidemiological description of acute intestinal obstruction in a tertiary care hospital in Eastern India.
Materials and Methods:
This was a retrospective study of patients admitted in our unit with a diagnosis of acute intestinal obstruction between the years 2005 and 2008 at Medical College, Calcutta. The study comprised of 367 patients.
Results:
Acute intestinal obstruction was the diagnosis in 9.87% of all patients admitted with males (75.20%) grossly outnumbering females. The commonest age group affected was 20-60 years. In our patients, the main cause of obstruction was obstructed hernia followed by malignancy with adhesions coming third. Intestinal tuberculosis was an important cause for obstruction in our patients comprising 14.17% of patients. Conservative management was advocated in 79 patients while the rest underwent surgery. Postoperative complications occurred in 95 patients and of these, 38 patients had a single complication and the rest, more than 1. The main complications were wound infection, basal atelectasis, burst abdomen and prolonged ileus. The mortality rate was 7.35% (27 patients). The highest mortality occurred in those with intestinal tuberculosis.
Conclusion:
This study demonstrates that the pattern of intestinal obstruction differs from the Western world with obstructed hernias being the most important cause and also emphasizes the fact that intestinal tuberculosis assumes a prominent role. It also highlights the necessity of using universal precautions because of the ever increasing number of HIV patients in those with intestinal obstruction.
doi:10.4103/1319-3767.70617
PMCID: PMC2995099  PMID: 20871195
Etiology; outcome; intestinal obstruction
23.  Robot-assisted surgery in children: current status 
Journal of Robotic Surgery  2008;1(4):243-246.
The horizon of robotic paediatric surgery has grown in leaps and bounds with advances in technology. The aim of this study was to analyse the extent of robotic involvement in paediatric surgical practice. A systematic database search was performed. Data about children who had undergone robot-assisted procedures were reviewed retrospectively from all published reports up to October 2007. Success rates were defined in term of completion of the procedures, their complications, and the time taken. These results were further studied in comparison with the procedures performed by open and laparoscopic methods. A total of 31 studies were identified describing 566 patients. Of these, four studies were case control, comparing with either laparoscopic or open procedures, one study was a prospective trial, and the rest of the studies were either case reports or series. The most common robotic system used was the da Vinci (23 studies) followed by the Zeus (four studies). The mean age of the children was 8.3 years. The commonest operation was pyeloplasty (141 cases), followed by fundoplication (122 cases) and patent ductus arteriosus ligation (50 cases). The mean operation time for robot-assisted pyeloplasty was 221 min (open pyeloplasty 214 min). The mean operation times for fundoplication were robotic, 170 min, laparoscopic, 158 min, and open, 121 min. The mean operation times for patent ductus arteriosus ligation were 166 min (robotic) and 83 min (open). Overall conversion rate for all paediatric robotic procedures was 4.7% and complications ranged from 0 to 15%. For robotic fundoplications the conversion and complication rates were 0.8 and 3.3%, respectively. For robotic pyeloplasties the conversion and complication rates were 2.1 and 3.5%, respectively. Many other major operations were performed successfully. All studies recommended robotic procedure as safe and feasible. Currently, the most common robotic operations in practice are pyeloplasties and fundoplications. Most of the authors concluded that, despite taking more time, robotic surgery enables more refined hand–eye coordination, superior suturing skills, better dexterity, and precise dissection with minimal conversion and complication rates. The widespread acceptance of this technology largely depends on solving the issues: learning curve; suitable machine size for neonates and infants; ensuring efficacy and safety in all operations; and, most importantly, making this procedure cost effective, so as to cater for the needs of most, if not all, children.
doi:10.1007/s11701-007-0054-6
PMCID: PMC4247450  PMID: 25484971
Children; Robotic; Paediatric surgery
24.  Diversity of arsenite oxidizing bacterial communities in arsenic-rich deltaic aquifers in West Bengal, India 
High arsenic (As) concentration in groundwater has affected human health, particularly in South-East Asia putting millions of people at risk. Biogeochemical cycling of As carried out by different bacterial groups are suggested to control the As fluxes in aquifers. A functional diversity approach in link with As precipitation was adopted to study bacterial community structures and their variation within the As contaminated Bengal Delta Plain (BDP) aquifers of India. Groundwater samples collected from two shallow aquifers in Karimpur II (West Bengal, India), during years 2010 and 2011, were investigated to trace the effects immediately after monsoon period (precipitation) on community structure and diversity of bacterial assemblages with a focus on arsenite oxidizing bacterial phyla for two successive years. The study focused on amplification, clone library generation and sequencing of the arsenite oxidase large sub-unit gene aioA and 16S rRNA marker, with respect to changes in elemental concentrations. New set of primers were designed to amplify the aioA gene as a phylogenetic marker to study taxonomically diverse arsenite oxidizing bacterial groups in these aquifers. The overall narrow distribution of bacterial communities based on aioA and 16S rRNA sequences observed was due to poor nutrient status and anoxic conditions in these As contaminated aquifers. Proteobacteria was the dominant phylum detected, within which Acidovorax, Hydrogenophaga, Albidiferax, Bosea, and Polymorphum were the major arsenite oxidizing bacterial genera based on the number of clones sequenced. The structure of bacterial assemblages including those of arsenite oxidizing bacteria seems to have been affected by increase in major elemental concentrations (e.g., As, Fe, S, and Si) within two sampling sessions, which was supported by statistical analyses. One of the significant findings of this study is detection of novel lineages of 16S rRNA-like bacterial sequences indicating presence of indigenous bacterial communities BDP wells that can play important role in biogeochemical cycling of elements including As.
doi:10.3389/fmicb.2014.00602
PMCID: PMC4240177  PMID: 25484877
Arsenic; aquifer; arsenite oxidation; aioA gene; phylogeny
25.  VEGFR-3 and CXCR4 as predictive markers for treatment with fluorouracil, leucovorin plus either oxaliplatin or cisplatin in patients with advanced esophagogastric cancer: a comparative study of the Arbeitsgemeinschaft Internistische Onkologie (AIO) 
BMC Cancer  2014;14:476.
Background
Combination of fluoropyrimidines and a platinum derivative are currently standards for systemic chemotherapy in advanced adenocarcinoma of the stomach and gastroesophageal junction (GEJ). Nevertheless, individual likelihood for response to these therapeutic regimes remains uncertain. Even more, no predictive markers are available to determine which patients may benefit more from oxaliplatin versus cisplatin or vice versa. The new invasion and stem cell markers VEGFR-3 and CXCR4 have been linked prognostically with more aggressive esophagogastric cancer types. Thus, we aimed to assess correlations of VEGFR-3 and CXCR4 expression levels with clinical outcome in a randomized phase III study of patients with oxaliplatin/leucovorin/5-FU (FLO) versus cisplatin/leucovorin/5-FU (FLP).
Methods
The patients data examined in this study (n = 72) were from the collective of the FLO vs. FLP phase III AIO trial. Tumour tissues were stained via immunohistochemistry for VEGFR-3 and CXCR4 expression and results were evaluated by two independent, blinded investigators.
Outcome parameter: Survival analysis was calculated for patients receiving FLO vs. FLP in relation to VEGFR-3 and CXCR4 expression.
Results
54% and 36% of the examined tumour tissues showed strong positive expression of VEGFR-3 and CXCR4 respectively. No superiority of each regime was detected in terms of overall survival (OS) in the whole population. Patients with strong expression of CXCR4 on their tumour tissues profited more in terms of OS under the treatment of FLP (mOS: 28 vs 15 months, p = 0.05 respectively). Patients with negative VEGFR-3 and CXCR4 expression had a trend to live longer when FLO regime was applied (mOS: 22 vs. 9 months, p = 0.099 and 20 vs. 10 months, p = 0.073 respectively). In an exploratory analysis of patients older than 60 years at diagnosis, we observed a significant benefit in overall survival for VEGFR-3 and CXCR4-positive patients when treated with FLP (p = 0.002, p = 0.021 respectively).
Conclusions
CXCR4 positive patients profited in terms of OS from FLP, whereas FLO proved to be more effective in CXCR4 and VEGFR-3 negative patients. Our results suggest, despite the limited size of the study, a predictive value of these biomarkers concerning chemotherapy with FLP or FLO in advanced esophagogastric cancer.
doi:10.1186/1471-2407-14-476
PMCID: PMC4094395  PMID: 24981311
VEGFR-3; CXCR4; Advanced esophagogastric cancer; FLO; FLP; Biomarkers

Results 1-25 (1597113)