Resilience, political ecology, and well-being: An interdisciplinary approach to analysing social-ecological change in coastal Bangladesh

The commodification of peasant livelihoods through export-oriented aquaculture has brought about significant social-ecological changes in low-lying coastal areas in many parts of Asia. A better understanding of the underlying drivers and distributional effects of these changes requires integration of social and ecological approaches that often have different epistemological origins. Resilience thinking has gained increased traction in social-ecological systems research because it provides a dynamic analysis of the cross-scalar interactions between multiple conditions and processes. However, the system-oriented perspective inherent in resilience thinking fails to acknowledge the heterogeneous values, interests, and power of social actors and their roles in navigating social-ecological change. Incorporation of political ecology and well-being perspectives can provide an actor-oriented analysis of the trade-offs associated with change and help to determine which state is desirable for whom. However, empirical demonstrations of such interdisciplinary approaches remain scarce. Here, we explore the combined application of resilience, political ecology, and well-being in investigating the root causes of social-ecological change and identifying the winners and losers of system transformation through empirical analysis of the differential changes in farming systems in two villages in coastal Bangladesh. Using the adaptive cycle as a structuring model, we examine the evolution of the shrimp aquaculture system over the past few decades, particularly looking at the power dynamics between households of different wealth classes. We found that although asymmetric land ownership and political ties enabled the wealthier households to reach their desired farming system in one village, social resilience achieved through memory, leadership, and crisis empowered poorer households to exercise their agency in another village. Material dimensions such as improved living standards, food security, and cash incomes were evidently important; however, freedom to pursue desired livelihood activities, better environmental quality, mental peace, and cultural identities had significant implications for relational and subjective well-being

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes

<p>Abstract</p> <p>Background</p> <p>We investigate if pooling BAC clones and sequencing the pools can provide for more accurate assembly of genome sequences than the "whole genome shotgun" (WGS) approach. Furthermore, we quantify this accuracy increase. We compare the pooled BAC and WGS approaches using <it>in silico </it>simulations. Standard measures of assembly quality focus on assembly size and fragmentation, which are desirable for large whole genome assemblies. We propose additional measures enabling easy and visual comparison of assembly quality, such as rearrangements and redundant sequence content, relative to the known target sequence.</p> <p>Results</p> <p>The best assembly quality scores were obtained using 454 coverage of 15× linear and 5× paired (3kb insert size) reads (15L-5P) on <it>Arabidopsis</it>. This regime gave similarly good results on four additional plant genomes of very different GC and repeat contents. BAC pooling improved assembly scores over WGS assembly, coverage and redundancy scores improving the most.</p> <p>Conclusions</p> <p>BAC pooling works better than WGS, however, both require a physical map to order the scaffolds. Pool sizes up to 12Mbp work well, suggesting this pooling density to be effective in medium-scale re-sequencing applications such as targeted sequencing of QTL intervals for candidate gene discovery. Assuming the current Roche/454 Titanium sequencing limitations, a 12 Mbp region could be re-sequenced with a full plate of linear reads and a half plate of paired-end reads, yielding 15L-5P coverage after read pre-processing. Our simulation suggests that massively over-sequencing may not improve accuracy. Our scoring measures can be used generally to evaluate and compare results of simulated genome assemblies.</p

A novel pathway producing dimethylsulphide in bacteria is widespread in soil environments

The volatile compound dimethylsulphide (DMS) is important in climate regulation, the sulphur cycle and signalling to higher organisms. Microbial catabolism of the marine osmolyte dimethylsulphoniopropionate (DMSP) is thought to be the major biological process generating DMS. Here we report the discovery and characterisation of the first gene for DMSP-independent DMS production in any bacterium. This gene, mddA, encodes a methyltransferase that methylates methanethiol (MeSH) and generates DMS. MddA functions in many taxonomically diverse bacteria including sediment-dwelling pseudomonads, nitrogen-fixing bradyrhizobia and cyanobacteria, and mycobacteria, including the pathogen Mycobacterium tuberculosis. The mddA gene is present in metagenomes from varied environments, being particularly abundant in soil environments, where it is predicted to occur in up to 76% of bacteria. This novel pathway may significantly contribute to global DMS emissions, especially in terrestrial environments, and could represent a shift from the notion that DMSP is the only significant precursor of DMS

Clinical examination, MRI and arthroscopy in meniscal and ligamentous knee Injuries – a prospective study

Data from 565 knee arthroscopies performed by two experienced knee surgeons between 2002 and 2005 for degenerative joint disorders, ligament injuries, loose body removals, lateral release of the patellar retinaculum, plica division, and adhesiolysis was prospectively collected. A subset of 109 patients from the above group who sequentially had clinical examination, MRI and arthroscopy for suspected meniscal and ligament injuries were considered for the present study and the data was reviewed. Patients with previous menisectomies, knee ligament repairs or reconstructions and knee arthroscopies were excluded from the study. Patients were categorised into three groups on objective clinical assessment: Those who were positive for either meniscal or cruciate ligament injury [group 1]; both meniscal and cruciate ligament injury [group 2] and those with highly suggestive symptoms and with negative clinical signs [group 3]. MRI was requested for confirmation of diagnosis and for additional information in all these patients. Two experienced radiologists reported MRI films. Clinical and MRI findings were compared with Arthroscopy as the gold standard. A thorough clinical examination performed by a skilled examiner more accurately correlated at Arthroscopy. MRI added no information in group 1 patients, valuable information in group 2 and was equivocal in group 3 patients. A negative MRI did not prevent an arthroscopy. In this study, specificity, positive and negative predictive values were more favourable for clinical examination though MRI was more sensitive for meniscal injuries. The use of MRI as a supplemental tool in the management of meniscal and ligament injuries should be highly individualised by an experienced surgeon

Medial patellofemoral ligament injury patterns and associated pathology in lateral patella dislocation: an MRI study

BACKGROUND: Lateral Patella dislocations are common injuries seen in the active and young adult populations. Our study focus was to evaluate medial patellofemoral ligament (MPFL) injury patterns and associated knee pathology using Magnetic Resonance Imaging studies. METHODS: MRI studies taken at one imaging site between January, 2007 to January, 2008 with the final diagnosis of patella dislocation were screened for this study. Of the 324 cases that were found, 195 patients with lateral patellar dislocation traumatic enough to cause bone bruises on the lateral femoral trochlea and the medial facet of the patella were selected for this study. The MRI images were reviewed by three independent observers for location and type of MPFL injury, osteochondral defects, loose bodies, MCL and meniscus tears. The data was analyzed as a single cohort and by gender. RESULTS: This study consisted of 127 males and 68 females; mean age of 23 yrs. Tear of the MPFL at the patellar attachment occurred in 93/195 knees (47%), at the femoral attachment in 50/195 knees (26%), and at both the femoral and patella attachment sites in 26/195 knees (13%). Attenuation of the MPFL without rupture occurred in 26/195 knees (13%). Associated findings included loose bodies in 23/195 (13%), meniscus tears 41/195 (21%), patella avulsion/fracture in 14/195 (7%), medial collateral ligament sprains/tears in 37/195 (19%) and osteochondral lesions in 96/195 knees (49%). Statistical analysis showed females had significantly more associated meniscus tears than the males (27% vs. 17%, p = 0.04). Although not statistically significant, osteochondral lesions were seen more in male patients with acute patella dislocation (52% vs. 42%, p = 0.08). CONCLUSION: Patients who present with lateral patella dislocation with the classic bone bruise pattern seen on MRI will likely rupture the MPFL at the patellar side. Females are more likely to have an associated meniscal tear than males; however, more males have underlying osteochondral lesions. Given the high percentage of associated pathology, we recommend a MRI of the knee in all patients who present with acute patella dislocation

Role of image-guided fine-needle aspiration biopsy in the management of patients with splenic metastasis

BACKGROUND: Splenic metastases are very rare and are mostly diagnosed at the terminal phase of the disease or at the time of autopsy. The cytohistological diagnosis, when done, is made prevalently by splenectomy. Reports on splenic percutaneous biopsies in the diagnosis of splenic metastasis are fragmentary and very poor. The aims of this study are to analyse retrospectively the accuracy, safety and the clinical impact of ultrasound (US)-guided fine-needle aspiration biopsy (UG-FNAB) in patients with suspected splenic metastasis. METHODS: A retrospective analysis of 1800 percutaneous abdominal biopsies performed at our institute during the period from 1993 to 2003 was done and 160 patients that underwent splenic biopsy were found. Among these 160 patients, 12 cases with the final diagnosis of solitary splenic metastases were encountered and they form the basis of this report. The biopsies were performed under US guidance using a 22-gauge Chiba needle. All the patients underwent laboratory tests, CT examination of the abdomen and chest, US examination of abdomen and pelvis. RESULTS: There were 5 women and 7 men, median age 65 years (range 48–80). Eight patients had a known primary cancer at the time of the diagnosis of splenic metastasis: 3 had breast adenocarcinoma, 2 colon adenocarcinoma, 2 melanoma and 1 lung adenocarcinoma. Four patients were undiagnosed at the time of the appearance of splenic metastasis and subsequent investigations showed adenocarcinoma of the lung in 2 patients and colon adenocarcinoma in the remaining 2. There was a complete correspondence between the US and Computed Tomography (CT) in detecting focal lesions of the spleen. The splenic biopsies allowed a cytological diagnosis of splenic metastasis in all the 12 patients and changed clinical management in all cases. Reviewing the 160 patients that underwent UG-FNAB of the spleen we found no complications related to the biopsies. CONCLUSION: These results indicate that UG-FNAB is a successful technique for diagnosis of splenic metastasis allowing an adequate treatment of the affected patients

Phase I Study of Safety and Immunogenicity of an Escherichia coli-Derived Recombinant Protective Antigen (rPA) Vaccine to Prevent Anthrax in Adults

The fatal disease caused by Bacillus anthracis is preventable with a prophylactic vaccine. The currently available anthrax vaccine requires a lengthy immunization schedule, and simpler and more immunogenic options for protection against anthrax are a priority for development. In this report we describe a phase I clinical trial testing the safety and immunogenicity of an anthrax vaccine using recombinant Escherichia coli-derived, B. anthracis protective antigen (rPA).A total of 73 healthy adults ages 18-40 were enrolled and 67 received 2 injections separated by 4 weeks of either buffered saline placebo, or rPA formulated with or without 704 µg/ml Alhydrogel® adjuvant in increasing doses (5, 25, 50, 100 µg) of rPA. Participants were followed for one year and safety and immunologic data were assessed. Tenderness and warmth were the most common post-injection site reactions. No serious adverse events related to the vaccine were observed. The most robust humoral immune responses were observed in subjects receiving 50 µg of rPA formulated with Alhydrogel® with a geometric mean concentration of anti-rPA IgG antibodies of 283 µg/ml and a toxin neutralizing geometric 50% reciprocal geometric mean titer of 1061. The highest lymphoproliferative peak cellular response (median Lymphocyte Stimulation Index of 29) was observed in the group receiving 25 µg Alhydrogel®-formulated rPA.The vaccine was safe, well tolerated and stimulated a robust humoral and cellular response after two doses.ClinicalTrials.gov NCT00057525

Syncope: experience at a tertiary care hospital in Karachi, Pakistan

Introduction:Our aim was to determine the characteristics of Patients presenting with syncope at a tertiary care hospital in Karachi, Pakistan.Methods: A review of medical records was conducted retrospectively at the Department of Medicine, Aga Khan University Hospital, Karachi. Patients aged 16 and above, admitted from January 2000 to December 2005 with the diagnosis of syncope made by the attending physician were included.Results:A total of 269 Patients were included (75% males, mean age: 57.4 years). Neurogenic (vasovagal) syncope was the most common cause (47%), followed by cardiogenic syncope (18%) and orthostatic syncope (9%). A total of 24% were discharged undiagnosed. Twenty Patients (7.4%) did not have any prodrome. Common prodromal symptoms included dizziness (61%), sweating (25%), palpitations (19%), nausea/vomiting (19%) and visual symptoms (17%). The distribution of symptoms according to cause of syncope revealed only breathlessness to be significantly associated with cardiogenic syncope (p = 0.002). Most Patients with cardiogenic syncope were aged above 40 (98%, p \u3c 0.001), had coronary artery disease (72%, p \u3c 0.001) and abnormal electrocardiogram at presentation (92%, p \u3c 0.001).Conclusion:Despite differences in burden of diseases, our findings were similar to those of published syncope literature. Further studies are needed to develop a protocol to expedite the evaluation and limit the work-up and admission in low-risk Patients

Comparative study of imaging at 3.0 T versus 1.5 T of the knee

The objectives of the study were to compare MR imaging at 1.5 and 3.0 T in the same patients concerning image quality and visualization of cartilage pathology and to assess diagnostic performance using arthroscopy as a standard of reference. Twenty-six patients were identified retrospectively as having comparative 1.5 and 3.0 T MR studies of the knee within an average of 102 days. Standard protocols included T1-weighted and fat-saturated intermediate-weighted fast spin-echo sequences in three planes; sequence parameters had been adjusted to account for differences in relaxation at 3.0 T. Arthroscopy was performed in 19 patients. Four radiologists reviewed each study independently, scored image quality, and analyzed pathological findings. Sensitivities, specificities, and accuracies in diagnosing cartilage lesions were calculated in the 19 patients with arthroscopy, and differences between 1.5 and 3.0 T exams were compared using paired Student’s t tests with a significance threshold of p &lt; 0.05. Each radiologist scored the 3.0 T studies higher than those obtained at 1.5 T in visualizing anatomical structures and abnormalities (p &lt; 0.05). Using arthroscopy as a standard of reference, diagnosis of cartilage abnormalities was improved at 3.0 T with higher sensitivity (75.7% versus 70.6%), accuracy (88.2% versus 86.4%), and correct grading of cartilage lesions (51.3% versus 42.9%). Diagnostic confidence scores were higher at 3.0 than 1.5 T (p &lt; 0.05) and signal-to-noise ratio at 3.0 T was approximately twofold higher than at 1.5 T. MRI at 3.0 T improved visualization of anatomical structures and improved diagnostic confidence compared to 1.5 T. This resulted in significantly better sensitivity and grading of cartilage lesions at the knee