Dynamics of suspended sediment transport and yield in a large agricultural catchment, southwest France

The dynamics of suspended sediment transport were monitored continuously in a large agricultural catchment in southwest France from January 2007 to March 2009. The objective of this paper is to analyse the temporal variability in suspended sediment transport and yield in that catchment. Analyses were also undertaken to assess the relationships between precipitation, discharge and suspended sediment transport, and to interpret sediment delivery processes using suspended sediment-discharge hysteresis patterns. During the study period, we analysed 17 fl ood events, with high resolution suspended sediment data derived from continuous turbidity and automatic sampling. The results revealed strong seasonal, annual and inter-annual variability in suspended sediment transport. Sediment was strongly transported during spring, when frequent fl ood events of high magnitude and intensity occurred. Annual sediment transport in 2007 yielded 16 614 tonnes, representing 15 t km−2 (85% of annual load transport during fl oods for 16% of annual duration), while the 2008 sediment yield was 77 960 tonnes, representing 70 t km−2 (95% of annual load transport during fl oods for 20% of annual duration). Analysis of the relationships between precipitation, discharge and suspended sediment transport showed that there were signifi cant correlations between total precipitation, peak discharge, total water yield, fl ood intensity and sediment variables during the fl ood events, but no relationship with antecedent conditions. Flood events were classifi ed in relation to suspended sediment concentration (SSC)–discharge hysteretic loops, complemented with temporal dynamics of SSC–discharge ranges during rising and falling fl ow. The hysteretic shapes obtained for all flood events refl ected the distribution of probable sediment sources throughout the catchment. Regarding the sediment transport during all fl ood events, clockwise hysteretic loops represented 68% from river deposited sediments and nearby source areas, anticlockwise 29% from distant source areas, and simultaneity of SSC and discharge 3%

Depressive Symptoms and Category Learning: A Preregistered Conceptual Replication Study

We present a fully preregistered, high-powered conceptual replication of Experiment 1 by Smith, Tracy, and Murray (1993). They observed a cognitive deficit in people with elevated depressive symptoms in a task requiring flexible analytic processing and deliberate hypothesis testing, but no deficit in a task assumed to require more automatic, holistic processing. Specifically, they found that individuals with depressive symptoms showed impaired performance on a criterial-attribute classification task, requiring flexible analysis of the attributes and deliberate hypothesis testing, but not on a family-resemblance classification task, assumed to rely on holistic processing. While deficits in tasks requiring flexible hypothesis testing are commonly observed in people diagnosed with a major depressive disorder, these deficits are much less commonly observed in people with merely elevated depressive symptoms, and therefore Smith et al.’s (1993) finding deserves further scrutiny. We observed no deficit in performance on the criterial-attribute task in people with above average depressive symptoms. Rather, we found a similar difference in performance on the criterial-attribute versus family-resemblance task between people with high and low depressive symptoms. The absence of a deficit in people with elevated depressive symptoms is consistent with previous findings focusing on different tasks

Effectiveness of antiretroviral therapy and development of drug resistance in HIV-1 infected patients in Mombasa, Kenya

Access to antiretroviral therapy (ART) is increasing in resource-limited settings (RLS) and can successfully reduce HIV-related morbidity and mortality. However, virologic failure and development of viral drug resistance can result in reduced treatment options and disease progression. Additionally, transmission of resistant virus, and particularly multi-drug resistance, could become a public health concern. This study evaluated treatment success and development of ART drug resistance after short-term treatment among patients attending the Comprehensive HIV Care Centre (CCC) of Coast Province General Hospital, Mombasa, Kenya. One hundred and fifty HIV-infected individuals receiving ART were consecutively recruited to participate in the study. After determination of plasma viral load, patients with detectable viral load levels were subjected to genotypic drug resistance testing. At the time of sampling, 132 of the 150 participants were on ART for more than 6 months (median 21 months, IQR = 12–26). An efficient viral load reduction to below 50 copies/ml was observed in 113 (85.6%) of them. Of the 19 patients with a detectable viral load, sequencing of the protease (PR) and reverse transcriptase (RT) gene was successful in 16. Eleven (11) of these 16 patients were infected with a subtype A1 virus. Major PR mutations were absent, but mutations associated with drug resistance in RT were detected in 14 of the 16 patients (87.5%). High-level resistance against at least 2 drugs of the ART regimen was observed in 9/14 (64.3%). The 3TC mutation M184V and the NNRTI mutation K103N were most frequent but also the multi-drug resistance Q151M and the broad NRTI cross-resistance K65R were observed. The results of this study revealed a high rate of treatment success after short term ART in patients treated at a public provincial hospital in a RLS. Nevertheless, the observed high risk of accumulation of resistance mutations among patients failing treatment and the selection of multi-drug resistance mutations in some, remains of great concern for future treatment options and potential transmission to partners

[37th] ANNUAL REPORT OF THE FACULTY OF THE COLLEGE OF THE CITY OF NEW YORK TO THE BOARD OF TRUSTEES, FOR THE YEAR ENDING JUNE 21, 1888.

Report fourteen from the sixth bound volume of ten which documents in part the first nineteen years of The Free Academy, the predecessor of the educational institution, City College of New York. COLLEGE OF THE CITY OF NEW YORK. 1856-96. REPORTS OF THE FACULTY II, includes 21 individual reports. At a time when municipal education constituted primary schooling, citizens united in response to arguments presented by a merchant and Board of Education President, Townsend Harris, for the necessity of an institution that would provide advanced training for future generations of citizens to fully engage in the professions advantageous to an expanding urban center. Includes preliminary reports that commented on the application of resources for the creation of the institution and the annual reports of the faculty, demonstrating accountability to the Board of Education with regard to the operation of the facility., [37th] ANNUAL REPORT OF THE FACULTY OF THE COLLEGE OF THE CITY OF NEW YORK TO THE BOARD OF TRUSTEES, FOR THE YEAR ENDING JUNE 21, 1888. [6 pages ([325]-330), 1888], RG

A Synthetic HIV-1 Subtype C Backbone Generates Comparable PR and RT Resistance Profiles to a Subtype B Backbone in a Recombinant Virus Assay

In order to determine phenotypic protease and reverse transcriptase inhibitor-associated resistance in HIV subtype C virus, we have synthetically constructed an HIV-1 subtype C (HIV-1-C) viral backbone for use in a recombinant virus assay. The in silico designed viral genome was divided into 4 fragments, which were chemically synthesized and joined together by conventional subcloning. Subsequently, gag-protease-reverse-transcriptase (GPRT) fragments from 8 HIV-1 subtype C-infected patient samples were RT-PCR-amplified and cloned into the HIV-1-C backbone (deleted for GPRT) using In-Fusion reagents. Recombinant viruses (1 to 5 per patient sample) were produced in MT4-eGFP cells where cyto-pathogenic effect (CPE), p24 and Viral Load (VL) were monitored. The resulting HIV-1-C recombinant virus stocks (RVS) were added to MT4-eGFP cells in the presence of serial dilutions of antiretroviral drugs (PI, NNRTI, NRTI) to determine the fold-change in IC50 compared to the IC50 of wild-type HIV-1 virus. Additionally, viral RNA was extracted from the HIV-1-C RVS and the amplified GPRT products were used to generate recombinant virus in a subtype B backbone. Phenotypic resistance profiles in a subtype B and subtype C backbone were compared. The following observations were made: i) functional, infectious HIV-1 subtype C viruses were generated, confirmed by VL and p24 measurements; ii) their rate of infection was slower than viruses generated in the subtype B backbone; iii) they did not produce clear CPE in MT4 cells; and iv) drug resistance profiles generated in both backbones were very similar, including re-sensitizing effects like M184V on AZT

HIV-1 Phenotypic Reverse Transcriptase Inhibitor Drug Resistance Test Interpretation Is Not Dependent on the Subtype of the Virus Backbone

To date, the majority of HIV-1 phenotypic resistance testing has been performed with subtype B virus backbones (e.g. HXB2). However, the relevance of using this backbone to determine resistance in non-subtype B HIV-1 viruses still needs to be assessed. From 114 HIV-1 subtype C clinical samples (36 ARV-naïve, 78 ARV-exposed), pol amplicons were produced and analyzed for phenotypic resistance using both a subtype B- and C-backbone in which the pol fragment was deleted. Phenotypic resistance was assessed in resulting recombinant virus stocks (RVS) for a series of antiretroviral drugs (ARV's) and expressed as fold change (FC), yielding 1660 FC comparisons. These Antivirogram® derived FC values were categorized as having resistant or sensitive susceptibility based on biological cut-off values (BCOs). The concordance between resistance calls obtained for the same clinical sample but derived from two different backbones (i.e. B and C) accounted for 86.1% (1429/1660) of the FC comparisons. However, when taking the assay variability into account, 95.8% (1590/1660) of the phenotypic data could be considered as being concordant with respect to their resistance call. No difference in the capacity to detect resistance associated with M184V, K103N and V106M mutations was noted between the two backbones. The following was concluded: (i) A high level of concordance was shown between the two backbone phenotypic resistance profiles; (ii) Assay variability is largely responsible for discordant results (i.e. for FC values close to BCO); (iii) Confidence intervals should be given around the BCO's, when assessing resistance in HIV-1 subtype C; (iv) No systematic resistance under- or overcalling of subtype C amplicons in the B-backbone was observed; (v) Virus backbone subtype sequence variability outside the pol region does not contribute to phenotypic FC values. In conclusion the HXB2 virus backbone remains an acceptable vector for phenotyping HIV-1 subtype C pol amplicons

Seasonal surface drainage of sloping farmland : a review of its hydrogeomorphic impacts

The combination of runoff-generating areas (saturated soils) and overland flow concentration in features such as drainage ditches makes sloping farmland vulnerable to soil erosion. The establishment of drainage ditches aims at draining the excess of water from the farmland, particularly in areas where soils are saturated in the rainy season. The hydrogeomorphic impacts on the farmland itself and on downstream areas need however also to be studied. Off site, downstream problems comprise higher peak discharges, leading to gully initiation, an increase in sediment load, and flooding problems. On-site problems such as the development of the drainage ditches into (ephemeral) gullies are less documented, although they may be important, as illustrated in the Lake Tana Basin (Ethiopia). The similarities and interactions between ephemeral gully channels and drainage ditches have to be considered to better understand all effects of drainage. Drainage ditches are a potential source of conflict between farmers with different interests and power, as well as between upstream and downstream users. A case study on drainage ditches on sloping farmlands in the Lake Tana Basin showed that nine out of ten catchments had drainage densities by ditches ranging from 53 to 510 m ha−1. Drainage ditches were constructed with an average top width of 27 (±9) cm. A significant correlation was found between stone bund density (physical conservation structures) and ditch drainage density (R = −0·72), in line with the Ethiopian government's ban on drainage ditches in farmlands where stone bunds have been constructed

A comparative analysis of HIV drug resistance interpretation based on short reverse transcriptase sequences versus full sequences

<p>Abstract</p> <p>Background</p> <p>As second-line antiretroviral treatment (ART) becomes more accessible in resource-limited settings (RLS), the need for more affordable monitoring tools such as point-of-care viral load assays and simplified genotypic HIV drug resistance (HIVDR) tests increases substantially. The prohibitive expenses of genotypic HIVDR assays could partly be addressed by focusing on a smaller region of the HIV reverse transcriptase gene (RT) that encompasses the majority of HIVDR mutations for people on ART in RLS. In this study, an <it>in silico </it>analysis of 125,329 RT sequences was performed to investigate the effect of submitting short RT sequences (codon 41 to 238) to the commonly used virco^®TYPE and Stanford genotype interpretation tools.</p> <p>Results</p> <p>Pair-wise comparisons between full-length and short RT sequences were performed. Additionally, a non-inferiority approach with a concordance limit of 95% and two-sided 95% confidence intervals was used to demonstrate concordance between HIVDR calls based on full-length and short RT sequences.</p> <p>The results of this analysis showed that HIVDR interpretations based on full-length versus short RT sequences, using the Stanford algorithms, had concordance significantly above 95%. When using the virco^®TYPE algorithm, similar concordance was demonstrated (>95%), but some differences were observed for d4T, AZT and TDF, where predictions were affected in more than 5% of the sequences. Most differences in interpretation, however, were due to shifts from fully susceptible to reduced susceptibility (d4T) or from reduced response to minimal response (AZT, TDF) or vice versa, as compared to the predicted full RT sequence. The virco^®TYPE prediction uses many more mutations outside the RT 41-238 amino acid domain, which significantly contribute to the HIVDR prediction for these 3 antiretroviral agents.</p> <p>Conclusions</p> <p>This study illustrates the acceptability of using a shortened RT sequences (codon 41-238) to obtain reliable genotype interpretations by virco^®TYPE and Stanford algorithms. Implementation of this simplified protocol could significantly reduce the cost of both resistance testing and ARV treatment monitoring in RLS.</p