LLukas22/scidocs huggingface dataset:
Trade-offs between on-farm varietal diversity and highly client-oriented breeding — a case study of upland rice in India

On-farm varietal diversity is now highest in marginal agricultural environments because, unlike the case in more favourable areas, modern varieties have not been a sufficiently attractive option for farmers to replace their landraces. However, the continued survival of landraces on farm is dependent on the continuing failure of plant breeding to provide better alternatives. Highly client-oriented breeding can produce suitable modern varieties for areas that were dominated by landraces. We examine here the case of the adoption of two upland rice varieties in three states in eastern India, Jharkhand, West Bengal and Orissa, where our surveys had confirmed low adoption of modern varieties in the upland ecosystem. The two new upland varieties were readily accepted by farmers who rapidly adopted them on large proportions of their land. On-farm diversity is maintained by the need to trade-off among varieties but once a variety with overall superiority was found this incentive was removed. The new varieties from the client-oriented breeding did not have weaknesses that farmers had to trade-off against their landraces so they were more likely to replace them. They also replaced older modern varieties. Farmers had previously maintained them along with landraces because they had to trade-off the higher yield of Kalinga III against the more stable yield of landraces or the higher yield of Vandana against the higher gain quality of the landraces. Only mean count per household could be used to test the significance of the differences between individual years. In all states, this revealed a significant reduction in landrace diversity with the adopting farmers when the addition of the two new varieties was not considered. Trends across years for mean varietal count, total count and Shannon–Wiener index showed a significant decline in Orissa, irrespective of whether the two new varieties were included in the analysis or not. In Jharkhand there was a significant decline only for mean count when the new varieties were not included. In Orissa, it was possible to test if rare landraces were as readily replaced as more common ones. Landrace replacement was unmitigated by increasing rarity yet the most rare landraces have the highest priority for genetic conservation. Some landraces were completely replaced by the farmers in the sample despite a diverse variety portfolio being a risk-reducing strategy in a region where there is a high risk of crop failure. There was little environmental heterogeneity in the marginal, drought-prone areas to slow this decline. The new varieties had an impact on the farming system because sometimes farmers brought additional upland into cultivation. They also introduced these varieties into more favourable, medium land. The strategy of releasing two new upland varieties met with some success in maintaining diversity.
Predominant floodplain over mountain weathering of Himalayan sediments (Ganga basin)

We present an extensive river sediment dataset covering the Ganga basin from the Himalayan front downstream to the Ganga mainstream in Bangladesh. These sediments were mainly collected over several monsoon seasons and include depth profiles of suspended particles in the river water column. Mineral sorting is the first order control on the chemical composition of river sediments. Taking into account this variability we show that sediments become significantly depleted in mobile elements during their transit through the floodplain. By comparing sediments sampled at the Himalayan front with sediments from the Ganga mainstream in Bangladesh it is possible to budget weathering in the floodplain. Assuming a steady state weathering regime in the floodplain, the weathering of Himalayan sediments in the Gangetic floodplain releases ca. (189 ± 92) 10 and (69 ± 22) 10 mol/yr of carbonate bound Ca and Mg to the dissolved load, respectively. Silicate weathering releases (53 ± 18) 10 and (42 ± 13) 10 mol/yr of Na and K while the release of silicate Mg and Ca is substantially lower, between ca. 0 and 20 10 mol/yr. Additionally, we show that sediment hydration, [H2O ], is a sensitive tracer of silicate weathering that can be used in continental detrital environments, such as the Ganga basin. Both [H2O ] content and the D/H isotopic composition of sediments increases during floodplain transfer in response to mineral hydrolysis and neoformations associated to weathering reactions. By comparing the chemical composition of river sediments across the floodplain with the composition of the eroded Himalayan source rocks, we suggest that the floodplain is the dominant location of silicate weathering for Na, K and [H2O ]. Overall this work emphasizes the role of the Gangetic floodplain in weathering Himalayan sediments. It also demonstrates how detrital sediments can be used as weathering tracers if mineralogical and chemical sorting effects are properly taken into account. 2012 Elsevier Ltd. All rights reserved.
Costs to Achieve Undetectable HIV RNA with Darunavir-Containing Highly Active Antiretroviral Therapy in Highly Pretreated Patients

Background: Very few studies have evaluated the cost of highly active antiretroviral therapy (HAART) per successful treatment in HIV-infected patients. Objectives: To evaluate the cost of achieving undetectable plasma HIV-RNA levels in highly treatment-experienced, HIV-1-infected adults receiving darunavir/ritonavir (DRV/r 600 mg/100mg twice a day) or control protease inhibitor (PI)-based HAART. Methods: The mean annual per-patient cost of DRV/r and control PI-based HAART was determined from the proportional use of antiretroviral agents in the DRV/r and control PI arms of the pooled POWER 1 and 2 trials, applying drug acquisition costs for 13 healthcare settings. The mean annual cost per patient of achieving undetectable plasma HIV-RNA levels (<50 copies/mL) was calculated by dividing the cost of each treatment by the proportion of patients with undetectable plasma HIV-RNA levels after 48 weeks in the DRV/r (45%) and control PI (10%) arms of the POWER trials. Results: Whereas absolute costs of treatment were 1–19% higher with DRV/r versus control PI-based HAART depending on the healthcare setting, the mean annual per-patient cost of achieving undetectable plasma HIV-RNA levels was 73–78%lower. These cost savings were maintained in the sensitivity analyses, adjusting for control PI and enfuvirtide use, and the number of active drugs in the background regimen. The incremental annual cost per additional patient achieving undetectable plasma HIV-RNA levels with DRV/r versus control PI-based HAART in POWER 1 and 2 (d4148) compared favourably with that determined for enfuvirtide (d137 740; TORO trials) and tipranavir/ritonavir (d32 176; RESIST) versus control therapy. Conclusions: DRV/r-based HAART provided consistent reductions in the cost of achieving undetectable plasma HIV-RNA levels compared with control PI-based therapy in highly treatment-experienced patients across various healthcare settings. The incremental cost per additional patient achieving undetectable plasma HIV-RNA levels with DRV/r versus control PI-based HAART was also lower than that calculated for other treatment options in this population. These results suggest that DRV/r is an economically viable option for highly treatment-experienced patients.
The Neoclassical Revival in Growth Economics: Has It Gone Too Far?

In our view there has been a "Neoclassical Revival" in growth economics spurred by the empirical findings of Mankiw, Romer, and Weil (1992), Barro and Sala-i-Martin (1995), and Young (1994 and 1995). By this we mean a revival of the neoclassical growth model which features a common level of productivity but different levels of human and physical capital across countries as a viable candidate for explaining the major part of country differences in levels and growth rates of output per worker. Marshaling evidence from the labor literature on the returns to schooling and experience, we construct new measures of human capital across countries. We find that productivity differences are the dominant source of the large international dispersion in levels and growth rates of output per worker. We conclude that, although models that focus on physical and human capital are clearly important, research needs to be re-focused on explaining the causes of productivity differences across countries.
A review of 100 consecutive secondary augmentation/mastopexies.

BACKGROUND
Simultaneous breast augmentation and mastopexy has historically been a controversial topic, and it has been considered by some to be a difficult and unpredictable procedure. Secondary breast augmentation and mastopexy after previous breast surgery is rarely discussed in the literature, and little is known about the outcomes of these secondary procedures.


OBJECTIVE
The authors present the indications, surgical techniques, and outcomes in a series of 100 consecutive secondary simultaneous breast augmentation and mastopexy cases.


METHODS
One hundred consecutive patients who underwent secondary combined augmentation mammaplasty and mastopexy from 1992 to 2005 were retrospectively reviewed. The complications and revision rates in this group of patients were analyzed and compared with primary mastopexy alone, as well as with primary combined augmentation and mastopexy. Independent variables such as patient age, history of smoking, body mass index, type and size of implant, and type of mastopexy incision were analyzed for correlation with complication and revision rates.


RESULTS
No major complications were noted in an average of 3.5 years follow-up (range 13 months to 13 years). Minor complications occurred in 13 patients, of whom 8 required revision surgery. The most common tissue-related complications were poor scarring (3%) and recurrent ptosis (3%). The most common implant-related complications were infection (3%) and capsular contracture (2%). In addition, 6 patients underwent reoperation for implant size exchange, and 1 patient underwent revision surgery to receive silicone implants. Patient age, history of smoking, body mass index, type and size of implant, type of mastopexy incision, type and number of previous breast surgeries, surgical time, concurrent non-breast operations, and preoperative ptosis grade were not statistically significant risks when correlated to the complication and revision rate.


CONCLUSIONS
Simultaneous breast augmentation and mastopexy after previous breast surgery is a commonly performed procedure that is not adequately reported in the literature. Our study indicates that the procedure is safe and has complication and revision rates comparable to primary augmentation/mastopexy.
Statistical limitations of percent ideal body weight as measure for nutritional failure in patients with cystic fibrosis.

BACKGROUND
For the past decade, percentage of ideal body weight (%IBW) was recommended by European and US nutrition consensus reports as preferred clinical measure of nutritional status in children with cystic fibrosis (CF). We and others have demonstrated that the %IBW method underestimates the prevalence of nutritional failure in CF, but the underlying mechanism for this methodological flaw remains incompletely defined.


DESIGN
We performed model calculations from cross sectional growth data of healthy and CF-children to assess the methodological limitations of %IBW calculation.


RESULTS
Here we demonstrate that an intrinsic limitation of %IBW method is that it largely ignores the statistical principle of regression to the mean. The key assumption of %IBW is that ideal weight-for-age is on exactly the same percentile ranking as height-for-age. We show that this assumption is only valid if the individual's height is close to the reference median. When the stature deviates from the median of the reference population, however, the increments of height-for-age and weight-for-age percentiles are not the same. In consequence, %IBW method systematically underestimates the ideal weight for smaller-than-average individuals, like CF-patients, which results in significant underestimation of the prevalence of malnutrition in this group of patients.


CONCLUSION
There is increasing scientific evidence that calculation of %IBW as a measure of nutritional status in children with CF is flawed and should be discontinued. It is expected that future guidelines will recommend the use of alternative measures of weight-for-height proportion, e.g. BMI percentiles, to assess underweight and malnutrition in patients with CF.
Educational Systems, Growth and Income Distribution: A Quantitative Study

This paper studies how human capital connects economic growth with income distribution under imperfect credit markets. We construct a model where households can choose between private and public schools. The government provides public education and public support for private education through voucher programs. We find that in a mixed educational system, the government can control economic performance by changing the structure of the educational system. If the government wishes to reduce income inequality, a policy to increase the enrollment rate in public schools should be adopted. However, having a high enrollment rate in private schools with the liberalization of credit markets can keep the growth rate high. JEL Classification: E17, I28, O11, O15, H31.
Effect of long-term belimumab treatment on B cells in systemic lupus erythematosus: extension of a phase II, double-blind, placebo-controlled, dose-ranging study.

OBJECTIVE
To understand the effects of long-term BLyS inhibition in human systemic lupus erythematosus (SLE).


METHODS
Seventeen patients with SLE who were enrolled in a clinical trial of belimumab, a BLyS-specific inhibitor, plus standard of care therapy were studied. Phenotypic analysis of lymphocytes was performed using flow cytometry. Circulating antibody-secreting cells were enumerated using enzyme-linked immunospot assay. Serum was analyzed by enzyme-linked immunosorbent assay using an antibody that recognizes products of the V(H)4-34 gene. Lymphocyte counts, Ig levels, and anti-double-stranded DNA antibody levels were available as part of the clinical trial analyses.


RESULTS
Samples were collected on days 0, 84, 168, 365, and 532 and after day 730. The total number of B cells started to decrease from baseline between days 84 and 168. This was due to a decrease in naive and transitional B cells. CD27+IgD+ memory B cells and plasmablasts decreased only after 532 days, whereas CD27+IgD- memory B cells were not affected, and there were no changes in T cells. Serum IgM levels began to decline between days 84 and 168, but there were no changes in serum levels of IgG, IgG anti-DNA antibodies, or V(H)4-34 antibodies during the study. SLE patients had more IgM-, IgG-, and autoantibody-producing B cells than did normal controls on day 0. There was only a modest decrease in the frequency of total IgM-producing, but not IgG-producing, cells on days 365 and 532, consistent with the phenotypic and serologic data.


CONCLUSION
Our data confirm the dependence of newly formed B cells on BLyS for survival in humans. In contrast, memory B cells and plasma cells are less susceptible to selective BLyS inhibition.
Integrated threat assessment and control design for roadway departure avoidance

This paper presents the design of an active safety system for prevention of unintended roadway departures. In normal driving conditions, the driver fully commands the vehicle while the safety system corrects the driver's steering and braking action in case there's a risk that the vehicle unintentionally departs the road. A model of the driver's nominal behavior is first estimated based on his or her observed behavior. A nonlinear model of the vehicle in closed loop with the driver is then used to reformulate the threat assessment and control problems as a combined optimization problem. The resulting predictive controller is always active and mode switching is not necessary. Experimental data collected using human drivers in a driver simulator demonstrate the capability of the suggested controller to detect and avoid roadway departures while avoiding unnecessary interventions.
Feedback with Carry Shift Registers over Finite Fields (extended abstract)

Academic Positions 2001–present, Professor, Department of Computer Science, University of Kentucky, Lexington, KY. 1997–2001, Associate Professor, Department of Computer Science, University of Kentucky, Lexington, KY. 1993–1997, Assistant Professor, Department of Computer Science, University of Kentucky, Lexington, KY. 1991–1993, Assistant/Associate Professor, Computer Science Department, University of Manitoba, Winnipeg, Manitoba. 1984–1991, Assistant Professor, College of Computer Science, Northeastern University, Boston, MA. 1981–1984, Postdoctoral Fellow, Assistant Professor, Department of Mathematics and Computer Science, Clark University, Worcester, MA.
Cyclegen: Cyclic consistency based product review generator from attributes

In this paper we present an automatic review generator system which can generate personalized reviews based on the user identity, product identity and designated rating the user wishes to allot to the review. We combine this with a sentiment analysis system which performs the complimentary task of assigning ratings to reviews based purely on the textual content of the review. We introduce an additional loss term to ensure cyclic consistency of the sentiment rating of the generated review with the conditioning rating used to generate the review. The introduction of this new loss term constraints the generation space while forcing it to generate reviews adhering better to the requested rating. The use of ‘soft’ generation and cyclic consistency allows us to train our model in an end to end fashion. We demonstrate the working of our model on product reviews from Amazon dataset.
A proof–theoretic study of the correspondence of hybrid logic and classical logic

In this paper, we show the equivalence between the provability of a proof system of basic hybrid logic and that of translated formulas of the classical predicate logic with equality and explicit substitution by a purely proof–theoretic method. Then we show the equivalence of two groups of proof systems of hybrid logic: the group of labelled deduction systems and the group of modal logic-based systems.
Effectiveness of financial incentives to improve adherence to maintenance treatment with antipsychotics: cluster randomised controlled trial

OBJECTIVE
To test whether offering financial incentives to patients with psychotic disorders is effective in improving adherence to maintenance treatment with antipsychotics.


DESIGN
Cluster randomised controlled trial.


SETTING
Community mental health teams in secondary psychiatric care in the United Kingdom.


PARTICIPANTS
Patients with a diagnosis of schizophrenia, schizoaffective disorder, or bipolar disorder, who were prescribed long acting antipsychotic (depot) injections but had received 75% or less of the prescribed injections. We randomly allocated 73 teams with a total of 141 patients. Primary outcome data were available for 35 intervention teams with 75 patients (96% of randomised) and for 31 control teams with 56 patients (89% of randomised).


INTERVENTIONS
Participants in the intervention group were offered £15 (€17; $22) for each depot injection over a 12 month period. Participants in the control condition received treatment as usual.


MAIN OUTCOME MEASURE
The primary outcome was the percentage of prescribed depot injections given during the 12 month intervention period.


RESULTS
73 teams with 141 consenting patients were randomised, and outcomes were assessed for 131 patients (93%). Average baseline adherence was 69% in the intervention group and 67% in the control group. During the 12 month trial period adherence was 85% in the intervention group and 71% in the control group. The adjusted effect estimate was 11.5% (95% confidence interval 3.9% to 19.0%, P=0.003). A secondary outcome was an adherence of ≥ 95%, which was achieved in 28% of the intervention group and 5% of the control group (adjusted odds ratio 8.21, 95% confidence interval 2.00 to 33.67, P=0.003). Although differences in clinician rated clinical improvement between the groups failed to reach statistical significance, patients in the intervention group had more favourable subjective quality of life ratings (β=0.71, 95% confidence interval 0.26 to 1.15, P=0.002). The number of admissions to hospital and adverse events were low in both groups and did not show substantial differences.


CONCLUSION
Offering modest financial incentives to patients with psychotic disorders is an effective method for improving adherence to maintenance treatment with antipsychotics.


TRIAL REGISTRATION
Current Controlled Trials ISRCTN77769281.
REGIONAL CLUSTERS, REGIONAL COMPETENCIES AND REGIONAL COMPETITION

Paper delivered at the International Conference on " Cluster management in structural policy – International experiences and consequences for Northrhine-Westfalia " , Duisburg, december 5 th
Business and Information Systems MisAlignment Model ( BISMAM ) : an Holistic Model Leveraged on Misalignment and Medical Sciences Approaches

Organizations aim to achieve business and information systems alignment, but actually “feel” and “suffer”, on a daily basis, the difficulties that inhibits the alignment achievement, in other words, the misalignments. This paper proposes a model, the Business and Information Systems MisAlignment Model (BISMAM), to understand, to classify and to manage misalignments. This proposal addresses the alignment problem combining misalignment approach with medical sciences approach based on a metaphor between misalignment and disease. The authors believe that the misalignment approach is closer to organizations real life and that medical sciences approach provides the relevant concepts and techniques for misalignment classification and management. Based on both academic research and years of professional consultancy, the authors propose an initial and possible instantiation to the BISMAM model, establishing a misalignment classification scheme that links enterprise architecture views, misalignment symptoms and causes, and defining techniques to detect, correct and prevent misalignments.
Shared decision making in public mental health care: perspectives from consumers living with severe mental illness.

OBJECTIVE
Most theoretical and empirical work regarding decision making in mental health suggests that mental health consumers have better outcomes when their preferences are integrated into quality of life decisions. A wealth of research, however, indicates that providers have difficulty predicting what their clients' priorities are. This study investigates consumer decision-making preferences and understanding of construction of decisions in community mental health.


METHODS
People living with severe mental illness being treated in the public mental health care system (N=16) participated in qualitative interviews regarding case management decision making as a part of a larger study investigating a decision support system to facilitate shared decision making. Interviews were transcribed, coded, and cross-case thematic analyses were conducted.


RESULTS
Mental health consumers generally endorse a "shared" style of decision making. When asked what "shared" means, however, consumers describe a two-step process which first prioritizes autonomy, and if that is not possible, defers to case managers' judgment. Consumers also primarily focused on the relationship and affective components of decision making, rather than information-gathering or deliberating on options. Finally, when disagreements arose, consumers primarily indicated they handled them.


CONCLUSIONS
Mental health consumers may have a different view of decision making than the literature on shared decision making suggests. Mental health consumers may consciously decide to at least verbally defer to their case managers, and remain silent about their preferences or wishes.