LLukas22/scidocs huggingface dataset:
Family effect on cultured pearl quality in black-lipped pearl oyster Pinctada margaritifera and insights for genetic improvement

Individual Pinctada margaritifera molluscs were collected from the Takapoto atoll (Tuamotu Archipelago, French Polynesia) and used to produce ten first generation full-sib families in a hatchery system, following artificial breeding protocols. After three years of culture, these progenies were transferred to Rangiroa atoll (Tuamotu Archipelago, French Polynesia) and tested for their potential as graft donors. A large-scale grafting experiment of 1500 grafts was conducted, in which a single professional grafter used ten individual donor oysters from each of the ten families, grafting 15 recipient oysters from each donor. The recipient oysters were all obtained from wild spat collection in Ahe (Tuamotu Archipelago, French Polynesia). After 18 months of culture, 874 pearls were harvested. Highly significant donor family effects were found for nucleus retention, nacre thickness, nacre weight, pearl colour darkness and visually-perceived colour (bodycolor and overtone), pearl shape categories, surface defects and lustre, the last two of which are components of the Tahitian classification grade. No significant difference was recorded between the ten G1 families for the absence or presence of rings. The progenies could be ranked from “best” (i.e., the donor whose grafts produced the greatest number of grade A pearls) to the “worst”. Some progenies had extreme characteristics: family B presented the greatest number of pearls with lustre (98%) and a high proportion of dark gray to black with green overtone pearls (70%). These results have important implications for the selective breeding of donor pearl oysters: it may be possible to reach a point where specific donor lines whose grafts produce pearls with specific quality traits could be identified and maintained as specific breeding lines.
Quantifying sediment transport across an undisturbed prairie landscape using cesium-137 and high resolution topography

Soil erosion is a global environmental problem, and anthropogenic fallout radionuclides offer a promising tool for describing and quantifying soil redistribution on decadal time scales. To date, applications of radioactive fallout to trace upland sediment transport have been developed primarily on lands disturbed by agriculture, grazing, and logging. Here we use Cs to characterize and quantify soil erosion at the Konza Prairie Long-Term Ecological Research (LTER) site, an undisturbed grassland in northeastern Kansas. We report on the small scale (b10 m) and landscape scale (10 to 1000 m) distribution of fallout Cs, and show significant variability in the concentrations and amounts of Cs in soils at our site. Cs soil concentrations and amounts typically vary by 10% to 30% on small scales, which most likely represents the spatial heterogeneity of the depositional processes. Landscape scale variability of soil Cs was significantly higher than small scale variability. Most notably, soils collected on convex (divergent) landforms had Cs inventories of 2500 to 3000 Bq m, which is consistent with the expected atmospheric inputs to the study area during the 1950s and 1960s. Concave landforms, however, had statistically lower inventories of 1800 to 2300 Bq m. The distribution of Cs on this undisturbed landscape contrasts significantly with distributions observed across disturbed sites, which generally have accumulations of radioactive fallout in valley bottoms. Because the upslope contributing area at each sampling point had a significant negative correlation with the soil inventory of Cs, we suggest that overland flow in convergent areas dominates soil erosion at Konza on time scales of decades. Very few points on our landscape had Cs inventories significantly above that which would be predicted from direct deposition of Cs on the soil surface; we conclude therefore that there is little net sediment storage on this undisturbed landscape. © 2005 Elsevier B.V. All rights reserved.
Sentinel node biopsy compared with complete axillary dissection for staging early breast cancer with clinically negative lymph nodes: results of randomized trial.

BACKGROUND
Sentinel lymph node (SLN) staging is currently used to avoid complete axillary dissection in breast cancer patients with negative SLNs. Evidence of a similar efficacy, in terms of survival and regional control, of this strategy as compared with axillary resection is based on few clinical trials. In 1998, we started a randomized study comparing the two strategies, and we present here its results.


MATERIALS AND METHODS
Patients were randomly assigned to sentinel lymph node biopsy (SLNB) and axillary dissection [axillary lymph node dissection (ALND arm)] or to SLNB plus axillary resection if SLNs contained metastases (SLNB arm). Main end points were overall survival (OS) and axillary recurrence.


RESULTS
One hundred and fifteen patients were assigned to the ALND arm and 110 to the SLNB arm. A positive SLN was found in 27 patients in the ALND arm and in 31 in the SLNB arm. Overall accuracy of SLNB was 93.0%. Sensitivity and negative predictive values were 77.1% and 91.1%, respectively. At a median follow-up of 5.5 years, no axillary recurrence was observed in the SLNB arm. OS and event-free survival were not statistically different between the two arms.


CONCLUSIONS
The SLNB procedure does not appear inferior to conventional ALND for the subset of patients here considered.
Continuous integration processes for modern client-side web applications

Continuous Integration (CI) is very useful for applications that involve many files and multiple developers. Unfortunately, not all types of applications can easily apply this approach. Apparently, CI does not gain a lot of attention with Modern Client-Side Web Application (MCSWA) because it requires complicated testing, i.e. the running environments are browsers. There is no compiler or error warning when a developer writes bad code and the build behavior in the usual CI practice is different from the build process in MCSWA. If the integration process is done manually by an integration expert, unexpected errors are found not only while integrating but also when performing manual tests to verify it. Moreover, it is problematic and elaborate if a developer needs to test the features by clicking around with repeated user-interaction in different browsers; especially, he might create human errors or miss some steps. This indicates that manual processes consume a lot of time and they are stressful. Therefore, the intent of this paper is to demonstrate a new approach for a CI process which specifically applies to MCSWA. It also provides a precise cycle for web development teams on how these repeated processes are important to run automatically with effective expected outcomes.
Study of compliance with a clinical pathway for suspected pulmonary embolism.

BACKGROUND/AIMS
Clinical pathways to guide the investigation of suspected pulmonary embolism have been increasingly adopted by emergency departments worldwide. This study evaluated the compliance with a clinical pathway that combines risk assessment (Wells score) with d-dimer, ventilation-perfusion scanning or computed tomographic pulmonary angiography (CTPA). The aims of this study were to identify factors that contribute to compliance and to assess patient outcomes and resource utilization.


METHODS
Repeated retrospective chart reviews of 239 patients who underwent investigation for pulmonary embolism through our emergency department extracted patient demographics, pathway parameters and patient outcomes. A phone interview at 3-month follow up was carried out.


RESULTS
Incidence of pulmonary embolism was 8.4% (n= 20). Compliance to the clinical pathway occurred in 120 subjects (50.2%). Non-compliance occurred in 71 subjects (29.7%). Forty-eight subjects (20.1%) underwent risk assessments, but subsequent diagnostic tests did not conform to the stated pathway (partial compliance). Compliance was poor in subjects assessed by non-emergency department doctors (χ(2) = 27.95, P≤ 0.001). Compliance occurred less in pregnant subjects (χ(2) = 7.27, P= 0.007) and those with chronic respiratory disease (χ(2) = 5.31, P= 0.021). Subjects in the compliant group were less likely to undergo CTPA (odds ratio 2.07 (1.16-3.70), P= 0.012).


CONCLUSIONS
Compliance with this clinical pathway allowed emergency department doctors in an Australian university teaching hospital to complete diagnostic testing for suspected pulmonary embolism appropriately unless non-emergency department doctors became involved. Compliance with this pathway altered the distribution of diagnostic tests performed with less reliance on CTPA, but was not associated with better patient outcomes.
A System for Automatic Image Categorization

Traditional multimedia classification techniques are based on the analysis of either low-level features or annotated textual information. Instead, the semantic gap between rough data and its content is still a challenging task. In this paper, we describe a novel solution which automatically associates the image analysis and processing algorithms to keywords and human annotation. We use the well known \FLICK\ system, that contains images, tags, keywords and sometimes useful annotation describing both the content of an image and personal interesting information describing the scene. We have carried out several experiments demonstrating that the proposed categorization process achieves quite good performances in terms of efficiency and effectiveness.
Detrimental cross-talk between sepsis and acute kidney injury: new pathogenic mechanisms, early biomarkers and targeted therapies

This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency medicine 2016. Other selected articles can be found online at http://www.biomedcentral.com/collections/annualupdate2016. Further information about the Annual Update in Intensive Care and Emergency Medicine is available from http://www.springer.com/series/8901.
Scaffolding game-based learning: Impact on learning achievements, perceived learning, and game experiences

One of the central challenges of integrating game-based learning in school settings is helping learners make the connections between the knowledge learned in the game and the knowledge learned at school, while maintaining a high level of engagement with game narrative and gameplay. The current study evaluated the effect of supplementing a business simulation game with an external conceptual scaffold, which introduces formal knowledge representations, on learners’ ability to solve financial-mathematical word problems following the game, and on learners’ perceptions regarding learning, flow, and enjoyment in the game. Participants (Mage 1⁄4 10.10 years) were randomly assigned to three experimental conditions: a “study and play” condition that presented the scaffold first and then the game, a “play and study” condition, and a “play only” condition. Although no significant gains in problem-solving were found following the intervention, learners who studied with the external scaffold before the game performed significantly better in the post-game problem-solving assessment. Adding the external scaffold before the game reduced learners’ perceived learning. However, the scaffold did not have a negative impact on reported flow and enjoyment. Flow was found to significantly predict perceived learning and enjoyment. Yet, perceived learning and enjoyment did not predict problem-solving and flow directly predicted problem solving only in the “play and study” condition. We suggest that presenting the scaffold may have “problematized” learners’ understandings of the game by connecting them to disciplinary knowledge. Implications for the design of scaffolds for game-based learning are discussed. 2013 Elsevier Ltd. All rights reserved.
Project scheduling under resource and mode identity constraints: Model, complexity, methods, and application

A recurring problem in project management involves the allocation of scarce resources to the individual jobs comprising the project. In many situations such as audit-staff scheduling, timetabling, and course scheduling, the resources correspond to individuals (skilled labour). This naturally leads to an assignment-type project scheduling problem, i.e. a project has to be performed by assigning one or more of several individuals (resources) to each job. In this paper we consider the nonpreemptive variant of a resource-constrained project scheduling problem with mode identity. Mode identity refers to a generalization of the multi-mode case where the set of all jobs is partitioned into disjoint subsets while all jobs forming one subset have to be processed in the same mode. Both time and cost incurred by processing a subset of jobs depend on the resources assigned to it. This problem is a substantial and non-trivial generalization of the well-known multi-mode case. Regarding precedence and temporal relations as well as release dates and deadlines, the question arises to which jobs resources should be assigned in order to minimize overall costs. For solving this time-resource-cost-tradeoff problem we present a tailored parallel randomized solution approach called RAMSES into which both static and dynamic priority rules can be incorporated. The results of an extensive computational study on a practical application from the field of audit-staff scheduling indicate that RAMSES is capable of producing "good" solutions in neglectable amounts of time.
Investigating the Energy Consumption of a Wireless Network Interface in an Ad Hoc Networking Environment

Energy-aware design and evaluation of network protocols r equires knowledge of the energy consumption behavior of actu al wireless interfaces. But little practical information is available about the energy consumption behavior of well-known wireless network interfaces and device specifications do not provide information in a form that is helpful to protocol developers. This paper describes a series of exper iments which obtained detailed measurements of the energy consumption of a n IEEE 802.11 wireless network interface operating in an ad hoc networking environment. The data is presented as a collection of linear equations for calculating the energy consumed in sending, receiving and discarding broad cast and pointto-point data packets of various sizes. Some implications f or protocol design and evaluation in ad hoc networks are discussed. Keywords—energy consumption, IEEE 802.11, ad hoc networks
The functional neuroanatomy of the placebo effect.

OBJECTIVE
Administration of placebo can result in a clinical response indistinguishable from that seen with active antidepressant treatment. Functional brain correlates of this phenomenon have not been fully characterized.


METHOD
Changes in brain glucose metabolism were measured by using positron emission tomography in hospitalized men with unipolar depression who were administered placebo as part of an inpatient imaging study of fluoxetine. Common and unique response effects to administration of placebo or fluoxetine were assessed after a 6-week, double-blind trial.


RESULTS
Placebo response was associated with regional metabolic increases involving the prefrontal, anterior cingulate, premotor, parietal, posterior insula, and posterior cingulate and metabolic decreases involving the subgenual cingulate, parahippocampus, and thalamus. Regions of change overlapped those seen in responders administered active fluoxetine. Fluoxetine response, however, was associated with additional subcortical and limbic changes in the brainstem, striatum, anterior insula, and hippocampus, sources of efferent input to the response-specific regions identified with both agents.


CONCLUSIONS
The common pattern of cortical glucose metabolism increases and limbic-paralimbic metabolism decreases in placebo and fluoxetine responders suggests that facilitation of these changes may be necessary for depression remission, regardless of treatment modality. Clinical improvement in the group receiving placebo as part of an inpatient study is consistent with the well-recognized effect that altering the therapeutic environment may significantly contribute to reducing clinical symptoms. The additional subcortical and limbic metabolism decreases seen uniquely in fluoxetine responders may convey additional advantage in maintaining long-term clinical response and in relapse prevention.
Structural Basis of Zika Virus-Specific Antibody Protection

Zika virus (ZIKV) infection during pregnancy has emerged as a global public health problem because of its ability to cause severe congenital disease. Here, we developed six mouse monoclonal antibodies (mAbs) against ZIKV including four (ZV-48, ZV-54, ZV-64, and ZV-67) that were ZIKV specific and neutralized infection of African, Asian, and American strains to varying degrees. X-ray crystallographic and competition binding analyses of Fab fragments and scFvs defined three spatially distinct epitopes in DIII of the envelope protein corresponding to the lateral ridge (ZV-54 and ZV-67), C-C' loop (ZV-48 and ZV-64), and ABDE sheet (ZV-2) regions. In vivo passive transfer studies revealed protective activity of DIII-lateral ridge specific neutralizing mAbs in a mouse model of ZIKV infection. Our results suggest that DIII is targeted by multiple type-specific antibodies with distinct neutralizing activity, which provides a path for developing prophylactic antibodies for use in pregnancy or designing epitope-specific vaccines against ZIKV.
Economic and environmental analysis of micro hydropower system for rural power supply

This paper discusses the advantages of using renewable energy sources in the architecture of an off-grid hybrid power system in rural areas. The studied system is composed of a diesel generator to which a micro hydropower plant is added. Simulations using the Hybrid Optimization Model for Electric Renewable (HOMER) are performed for given annual values of hydro resources, power demands and hybrid system component costs. The results highlight the cost-effectiveness character and the reduction of gas pollutant emissions achieved by using such a system rather than a diesel generator to supply the same load.
Fault tolerant longitudinal aircraft control using non-linear integral sliding mode

This paper proposes a novel nonlinear fault tolerant scheme for longitudinal control of an aircraft system, comprising an integral sliding mode control allocation scheme and a backstepping structure. In fault free conditions, the closed loop system is governed by the backstepping controller and the integral sliding mode control allocation scheme only influences the performance if faults/failures occur in the primary control surfaces. In this situation the allocation scheme redistributes the control signals to the secondary control surfaces and the scheme is able to tolerate total failures in the primary actuator. A backstepping scheme taken from the existing literature is designed for flight path angle tracking (based on the nonlinear equations of motion) and this is used as the underlying baseline controller in nominal conditions. The efficacy of the scheme is demonstrated using a high fidelity aircraft benchmark model. Excellent results are obtained in the presence of plant/model uncertainty in both fault-free and faulty conditions. Keyword: Fault tolerant control (FTC), integral sliding mode (ISM) control.
Building credit scoring models using genetic programming

Credit scoring models have been widely studied in the areas of statistics, machine learning, and artificial intelligence (AI). Many novel approaches such as artificial neural networks (ANNs), rough sets, or decision trees have been proposed to increase the accuracy of credit scoring models. Since an improvement in accuracy of a fraction of a percent might translate into significant savings, a more sophisticated model should be proposed to significantly improving the accuracy of the credit scoring mode. In this paper, genetic programming (GP) is used to build credit scoring models. Two numerical examples will be employed here to compare the error rate to other credit scoring models including the ANN, decision trees, rough sets, and logistic regression. On the basis of the results, we can conclude that GP can provide better performance than other models. q 2005 Elsevier Ltd. All rights reserved.
Sexual activity and Kaposi's sarcoma among human immunodeficiency virus type 1 and human herpesvirus type 8-coinfected men.

PURPOSE
There is notable heterogeneity in the progression to Kaposi's sarcoma (KS) among men coinfected with HIV-1 and human herpesvirus type 8 (HHV-8); additional determinants of KS likely exist. Here, we explore sexual activity as a proxy for a sexually transmitted determinant beyond HIV-1 and HHV-8.


METHODS
The association between sexual activity and incident KS was estimated with data from 1354 HIV-1- and HHV-8-coinfected homosexual men who were followed for up to 10 years in the Multicenter AIDS Cohort Study.


RESULTS
As expected, white race, low CD4 cell count, and the acquisition of HHV-8 after HIV-1 infection increased, whereas smoking decreased, the hazard of KS. The unadjusted hazard of KS among those with high sexual activity was 0.68 relative to the hazard of those with low sexual activity (95% confidence interval, 0.49-0.93) and was somewhat muted after adjustment for characteristics measured at study entry (i.e., race, smoking, CD4 cell count, infection order, history of sexual activity, and sexually transmitted diseases). However, adjustment for time-varying covariates, particularly CD4 cell count, resulted in a nullification of the association (adjusted hazard ratio = 1.06; 95% confidence interval, 0.77-1.48).


CONCLUSION
Once HIV-1 and HHV-8 coinfection is established in homosexual men, progression to KS does not appear to be caused by a third pathogen transmitted by sexual activity.
Smallpox vaccine–induced antibodies are necessary and sufficient for protection against monkeypox virus

Vaccination with live vaccinia virus affords long-lasting protection against variola virus, the agent of smallpox. Its mode of protection in humans, however, has not been clearly defined. Here we report that vaccinia-specific B-cell responses are essential for protection of macaques from monkeypox virus, a variola virus ortholog. Antibody-mediated depletion of B cells, but not CD4+ or CD8+ T cells, abrogated vaccine-induced protection from a lethal intravenous challenge with monkeypox virus. In addition, passive transfer of human vaccinia-neutralizing antibodies protected nonimmunized macaques from severe disease. Thus, vaccines able to induce long-lasting protective antibody responses may constitute realistic alternatives to the currently available smallpox vaccine (Dryvax).