Miracle-dz/UniFAR-FTUs huggingface dataset:
Response of life‐history traits to artificial and natural selection for virulence and nonvirulence in a Drosophila parastitoid, Asobara tabida

Co‐evolution of host–parasitoid interactions is determined by the costs of host resistance, which received empirical evidence, and the costs of parasitoid virulence, which have been mostly hypothesized. Asobara tabida is a parasitoid, which mainly parasitizes Drosophila melanogaster and D. subobscura, the first species being able to resist to the parasitoid development while the second species is not. To parasitize resistant hosts, including D. melanogaster, A. tabida develops sticky eggs, which prevent encapsulation, but this virulence mechanism may be costly. Interindividual and interpopulation variation in the proportion of sticky eggs respectively allowed us to (i) artificially select and compare life‐history traits of a virulent and a nonvirulent laboratory strain, and (ii) compare a virulent and a nonvirulent field strain, to investigate the hypothetical costs of virulence. We observed strong differences between the 2 laboratory strains. The nonvirulent strain invested fewer resources in reproduction and walked less than the virulent one but lived longer. Concerning the field strains, we observed that the nonvirulent strain had larger wings while the virulent one walked more and faster. All together, our results suggest that virulence may not always be costly, but rather that different life histories associated with different levels of virulence may coexist at both intra‐ and interpopulation levels.
Finish line plant–insect interactions mediated by insect feeding mode and plant interference: a case study of Brassica interactions with diamondback moth and turnip aphid

There are gaps in our understanding of plant responses under different insect phytophagy modes and their subsequent effects on the insect herbivores’ performance at late season. Here we compared different types of insect feeding by an aphid, Lipaphis erysimi, and a lepidopteran, Plutella xylostella, and how this affected defensive metabolites in leaves of 2 Brassica species when plants gain maturity. Thiocyanate concentrations after P. xylostella and L. erysimi feeding activities were the same. Total phenolics was higher after the phloem feeder feeding than the folivore activity. The plants compensatory responses (i.e., tolerance) to L. erysimi feeding was significantly higher than the responses to P. xylostella. This study showed that L. erysimi had higher carbon than P. xylostella whereas nitrogen in P. xylostella was 1.42 times that in L. erysimi. Population size of the phloem feeder was not affected by plant species or insect coexistence. However, there was no correlation between plant defensive metabolites and both insects’ population size and biomass. This suggests that plant root biomass and tolerance index after different insect herbivory modes are not necessarily unidirectional. Importantly, the interaction between the folivore and the phloem feeder insects is asymmetric and the phloem feeder might be a trickier problem for plants than the folivore. Moreover, as both plants’ common and special defenses decreased under interspecific interference, we suggest that specialist insect herbivores can be more challenged in ecosystems in which plants are not involved in interspecific interference.
Cause-Specific Excess Deaths Associated With Underweight, Overweight, and Obesity

This study examined the association of body mass index (BMI) with cause-specific mortality. Data were taken from the National Health and Nutrition Examination Survey (NHANES) for the years 1971-1980 and 1988-1994, with mortality follow-up through 2000. Person-years of follow-up totalling 571,042 were combined with data from NHANES 1999-2002. Cause of death information was available for 2.3 million adults aged 25 and older. BMI categories included underweight (BMI less than 18.5), overweight (BMI of 25-29), and obese (BMI of 30 and above). Obesity but not overweight was significantly and positively associated with excess mortality from cardiovascular disease (CVD). The association held for coronary heart disease and other cardiovascular causes such as stroke. No significant association was found between excess mortality and BMI categories. Analysis of non-CVD, noncancer mortality disclosed an association with being underweight. Overweight was associated with significantly decreased mortality from causes other than CVD and cancer. Obesity was associated with significantly increased mortality from CVD but not with cancer nor noncancer, non-CVD mortality. Overweight and obesity combined were associated with increased mortality from diabetes and kidney disease and with decreased mortality from other noncancer, non-CVD mortality. Obesity was associated with increased mortality from cancers considered to be obesity-related. The association of obesity with CVD mortality appeared to decrease over time. In this large-scale survey, being overweight was associated with significantly decreased all-cause mortality overall. The findings affirm that relationships between BMI and mortality vary considerably with the cause of death.
A biotrophic fungal infection of the great burnet Sanguisorba officinalis indirectly affects caterpillar performance of the endangered scarce large blue butterfly Phengaris teleius

Interactions between ecological communities of herbivores and microbes are commonly mediated by a shared plant. A tripartite interaction between a pathogenic fungus–host plant–herbivorous insect is an example of such mutual influences. In such a system a fungal pathogen commonly has a negative influence on the morphology and biochemistry of the host plant, with consequences for insect herbivore performance. Here we studied whether the biotrophic fungus Podosphaera ferruginea, attacking the great burnet Sanguisorba officinalis, affects caterpillar performance of the endangered scarce large blue butterfly Phengaris teleius. Our results showed that the pathogenic fungus affected the number and size of inflorescences produced by food‐plants and, more importantly, had indirect, plant‐mediated effects on the abundance, body mass and immune response of caterpillars. Specifically, we found the relationship between caterpillar abundance and variability in inflorescence size on a plant to be positive among healthy food‐plants, and negative among infected food‐plants. Caterpillars that fed on healthy food‐plants were smaller than those that fed on infected food‐plants in one studied season, while there was no such difference in the other season. We observed the relationship between caterpillar immune response and the proportion of infected great burnets within a habitat patch to be positive when caterpillars fed on healthy food‐plants, and negative when caterpillars fed on infected food‐plants. Our results suggest that this biotrophic fungal infection of the great burnet may impose a significant indirect influence on P. teleius caterpillar performance with potential consequences for the population dynamics and structure of this endangered butterfly.
Snow chemistry of the Cascade-Sierra Nevada Mountains.

This investigation assesses geographic variations in atmospheric deposition in Washington, Oregon, and California using snow cores from the Cascade-Sierra Nevada Mountains, collected from late February to mid-March 1983. A statistical analysis of the analytical and sampling precision was made. The snowpack in the higher Cascades and Sierra Nevada is not strongly influenced by anthropogenic activities at present. The pH of snow samples ranges from 5.11 to 5.88. Sulfate and nitrate correlate with H/sup +/ in some segments of the sample traverse. The SO/sub 4/ data show apparent influence from major source areas in Washington and California; nitrate does not. An apparent decrease in NH/sub 4/ in snow in Washington and California suggests atmospheric interactions resulting in the removal of NH/sub 4/. The NH/sub 4/ reduction raises questions about nutrient supply in the mountain vegetation. Heavy-metal correlations included Cd, Cu, and Fe with Pb, and Mn with K and DOC, among others. No correlation was found between constituents and snow-water content. 47 references, 11 figures, 7 tables.
Dialysate Vascular Endothelial Growth Factor Is an Independent Determinant of Serum Albumin Levels and Predicts Future Withdrawal From Peritoneal Dialysis in Uremic Patients

Peritoneal protein loss due to high peritoneal permeability may contribute to hypoalbuminemia and early withdrawal from peritoneal dialysis (PD) therapy in end stage renal disease (ESRD) patients. We have found that pigment epithelium‐derived factor (PEDF) has anti‐vasopermeability properties both in cell culture and animal models by counteracting the biological actions of vascular endothelial growth factor (VEGF). However, it remains unknown which clinical variables, including dialysate VEGF and PEDF, are associated with decreased serum albumin levels and could predict early withdrawal from the PD in ESRD patients. We address these issues. Twenty‐seven ESRD patients undergoing PD were enrolled. Clinical variables were measured at 6 months after commencing PD. We examined the independent correlates of serum albumin in PD patients and then prospectively investigated the predictors of withdrawal from the PD therapy over 4 years. Dialysate VEGF was associated with peritoneal solute transport rate (P = 0.002), serum albumin (inversely, P < 0.001) and dialysate PEDF levels (P < 0.001). In multiple stepwise regression analysis, age (P = 0.002) and dialysate VEGF levels (P < 0.001) were independent determinants of serum albumin levels. High VEGF (>27 pg/mL), low serum albumin (≤3.31 g/dL) and low hemoglobin (≤11.2 g/dL) were correlated with withdrawal from the PD therapy during the 4 years. The odds ratio of dialysate VEGF for early withdrawal from the PD was 6.310 (P = 0.035). The present study demonstrated that increased dialysate VEGF was associated with decreased serum albumin and early withdrawal from the PD therapy. Inhibition of peritoneal VEGF production may be a therapeutic target in PD patients.
Spectrum bias: why generalists and specialists do not connect

Coronary artery disease (CAD) exists in a spectrum: it ranges from the early lesions seen in young victims of trauma1 through to sudden cardiac death or myocardial infarction with cardiogenic shock. Yet diagnostic studies that compare the clinical features and diagnostic tests with a reference standard usually act as if the disease was a homogeneous entity. This dichotomous approach to diagnostic accuracy is measured as sensitivity and specificity, likelihood ratios, diagnostic odds ratios, and the area under the receiver-operator characteristic curve.2 Ransahoff and Feinstein recognised that “unless an appropriately broad spectrum is chosen for the diseased and non-diseased patients who comprise the study population,” the diagnostic test may result in spurious estimates of diagnostic performance.3 However, this article argues that it is not possible to have a sufficiently broad spectrum of patients to be of value in a single description of diagnosis, prognosis, and therapy of any common condition such as CAD. The clinical and diagnostic features of disease such as CAD change with increasing severity of the disease. Generalists, particularly primary care clinicians, are likely to see less severe manifestations of CAD than specialists. Hence, depending on the level of specialisation of the clinician, disease presentation may create spurious clinical associations or miss legitimate clinical associations. The solution proposed for this differing disease presentation in different clinical contexts is to recognise that …
Parallel out-of-core matrix inversion

This paper presents a parallel out-of-core algorithm to invert huge dense matrices, that is matrices larger than the available physical memory by one or more orders of magnitude. Preliminary performance results are shown for a commodity cluster. An accurate prediction performance model of the algorithm is given. Thanks to the prediction model, optimizations that avoid the overhead of the out-of-core algorithm are derived. Performance of the optimized algorithm using O(N) memory size are similar to the performance of the best known parallel in-core algorithm using O(N2) memory size (where N is the matrix order). There is no memory restriction for inversion of huge matrices!
Metrics for reconfigurable architectures characterization: remanence and scalability

Target applications for mobile devices such as PDA and cellular telephones require increasingly powerful architectures. This challenge has spawned different hardware acceleration styles like configurable instruction set processors, coprocessors, and ASIC. Despite acceptable, these solutions show today a lack of flexibility considering rapidly changing standards. Structurally programmable architectures can today provide a trade-off between performance of hardwired logic and flexibility of processors. More and more reconfigurable architectures are today available as IP cores for SoC designers. These ones often differ according to several parameters (granularity, reconfiguration mode, topology.). Therefore, it is not straightforward to compare different architectures and choose the right one considering both actual and future requirements. This paper proposes a general model for reconfigurable architectures and gives a set of metrics which prove useful for architecture characterization. The methodology is illustrated on a dynamically reconfigurable architecture: the systolic ring.
Optimizing the Fast Fourier Transform on a Multi-core Architecture

The rapid revolution in microprocessor chip architecture due to multicore technology is presenting unprecedented challenges to the application developers as well as system software designers: how to best exploit the parallelism potential due to such multi-core architectures? In this paper, we report an in-depth study on such challenges based on our experience of optimizing the fast Fourier transform (FFT) on the IBM Cyclops-64 chip architecture - a large-scale multi-core chip architecture consisting 160 thread units, associated memory banks and an interconnection network that connect them together in a shared memory organization. We demonstrate how multi-core architectures like the C64 could be used to achieve a high performance implementation of FFT both in 1D and 2D cases. We analyze the optimization challenges and opportunities including problem decomposition, load balancing, work distribution, and data-reuse, together with the exploiting of the C64 architecture features such as the multi-level of memory hierarchy and large register files. Furthermore, the experience learned during the hand-tuned optimization process have provided valuable guidance in our compiler optimization design and implementation. The main contributions of this paper include: 1) our study demonstrates that successful optimization for C64-like large-scale multi-core architectures requires a careful analysis that can identify certain domain-specific features of a target application (e.g. FFT) and match them well with some key multi-core architecture features; 2) our optimization, assisted with hand-tuned process, provided quantitative evidence on the importance of each optimization identified in 1); 3) automatic optimization by our compiler, the design and implementation of which is guided by the feedbacks from 1) and 2), shows excellent results that are often comparable to the results derived from our time-consuming hand-tuned code.
Prevalence of and Predictive Factor for Abdominal Aortic Calcification in Thai Chronic Kidney Disease Patients

Presence and severity of cardiovascular calcifications strongly predict cardiovascular morbidity and mortality in patients with CKD. This multicenter, cross‐sectional study primarily aimed to determine prevalence of abdominal aortic calcification (AAC) detected by plain lateral abdominal radiograph, and secondarily aimed to assess predictive factors for AAC. Patients (N = 1500), aged 18–70 years, with CKD stages 3–5D for ≥3 months prior to evaluation, were enrolled at 24 study centers in Thailand; 54.3% were non‐dialysis patients. The prevalence of AAC was 70.6% and 70.8% in non‐dialysis and dialysis patients, respectively. Patient's advanced age and widening pulse pressure were identified as predictive factors for AAC ≥ 5 in non‐dialysis patients, while patient's age, history of coronary heart disease or diabetes, longer dialysis vintage, and increasing corrected serum calcium or high‐sensitivity C‐reactive protein were identified as such in dialysis patients. With additional regression having covariates in binary, corrected serum calcium ≥9.5 mg/dL gave an OR 1.974 (95% CI: 1.324–2.943) for AAC ≥ 5 among the dialysis patients. AAC in diabetes subgroup (N = 692) was additionally evaluated and found that it was prevalent at 84.7% with increased phosphorus as predictive factor (OR, 1.178; 95% CI: 1.032–1.344) and 1,25 (OH)2 vitamin D as protective factor (OR, 0.983; 95% CI, 0.970–0.996). The prevalence of AAC in the Thai CKD population is lower than that reported in the literature, and yet the burden is prominent in patients coexisting with diabetes. Variable relationships identified in this study may guide preventive measures against cardiovascular complications in CKD patients.
New ACC-AHA cholesterol guidelines significantly increase potential eligibility for statin treatment

Commentary on : Pencina MJ, Navar-Boggan AM, D’Agostino RB Sr., et al. Application of new cholesterol guidelines to a population-based sample. N Engl J Med 2014;370:1422–31. [OpenUrl][1][CrossRef][2][PubMed][3][Web of Science][4] In 2013, new guidelines for the treatment of cholesterol for the prevention of cardiovascular disease (CVD) were issued by the American College of Cardiology and the American Heart Association (ACC-AHA), based on a systematic review of lipid lowering trials and meta-analyses evaluating treatment impact on CVD morbidity and mortality, and quantitated adverse effects of lipid-lowering therapy.1 Many of these trials were reported after publication of the NIH-issued Third Adult Treatment Panel (ATPIII) lipid-lowering guidelines.2 The new guidelines feature modified eligibility criteria for cholesterol-lowering treatment based on estimation of benefits and harms of therapy in specific population subsets, and recommend use of a new risk calculator which … [1]: {openurl}? query=rft.jtitle%253DN%2BEngl%2BJ%2BMed%26rft.volume%253D370%26rft.spage%253D1422%26rft_id%253Dinfo%253Adoi%252F10.1056%252FNEJMoa1315665%26rft_id%253Dinfo%253Apmid%252F24645848%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [2]: /lookup/external-ref? access_num=10.1056/NEJMoa1315665&link_type=DOI [3]: /lookup/external-ref? access_num=24645848&link_type=MED&atom=%2Febmed%2Fearly%2F2014%2F07%2F09%2Febmed-2014-110029.atom [4]: /lookup/external-ref? access_num=000334095200010&link_type=ISI
Fast and Efficient Graph Traversal Algorithm for CPUs: Maximizing Single-Node Efficiency

Graph-based structures are being increasingly used to model data and relations among data in a number of fields. Graph-based databases are becoming more popular as a means to better represent such data. Graph traversal is a key component in graph algorithms such as reachability and graph matching. Since the scale of data stored and queried in these databases is increasing, it is important to obtain high performing implementations of graph traversal that can efficiently utilize the processing power of modern processors. In this work, we present a scalable Breadth-First Search Traversal algorithm for modern multi-socket, multi-core CPUs. Our algorithm uses lock- and atomic-free operations on a cache-resident structure for arbitrary sized graphs to filter out expensive main memory accesses, and completely and efficiently utilizes all available bandwidth resources. We propose a work distribution approach for multi-socket platforms that ensures load-balancing while keeping cross-socket communication low. We provide a detailed analytical model that accurately projects the performance of our single- and multi-socket traversal algorithms to within 5-10% of obtained performance. Our analytical model serves as a useful tool to analyze performance bottlenecks on modern CPUs. When measured on various synthetic and real-world graphs with a wide range of graph sizes, vertex degrees and graph diameters, our implementation on a dual-socket Intel® Xeon® X5570 (Intel microarchitecture code name Nehalem) system achieves 1.5X-13.2X performance speedup over the best reported numbers. We achieve around 1 Billion traversed edges per second on a scale-free R-MAT graph with 64M vertices and 2 Billion edges on a dual-socket Nehalem system. Our optimized algorithm is useful as a building block for efficient multi-node implementations and future exascale systems, thereby allowing them to ride the trend of increasing per-node compute and bandwidth resources.
The Pediatric Obesity Initiative: Development, implementation, and evaluation

Purpose: Pediatric obesity rates have nearly tripled over the past three decades contributing to increased morbidity and mortality in the United States and around the world. Pediatric obesity is most prevalent in developed countries and affects all races, ethnicities, cultures, and age groups. To combat this epidemic locally, a team of dedicated providers developed a comprehensive evidenced‐based toolkit and training program for clinical practices providing primary care services to children in a North Carolina county. Data sources: The toolkit and training program were developed using the most current treatment guidelines for pediatric obesity and included resources developed by Healthy Carolinians. One unique feature of the training was a demonstration of motivational interviewing with additional resources included in the toolkit. Conclusions: Staff and providers in three pediatric practices and the local Health Department received the training. In a 3 months follow‐up survey after the training, the providers indicated that the toolkit and training program were useful but that they still did not consistently use the guidelines or tools. Implications for practice: Ensuring the use of available guidelines and resources by providers remains a challenge. Further study is needed on how to improve implementation of guidelines in primary care settings.
Linear solvation energy relationships. 44. Parameter estimation rules that allow accurate prediction of octanol/water partition coefficients and other solubility and toxicity properties of polychlorinated biphenyls and polycyclic aromatic hydrocarbons.

Methods are presented for estimation of V{sub I} (intrinsic molar volume), {pi}*, and {beta} of polychlorinated biphenyls and polycyclic aromatic hydrocarbons. Taken with the equation log K{sub OW} = 0.45 + 5.15V{sub I}/100-1.29 ({pi}* - 0.40{delta}) - 3.60{beta} reported recently by Leahy, these parameter estimation rules allow prediction of log K{sub OW} with a precision that is better than the usual reproducibility of the measurements between laboratories.
Improving the QoS of Web Applications across Multiple Virtual Machines in Cloud Computing Environment

Cloud computing is a hot topic in both industrial and academic areas. Virtualization employed on large data centers forms the basis of cloud computing, which includes CPU, I/O and memory virtualization. Time-sharing of CPU cycles for multiple virtual machines (VMs) has been the main bottleneck of system-level virtualization. How to schedule CPU cycles for multi-VMs to improve the QoS of web applications need further study. This paper first proposes a CPU management architecture for multi-VMs. Then, we convert the CPU scheduling problem into an integer programming problem. Importantly, we put forward a CPU scheduling algorithm based on utility optimization theory (UOCRS) to increase the global utility. Experiments show that our scheme improves the performance of Web applications remarkably.