Miracle-dz/UniFAR-FTUs huggingface dataset:
Metagenomics: Read Length Matters

ABSTRACT Obtaining an unbiased view of the phylogenetic composition and functional diversity within a microbial community is one central objective of metagenomic analysis. New technologies, such as 454 pyrosequencing, have dramatically reduced sequencing costs, to a level where metagenomic analysis may become a viable alternative to more-focused assessments of the phylogenetic (e.g., 16S rRNA genes) and functional diversity of microbial communities. To determine whether the short (∼100 to 200 bp) sequence reads obtained from pyrosequencing are appropriate for the phylogenetic and functional characterization of microbial communities, the results of BLAST and COG analyses were compared for long (∼750 bp) and randomly derived short reads from each of two microbial and one virioplankton metagenome libraries. Overall, BLASTX searches against the GenBank nr database found far fewer homologs within the short-sequence libraries. This was especially pronounced for a Chesapeake Bay virioplankton metagenome library. Increasing the short-read sampling depth or the length of derived short reads (up to 400 bp) did not completely resolve the discrepancy in BLASTX homolog detection. Only in cases where the long-read sequence had a close homolog (low BLAST E-score) did the derived short-read sequence also find a significant homolog. Thus, more-distant homologs of microbial and viral genes are not detected by short-read sequences. Among COG hits, derived short reads sampled at a depth of two short reads per long read missed up to 72% of the COG hits found using long reads. Noting the current limitation in computational approaches for the analysis of short sequences, the use of short-read-length libraries does not appear to be an appropriate tool for the metagenomic characterization of microbial communities.
Delay-Guaranteed Cross-Layer Scheduling in Multihop Wireless Networks

In this paper, we propose a cross-layer scheduling algorithm that achieves a throughput “ ε-close” to the optimal throughput in multihop wireless networks with a tradeoff of O([1/(ε)]) in average end-to-end delay guarantees. The algorithm guarantees finite buffer sizes and aims to solve a joint congestion control, routing, and scheduling problem in a multihop wireless network while satisfying per-flow average end-to-end delay constraints and minimum data rate requirements. This problem has been solved for both backlogged as well as arbitrary arrival rate systems. Moreover, we discuss the design of a class of low-complexity suboptimal algorithms, effects of delayed feedback on the optimal algorithm, and extensions of the proposed algorithm to different interference models with arbitrary link capacities.
CHANGE DETECTION - CELLULAR AUTOMATA METHOD FOR URBAN GROWTH MODELING

This paper describes an on-going work on the development and implementation of cellular automata based urban growth modeling using multitemporal satellite imagery. The algorithm is designed to simulate the historical growth as a function of local neighbourhood structure of the input data. Transition rules in the algorithm drive the urban growth over time. Calibration is introduced in the cellular automata model. Spatial and temporal calibration schemes are used to improve the prediction accuracy. Spatially, the model is calibrated on a township basis to take into account the effect of site specific features, while the temporal calibration is set up to adapt the model to the changes in the growth pattern over time. Calibration provides the optimal values for the transition rules to achieve accurate urban growth modeling. The paper discusses at the end a proposed automatic rule calibration method using genetic algorithm. The aim is to optimize the transition rule values. Prediction accuracy is selected as the fitness function. A set of strings are used as initial population over which the genetic algorithm runs till convergence. The cellular automata model is tested over city Indianapolis, IN, USA to model its urban growth over a period of 30 years. Besides the land use data derived from the satellite imagery, population density is used. Results indicate good accuracy on a township basis for short term (5 years) and long term (11 years) prediction. The model succeeds in adapting to the dynamic growth pattern. Genetic algorithm shows promising potential in the calibration process.
A comparative study between two neutron facilities regarding SEU

We report on a comparative study between two neutron facilities used for SEU studies, namely the Weapons Neutron Research facility at Los Alamos National Laboratory (a white neutron source), and the The Svedberg Laboratory in Sweden (a quasimono-energetic neutron source). The soft error rates generated from TSL are in excellent agreement with those from WNR. Moreover, an increase of the SER for small process technologies was observed.
Suburbanization, estrogen contamination, and sex ratio in wild amphibian populations

Significance We focus on a critical issue, the influence of human-derived contaminants on wildlife populations. Endocrine disrupting chemicals that act through hormonal pathways are capable of having large influences even when concentrations are relatively low. While there is evidence that such endocrine disruption can result from the application of agricultural pesticides and through exposure to wastewater effluent, we have identified a diversity of endocrine disrupting chemicals within suburban neighborhoods. Sampling populations of a local frog species, we found a strong association between the degree of landscape development and frog offspring sex ratio. Our study points to rarely studied contamination sources, like vegetation landscaping and impervious surface runoff, that may be associated with endocrine disruption environments around suburban homes. Research on endocrine disruption in frog populations, such as shifts in sex ratios and feminization of males, has predominantly focused on agricultural pesticides. Recent evidence suggests that suburban landscapes harbor amphibian populations exhibiting similar levels of endocrine disruption; however the endocrine disrupting chemical (EDC) sources are unknown. Here, we show that sex ratios of metamorphosing frogs become increasingly female-dominated along a suburbanization gradient. We further show that suburban ponds are frequently contaminated by the classical estrogen estrone and a variety of EDCs produced by plants (phytoestrogens), and that the diversity of organic EDCs is correlated with the extent of developed land use and cultivated lawn and gardens around a pond. Our work also raises the possibility that trace-element contamination associated with human land use around suburban ponds may be contributing to the estrogenic load within suburban freshwaters and constitutes another source of estrogenic exposure for wildlife. These data suggest novel, unexplored pathways of EDC contamination in human-altered environments. In particular, we propose that vegetation changes associated with suburban neighborhoods (e.g., from forests to lawns and ornamental plants) increase the distribution of phytoestrogens in surface waters. The result of frog sex ratios varying as a function of human land use implicates a role for environmental modulation of sexual differentiation in amphibians, which are assumed to only have genetic sex determination. Overall, we show that endocrine disruption is widespread in suburban frog populations and that the causes are likely diverse.
Preparing doctoral candidates for the viva: issues for students and supervisors

The PhD viva has been described as mysterious (Burnham 1994; Morley et al. 2002), unpredictable (Rugg & Petre 2004) and potentially frightening for students (Delamont et al. 2004), with its form and duration a function of the predilections of individual examiners as well as a function of differences across disciplines. Despite its myriad manifestations, the PhD viva voce (live voice), as oral examination of the doctoral thesis, constitutes the final ‘test’ of the PhD endeavour. In the UK, this is a private event, though in some countries such as Belgium and the Netherlands, for example, the viva is conducted in a public arena (Delamont et al. 2004). Although there is no standard or prescribed format, students across all disciplines can expect to defend their thesis through a process involving questioning, clarification and discussion of key elements. This critical commentary discusses a number of issues that inform the preparation of students, focusing on the role of the internal and external examiner, the viva voce process, guidance for students and some practical suggestions for supervisors and students, particularly the value of full role-play in building students’ confidence. The extent to which the doctoral viva, in its current ‘secret’ form, can be seen as a fully accountable and independently rigorous process is taken up in the conclusion that highlights the phenomenon of ‘cosy’ reciprocal examining arrangements, the spectre of litigation when things go wrong and the need to consider a fundamental review of both the purpose and conduct of the viva.
Fatty acid regulation of hepatic lipid metabolism

Purpose of reviewTo discuss transcriptional mechanisms regulating hepatic lipid metabolism. Recent findingsHumans who are obese or have diabetes (NIDDM) or metabolic syndrome (MetS) have low blood and tissue levels of C20–22 polyunsaturated fatty acids (PUFAs). Although the impact of low C20–22 PUFAs on disease progression in humans is not fully understood, studies with mice have provided clues suggesting that impaired PUFA metabolism may contribute to the severity of risk factors associated with NIDDM and MetS. High fat diets promote hyperglycemia, insulin resistance and fatty liver in C57BL/6J mice, an effect that correlates with suppressed expression of enzymes involved in PUFA synthesis and decreased hepatic C20–22 PUFA content. A/J mice, in contrast, are resistant to diet-induced obesity and diabetes; these mice have elevated expression of hepatic enzymes involved in PUFA synthesis and C20–22 PUFA content. Moreover, loss-of-function and gain-of-function studies have identified fatty acid elongase (Elovl5), a key enzyme involved in PUFA synthesis, as a regulator of hepatic lipid and carbohydrate metabolism. Elovl5 activity regulates hepatic C20–22 PUFA content, signaling pathways (Akt and PP2A) and transcription factors (SREBP-1, PPARα, FoxO1 and PGC1α) that control fatty acid synthesis and gluconeogenesis. SummaryThese studies may help define novel strategies to control fatty liver and hyperglycemia associated with NIDDM and MetS.
Cancer incidence among Norwegian airline cabin attendants.

BACKGROUND Cabin crews are exposed to cosmic radiation at work and this may increase their incidence of radiation-induced cancers. Former studies indicate an increased risk of breast cancer. METHODS A retrospective cohort study was performed. The cohort was established from the files of the Civil Aviation Administration and included people with a valid licence as a cabin attendant between 1950 and 1994. The cohort was linked to the Cancer Registry of Norway. Observed number of cases was compared with expected, based on national rates. Breast cancer incidence was analysed, adjusting for individual fertility variables. RESULTS A group of 3693 cabin attendants were followed over 72 804 person-years. Among the women, 38 cases of breast cancer were observed (standardized incidence ratio (SIR) = 1.1, 95% CI : 0.8-1.5). Among men excess risks were found for cancers in the upper respiratory and gastric tract (SIR = 6.0, 95% CI : 2.7-11.4) and cancer of the liver (two cases, SIR = 10.8, 95% CI : 1.3-39.2). For both sexes elevated risks were found for malignant melanoma and non-melanoma skin cancer; for men these were SIR = 2.9 (95% CI : 1.1-6.4) and SIR = 9.9 (95% CI : 4.5-18.8) respectively, while for women these were SIR = 1.7 (95% CI : 1.0-2.7) and SIR = 2.9 (95% CI : 1.0-6.9) respectively. For no cancer site was a significant decreased risk found. CONCLUSIONS An increased risk of radiation-induced cancers was not observed. The excess risks of some other cancers are more probably explained by factors related to lifestyle.
Image Watermarking Based on DC Component in DCT

The peak signal-to-noise ratio (PSNR) is a simple and widely used fidelity measure in the image watermarking. The position of watermarking plays an important role when the tradeoff between robustness and invisibility is considered. In the paper we analyze the mathematical relationship between the embeddable position and the PSNR in the DCT (discrete cosine transform) domain. We consider DC (direct current) coefficient to tradeoff robustness and invisibility. And a blind watermarking scheme is implemented through quantization index modulation (QIM) technology. Experimental results show watermarking is robust to common signal processing operation such as additional noise, filtering, resizing and JPEG compressing, and invisibility is satisfaction.
Acetaminophen, aspirin, and chronic renal failure.

BACKGROUND Several epidemiologic studies have demonstrated an association between heavy consumption of nonnarcotic analgesics and the occurrence of chronic renal failure, but it is unclear which is the cause and which is the effect METHODS In a nationwide, population-based, case-control study of early-stage chronic renal failure in Sweden, face-to-face interviews were conducted with 926 patients with newly diagnosed renal failure and 998 control subjects, of whom 918 and 980, respectively, had complete data. We used logistic-regression models to estimate the relative risks of disease-specific types of chronic renal failure associated with the use of various analgesics RESULTS Aspirin and acetaminophen were used regularly by 37 percent and 25 percent, respectively, of the patients with renal failure and by 19 percent and 12 percent, respectively, of the controls. Regular use of either drug in the absence of the other was associated with an increase by a factor of 2.5 in the risk of chronic renal failure from any cause. The relative risks rose with increasing cumulative lifetime doses, rose more consistently with acetaminophen use than with aspirin use, and were increased for most disease-specific types of chronic renal failure. When we disregarded the recent use of analgesics, which could have occurred in response to antecedents of renal disease, the associations were only slightly attenuated CONCLUSIONS Our results are consistent with the existence of exacerbating effects of acetaminophen and aspirin on chronic renal failure. However, we cannot rule out the possibility of bias due to the triggering of analgesic consumption by predisposing conditions.
SYMMETRIC, COHERENT, CHOQUET CAPACITIES

Choquet capacities are a generalization of probability measures that arise in robustness, decision theory and game theory. Many capacities that arise in robustness are symmetric or can be transformed into sym­ metric capacities. We characterize the extreme points of the set of upper distribution functions corresponding to coherent, symmetric Choquet ca­ pacities on [0,1]. We also show that the set of 2-altemating capacities is a simplex and we give a Choquet representation of this set.
Long paths and cycles in random subgraphs of graphs with large minimum degree

For a given finite graph G of minimum degree at least k, let Gp be a random subgraph of G obtained by taking each edge independently with probability p. We prove that (i) if p≥ω/k for a function ω=ω(k) that tends to infinity as k does, then Gp asymptotically almost surely contains a cycle (and thus a path) of length at least (1−o(1))k , and (ii) if p≥(1+o(1))lnk/k , then Gp asymptotically almost surely contains a path of length at least k. Our theorems extend classical results on paths and cycles in the binomial random graph, obtained by taking G to be the complete graph on k + 1 vertices. © Wiley Periodicals, Inc. Random Struct. Alg. , 46, 320–345, 2015
Cytokinin-Induced Parthenocarpic Fruit Development in Tomato Is Partly Dependent on Enhanced Gibberellin and Auxin Biosynthesis

Fruit set of plants largely depends on the biosynthesis and crosstalk of phytohormones. To date the role of cytokinins (CKs) in the fruit development is less understood. Here, we showed that parthenocarpic fruit could be induced by 1-(2-chloro-4-pyridyl)-3-phenylurea (CPPU, an active CK) in tomato ( Solanum lycopersicum cv. Micro-Tom). The fresh weight of CPPU-induced parthenocarpic fruits was comparable with that induced by GA3. Importantly, CPPU-induced parthenocarpy was found to be compromised by simultaneous application of paclobutrazol (a GA biosynthesis inhibitor), and this effect could be restored by exogenous GA3. Like pollination, CPPU-induced fruit showed enhanced accumulation of GA1+3 and indole-3-acetic (IAA), which were accompanied by elevated expression of GA biosynthesis genes like SlGPS, SlGA20ox1, SlGA20ox2 and SlGA3ox1, and IAA biosynthesis gene ToFZY. Elevated GAs level in CPPU-induced fruits was also associated with down-regulation of GA inactivation genes, namely SlGA2ox1,2,3,4,5 in comparison with untreated control. These results suggested that CKs may induce parthenocarpy in tomato partially through modulation of GA and IAA metabolisms.
Why Race-to-Finish is Energy-Inefficient for Continuous Multimedia Workloads

It is often believed that a "race-to-finish" approach, where processing is finished quickly, is the best way to conserve energy on modern mobile architectures. However, from earlier work we know that for continuous multimedia workloads, the best way to conserve energy is to minimise processor frequency such that application deadlines are met. In this paper, we investigate the reasons behind this. We develop an original method to model dynamic and static power on individual power rails of the Tegra K1 by only measuring the total power usage of the board. Our model has an average error of only 8 %. We find that the way an application scales performance with frequency is very important for energy efficiency. We demonstrate a 37 % energy saving by minimising processor and memory frequency of a video processing filter such that a framerate of 20 FPS is met.
Coagulation Activity and Emboli Counts in Patients With Prosthetic Cardiac Valves

Background and Purpose The underlying embolic material detected by transcranial Doppler ultrasound in patients with prosthetic heart valves remains unknown. We undertook this study to evaluate the relation between the number of Doppler emboli signals and the activity of the coagulation system. Methods Patients with various types of prosthetic valves (n=120) and patients in atrial fibrillation (n=20) were monitored for 30 minutes using transcranial Doppler with a 2-MHz probe. The plasma concentrations of cross-linked D-dimer, antithrombin-III, and thrombin-antithrombin III complex were measured. Results No correlation between the levels of any of the hematologic parameters and the number of emboli was demonstrated in the studied groups. The D-dimer levels were significantly higher in patients with mechanical prosthetic valves with an international normalized ratio under 2.0 compared with those with an international normalized ratio between 2 and 3.5 or above 3.5, and in patients with Medtronic-Hall versus Björk-Shiley or Carpentier-Edwards valve prostheses. Conclusions The lack of correlation between the activity of the coagulation system and the number of Doppler emboli in patients with prosthetic valves suggests that the underlying embolic material in these patients is not thrombotic. Our results also suggest that an increase of the anticoagulation intensity to an international normalized ratio above 3.5 does not result in a further decrease of the activity of the unstimulated coagulation system in patients with mechanical prosthetic valves.
The complexity of the union of (α, β)-covered objects

An (α, β)-covered object is a simply connected planar region c with the property that for each point p ∈ ∂c there exists a triangle contained in c and having p as a vertex, such that all its angles are at least α and all its edges are at least β · diam(c)long. This notion extends that of fat convex objects. We show that the combinatorial complexity of the union of n (α, β)-covered objects of ‘constant description complexity’ is O(λs+2(n) log 2 n log logn), where s is the maximum number of intersections between the boundaries of any pair of the given objects.
Immortalized Adult Rodent Schwann Cells as In Vitro Models to Study Diabetic Neuropathy

We have established spontaneously immortalized Schwann cell lines from normal adult mice and rats and murine disease models. One of the normal mouse cell lines, IMS32, possesses some biological properties of mature Schwann cells and high proliferative activities. The IMS32 cells under hyperglycemic and/or hyperlipidemic conditions have been utilized to investigate the pathogenesis of diabetic neuropathy, especially the polyol pathway hyperactivity, glycation, increased oxidative stress, and reduced synthesis of neurotrophic factors. In addition to the mouse cell lines, our current study focuses on the characterization of a normal rat cell line, IFRS1, under normal and high glucose conditions. These Schwann cell lines can be valuable tools for exploring the detailed mechanisms leading to diabetic neuropathy and novel therapeutic approaches against that condition.
Communicating Uncertainty in Surgical Pathology Reports

In order to document perceptions of text comments appearing in surgical pathology reports, questionnaires were distributed to 4 groups of caregivers: university staff pathologists, resident pathologists, faculty clinicians (other than pathologists), and resident clinicians at a teaching hospital. Results of this pilot study showed a wide degree of variability existed within each group of surgical pathology report users, with respect to percent confidence assigned to various phrases, commonly used to express diagnostic uncertainty, appearing often as free-text comments in surgical pathology reports. The unavailability of immunohistochemistry tests, or ambiguous immunohistochemistry test results, was especially problematic. With respect to modes of communication between the surgical pathology laboratory and its service users, clinicians indicated they preferred to use tumor boards/interdisciplinary conferences, face-to-face meetings, and phone calls to clarify their interpretations of a pathologist’s diagnoses, as compared with simply reading free-text comments. On the other hand, surgical pathologists rely heavily on their use of the comment portion of a surgical pathology report to clarify, modify, or expand on the diagnoses they render. The majority of clinicians stated that they “always” read the free-text comment portion of a surgical pathology report, whereas some acknowledged they do not always read it. Pathology residents had significantly less confidence in the ability of a free-text comment on a surgical pathology report to clarify a diagnosis (χ2 = 46.36, P < .0001). Pathology departments should consider standardizing definitions and weighting the words and phrases they use in their free-text comment sections of surgical pathology reports.