Miracle-dz/UniFAR-FTUs huggingface dataset:
Conspecific Plasticity and Invasion: Invasive Populations of Chinese Tallow (Triadica sebifera) Have Performance Advantage over Native Populations Only in Low Soil Salinity

Global climate change may increase biological invasions in part because invasive species may have greater phenotypic plasticity than native species. This may be especially important for abiotic stresses such as salt inundation related to increased hurricane activity or sea level rise. If invasive species indeed have greater plasticity, this may reflect genetic differences between populations in the native and introduced ranges. Here, we examined plasticity of functional and fitness-related traits of Chinese tallow (Triadica sebifera) populations from the introduced and native ranges that were grown along a gradient of soil salinity (control: 0 ppt; Low: 5 ppt; Medium: 10 ppt; High: 15 ppt) in a greenhouse. We used both norm reaction and plasticity index (PIv) to estimate the conspecific phenotypic plasticity variation between invasive and native populations. Overall, invasive populations had higher phenotypic plasticity of height growth rate (HGR), aboveground biomass, stem biomass and specific leaf area (SLA). The plasticity Index (PIv) of height growth rate (HGR) and SLA each were higher for plants from invasive populations. Absolute performance was always comparable or greater for plants from invasive populations versus native populations with the greatest differences at low stress levels. Our results were consistent with the “Master-of-some” pattern for invasive plants in which the fitness of introduced populations was greater in more benign conditions. This suggests that the greater conspecific phenotypic plasticity of invasive populations compared to native populations may increase invasion success in benign conditions but would not provide a potential interspecific competitive advantage in higher salinity soils that may occur with global climate change in coastal areas.
PCMO RRAM for Integrate-and-Fire Neuron in Spiking Neural Networks

Resistance random access memories (RRAM) or memristors with an analog change of conductance are widely explored as an artificial synapse, e.g., Pr0.7Ca0. 3MnO3 (PCMO) RRAM-based synapses. In addition to synapses, scaled neurons are essential to enable a neuromorphic hardware. In this letter, we propose a PCMO RRAM for integrate and fire (IF) neuron. The analog conductance increase during SET process enables integration function. Upon exceeding a conductance threshold (i.e., fire) during a READ operation, a hard RESET is performed to reduce the conductance. The SET, READ, and RESET are performed in different phases of a clock to enable a PCMO for IF neuron. The availability of a non-volatile PCMO-based synapse makes PCMO for IF neuron attractive. Finally, PCMO-based neuron in spiking neural network yields software-equivalent classification accuracy as demonstrated on standard Fischer’s Iris flower data set.
Application of Sculptured Thin Film Technology to Metal Oxide Gas Sensors

KIETHER, WILLIAM JAY. Application of Sculptured Thin Film Technology to Metal Oxide Gas Sensors. (Under the direction of Dr. H. Troy Nagle.) The main goal of this research has been the application of glancing angle deposition (GLAD) techniques to create highly porous sculptured thin films (STF) structures for use as gas sensors. The glancing angle technique utilizes physical vapor depositions at highly oblique (>70o) angles of incidence to form porous film structures. Process conditions including the deposition rate, rotation speed, and flux angle were investigated to produce pillar and chevron formations. Control of the anatase/rutile percentages in TiO2 gas sensors is critical for design and development. Thin films were deposited using reactive e-beam evaporation with a titanium source melt at various partial pressures of oxygen and argon. Post deposition anneal studies were conducted in air from 150-900 °C. The combination of reactive evaporation at high oxygen partial pressures and low temperature (150 °C) anneals in air formed films with the highest percentage of anatase. Depositions at lower oxygen partial pressures yielded films with a higher percentage of rutile, which supports the role of oxygen vacancies as nucleation centers for the anatase to rutile transformation. Higher temperature annealing produced rutile films as expected from the thermodynamics of the TiO2 system. After the formation of anatase STF structures, the films displayed a high degree of temperature stability during subsequent annealing. Anatase structures were still evident even after annealing at 1200 oC in air. The GLAD technique produces films with preferred crystal orientations which differ based on the deposition angle. A series of experiments looked at the effect of the angle of incidence, the deposition conditions, and the substrate material on the crystal structure of the STF structures. The titanium films show a dependence of the crystalline structure on the angle of incidence for both as-deposited films and after oxidation at 900 oC in air. A conductive MOS sensor was designed based on an anatase chevron formation. Following the fabrication of a sensor test chamber, the sensor response was characterized versus temperature for inert, oxidizing, and reducing atmospheres. Application of Sculptured Thin Film Technology to Metal Oxide Gas Sensors By William Jay Kiether A dissertation submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy ELECTRICAL ENGINEERING Raleigh, North Carolina 2007
A Cohort Study of Adolescent and Midlife Diet and Pancreatic Cancer Risk in the NIH-AARP Diet and Health Study

Given the long latency period of pancreatic cancer, exploring the influence of early and midlife exposures will further advance our understanding of the disease. We assessed associations between diet and pancreatic cancer incidence in the National Institutes of Health (NIH)-AARP (formerly American Association of Retired Persons) Diet and Health Study. In 1996, a total of 303,094 participants completed 2 food frequency questionnaires that assessed diet at ages 12-13 years and 10 years previously. We used Cox proportional hazards regression to estimate adjusted hazard ratios and 95% confidence intervals. Through the end of 2006, a total of 1,322 pancreatic cancer cases occurred (average follow up time = 10.1 years). When comparing the highest tertiles with the lowest, carbohydrate intake during adolescence (hazard ratio (HR) = 0.87, 95% confidence interval (CI): 0.76, 0.99), but not 10 years before baseline, was inversely associated with pancreatic cancer risk. Total fat intake 10 years before baseline was significantly associated with increased risk (HR = 1.17, 95% CI: 1.02, 1.34), while risk was higher for high fat intake during both adolescence and midlife. Calcium intake 10 years before baseline was associated with reduced risk (HR = 0.87, 95% CI: 0.76, 0.99), as was a change from low intake in adolescence to high intake in midlife (HR = 0.71, 95% CI: 0.54, 0.93). Our study found a number of dietary factors present during adolescence and midlife to be associated with pancreatic cancer.
Anderson localization of light in a random configuration of nanocolumns

We show pseudogap maps of Anderson localization of light adopting the parameters of self-organized nanocolumn samples, which consist of random arrays of parallel nanosized columnar semiconductor crystals. The maps indicate the parametric dependence of the localization effect. To obtain the maps, we simulated light propagation in open random media using the two-dimensional finite-difference time-domain method and analyzed the simulation results by Fourier transformation. We found that the shape of the pseudogaps is close to the one of bandgaps in photonic crystals. We conclude that strong localization of light occurs because of interference by average Bragg diffraction, not strong Mie resonant peaks.
Adaptive probability marking traceback scheme to enhance security in wireless sensor networks

Security is a pivotal issue for Wireless sensor networks (WSNs) which are emerging as a promising platform that enable a wide range of applications in military, scientific, industrial and commercial applications. Traceback as one of key cyber forensics technologies can play an important role to trace and locate malicioussource as to guarantee cyber security. An adaptive probability marking traceback (APMT) scheme is proposed to enhance security for WSNs. In APMT scheme, the marking probability is adaptive adjust according to the requirement of the security which can substantial reduce marking tuples and improve lifetime. The results of experimental show that: the number of total marking tuples can be reduced by 13.20%-73.70% in APMT scheme, it can improve the network lifetime, at the same time, and the traceback time can be reduced by more than 80%.
Investigation on structural behavior of an innovative orthogonal-diagonal steel open-web sandwich floor system

A new orthogonal-diagonal steel open-web sandwich floor system has been developed by the authors in the past few years to replace the conventional methodology. This floor system owns excellent structural mechanical characteristics to be applied in civil engineering applications. The three-dimensional structural characteristics are achieved by letting the top and bottom chords of the space truss that constitutes the floor inclined 45° toward the edge of the boundary lines. The present work focuses on the fabrication and erection of the proposed floor and its structural behavior subjected to partial loadings. Field partially-loaded test was conducted and the performance was evaluated in terms of the deflection distribution and stress response at different load levels. A three-dimensional numerical finite element model was developed and calibrated against the test results. The results demonstrate that the new floor system offers satisfactory structural performance.
Frequency Change of Tension-Shear Two Spot Welds During Fatigue

Fatigue tests on tension-shear spot welds of single-spot and two-spot were carried out.The crack initiation location and crack shape were observed,changes of natural frequency were obtained.Deformation of two kinds of specimens was analyzed by finite element method.Comparison of the load amplitude-life relationship between two kinds of spot welds showed that under same fatigue life,two-spot welds bear twice the loadings of single-spot welds.Change of natural frequency were analysed with finite element analysis,according frequency test results, frequency ration at failure were defined,with which damage during fatigue process was calculated.
Automatic quantification of ejection fraction from gated myocardial perfusion SPECT.

UNLABELLED We have developed a completely automatic algorithm to quantitatively measure left ventricular ejection fraction (LVEF) from gated 99mTc-sestamibi myocardial perfusion SPECT images. METHODS The algorithm operates in the three-dimensional space and uses gated short-axis image volumes. It segments the left ventricle (LV), estimates and displays endocardial and epicardial surfaces for all gating intervals in the cardiac cycle, calculates the relative left ventricular cavity volumes and derives the global EF from the end-diastolic and end-systolic volume, all without operator interaction. The algorithm for measuring LVEF was tested in 65 clinical patients undergoing 16-interval and 8-interval rest-gated SPECT and validated against first-pass radionuclide ventriculography. RESULTS Automatic segmentation and contouring of the LV was successful in 65/65 (100%) of the studies. Agreement between EFs measured from 8-interval gated SPECT and EFs calculated from first-pass data was high (y = 2.44 + 1.03x, r = 0.909, p < 0.001, s.e.e. = 6.87). Agreement between EF values measured from 16-interval and 8-interval gated SPECT was excellent (y = -2.7 + 0.97x, r = 0.988, p < 0.001, s.e.e. = 2.65), the latter being on average lower by 3.71 percentage points. CONCLUSION Our automatic method is rapid and highly agrees with conventional radionuclide measurements of EF, thus providing clinically useful additional information to complement myocardial perfusion studies.
Structured Output Learning with Abstention: Application to Accurate Opinion Prediction

Motivated by Supervised Opinion Analysis, we propose a novel framework devoted to Structured Output Learning with Abstention (SOLA). The structure prediction model is able to abstain from predicting some labels in the structured output at a cost chosen by the user in a flexible way. For that purpose, we decompose the problem into the learning of a pair of predictors, one devoted to structured abstention and the other, to structured output prediction. To compare fully labeled training data with predictions potentially containing abstentions, we define a wide class of asymmetric abstention-aware losses. Learning is achieved by surrogate regression in an appropriate feature space while prediction with abstention is performed by solving a new pre-image problem. Thus, SOLA extends recent ideas about Structured Output Prediction via surrogate problems and calibration theory and enjoys statistical guarantees on the resulting excess risk. Instantiated on a hierarchical abstention-aware loss, SOLA is shown to be relevant for fine-grained opinion mining and gives state-of-the-art results on this task. Moreover, the abstention-aware representations can be used to competitively predict user-review ratings based on a sentence-level opinion predictor.
Association rule mining for finding usability problem patterns: A case study on StackOverflow

Usually, developers suffer from usability related problems during working with software development tools. Such problems should be detected to improve developer team performance. To tackle this problem, pattern discovery techniques can be used to locate usability problems by analyzing the feedback of users extracted from software repositories. In this paper, a comprehensive data analysis methodology is presented to extract hidden knowledge for acquiring user challenges regarding tools interaction. The main motivation of this paper is to involve the role of knowledge in software development process such as Agile development. Rich user feedback datasets from StackOverflow programming Question and Answer (Q&A) repository have been used as the input of Apriori algorithm while required preprocessing has been considered. The generated results are association rules representing the usability problem patterns among tools and technologies interactions. The results can also be used for effort planning when a software upgrade needs to be considered.
SETD6 dominant negative mutation in familial colorectal cancer type X

Familiar colorectal cancer type X (FCCTX) comprises families that fulfill the Amsterdam criteria for hereditary non-polyposis colorectal cancer, but that lack the mismatch repair deficiency that defines the Lynch syndrome. Thus, the genetic cause that increases the predisposition to colorectal and other related cancers in families with FCCTX remains to be elucidated. Using whole-exome sequencing, we have identified a truncating mutation in the SETD6 gene (c.791_792insA, p.Met264IlefsTer3) in all the affected members of a FCCTX family. SETD6 is a mono-methyltransferase previously shown to modulate the NF-κB and Wnt signaling pathways, among other. In the present study, we characterized the truncated version of SETD6, providing evidence that this SETD6 mutation may play a role in the cancer inheritance in this family. Here we demonstrate that the truncated SETD6 lacks its enzymatic activity as a methyltransferase, while maintaining other properties such as its expression, localization and substrate-binding ability. In addition, we show that the mutant allele is expressed and that the resulting protein competes with the wild type for their substrates, pointing to a dominant negative nature. These findings suggest that the identified mutation impairs the normal function of SETD6, which may result in the deregulation of the different pathways in which it is involved, contributing to the increased susceptibility to cancer in this FCCTX family.
Genetic Determinants of High-Level Oxacillin Resistance in Methicillin-Resistant Staphylococcus aureus

ABSTRACT Methicillin-resistant Staphylococcus aureus (MRSA) strains carry either a mecA- or a mecC-mediated mechanism of resistance to beta-lactam antibiotics, and the phenotypic expression of resistance shows extensive strain-to-strain variation. In recent communications, we identified the genetic determinants associated with the stringent stress response that play a major role in the antibiotic resistant phenotype of the historically earliest “archaic” clone of MRSA and in the mecC-carrying MRSA strain LGA251. Here, we sought to test whether or not the same genetic determinants also contribute to the resistant phenotype of highly and homogeneously resistant (H*R) derivatives of a major contemporary MRSA clone, USA300. We found that the resistance phenotype was linked to six genes (fruB, gmk, hpt, purB, prsA, and relA), which were most frequently targeted among the analyzed 20 H*R strains (one mutation per clone in 19 of the 20 H*R strains). Besides the strong parallels with our previous findings (five of the six genes matched), all but one of the repeatedly targeted genes were found to be linked to guanine metabolism, pointing to the key role that this pathway plays in defining the level of antibiotic resistance independent of the clonal type of MRSA.
Viral Fitness Correlates with the Magnitude and Direction of the Perturbation Induced in the Host’s Transcriptome: The Tobacco Etch Potyvirus—Tobacco Case Study

Abstract Determining the fitness of viral genotypes has become a standard practice in virology as it is essential to evaluate their evolutionary potential. Darwinian fitness, defined as the advantage of a given genotype with respect to a reference one, is a complex property that captures, in a single figure, differences in performance at every stage of viral infection. To what extent does viral fitness result from specific molecular interactions with host factors and regulatory networks during infection? Can we identify host genes in functional classes whose expression depends on viral fitness? Here, we compared the transcriptomes of tobacco plants infected with seven genotypes of tobacco etch potyvirus that differ in fitness. We found that the larger the fitness differences among genotypes, the more dissimilar the transcriptomic profiles are. Consistently, two different mutations, one in the viral RNA polymerase and another in the viral suppressor of RNA silencing, resulted in significantly similar gene expression profiles. Moreover, we identified host genes whose expression showed a significant correlation, positive or negative, with the virus' fitness. Differentially expressed genes which were positively correlated with viral fitness activate hormone- and RNA silencing-mediated pathways of plant defense. In contrast, those that were negatively correlated with fitness affect metabolism, reducing growth, and development. Overall, these results reveal the high information content of viral fitness and suggest its potential use to predict differences in genomic profiles of infected hosts.
Elements of Physical Biology.

FOR a long time methods analogous to those of statistical mechanics have been applied to animal and plant communities. But just as in physical chemistry these methods soon become intolerably cumbrous and may generally be replaced by thermodynamical calculations which ignore the individual molecule, so in the book before us the author has applied to biological problems a treatment of the type familiar in chemical statics and kinetics. These methods are applied to the growth of populations, whether of bacteria, insects, men,. or railway engines, and to relationships between different species, for example, between a parasite and one or more hosts. The author has the problem of evolution always before him, and considers analytically the effect on population of a change in the behaviour of individuals.Elements of Physical Biology.By Dr. Alfred J. Lotka. Pp. xxx + 460. (Baltimore, Md.: Williams and Wilkins Co.; London: Baillière, Tindall and Cox, 1925.) 25s. net.
Gaze-Informed Egocentric Action Recognition for Memory Aid Systems

Egocentric action recognition has been intensively studied in the fields of computer vision and clinical science with applications in pervasive health-care. The majority of the existing egocentric action recognition techniques utilize the features extracted from either the entire contents or the regions of interest (ROI) in video frames as the inputs of action classifiers. The former might suffer from moving backgrounds or irrelevant foregrounds usually associated with egocentric action videos, while the latter may be impaired by the mismatch between the calculated and the ground truth ROI. This paper proposes a new gaze-informed feature extraction approach, by which the features are extracted from the regions around the gaze points and thus representing the genuine ROI from a first person of view. The activity of daily life can then be classified based only on the identified regions using the extracted gaze-informed features. The proposed approach has been further applied to a memory support system for people with poor memory, such as those with amnesia or dementia, and their carers. The experimental results demonstrate the efficacy of the proposed approach in egocentric action recognition, and thus the potential of the memory support tool in health care.
Discovery of Potential Therapeutic miRNA Targets in Cardiac Ischemia–Reperfusion Injury

Background: A highly efficient approach to select microRNA (miRNA) targets is a key to develop a miRNA-based therapeutic approach to cardiac ischemia–reperfusion (I/R). To reverse the change induced by disease, I/R in this case, is the traditional strategy to develop therapeutic drugs. However, examples show that it will not always serve the purpose. In this study, we demonstrate an additional approach of selecting miRNA targets with therapeutic potential following cues from cardioprotection-induced changes rather than by reversing disease-induced changes in cardiac I/R. Methods: Isolated perfused rat hearts subjected to I/R were treated with 50 μmol/L sodium hydrosulfide (NaHS) or 10 nmol/L urocortin 2 (UCN2). Cardiac miRNA regulations were determined by miRNA array. Functional screening of selected miRNA mimics, assessed by WST (2-(4-Iodophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium, monosodium salt) activity and lactate dehydrogenase (LDH) release, was performed in H9c2 and neonatal rat ventricular myocytes (NRVMs) with hypoxia/reoxygenation. RNA-induced silencing complex (RISC)-loaded miRNAs caused by mimic transfection were quantified following argonaute-2 immunoprecipitation. Gene regulations of 1 selected miRNA were determined by quantitative polymerase chain reaction and Western blot. Results: Treatment with NaHS and UCN2 significantly improved cardiac function and reduced LDH release. The miRNA array indicated a panel of commonly up- and downregulated miRNAs. Among them, 10 upregulated miRNAs with antiapoptotic and antiautophagy potentials were selected for further screening. Mimics of miRNA-221, -150, and -206 were protective in both H9c2 and NRVM. RISC-loaded miRNAs were up by ∼20-fold above. To further prove the feasibility of this approach, miRNA-221 was studied. It reduced I/R-induced caspase 3/7 activity and LC3-II (microtubule-associated protein 1 light chain 3). Measuring genes predicted to regulate apoptosis and autophagy, miRNA-221 mimic decreased Ddit4, TP53inp1, and p27 at both messenger RNA (mRNA) and protein levels, and reduced mRNA of Bak1 and Puma and proteins of Bim and Bmf. Conclusion: Mimicking miRNA changes caused by cardioprotective agents, combined with functional screening, enables investigators to efficiently identify novel miRNAs with therapeutic potential in cardiac I/R.