Miracle-dz/UniFAR-FTUs huggingface dataset:
Simulation of Interfacial Phonon Transport in Si–Ge Heterostructures Using an Atomistic Green’s Function Method

An atomistic Green 's function method is developed to simulate phonon transport across a strained germanium (or silicon) thin film between two semi-infinite silicon (or germanium) contacts. A plane-wave formulation is employed to handle the translational symmetry in directions parallel to the Interfaces. The phonon transmission function and thermal conductance across the thin film are evaluated for various atomic configurations. The contributions from lattice straining and material heterogeneity are evaluated separately, and their relative magnitudes are characterized. The dependence of thermal conductance on film thickness is also calculated, verifying that the thermal conductance reaches an asymptotic value for very thick films. The thermal boundary resistance of a single Si/Ge interface is computed and agrees well with analytical model predictions. Multiple-interface effects on thermal resistance are investigated, and the results indicate that the first few interfaces have the most significant effect on the overall thermal resistance.
Evolving Guide Trees in Progressive Multiple Sequence Alignment

We present a novel application of genetic algorithms to the problem of aligning multiple biological sequences through the optimization of guide trees. Individual guide trees are represented as coalescing binary trees which provide for efficient and meaningful crossover and mutation operations. We hypothesize that our technique avoids the limitations of other heuristic tree-building techniques, and is therefore capable of producing better trees, as measured by higher quality alignments. Further, our approach is more scalable than commonly used progressive alignment techniques when aligning large datasets.
Embedding Knowledge Exchange Within Irish Universities- International Shifts Towards A Hybrid Academic?

The recent literature is comprehensive in outlining how higher education internationally is immersed in operational and cultural change with fiscal challenges placing immense focus on competition. This paper is primarily focused on the knowledge exchange policy/practice nexus in Ireland. The term knowledge exchange is adopted while recognizing the evident overlap with many other related concepts such as knowledge transfer, university community engagement, integrative applied research, and engaged scholarship. This paper provides an overview of recent international shifts on responding and supporting a more coordinated approach to knowledge exchange initiatives as a response for universities to provide for greater social accountability. This paper will reflect on the new demands on Irish universities and argues for the need for more attention and support to be given on the collaborative capacity of researchers and support staff in order to embed knowledge exchange fully.
The functional significance of chronotropic incompetence during dobutamine stress test

OBJECTIVE To investigate the functional significance of chronotropic incompetence during dobutamine stress echocardiography. PATIENTS AND METHODS The functional significance of chronotropic incompetence was evaluated during dobutamine stress echocardiography in 512 patients without β blocker treatment who underwent dobutamine stress echocardiography (up to 40 μg/kg/min) and completed the protocol or reached the target heart rate. Mean (SD) age was 60 (12) years (313 men, 199 women). Chronotropic incompetence was defined as failure to achieve 85% of the maximum exercise heart rate predicted for age and sex (220 − age in men; 200 − age in women) at maximum dobutamine dose. RESULTS Chronotropic incompetence occurred in 196 patients (38%). Affected patients were significantly younger, more likely to be men (both p << 0.001) and smokers (p < 0.05), had a higher prevalence of previous myocardial infarction (p < 0.005) and resting wall motion abnormalities (p < 0.05), and had a lower resting heart rate (p << 0.001) and systolic blood pressure (p << 0.001) than patients without chronotropic incompetence, but there was no difference in the overall prevalence of ischaemia and significant coronary artery disease. By multivariate analysis, independent predictors of chronotropic incompetence were a lower resting heart rate (p << 0.001), younger age (p << 0.001), and male sex (p << 0.001). CONCLUSIONS The relations among sex, age, and chronotropic incompetence show the need to titrate the dobutamine dose using specific data based on age and sex related heart rate responses to dobutamine rather than to an exercise stress test. Obtaining specific heart rate criteria is necessary to determine whether chronotropic incompetence represents a real failure to achieve a normal response or is the result of applying an inappropriate gold standard.
Paraprofessional-Led Phonological Awareness Training With Youngsters at Risk for Reading and Behavioral Concerns

This study examined the efficacy of a paraprofessional-led supplemental early intervention for first-grade students with poor early literacy skills and behavioral concerns. The goal was to determine if (a) the relatively brief intervention was effective in improving phonological skills, and (b) improvements in academic skills would be accompanied by behavioral and social improvements. The results indicated that the students in the treatment condition experienced significant, lasting increases in phonological awareness and moderate improvement in word attack skills. However, significant collateral effects on social and behavioral performance were not observed. Limitations and directions for future investigation are offered.
An Enhanced Dragonfly Key Exchange Protocol against Offline Dictionary Attack

Dragonfly is Password Authenticated Key Exchange protocol that uses a shared session key to authenticate parties based on pre-shared secret password. It was claimed that this protocol was secure against off-line dictionary attack, but a new research has proved its vulnerability to off-line dictionary attack and proving step was applied by using “Patched Protocol” which was based on public key validation. Unfortunately, this step caused a raise in the computation cost, which made this protocol less appealing than its competitors. We proposed an alternate enhancement to keep this protocol secure without any extra computation cost that was known as “Enhanced Dragonfly”. This solution based on two-pre-shared secret passwords instead of one and the rounds between parties had compressed into two rounds instead of four. We prove that the enhanced-Dragonfly protocol is secure against off-line dictionary attacks by analyzing its security properties using the Scyther tool. A simulation was developed to measure the execution time of the enhanced protocol, which was found to be much less than the execution time of patched Dragonfly. The off-line dictionary attack time is consumed for few days if the dictionary size is 10,000. According to this, the use of the enhanced Dragonfly is more efficient than the patched Dragonfly.
Association of low-level ozone and fine particles with respiratory symptoms in children with asthma.

CONTEXT Exposure to ozone and particulate matter of 2.5 microm or less (PM2.5) in air at levels above current US Environmental Protection Agency (EPA) standards is a risk factor for respiratory symptoms in children with asthma. OBJECTIVE To examine simultaneous effects of ozone and PM2.5 at levels below EPA standards on daily respiratory symptoms and rescue medication use among children with asthma. DESIGN, SETTING, AND PARTICIPANTS Daily respiratory symptoms and medication use were examined prospectively for 271 children younger than 12 years with physician-diagnosed, active asthma residing in southern New England. Exposure to ambient concentrations of ozone and PM2.5 from April 1 through September 30, 2001, was assessed using ozone (peak 1-hour and 8-hour) and 24-hour PM2.5. Logistic regression analyses using generalized estimating equations were performed separately for maintenance medication users (n = 130) and nonusers (n = 141). Associations between pollutants (adjusted for temperature, controlling for same- and previous-day levels) and respiratory symptoms and use of rescue medication were evaluated. MAIN OUTCOME MEASURES Respiratory symptoms and rescue medication use recorded on calendars by subjects' mothers. RESULTS Mean (SD) levels were 59 (19) ppb (1-hour average) and 51 (16) ppb (8-hour average) for ozone and 13 (8) microg/m3 for PM2.5. In copollutant models, ozone level but not PM2.5 was significantly associated with respiratory symptoms and rescue medication use among children using maintenance medication; a 50-ppb increase in 1-hour ozone was associated with increased likelihood of wheeze (by 35%) and chest tightness (by 47%). The highest levels of ozone (1-hour or 8-hour averages) were associated with increased shortness of breath and rescue medication use. No significant, exposure-dependent associations were observed for any outcome by any pollutant among children who did not use maintenance medication. CONCLUSION Asthmatic children using maintenance medication are particularly vulnerable to ozone, controlling for exposure to fine particles, at levels below EPA standards.
Validity and Reliability of Accelerometers in Patients With COPD: A SYSTEMATIC REVIEW

Purpose: Reduced physical activity is associated with poor prognosis in chronic obstructive pulmonary disease (COPD). Accelerometers have greatly improved quantification of physical activity by providing information on step counts, body positions, energy expenditure, and magnitude of force. The purpose of this systematic review was to compare the validity and reliability of accelerometers used in patients with COPD. Methods: An electronic database search of MEDLINE and CINAHL was performed. Study quality was assessed with the Strengthening the Reporting of Observational Studies in Epidemiology checklist while methodological quality was assessed using the modified Quality Appraisal Tool for Reliability Studies. Results: The search yielded 5392 studies; 25 met inclusion criteria. The SenseWear Pro armband reported high criterion validity under controlled conditions (r = 0.75-0.93) and high reliability (ICC = 0.84-0.86) for step counts. The DynaPort MiniMod demonstrated highest concurrent validity for step count using both video and manual methods. Discussion: Validity of the SenseWear Pro armband varied between studies especially in free-living conditions, slower walking speeds, and with addition of weights during gait. A high degree of variability was found in the outcomes used and statistical analyses performed between studies, indicating a need for further studies to measure reliability and validity of accelerometers in COPD. Conclusion: The SenseWear Pro armband is the most commonly used accelerometer in COPD, but measurement properties are limited by gait speed variability and assistive device use. DynaPort MiniMod and Stepwatch accelerometers demonstrated high validity in patients with COPD but lack reliability data.
Effects of selective vagal and stellate ganglion stimulation of atrial refractoriness.

This study reports results of selective right and left vagosympathetic trunk (VST) and stellate ganglion stimulation (supra-maximal intensity) on atrial refractory period (ARP) in dogs. The effect of selective stellate stimulation on A-V conduction was also evaluated. During right and left VST stimulation, the region of the sinus node exhibited greater ARP shortening than most of the tested sites on the right atrium and all of the tested sites on the left atrium. The right VST exerted a greater effect on the right atrium than on the left atrium. Right VST stimulation shortened ARP at most tested right atrial sites more than did left VST stimulation. Selective vagal stimulation could result in three-fold difference in ARPs at the same electrode site. During right or left stellate ganglion stimulation, the refractory period change at any atrial site was usually minimal and often did not change at all. Supra-maximal right or left stellate stimulation shortened A-H (nodal) conduction by 50% or more in some experiments but shortened conduction time distal to the bundle of His by only 1 to 3 msec.
The effects of sodium oxybate on core body and skin temperature regulation in narcolepsy

Patients suffering from narcolepsy type 1 show altered skin temperatures, resembling the profile that is related to sleep onset in healthy controls. The aim of the present study is to investigate the effects of sodium oxybate, a widely used drug to treat narcolepsy, on the 24‐h profiles of temperature and sleep‐wakefulness in patients with narcolepsy and controls. Eight hypocretin‐deficient male narcolepsy type 1 patients and eight healthy matched controls underwent temperature measurement of core body and proximal and distal skin twice, and the sleep–wake state for 24 h. After the baseline assessment, 2 × 3 g of sodium oxybate was administered for 5 nights, immediately followed by the second assessment. At baseline, daytime core body temperature and proximal skin temperature were significantly lower in patients with narcolepsy (core: 36.8 ± 0.05 °C versus 37.0 ± 0.05 °C, F = 8.31, P = 0.01; proximal: 33.4 ± 0.26 °C versus 34.3 ± 0.26 °C, F = 5.66, P = 0.03). In patients, sodium oxybate administration increased proximal skin temperature during the day (F = 6.46, P = 0.04) to a level similar as in controls, but did not affect core body temperature, distal temperature or distal–proximal temperature gradient. Sodium oxybate administration normalised the predictive value of distal skin temperature and distal–proximal temperature gradient for the onset of daytime naps (P < 0.01). In conclusion, sodium oxybate administration resulted in a partial normalisation of the skin temperature profile, by increasing daytime proximal skin temperature, and by strengthening the known relationship between skin temperature and daytime sleep propensity. These changes seem to be related to the clinical improvement induced by sodium oxybate treatment. A causal relationship is not proven.
Predicting protein–DNA interactions by full search computational docking

Protein–DNA interactions are essential for many biological processes. X‐ray crystallography can provide high‐resolution structures, but protein‐DNA complexes are difficult to crystallize and typically contain only small DNA fragments. Thus, there is a need for computational methods that can provide useful predictions to give insights into mechanisms and guide the design of new experiments. We used the program DOT, which performs an exhaustive, rigid‐body search between two macromolecules, to investigate four diverse protein–DNA interactions. Here, we compare our computational results with subsequent experimental data on related systems. In all cases, the experimental data strongly supported our structural hypotheses from the docking calculations: a mechanism for weak, nonsequence‐specific DNA binding by a transcription factor, a large DNA‐binding footprint on the surface of the DNA‐repair enzyme uracil‐DNA glycosylase (UNG), viral and host DNA‐binding sites on the catalytic domain of HIV integrase, and a three‐DNA‐contact model of the linker histone bound to the nucleosome. In the case of UNG, the experimental design was based on the DNA‐binding surface found by docking, rather than the much smaller surface observed in the crystallographic structure. These comparisons demonstrate that the DOT electrostatic energy gives a good representation of the distinctive electrostatic properties of DNA and DNA‐binding proteins. The large, favourably ranked clusters resulting from the dockings identify active sites, map out large DNA‐binding sites, and reveal multiple DNA contacts with a protein. Thus, computational docking can not only help to identify protein–DNA interactions in the absence of a crystal structure, but also expand structural understanding beyond known crystallographic structures. Proteins 2013; 81:2106–2118. © 2013 Wiley Periodicals, Inc.
The cognitive psychology of auditory distraction: The 1997 BPS Broadbent Lecture

Recent research extending Broadbent's work on selective auditory attention is described through the medium of the irrelevant sound effect (the loss of efficiency when irrelevant sound is played during a serial short-term memory task). This breakdown of selective attention cannot be explained by interference at encoding, but rather as disruption following some obligatory entry of sound into memory. Within memory, interference does not arise as a result of the conflict between the contents of memory and the irrelevant sound, since neither phonological nor semantic similarity predicts its extent. Instead, the interference seems to be a product of the similarity in process - the degree of seriation - between rehearsal in short-term memory and the perceptual organization of the irrelevant sound. This type of breakdown in selectivity is likely to have relatively great practical impact, particularly since it is relatively insensitive to loudness and does not appear to diminish with repeated exposure.
Infrastructureless signal source localization using crowdsourced data for smart-city applications

As mobile crowdsourcing techniques are steering many smart-city and Internet-of-Things applications, a new challenge of signal source localization problem arises, which is to infer the locations of signal sources based on crowdsourced data. It will benefit real-world applications such as WiFi advisory systems by locating WiFi access points and urban noise monitoring systems by locating noise sources. However, crowdsourced data collected from diverse mobile devices are often sparse, fluctuating, and inconsistent. In this paper, we propose a source localization scheme to solve this problem, without the need of prior localization infrastructure or reference (anchor) nodes. We also implement a crowdsourcing WiFi advisory system and conduct real-world experiments to evaluate the performance of the proposed scheme. The results show that our scheme can locate the WiFi access points within a small error of 1 ~ 16 meters, and improve the accuracy of a conventional method by up to 50%.
Physiologic and Morphologic Studies on Atherosclerotic Pigeons.∗

Summary Middle-aged White Carneau pigeons were found to have mean systolic blood pressures of 204 ± 2.3 mm of Hg and diastolic pressures of 140 ± 1.5 mm of Hg. Serum cholesterol levels were found to be 313 ± 7.19 mg% and serum triglyceride levels were 217 ± 11.83 mg%. The aortic atherosclerosis of these birds involved 12.88 ± 0.71% of the intima of the thoracic aorta. The mean per cent of arteries with atherosclerotic lesions in 15 frozen sections of left ventricle and septum of the heart were 6.6 ± 0.85%. The levels of blood pressure among White Carneau pigeons were found to account for very little of the variability in either aortic or coronary artery atherosclerosis. No sex difference could be found in the amount of coronary or aortic atherosclerosis. Serum cholesterol levels were found to be correlated with aortic atherosclerosis among male but not female birds. Serum cholesterol and triglyceride levels were correlated with coronary artery atherosclerosis among female but not male White Carneau pigeons.
Seismic Full-waveform Inversion of Salt Geometry Using a Level Set Approach

An accurate definition of geometry of complex subsurface bodies, such as salt intrusions, is crucial for imaging below such targets. Full-waveform inversion (FWI) is a method for building high-resolution seismic velocity models from nonlinear iterative minimization of the misfit between observed and synthetic seismic data. The ability of FWI to accurately recover the geometry of salt bodies can be limited by several factors, with the lack of low frequencies in the data being one of them, thus, requiring the salt geometry to be often manually interpreted. In this paper we modify the FWI algorithm to use a level set representation to parameterize and invert for the geometry of salt bodies, without adding to computational cost of FWI.
Summary of the Survey of Fundamental Concerns Confronting the LD Field

Not surprisingly, respondents cited improvement in the quality of theoretical analyses as essential to upgrading research. In turn, better theory and research were seen as providing the foundation for improving practice, training, and policy, and as the key to maintaining the integrity of the field. For the majority, defining LD (e.g., arriving at conceptual and operational consensus of just what constitutes a learning disability) was of primary concern in efforts to advance the field. At the same time, the difficulty of arriving at consensus was reflected in the conflicting views of those who want the definition broadened versus those who want it narrowed. Also expressed were the need for (a) more and better programs to enhance public awareness, (b) improved legislation, and (c) less politicization of the field. With regard to who might provide guidance in resolving current problems and issues, it was implied that much of the field's future is in the hands of those working for government agencies, major research groups, the leaders of professional and lay organizations, and journal editors and editorial boards. A sample of some of the specific concerns raised by respondents is provided here. For a more detailed presentation, see the original report in JLD.
A two-microRNA signature as a potential biomarker for early gastric cancer

Gastric cancer (GC) is one of the most common malignant tumors worldwide. No fundamental improvements in the five-year survival rates of patients with GC have been reported due to a low early diagnosis rate. Therefore, the identification of novel biomarkers is urgently required for an early diagnosis of GC. A total of 86 patients were selected for the present study, including 44 patients with early stage GC (T1–T2 according to TNM staging criteria) and 42 normal gastric mucosa samples from non-cancer patients as controls. A total of 18 samples were used for the microRNA (miRNA) microarray experiments, including nine early GC and nine normal gastric mucosa samples. Bioinformatics algorithms, significant analysis of microarray (SAM), top scoring pair (TSP) and statistical receiver operating characteristic curves were used to identify the best signatures. Finally, quantitative PCR was used to validate the candidate biomarkers for early gastric cancer in the test samples (35 cancer and 33 normal samples). Using the SAM algorithm, 14 differential miRNAs were selected as candidate biomarkers. Using the TSP algorithm, hsa-miR-196a and hsa-miR-148a were obtained as a signature to differentiate between the early GC and normal samples. A coincidental result was observed in the test samples. hsa-miR-196a was upregulated and hsa-miR-148a was downregulated in the early GC samples. hsa-miR-196a and hsa-miR-148a have the potential to serve as candidate biomarkers for early GC.
A new subaperture approach to high squint SAR processing

A high squint subaperture (HSS) algorithm was developed from the perspective of a strip map synthetic aperture radar (SAR) system and has the ability to focus SAR data at extremely high squint angle of 55/spl deg/ with less than 1.27% mainlobe expansion or even higher squint angles if larger mainlobe expansion can be tolerated. The unique characteristic of this algorithm is that the subapertures are formed by multiplying the received signal with a set of overlapped complex conjugated reference signals where the chirp rate varies in the azimuth direction. This is done to solve the range focus problem that arises after the azimuth input signal undergoes the range walk removal procedure. As the IISS algorithm only involves short fast Fourier transforms (FFTs) and avoids interpolation, it is computationally efficient and allows for small data buffers and facilitates hardware real-time implementation. The distinct feature of this algorithm is its simplicity of implementation, which is vital in real time processing and motion compensation when the squint angle may be changing continuously.