Miracle-dz/UniFAR-FTUs huggingface dataset:
Using principal component analysis and support vector machine to predict protein structural class for low-similarity sequences via PSSM

The accurate identification of protein structure class solely using extracted information from protein sequence is a complicated task in the current computational biology. Prediction of protein structural class for low-similarity sequences remains a challenging problem. In this study, the new computational method has been developed to predict protein structural class by fusing the sequence information and evolution information to represent a protein sample. To evaluate the performance of the proposed method, jackknife cross-validation tests are performed on two widely used benchmark data-sets, 1189 and 25PDB with sequence similarity lower than 40 and 25%, respectively. Comparison of our results with other methods shows that the proposed method by us is very promising and may provide a cost-effective alternative to predict protein structural class in particular for low-similarity data-sets.
Complexity theory and curriculum reforms in Hong Kong

Abstract Hong Kong is embarking on curricular and pedagogic reforms which replace modernist, Tylerian approaches to the curriculum with recommendations that echo many features of complexity theory. The nature of complexity theory-based curricula are outlined, and these are used to interrogate three seminal curriculum reform documents in Hong Kong. The article suggests that they embody a paradigm shift in curriculum thinking. However, given that complexity theory is not without its problems for curricula, a case is made for an eclectic approach to curriculum planning, and it is this that is taking place in Hong Kong's reformist agenda.
Patient perceptions of service quality in group versus solo practice clinics.

OBJECTIVE To compare patient perceptions of service quality at solo and group practices, and to examine the association of perceptions with 'potential patient loyalty' (PPL), the potential for seeking future service from the same clinic. DESIGN A self-administered, cross-sectional survey of clinic outpatients, using an adapted SERVQUAL questionnaire translated into Chinese, with additional items on overall satisfaction and intent to return/recommend the clinic to others. Sampling and study subjects. Every third outpatient at all newly started group practices (four) and solo clinics (thirteen) in Taiwan in the preceding 4-7 months, including 150 and 50 patients from each group and solo practice, respectively, for a total of 1250 patients. MAIN OUTCOME MEASURES Perceived service quality on five dimensions-tangibles, reliability, responsiveness, assurance, and empathy-and PPL. All constructs were measured on a five-point scale. RESULTS After accounting for random effects of clinical and geographical location, group practice patients perceived significantly higher service quality on all dimensions relative to solo practice patients, after adjusting for age, gender, education, and illness type. All service quality dimensions except assurance were significantly positively associated with PPL after adjusting for age, gender, education, and illness type, and random effects at the clinical and geographical location levels. CONCLUSIONS Patients perceive better service quality at group practices compared with solo practices on all dimensions. Patients' quality perceptions are significant predictors of PPL. The implications for physician practices both internationally and in Taiwan are discussed, as well as policy implications for the Taiwan government.
Automatically generating commit messages from diffs using neural machine translation

Commit messages are a valuable resource in comprehension of software evolution, since they provide a record of changes such as feature additions and bug repairs. Unfortunately, programmers often neglect to write good commit messages. Different techniques have been proposed to help programmers by automatically writing these messages. These techniques are effective at describing what changed, but are often verbose and lack context for understanding the rationale behind a change. In contrast, humans write messages that are short and summarize the high level rationale. In this paper, we adapt Neural Machine Translation (NMT) to automatically "translate" diffs into commit messages. We trained an NMT algorithm using a corpus of diffs and human-written commit messages from the top 1k Github projects. We designed a filter to help ensure that we only trained the algorithm on higher-quality commit messages. Our evaluation uncovered a pattern in which the messages we generate tend to be either very high or very low quality. Therefore, we created a quality-assurance filter to detect cases in which we are unable to produce good messages, and return a warning instead.
Tight Bounds for Online TSP on the Line

We consider the online traveling salesperson problem (TSP), where requests appear online over time on the real line and need to be visited by a server initially located at the origin. We distinguish between closed and open online TSP, depending on whether the server eventually needs to return to the origin or not. While online TSP on the line is a very natural online problem that was introduced more than two decades ago, no tight competitive analysis was known to date. We settle this problem by providing tight bounds on the competitive ratios for both the closed and the open variant of the problem. In particular, for closed online TSP, we provide a 1.64-competitive algorithm, thus matching a known lower bound. For open online TSP, we give a new upper bound as well as a matching lower bound that establish the remarkable competitive ratio of 2.04. Additionally, we consider the online DIAL-A-RIDE problem on the line, where each request needs to be transported to a specified destination. We provide an improved non-preemptive lower bound of 1.75 for this setting, as well as an improved preemptive algorithm with competitive ratio 2.41. Finally, we generalize known and give new complexity results for the underlying offline problems. In particular, we give an algorithm with running time O(n2) for closed offline TSP on the line with release dates and show that both variants of offline DIAL-A-RIDE on the line are NP-hard for any capacity c≥ 2 of the server.
Improving Hard Disk Contention-Based Covert Channel in Cloud Computing

Steganographic methods allow the covert exchange of secret data between parties aware of the procedure. The cloud computing environment is a new and emerging target for steganographers, but currently not many solutions have been proposed. This paper proposes CloudSteg, which is a steganographic method that creates a covert channel based on hard disk contention between the two cloud instances that reside on the same physical machine. Experimental results conducted using open-source cloud environment Open Stack show that CloudSteg is able to achieve a bandwidth of about 0.1 bps, which is 1000 times higher than is known from the state-of-the-art version.
Endophytic Actinobacteria from the Brazilian Medicinal Plant Lychnophora ericoides Mart. and the Biological Potential of Their Secondary Metabolites

Endophytic actinobacteria from the Brazilian medicinal plant Lychnophora ericoides were isolated for the first time, and the biological potential of their secondary metabolites was evaluated. A phylogenic analysis of isolated actinobacteria was accomplished with 16S rRNA gene sequencing, and the predominance of the genus Streptomyces was observed. All strains were cultured on solid rice medium, and ethanol extracts were evaluated with antimicrobial and cytotoxic assays against cancer cell lines. As a result, 92% of the extracts showed a high or moderate activity against at least one pathogenic microbial strain or cancer cell line. Based on the biological and chemical analyses of crude extracts, three endophytic strains were selected for further investigation of their chemical profiles. Sixteen compounds were isolated, and 3‐hydroxy‐4‐methoxybenzamide (9) and 2,3‐dihydro‐2,2‐dimethyl‐4(1H)‐quinazolinone (15) are reported as natural products for the first time in this study. The biological activity of the pure compounds was also assessed. Compound 15 displayed potent cytotoxic activity against all four tested cancer cell lines. Nocardamine (2) was only moderately active against two cancer cell lines but showed strong activity against Trypanosoma cruzi. Our results show that endophytic actinobacteria from L. ericoides are a promising source of bioactive compounds.
Psychometric Properties of the Cervical Smear Belief Inventory for Chinese Women

This study examines the reliability and validity of the scores of Cervical Smear Belief Inventory (CSBI) among Chinese women in Taiwan. Women who were nonadherent to cervical screening guidelines were recruited (N = 424). Reliabilities showed good internal consistency for the perceived Pros, Cons, and Susceptibility scales (α ranged from .78 to .87). Factor analysis showed good construct validity of the scores of CSBI that revealed concordant patterns with existing social and behavioral theories, except that the Norms scale was loaded with the Pros scale. Moreover, two items in the Cons scale appeared to be “cultural belief toward virginity. ” Item-discrimination analysis showed that all items in the CSBI successfully discriminated women with favorable cervical smear beliefs from those with unfavorable beliefs (p < .001). In summary, many psychometric properties of the CSBI showed that the scores of the inventory were reliable and valid to assess belief toward cervical smear among Chinese women.
Exploiting content redundancy for web information extraction

We propose a novel extraction approach that exploits content redundancy on the web to extract structured data from template-based web sites. We start by populating a seed database with records extracted from a few initial sites. We then identify values within the pages of each new site that match attribute values contained in the seed set of records. To match attribute values with diverse representations across sites, we define a new similarity metric that leverages the templatized structure of attribute content. Specifically, our metric discovers the matching pattern between attribute values from two sites, and uses this to ignore extraneous portions of attribute values when computing similarity scores. Further, to filter out noisy attribute value matches, we exploit the fact that attribute values occur at fixed positions within template-based sites. We develop an efficient Apriori-style algorithm to systematically enumerate attribute position configurations with sufficient matching values across pages. Finally, we conduct an extensive experimental study with real-life web data to demonstrate the effectiveness of our extraction approach.
Music type classification by spectral contrast feature

Automatic music type classification is very helpful for the management of digital music databases. In this paper, the octave-based spectral contrast feature is proposed to represent the spectral characteristics of a music clip. It represented the relative spectral distribution instead of average spectral envelope. Experiments show that the octave-based spectral contrast feature performs well in music type classification. Another comparison experiment demonstrates that the octave-based spectral contrast feature has a better discrimination among different music types than mel-frequency cepstral coefficients (MFCC), which is often used in previous music type classification systems.
Public Service Motivation and Institutional-Occupational Motivations Among Undergraduate Students and ROTC Cadets

Given the current fiscal climate, budgetary pressures may have important implications for recruitment and retention of military personnel. In response to this issue, we join two literatures to study motivational differences in undergraduate college students and Reserve Officer Training Corps (ROTC) cadets: Moskos’ Institutional and Occupational (I-O) enlistment motivation model and Kim et al.’s revised Public Service Motivation (PSM) scale. We survey ROTC cadets and undergraduates at a mid-size public university and find that PSM is higher for ROTC cadets than regular undergraduates. We also find that for ROTC cadets, the institutional motivators for enlistment correlate positively with the rational, normative, and affective dimensions of PSM. In addition, we find increases in the Occupational motivator and the compassion PSM dimension reduce the likelihood of being an ROTC cadet whereas the Institutional motivator and the self-sacrifice PSM dimension are positively related with being an ROTC cadet.
Precise U‐Pb Zircon Constraints on the Earliest Magmatic History of the Carolina Terrane

The early magmatic and tectonic history of the Carolina terrane and its possible affinities with other Neoproterozoic circum‐Atlantic arc terranes have been poorly understood, in large part because of a lack of reliable geochronological data. Precise U‐Pb zircon dates for the Virgilina sequence, the oldest exposed part, constrain the timing of the earliest known stage of magmatism in the terrane and of the Virgilina orogeny. A flow‐banded rhyolite sampled from a metavolcanic sequence near Chapel Hill, North Carolina, yielded a U‐Pb zircon date of 632.9 +2.6/−1.9 Ma. A granitic unit of the Chapel Hill pluton, which intrudes the metavolcanic sequence, yielded a nearly identical U‐Pb zircon date of 633 +2/−1.5 Ma, interpreted as its crystallization age. A felsic gneiss and a dacitic tuff from the Hyco Formation yielded U‐Pb zircon dates of 619.9 +4.5/−3 Ma and 615.7 +3.7/−1.9 Ma, respectively. Diorite and granite of the Flat River complex have indistinguishable U‐Pb upper‐intercept dates of 613.9 +1.6/−1.5 Ma and 613.4 +2.8/−2 Ma. The Osmond biotite‐granite gneiss, which intruded the Hyco Formation before the Virgilina orogeny, crystallized at 612.4 +5.2/−1.7 Ma. Granite of the Roxboro pluton, an intrusion that postdated the Virgilina orogeny, yielded a U‐Pb upper intercept date of 546.5 +3.0/−2.4 Ma, interpreted as the time of its crystallization. These new dates both provide the first reliable estimates of the age of the Virgilina sequence and document that the earliest known stage of magmatism in the Carolina terrane had begun by 633 +2/−1.5 Ma and continued at least until 612.4 +5.2/−1.7 Ma, an interval of ∼25 m.yr. Timing of the Virgilina orogeny is bracketed between 612.4 +5.2/−1.7 Ma and \documentclass{aastex} \usepackage{amsbsy} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{bm} \usepackage{mathrsfs} \usepackage{pifont} \usepackage{stmaryrd} \usepackage{textcomp} \usepackage{portland,xspace} \usepackage{amsmath,amsxtra} \usepackage[OT2,OT1]{fontenc} \newcommand\cyr{ \renewcommand\rmdefault{wncyr} \renewcommand\sfdefault{wncyss} \renewcommand\encodingdefault{OT2} \normalfont \selectfont} \DeclareTextFontCommand{\textcyr}{\cyr} \pagestyle{empty} \DeclareMathSizes{10}{9}{7}{6} \begin{document} \landscape $$586\pm 10$$ \end{document} Ma (reported age of the upper Uwharrie Formation). The U‐Pb systematics of all units studied in the Virgilina sequence are simple and lack any evidence of an older xenocrystic zircon component, which would indicate the presence of a continental‐type basement. This observation, together with the juvenile Nd isotopic character of the Virgilina volcanic arc sequence, suggests that the oldest part of the Carolina terrane was built on oceanic crust away from a continental crustal influence.
Unexpected radiation hazard in dyes of textiles

Textile dyes are among the most problematic pollutants because of their toxicity on several organisms and ecosystems. Many of the chemicals used in the textile industry may represent some health concerns. The determination of the radioactivity in textile dyes is therefore very important for both human health and environment. The study was designated to determine, for the first time, the values of 238U, 232Th and 40K in nine different dyes employed in the textile industry using gamma spectrometry with a Hyper Pure Germanium (HPGe) detector. The mean activity concentrations of 238U, 232Th and 40K were 29.37 ± 4.48, 1.15 ± 0.13 and 565 ± 4 Bq/kg, respectively. The calculated radium equivalents for all samples were lower than the maximum admissible value (370 Bq/kg). The absorbed dose rates due to the natural radioactivity of the investigated samples ranged from 2.94 ± 0.05 to 166 ± 3 nGy/h. So, the absorbed dose rates for all samples of textile dyes were lower than the international recommended value (55 nGy/h) except the yellow dye (166 ± 3 nGy/h), which recorded a significant radiological hazard. The external hazard index was also calculated. Conclusively, the results have indicated that the textile dyes may possess a measurable amount of radioactivity that should be taken into account. Therefore, safety rules and precautions should be applied for dyes used in the textile industry and for people working in this field.
MR imaging of the amide‐proton transfer effect and the pH‐insensitive nuclear overhauser effect at 9.4 T

The amide proton transfer (APT) effect has emerged as a unique endogenous molecular imaging contrast mechanism with great clinical potentials. However, in vivo quantitative mapping of APT using the conventional asymmetry analysis is difficult due to the confounding nuclear Overhauser effect (NOE) and the asymmetry of the magnetization transfer effect. Here, we showed that the asymmetry of magnetization transfer contrast from immobile macromolecules is highly significant, and the wide spectral separation associated with a high magnetic field of 9.4 T delineates APT and NOE peaks in a Z‐spectrum. Therefore, high‐resolution apparent APT and NOE maps can be obtained from measurements at three offsets. The apparent APT value was greater in gray matter compared to white matter in normal rat brain and was sensitive to tissue acidosis and correlated well with apparent diffusion coefficient in the rat focal ischemic brain. In contrast, no ischemia‐induced contrast was observed in the apparent NOE map. The concentration dependence and the pH insensitivity of NOE were confirmed in phantom experiments. Our results demonstrate that in vivo apparent APT and NOE maps can be easily obtained at high magnetic fields and the pH‐insensitive NOE may be a useful indicator of mobile macromolecular contents. Magn Reson Med, 2013. © 2012 Wiley Periodicals, Inc.
Scheduling for mixed-criticality hypervisor systems in the automotive domain

This thesis focuses on scheduling for hypervisor systems in the automotive domain. Current practices are primarily implementation-agnostic or are limited by lack of visibility during the execution of partitions. The tasks executed within the partitions are classified as event-triggered or time-triggered. A scheduling model is developed using a pair of a deferrable server and a periodic server per partition to provide low latency for event-triggered tasks and maximising utilisation. The developed approach enforces temporal isolation between partitions and ensures that time-triggered tasks do not suffer from starvation. The scheduling model was extended to support three criticality levels with two degraded modes. The first degraded mode provides the partitions with additional capacity by trading-off low latency of event-driven tasks with lower overheads and utilisation. Both models were evaluated by forming a case study using real ECU application code. A second case study was formed inspired from the Olympus Attitude and Orbital Control System (AOCS) to further evaluate the proposed mixed-criticality model. To conclude, the contributions of this thesis are addressed with respect to the research hypothesis and possible avenues for future work are identified.
Policy Framework for Educational Research

A policy framework for analyzing educational research and development has been proposed. The framework consists of five primary elements focusing on the contexts in which educational R & D operates, its goals, its characteristics, its manpower, and its decision structures. These five primary elements interact to produce two secondary elements concerned with priorities and objectives, and strategies and tactics. The framework was applied to three current policy proposals in educational R & D including directed R & D programming in the U.S. Office of Education, the request for funds for experimental schools, and the proposed National Institute of Education. Rigorous application of the framework to major policy questions such as these three can help us examine issues before they arise. It can help prevent errors. Its application can provide greater assurance that primary, secondary, and tertiary consequences—those that arise from the interaction of the consequences we most directly perceive—will receive examination. This kind of consideration can help produce the desirable and intended effects and avoid the detrimental consequences of unanticipated impacts in unintended areas.
Grid-based Visual SLAM in Complex Environment

This paper presents a novel real-time SLAM method working in an unstructured indoor environment with a single forward viewing camera. Most existing visual SLAM methods extract features from the environment, associate them in different images and produce a feature map as a result. However, our approach estimates the distances between the robot and the obstacles by applying a visual sonar technique to the image and then associates this range data through an iterative closest point (ICP) based algorithm and finally produces the grid map. Here, we reconstruct a pseudo-dense scan pattern (PDSP) which is a temporal accumulation of the visual sonar readings based on odometry readings to overcome the sparseness of the visual sonar and then apply ICP based algorithm to associate this scan pattern with the previous one. In addition, we further correct the slight trajectory error included in the PDSP reconstruction step to get a much more refined map. Experimental results show that our method can obtain a grid map using a single camera alone unlike active sensor-based SLAMs
The Curious Anomaly of Skewed Judgment Distributions and Systematic Error in the Wisdom of Crowds

Judgment distributions are often skewed and we know little about why. This paper explains the phenomenon of skewed judgment distributions by introducing the augmented quincunx (AQ) model of sequential and probabilistic cue categorization by neurons of judges. In the process of developing inferences about true values, when neurons categorize cues better than chance, and when the particular true value is extreme compared to what is typical and anchored upon, then populations of judges form skewed judgment distributions with high probability. Moreover, the collective error made by these people can be inferred from how skewed their judgment distributions are, and in what direction they tilt. This implies not just that judgment distributions are shaped by cues, but that judgment distributions are cues themselves for the wisdom of crowds. The AQ model also predicts that judgment variance correlates positively with collective error, thereby challenging what is commonly believed about how diversity and collective intelligence relate. Data from 3053 judgment surveys about US macroeconomic variables obtained from the Federal Reserve Bank of Philadelphia and the Wall Street Journal provide strong support, and implications are discussed with reference to three central ideas on collective intelligence, these being Galton's conjecture on the distribution of judgments, Muth's rational expectations hypothesis, and Page's diversity prediction theorem.