Miracle-dz/UniFAR-FTUs huggingface dataset:
Protein Loop Dynamics Are Complex and Depend on the Motions of the Whole Protein

We investigate the relationship between the motions of the same peptide loop segment incorporated within a protein structure and motions of free or end-constrained peptides. As a reference point we also compare against alanine chains having the same length as the loop. Both the analysis of atomic molecular dynamics trajectories and structure-based elastic network models, reveal no general dependence on loop length or on the number of solvent exposed residues. Rather, the whole structure affects the motions in complex ways that depend strongly and specifically on the tertiary structure of the whole protein. Both the Elastic Network Models and Molecular Dynamics confirm the differences in loop dynamics between the free and structured contexts; there is strong agreement between the behaviors observed from molecular dynamics and the elastic network models. There is no apparent simple relationship between loop mobility and its size, exposure, or position within a loop. Free peptides do not behave the same as the loops in the proteins. Surface loops do not behave as if they were random coils, and the tertiary structure has a critical influence upon the apparent motions. This strongly implies that entropy evaluation of protein loops requires knowledge of the motions of the entire protein structure.
MIR141 Expression Differentiates Hashimoto Thyroiditis from PTC and Benign Thyrocytes in Irish Archival Thyroid Tissues

MicroRNAs (miRNAs) are small non-coding RNAs approximately 22 nucleotides in length that function as regulators of gene expression. Dysregulation of miRNAs has been associated with initiation and progression of oncogenesis in humans. Our group has previously described a unique miRNA expression signature, including the MIR200 family member MIR141, which can differentiate papillary thyroid cancer (PTC) cell lines from a control thyroid cell line. An investigation into the expression of MIR141 in a series of archival thyroid malignancies [n = 140; classic PTC (cPTC), follicular variant PTC, follicular thyroid carcinoma, Hashimoto thyroiditis (HT), or control thyrocytes] was performed. Each cohort had a minimum of 20 validated samples surgically excised within the period 1980–2009. A subset of the HT and cPTC cohorts (n = 3) were also analyzed for expression of TGFβR1, a key member of the TGFβ pathway and known target of MIR141. Laser capture microdissection was used to specifically dissect target cells from formalin-fixed paraffin-embedded archival tissue. Thyrocyte- and lymphocyte-specific markers (TSHR and LSP1, respectively), confirmed the integrity of cell populations in the HT cohort. RNA was extracted and quantitative RT-PCR was performed using comparative CT (ΔΔCT) analysis. Statistically significant (p < 0.05) differential expression profiles of MIR141 were found between tissue types. HT samples displayed significant downregulation of MIR141 compared to both cPTC and control thyrocytes. Furthermore, TGFβR1 expression was detected in cPTC samples but not in HT thyrocytes. It is postulated that the downregulation of this miRNA is due, at least in part, to its involvement in regulating the TGFβ pathway. This pathway is exquisitely involved in T-cell autoimmunity and has previously been linked with HT. In conclusion, HT epithelium can be distinguished from cPTC epithelium and control epithelium based on the relative expression of MIR141.
Child Nutrition, Child Health, and School Enrollment: A Longitudinal Analysis

Private behavioral choices and policies that affect the health and nutrition of children have far greater effects on school enroolment and thus on eventual productivity than most literature suggests. Better health and nutrition are thought to improve children's performance in school, and therefore their productivity after school. Most literature ignores the fact that child health and schooling reflect behavioral choices, so the estimated impact of health and nutrition on a child`s schooling reflects biases in the studies. Using an explicit dynamic model for preferred estimates, the authors use longitudinal data to investigate how children's health and nutrition affect school enrollment in rural Pakistan. They use price shocks when children were of preschool age to control for behavior determining the measure of children's health and nutrition stock. The authors find that children's health and nutrition is three times more important for enrollment than is suggested by naive estimates that assume that children's health and nutrition is predetermined rather that determined by household choices. Not only does improved nutrition increase enrollments, it does so more for girls, thus closing a portion of the gender gap. These results strongly reinforce the importance of using estimation methods that are consistent with the economic theory of households to explore the impact of some choice variables on others, using socioeconomic behavioral data. Private behaviors and public policies that affect the health and nutrition of children have much greater effect on school enrollment and on eventual productivity than suggested by early literature methods. This paper - a product of the Poverty and Human Resources Division, Policy Research Department - is part of a larger effort in the department to evaluate the economic impact of human resource investments.
Characterization and Mapping of a Shattering Mutant in Rice That Corresponds to a Block of Domestication Genes

Easy shattering reduces yield due to grain loss during harvest in cereals. Shattering is also a hindrance in breeding programs that use wild accessions because the shattering habit is often linked to desirable traits. We characterized a shattering mutant line of rice, Hsh, which was derived from a nonshattering japonica variety, Hwacheong, by N-methyl-N-nitrosourea (MNU) treatment. The breaking tensile strength (BTS) of the grain pedicel was measured using a digital force gauge to evaluate the degree of shattering of rice varieties at 5, 10, 15, 20, 25, 30, 35, and 40 days after heading (DAH). The BTS of Hwacheong did not decrease with increasing DAH, maintaining a level of 180–240 gf, while that of Hsh decreased greatly during 10–20 DAH and finally stabilized at 50 gf. Optical microscopy revealed that Hsh had a well-developed abscission layer similar to the wild rice Oryza nivara (accession IRGC105706), while Hwacheong did not produce an abscission layer, indicating that the shattering of Hsh was caused by differentiation of the abscission layer. On the basis of the BTS value and morphology of the abscission layer of F1 plants and segregation data in F2 populations, it was concluded that the easy shattering of Hsh was controlled by the single recessive gene sh-h. The gene sh-h was determined to be located on rice chromosome 7 by bulked segregant analysis. Using 14 SSR markers on rice chromosome 7, the gene sh-h was mapped between the flanking markers RM8262 and RM7161 at distances of 1.6 and 2.0 cM, respectively. An SSR marker Rc17 cosegregated with the gene sh-h. The locus sh-h for shattering was tightly linked to the Rc locus conferring red pericarp, as well as a QTL qSDs-7-1 for seed dormancy, implying that this region might represent a domestication block in the evolutionary pathway of rice.
Investment in U.S. Education and Training

The current high rates of return to human capital stimulate a supply response via increased investments in education and training. The so increased human capital stock exerts downward pressures on the rates of return that reduce the skill differential in wages. This paper reports estimates of: the responses of investments in post-secondary education, measured by enrollments, to changes in the rate of return; responses of investment in job training, measured by incidence; and effects of accumulated human capital stocks, measured by educational attainment, on educational wage differentials. Enrollment responses and attainment effects are shown to be separated by a time lag of about a decade. The parameter estimates are based on annual CPS and NCES data, covering a recent 25 year period. If demands for human capital cease their acceleration, the rate of return is expected to decline about 25% over the current decade, judging by the estimated parameters and lags.
Testosterone Regulates Androgen Receptor Immunoreactivity in the Copulatory, but not Courtship, Neuromuscular System in Adult Male Green Anoles

Androgens regulate the expression of male reproductive behaviour in diverse vertebrate species, often acting on androgen receptors (AR) to induce structural or functional changes in the nervous system and periphery. Male green anoles possess two sexually dimorphic neuromuscular systems, one controlling throat fan (dewlap) extension, which occurs during courtship, and the other mediating copulatory organ function. Although androgens are required for behavioural activation in both systems, testosterone has differential effects on the neuromuscular morphology. It increases the size of copulatory muscle fibres during the breeding season, but significant effects on dewlap muscle fibre size and motoneurone soma size in either system have not been detected. Corresponding to the lack of testosterone‐induced morphological effects in the courtship system, relatively low levels of AR are expressed in the associated motoneurones. The present experiment had two goals, aiming to determine whether: (i) the other courtship and copulatory neuromuscular tissues express AR and (ii) testosterone and/or seasonal environmental changes regulate AR expression. The percentage of AR+ nuclei was evaluated in both the breeding and nonbreeding seasons in gonadally intact adult males (Experiment 1) and in castrated males treated with either testosterone or vehicle (Experiment 2). AR was extensively expressed in the dewlap and copulatory muscles, and in a high percentage of the copulatory motoneurones, but immunoreactivity did not vary across season. Testosterone increased the percentage of AR+ nuclei in the copulatory muscles of both breeding and nonbreeding males but not in the dewlap muscle or copulatory motoneurones. Finally, the target structures for both systems (cartilages and hemipenes) expressed AR in all animals. Therefore, the effects of testosterone on AR immunoreactivity suggest that up‐regulation of the receptors may be important for morphological change. However, because all structures investigated in the present experiment expressed AR, the data also indicate that the receptors are involved with other functions.
Do Inflation Expectations Currently Pose a Risk to the Economy?

People’s expectations about future inflation play an important role in determining the current rate of inflation. There is a risk that the recent prolonged period of above-target inflation, which the Monetary Policy Committee (MPC) judges is more likely than not to continue over much of the next two years, may cause inflation expectations to become less well anchored. By pushing up wages and prices, higher inflation expectations could lead to inflation becoming more persistent. At the moment, most indicators are consistent with inflation expectations remaining anchored to the target, although there is tentative evidence that financial market measures of inflation expectations have become a little more responsive to developments in the economy. There are currently few signs to suggest that prices and wages have increased as a result of higher inflation expectations. The MPC will continue to monitor and assess indicators closely.
Coding rates and MCS using adaptive modulation for WiMAX in OFDM systems using GNU Radio

Various Various wireless technologies have been emerging with ever increasing demand for higher data rates along with low bit error rates (BER's). Adaptive modulation and coding (AMC) schemes, when incorporated into WiMAX helps the system to react dynamically to the channel variations thereby providing higher data rates and improve BER performance. Based on the channel state information, both the modulation and coding rates can be varied so as to achieve higher throughput and improve spectral efficiency. This work proposes an efficient adaptive modulation coding technique, which maximizes the throughput, while maintaining a target BER. It proposes to select a particular modulation coding scheme along with the corresponding coding rates based on the given threshold. The parameter values, such as SNR, BER, CINR, BLER channel attenuation factor, are accepted and then the modulation schemes with an appropriate coding rate are selected for the operation of a OFDM system in GNU Radio.
Versatile object tracking standard database for security surveillance

Object tracking has gained quite an interest from researchers all over the world. Even though there are numerous approaches to solve the problem of tracking multiple objects in visual clutter, it is still difficult to evaluate and compare the methods with one another, due to the lack of standard database available. Thus, the purpose of this paper is to address this issue and establish a standard database accessible for both public and research organization. The database introduced is basically divided into 2 categories; outdoor environment and indoor environment, and it covers different head population, pose, orientation, lighting conditions and etc. However, unlike other database available in the World Wide Web, this database is multipurpose and it can be used for either head tracking, body tracking, arms tracking or legs tracking. Also, the ground truth data for each video will be fully provided and opened for public.
AHA! Version 2.0, More adaptation flexibility for authors

AHA! is a simple Web-based adaptive hypermedia system. Because of this simplicity it has been studied and experimented with in several research groups, see e.g. (Cini & Valdeni de Lima, 2002), (Calvi & Cristea, 2002), (Romero et al., 2002). This paper identifies shortcomings in AHA! and presents AHA! version 2.0 which tries to overcome the known problems with AHA! while maintaining its biggest asset: simplicity. We illustrate how different user modeling and adaptation aspects can be expressed in the new AHA! system (that would be difficult in the old system, and impossible in most other systems).
Guided artificial bee colony algorithm

Artificial bee colony algorithm is an optimization algorithm based on a particular intelligent behaviour of honeybee swarms. In this paper we present a novel algorithm named GABC which integrates artificial bee colony algorithm (ABC) with self-adaptive guidance adjusted for engineering optimization problems. The novel algorithm speeds up the convergence and improves the algorithm's exploitation. We tested our guided algorithm on four standard engineering benchmark problems. The experimental results show that GABC algorithm can outperform ABC algorithm in most of the cases.
Gateless Treasure: How to Get Sensitive Information from Unprotected External Storage on Android Phones

With millions of apps that can be downloaded from official or third-party market, Android has become one of the most popular mobile platforms today. These apps help people in all kinds of ways and thus have access to lots of user's data that in general fall into three categories: sensitive data, data to be shared with other apps, and non-sensitive data not to be shared with others. For the first and second type of data, Android has provided very good storage models: an app's private sensitive data are saved to its private folder that can only be access by the app itself, and the data to be shared are saved to public storage (either the external SD card or the emulated SD card area on internal FLASH memory). But for the last type, i.e., an app's non-sensitive and non-shared data, there is a big problem in Android's current storage model which essentially encourages an app to save its non-sensitive data to shared public storage that can be accessed by other apps. At first glance, it seems no problem to do so, as those data are non-sensitive after all, but it implicitly assumes that app developers could correctly identify all sensitive data and prevent all possible information leakage from private-but-non-sensitive data. In this paper, we will demonstrate that this is an invalid assumption with a thorough survey on information leaks of those apps that had followed Android's recommended storage model for non-sensitive data. Our studies showed that highly sensitive information from billions of users can be easily hacked by exploiting the mentioned problematic storage model. Although our empirical studies are based on a limited set of apps, the identified problems are never isolated or accidental bugs of those apps being investigated. On the contrary, the problem is rooted from the vulnerable storage model recommended by Android. To mitigate the threat, we also propose a defense framework.
GOBoost: G-mean optimized boosting framework for class imbalance learning

Boosting-based methods are effective for class imbalance problem, where the numbers of samples in two or more classes are severely unequal. However, the classifier weights of existing boosting-based methods are calculated by minimizing the error rate, which is inconsistent with the objective of class imbalance learning. As a result, the classifier weights cannot represent the performance of individual classifiers properly when the data is imbalanced. In this paper, we therefore propose a G-mean Optimized Boosting (GOBoost) framework to assign classifier weights optimized on G-mean. Subsequently, high weights are assigned to the classifier with high accuracy on both the majority class and the minority class. The GOBoost framework can be applied to any AdaBoost-based method for class imbalance learning by simply replacing the calculation of classifier weights. Accordingly, we extend six AdaBoost-based methods to GOBoost-based methods for comparative studies in class imbalance learning. The experiments conducted on 12 real class imbalance data sets show that GOBoost-based methods significantly outperform the corresponding AdaBoost-based methods in terms of F1 and G-mean metrics.
Estimating the Effects of Dormitory Living on Student Performance

Many large universities require freshman to live in dormitories on the basis that living on campus leads to better classroom performance and lower drop out incidence. Large universities also provide a number of academic services in dormitories such as tutoring and student organizations that encourage an environment condusive to learning. A survey was administered to college students at a large state school to determine what impact dormitory living has on student performance. We use a handful of instrumental variable strategies to account for the possibly endogenous decision to live on campus. We find a robust result across model specifications and estimation techniques that on average, living on campus increases GPA by between 0.19 to 0.97. That is, the estimate for the degree of improvement to student performance caused by living on campus ranges between one-fifth to one full letter grade.
Quorum Sensing Activity of Hafnia alvei Isolated from Packed Food

Quorum sensing (QS) is a mechanism adopted by bacteria to regulate expression of genes according to population density. N-acylhomoserine lactones (AHLs) are a type of QS signalling molecules commonly found in Gram-negative bacteria which have been reported to play a role in microbial spoilage of foods and pathogenesis. In this study, we isolated an AHL-producing Hafnia alvei strain (FB1) from spherical fish pastes. Analysis via high resolution triple quadrupole liquid chromatography/mass spectrometry (LC/MS) on extracts from the spent supernatant of H. alvei FB1 revealed the existence of two short chain AHLs: N-(3-oxohexanoyl) homoserine lactone (3-oxo-C6-HSL) and N-(3-oxo- octanoyl) homoserine lactone (3-oxo-C8-HSL). To our knowledge, this is the first report of the production of AHLs, especially 3-oxo-C8-HSL, by H. alvei.
Refactoring trends across N versions of N Java open source systems : an empirical study

In the past few years, refactoring has emerged as an important consideration in the maintenance and evolution of software. Yet very little empirical evidence exists to support the claim about whether developers actively undertake refactoring, or whether as Fowler suggests that the benefits of doing refactoring are not short-term but too ‘long-term’ [8]. In this paper, we describe an empirical study of multiple versions of a range of open source Java systems in an attempt to understand whether refactoring does occur and, if so, which types of refactoring were most (and least) common. Fifteen refactorings were chosen as a basis (on seven Java systems) and the code analysed using an automated tool. Results confirmed that refactoring did take place, but the majority were of the simpler, less complex type. Interestingly, the most common refactorings empirically identified were those which, according to Fowler (and from a dependency graph of the ‘seventy two’ original refactorings), were central to larger more involved refactorings. One conclusion from the study is thus that developer time and effort for relatively large restructuring and testing of refactored code is prohibitive; making small, simple changes is preferred. A further conclusion from our study is that refactoring didn’t occur in the earliest or latest versions of the systems we investigated.
The Value of ABCD2F Scoring System (ABCD2 Combined with Atrial Fibrillation) to Predict 90-Day Recurrent Brain Stroke

Background. The ABCD2 score is now identified as a useful clinical prediction rule to determine the risk for stroke in the days following brain ischemic attacks. Aim. The present study aimed to introduce a new scoring system named “ABCD2F” and compare its value with the previous ABCD2 system to predict recurrent ischemic stroke within 90 days of the initial cerebrovascular accident (CVA). Methods. 138 consecutive patients with the final diagnosis of ischemic CVA or TIAs who referred to emergency ward of Rasoul-e-Akram general hospital in Tehran from September 2012 to December 2013 were eligible. By adding a new score in the presence of atrial fibrillation to ABCD2 system, the new scoring system as ABCD2F was introduced and the risk stratification was done again on this new system. Results. The area under the curve for ABCD2 was 0.434 and for ABCD2F it was 0.452 indicating low value of both systems for assessing recurrence of stroke within 90 days of primary event. Multivariable logistic regression analysis showed that none of the baseline factors could predict 90-day recurrent stroke. Conclusion. ABCD2 and/or atrial fibrillation are not good scoring candidates for assessing the risk of recurrent stroke within first 90 days.
Perceptual limits on 2D motion-field visualization

This paper examines perceptual issues in 2D motion-field visualization. Several aspects of motion-field perception are considered, including sensitivity to spatial gradients, number of motion layers, and motion blur. Our analysis concentrates on a specific popular method for 2D flow visualization, namely, line integral convolution (LIC). Using 2D spectral analysis, we examine a tradeoff that arises in dynamic LIC between the static motion blur cue, which indicates motion direction and the dynamic cue which indicates image speed. We also present a 2D spectral synthesis method for motion-field visualization, along with several examples. The synthesis method is simple to implement and to analyze in the frequency domain, which makes it a convenient tool for studying the perception of complex motion fields.
GIS Map Encryption Algorithm for Drone Security Based on Geographical Features

GIS map is used in Drone applications widely. In some cases, GIS map data is necessary to be protected from attacks. This paper present an encryption algorithm for GIS map data in Drone security. The proposed algorithm is based on the geographical features of GIS map data. Geometric objects are extracted from GIS map data to perform selective encryption in the frequency domain of discrete cosine transform. Experimental results verified that the entire map is changed after encryption.