Miracle-dz/UniFAR-FTUs huggingface dataset:
Generalizing evolutionary coupling with stochastic dependencies

Researchers have leveraged evolutionary coupling derived from revision history to conduct various software analyses, such as software change impact analysis (IA). The problem is that the validity of historical data depends on the recency of changes and varies with different evolution paths—thus, influencing the accuracy of analysis results. In this paper, we formalize evolutionary coupling as a stochastic process using a Markov chain model. By varying the parameters of this model, we define a family of stochastic dependencies that accounts for different types of evolution paths. Each member of this family weighs historical data differently according to their recency and frequency. To assess the utility of this model, we conduct IA on 78 releases of five open source systems, using 16 stochastic dependency types, and compare with the results of several existing approaches. The results show that our stochastic-based IA technique can provide more accurate results than these existing techniques.
Semi-supervised Learning of Naive Bayes Classifier with feature constraints

A BSTRACT Semi-supervised learning methods address the problem of building classiﬁers when labeled data is scarce. Text classiﬁcation is often augmented by rich set of labeled features representing a particular class. As tuple level labling is resource consuming, semi-supervised and weakly supervised learning methods are explored recently. Compared to labeling data instances (documents), feature labeling takes much less effort and time. Posterior regularization (PR) is a framework recently proposed for incorporating bias in the form prior knowledge into posterior for the label. Our work focuses on incorporating labeled features into a naive bayes classiﬁer in a semi-supervised setting using PR. Generative learning approaches utilize the unlabeled data more effectively compared to discriminative approaches in a semi-supervised setup. In the current study we formulate a classiﬁcation method which uses the labeled features as constraints for the posterior in a semi-supervised generative learning setting. Our empirical study shows that performance gains are signiﬁcant compared to an approach solely based on Generelized Expectation(GE) or limited amount of labeled data alone. We also show an application of our framework in a transfer learning setup for text classiﬁcation. As we allow labeled data as well as labeled features to be used, our setup allows the presence of limited amount of labeled data on the target side of transfer learning where feature constraints are used for transferring knowledge from source domain to target domain.
Ubuntu and the Quest for Conflict Resolution in Africa

Many postcolonial African states have experienced violent conflicts, prompting the quest for viable approaches to conflict resolution and peace-building. Certain groups’ desire to control power and resources at the expense of others lies at the heart of the racism, civil wars, armed insurrections, terrorism, ethnic conflict, genocide, xenophobia, and intracommunity and domestic conflict prevalent in Africa, particularly in countries that experienced prolonged foreign domination. The quest for peace and security led to the resurgence of Ubuntu, an African humanist ideology, as an indigenous approach to conflict resolution and peace-building. This article explores the place of Ubuntu in the continent’s peace and security projects. Despite the utility of Ubuntu’s principles in a few postconflict societies, the article highlights the difficulties involved in its adoption by state institutions, mainly due to the complex interactions exemplified by the modern state. However, adherence to the principles of Ubuntu by state and nonstate actors would drastically reduce threats to peace and security in Africa.
Unusually delayed presentation of persistent Descemet’s membrane tear and detachment after cataract surgery

A 51-year-old male who had undergone phacoemulsification in his left eye 11 months prior presented with complaint of sudden onset of blurred vision in the same eye. Review of his clinical course, slit-lamp exam, pachymetry, and specular endothelial microscopy led to the diagnosis of acute hydrops caused by Descemet’s membrane dehiscence at the site of the incision. He was initially managed with medical treatment and observation. In the subsequent months of follow-up, the corneal edema and the patient’s visual acuity did not improve. Intracameral gas injection was performed 7 months after presentation, but because of persistent corneal edema and nonattached Descemet’s membrane, penetrating keratoplasty was performed. Histopathologic examination confirmed the diagnosis. The patient has had a clear corneal graft since then. Although Descemet’s membrane detachment is a rather common complication after intraocular surgery, its unusually delayed presentation can also occur, and should not be confused with pseudophakic bullous keratopathy. Many mechanisms have been studied for the development of early tears and detachments after cataract surgery, but little is known about late presentations. The authors explore possible causes, and highlight the importance of instructing patients to avoid eye rubbing and any other type of trauma to the cornea after intraocular surgery.
Heterogeneous Agent Models in Economics and Finance

This paper surveys work on dynamic heterogeneous agent models (HAMs) in economics and finance. Emphasis is given to simple models that, at least to some extent, are tractable by analytic methods in combination with computational tools. Most of these models are behavioral models with boundedly rational agents using different heuristics or rule of thumb strategies that may not be perfect, but perform reasonably well. Typically these models are highly nonlinear, e.g. due to evolutionary switching between strategies, and exhibit a wide range of dynamical behavior ranging from a unique stable steady state to complex, chaotic dynamics. Aggregation of simple interactions at the micro level may generate sophisticated structure at the macro level. Simple HAMs can explain important observed stylized facts in financial time series, such as excess volatility, high trading volume, temporary bubbles and trend following, sudden crashes and mean reversion, clustered volatility and fat tails in the returns distribution.
2.6 GHz 4 watt GaN-HEMT two-stage power amplifier MMIC for LTE small-cell applications

This paper presents a two-stage PA MMIC using 0.4-μm GaN-HEMT. Two-stage structure is adopted to take its high gain property and simple inter-stage matching network. The size and loss of the inter-stage matching network can be reduced by including bond wires as a part of the shunt inductors in the matching network. The two-stage PA MMIC was fabricated with a size of 2.0×1.9 mm2 and was mounted on the 4×4 QFN package for evaluation. Using a downlink LTE signal with a PAPR of 6.5 dB and a channel bandwidth of 10 MHz at the 2.6 GHz band, the PA MMIC exhibited a gain of 30 dB, a DE of 32%, and an ACLR of -31.4 dBc at an average output power of 36 dBm. Using two PA MMICs for carrier and peaking amplifiers, DPA was designed and evaluated. At a 6-dB back-off output power level of 39 dBm, a gain of 24.7 dB and a DE of 43.5% were achieved.
Flicker correction for archived film sequences using a nonlinear model

A new model for the correction of flicker in archived film sequences is formulated from first principles. The model takes into account the Hurter-Driffield density versus log exposure characteristic to estimate image intensity errors caused by exposure inconsistencies. The model is shown to be highly nonlinear and can accommodate typical grayscale manipulations performed during film-to-video transfers. Motivated by the above model, an algorithm for the estimation of a correction profile across the available grayscale is developed. This profile is obtained from histogrammed gray-level differences between a reference and a degraded frame and is robust with respect to intensity changes due to scene and camera motion. Our results show that the proposed algorithm is very effective toward removing flicker for a variety of archived sequences and compares favorably with other state-of-the-art techniques developed for the same purpose. Additionally, the parametric form of the profile makes it particularly suitable for metadata use and allows fast inversion of the restoration process and recovery of the original material.
New clues on outburst mechanisms and improved spectroscopic elements of the black hole binary V4641 Sagittarii

We present spectroscopic observations of the black hole binary V4641 Sagittarii, obtained between 2004 July 4 and 2005 March 28, which cover the minor outburst of the star in early 2004 July and quiescence variations on 19 nights scattered over six months. During the outburst, the star peaked approximately 3 mag brighter than usual, and our spectra were dominated by broad hydrogen, helium and iron emission lines. The very first spectra showed P Cygni profiles, which disappeared within a few hours, indicating rapid changes in matter ejection. The Hα line had multiple components, one being a broad blueshifted wing exceeding 5000 km s -1 . During a simultaneously observed 10-min photometric flare up, the equivalent width of the Ha line temporarily decreased, implying that it was a flare of the continuum. The overall spectral appearance was similar to that observed in the 1999 September active phase, which suggests that similar mass-ejection processes were associated with both eruptions. In quiescence, the spectra were those of the early-type secondary star showing its orbital motion around the primary. By measuring cross-correlation radial velocities, we give an improved set of spectroscopic elements. Whereas we measure the same velocity amplitude (K 2 = 211.3 ± 1.0 km s -1 ), within errors, as Orosz et al., our centre-of-mass velocity (y = 72.7 ± 3.3 km s -1 ) differs significantly from the previously published value (107.4 ± 2.9 km s -1 ). However, we find evidence that the difference is caused by a systematic error in data reduction in the previous study, rather than by gravitational effects of an invisible third component.
The Antibody Response of Pregnant Cameroonian Women to VAR2CSA ID1-ID2a, a Small Recombinant Protein Containing the CSA-Binding Site

In pregnant women, Plasmodium falciparum-infected erythrocytes expressing the VAR2CSA antigen bind to chondroitin sulfate A in the placenta causing placental malaria. The binding site of VAR2CSA is present in the ID1-ID2a region. This study sought to determine if pregnant Cameroonian women naturally acquire antibodies to ID1-ID2a and if antibodies to ID1-ID2a correlate with absence of placental malaria at delivery. Antibody levels to full-length VAR2CSA and ID1-ID2a were measured in plasma samples from 745 pregnant Cameroonian women, 144 Cameroonian men, and 66 US subjects. IgM levels and IgG avidity to ID1-ID2a were also determined. As expected, antibodies to ID1-ID2a were absent in US controls. Although pregnant Cameroonian women developed increasing levels of antibodies to full-length VAR2CSA during pregnancy, no increase in either IgM or IgG to ID1-ID2a was observed. Surprisingly, no differences in antibody levels to ID1-ID2a were detected between Cameroonian men and pregnant women. For example, in rural settings only 8–9% of males had antibodies to full-length VAR2CSA, but 90–96% had antibodies to ID1-ID2a. In addition, no significant difference in the avidity of IgG to ID1-ID2a was found between pregnant women and Cameroonian men, and no correlation between antibody levels at delivery and absence of placental malaria was found. Thus, the response to ID1-ID2a was not pregnancy specific, but predominantly against cross-reactivity epitopes, which may have been induced by other PfEMP1 antigens, malarial antigens, or microbes. Currently, ID1-ID2a is a leading vaccine candidate, since it binds to the CSA with the same affinity as the full-length molecule and elicits binding-inhibitory antibodies in animals. Further studies are needed to determine if the presence of naturally acquired cross-reactive antibodies in women living in malaria endemic countries will alter the response to ID1-ID2a following vaccination with ID1-ID2a.
Detection of Protein Coding Sequences Using a Mixture Model for Local Protein Amino Acid Sequence

Locating protein coding regions in genomic DNA is a critical step in accessing the information generated by large scale sequencing projects. Current methods for gene detection depend on statistical measures of content differences between coding and noncoding DNA in addition to the recognition of promoters, splice sites, and other regulatory sites. Here we explore the potential value of recurrent amino acid sequence patterns 3-19 amino acids in length as a content statistic for use in gene finding approaches. A finite mixture model incorporating these patterns can partially discriminate protein sequences which have no (detectable) known homologs from randomized versions of these sequences, and from short (< or = 50 amino acids) non-coding segments extracted from the S. cerevisiea genome. The mixture model derived scores for a collection of human exons were not correlated with the GENSCAN scores, suggesting that the addition of our protein pattern recognition module to current gene recognition programs may improve their performance.
Laboratory and Field-Based Correlates of Off-Road Cycling Performance

iv LIST OF TABLES . viii LIST OF FIGURES . ix CHAPTER 1: INTRODUCTION . 1 Hypotheses . 6 Delimitations . 7 Limitations . 7 Definitions. 8 Lactate Threshold. 8 Maximum Aerobic Capacity . 8 Maximal Anaerobic Power . 8 Onset of Blood Lactate Accumulation . 8 Peak Aerobic Power . 8 Vertical Feet per Second . 8 CHAPTER 2: LITERATURE REVIEW . 9 Race Categories . 9 Road Racing . 9 Mountain Bike Racing . 10 Anthropometric Profiles of Off-Road Cyclists . 10
COG Complex Complexities: Detailed Characterization of a Complete Set of HEK293T Cells Lacking Individual COG Subunits

The Conserved Oligomeric Golgi complex is an evolutionarily conserved multisubunit tethering complex (MTC) that is crucial for intracellular membrane trafficking and Golgi homeostasis. The COG complex interacts with core vesicle docking and fusion machinery at the Golgi; however, its exact mechanism of action is still an enigma. Previous studies of COG complex were limited to the use of CDGII (Congenital disorders of glycosylation type II)-COG patient fibroblasts, siRNA mediated knockdowns, or protein relocalization approaches. In this study we have used the CRISPR approach to generate HEK293T knock-out (KO) cell lines missing individual COG subunits. These cell lines were characterized for glycosylation and trafficking defects, cell proliferation rates, stability of COG subunits, localization of Golgi markers, changes in Golgi structure, and N-glycan profiling. We found that all KO cell lines were uniformly deficient in cis/medial-Golgi glycosylation and each had nearly abolished binding of Cholera toxin. In addition, all cell lines showed defects in Golgi morphology, retrograde trafficking and sorting, sialylation and fucosylation, but severities varied according to the affected subunit. Lobe A and Cog6 subunit KOs displayed a more severely distorted Golgi structure, while Cog2, 3, 4, 5, and 7 knock outs had the most hypo glycosylated form of Lamp2. These results led us to conclude that every subunit is essential for COG complex function in Golgi trafficking, though to varying extents. We believe that this study and further analyses of these cells will help further elucidate the roles of individual COG subunits and bring a greater understanding to the class of MTCs as a whole.
Transport of Carbon Dioxide in the Presence of Storm Systems over a Northern Wisconsin Forest

Mixing ratios of CO2 often change abruptly in the presence of inclement weather and low pressure systems. Water vapor mixing ratio, temperature, wind speed, and wind direction data are used to infer that the abrupt changes in CO2 mixing ratios at a site in northern Wisconsin are due to tropospheric mixing, horizontal transport, or a combination of both processes. Four different scenarios are examined: the passage of a summer cold front, a summer convective storm, an early spring frontal passage, and a late autumn low pressure system. Each event caused CO2 mixing ratios to change rapidly when compared to biological processes. In one summer convective event, vertical mixing caused CO 2 mixing ratios to rise more than 22 ppm in just 90 s. Synoptic-scale transport was also evident in the presence of storm systems and frontal boundaries. In the cases examined, synoptic-scale transport changed CO2 mixing ratios as much as 15 ppm in a 1-h time period. The events selected here represent extremes in the rate of change of boundary layer CO2 mixing ratios, excluding the commonly observed venting of a shallow, stable boundary layer. The rapid changes in CO 2 mixing ratios that were observed imply that large mixing ratio gradients must exist, often over rather small spatial scales, in the troposphere over North America. These rapid changes may be utilized in inverse modeling techniques aimed at identifying sources and sinks of CO2 on regional to continental scales.
Linking Entrepreneurial Orientation and Export Intensity: How. Organizational Learning Capability and Innovation Performance affect this relationship?

Firms that partake in export activity are entrepreneurial in nature because exporting firms would benefit by proactively seeking new markets, engaging in innovative action to meet local market’s needs, and be able and willing to take risks by venturing into previously unknown markets. While prior studies have looked at the importance of entrepreneurial orientation, organizational learning or innovation in export strategy, they have overlooked the process view that allows understanding the way through which firms with this kind of characteristics are able to assure better export results. Through the use of structural equation modelling in a sample of 182 small and medium enterprises ceramic firms, the authors demonstrate that entrepreneurial orientation is a precursor of export intensity but this relationship is mediated by organizational learning and innovation performance. This result highlights the process view; those firms with entrepreneurial orientation are able to have the capability of learning and superior innovation performance which finally increases export intensity. Political implications could be done with our study. Governments that reinforce innovation policies in the firms are helping the openness of the companies indirectly.
Real Zeros and Normal Distribution for Statistics on Stirling Permutations Defined by Gessel and Stanley

We study Stirling permutations defined by Gessel and Stanley in [J. Combin. Theory Ser. A, 24 (1978), pp. 25-33]. We prove that their generating function according to the number of descents has real roots only. We use that fact to prove that the distribution of these descents and other equidistributed statistics on these objects converge to a normal distribution.
Perceived managerial and leadership effectiveness within a Moroccan Higher Education Institution

ABSTRACT The purpose of this research was to determine what behaviourally distinguishes effective and ineffective managers within a Moroccan Higher Education Institution (HEI). The critical incident technique (CIT) was the methodology deployed to collect data from participants in terms of how they perceive managers as either effective or ineffective. The collected data (CIs) were subjected to content and thematic analysis that resulted in derived positive and negative behavioural statements (BSs). A total of 42 participants/informants were interviewed and revealed a total of 418 CIs, of which 189 were positive CIs and 229 were negative. The analysis revealed a total of 49 BSs, of which 19 were positive and 30 were negative behavioural indicators. The findings of this investigation bring empirical evidence to understand what and how managers are perceived as effective or ineffective in the Moroccan academic context and, therefore, adds to the literature. The information obtained can also provide rich information/knowledge that can be used as a basis to address the behavioural developmental needs of managers in HEIs. This research adds value by following by following two previous replication studies in a French and a Hungarian HEI; moreover, this study is the first to be conducted in the Moroccan/North African region.
Explanations of recommendations

This thesis focuses on explanations of recommendations. Explanations can have many advantages, from inspiring user trust to helping users make good decisions. We have identified seven different aims of explanations, and in this thesis we will consider how explanations can be optimized for some of these aims. We will consider both an explanation's content and its presentation. As a domain, we are currently investigating explanations for a movie recommender, and developing a prototype system. This paper summarizes the goals of the thesis, the methodology we are using, the work done so far and our intended future work.
Risk Sharing Networks in Rural Philippines

Using detailed data on gifts, loans, and asset sales, this paper investigates how rural Filipino households deal with income and expenditure shocks. We find that shocks have a strong effect on gifts and informal loans, but little effect on sales of livestock and grain. Mutual insurance does not appear to take place at the village level; rather, households receive help primarily through networks of friends and relatives. Certain shocks are better insured than others. The evidence is consistent with models of quasi-credit where risk is shared within tightly knit networks through flexible, zero interest informal loans combined with pure transfers.
A Recurrent loss‐of‐function alanyl‐tRNA synthetase (AARS ) mutation in patients with charcot‐marie‐tooth disease type 2N (CMT2N)

Charcot‐Marie‐Tooth (CMT) disease comprises a heterogeneous group of peripheral neuropathies characterized by muscle weakness and wasting, and impaired sensation in the extremities. Four genes encoding an aminoacyl‐tRNA synthetase (ARS) have been implicated in CMT disease. ARSs are ubiquitously expressed, essential enzymes that ligate amino acids to cognate tRNA molecules. Recently, a p.Arg329His variant in the alanyl‐tRNA synthetase (AARS) gene was found to segregate with dominant axonal CMT type 2N (CMT2N) in two French families; however, the functional consequence of this mutation has not been determined. To investigate the role of AARS in CMT, we performed a mutation screen of the AARS gene in patients with peripheral neuropathy. Our results showed that p.Arg329His AARS also segregated with CMT disease in a large Australian family. Aminoacylation and yeast viability assays showed that p.Arg329His AARS severely reduces enzyme activity. Genotyping analysis indicated that this mutation arose on three distinct haplotypes, and the results of bisulfite sequencing suggested that methylation‐mediated deamination of a CpG dinucleotide gives rise to the recurrent p.Arg329His AARS mutation. Together, our data suggest that impaired tRNA charging plays a role in the molecular pathology of CMT2N, and that patients with CMT should be directly tested for the p.Arg329His AARS mutation. Hum Mutat 33:244–253, 2012. © 2011 Wiley Periodicals, Inc.