Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative Analysis of Field-Isolate and Monkey-Adapted Plasmodium vivax Genomes

Significant insights into the biology of Plasmodium vivax have been gained from the ability to successfully adapt human infections to non-human primates. P. vivax strains grown in monkeys serve as a renewable source of parasites for in vitro and ex vivo experimental studies and functional assays, or for studying in vivo the relapse characteristics, mosquito species compatibilities, drug susceptibility profiles or immune responses towards potential vaccine candidates. Despite the importance of these studies, little is known as to how adaptation to a different host species may influence the genome of P. vivax. In addition, it is unclear whether these monkey-adapted strains consist of a single clonal population of parasites or if they retain the multiclonal complexity commonly observed in field isolates. Here we compare the genome sequences of seven P. vivax strains adapted to New World monkeys with those of six human clinical isolates collected directly in the field. We show that the adaptation of P. vivax parasites to monkey hosts, and their subsequent propagation, did not result in significant modifications of their genome sequence and that these monkey-adapted strains recapitulate the genomic diversity of field isolates. Our analyses also reveal that these strains are not always genetically homogeneous and should be analyzed cautiously. Overall, our study provides a framework to better leverage this important research material and fully utilize this resource for improving our understanding of P. vivax biology.
Antihypertensive Peptide Activity in Dutch-Type Cheese Models Prepared with Different Additional Strains of Lactobacillus Genus Bacteria

The objective of this study was to determine the proteolytic activity of bacterial strains from the genus Lactobacillus and their capability in producing peptide inhibitors of angiotensin-converting enzyme (ACE) in cheese models prepared with their addition. After 5 weeks of ripening, all cheese models studied were characterized by a high ability of angiotensin convertase inhibition which exceeded 80%. The use of the adjunct bacterial cultures from the genus Lactobacillus contributed to lower IC50 values compared with the value determined for the control cheese model. The proteolytic activity of model cheeses varied in their increase through the period of ripening, with changes in values dependent on the adjunct lactic acid bacteria (LAB) strain used for cheesemaking. Starting from the first week of ripening, the lowest proteolytic activity was demonstrated for the control cheese models, whereas the highest activity throughout the ripening period was shown for the cheese models with the addition of Lb. rhamnosus 489.
Temporal Reasoning with Abductive Event Calculus

We present the SLDNFA procedure, which integrates two important nonmonotonic paradigms, negation as failure and abduction. The main diierence between SLDNFA and existing approaches is the improved treatment of non-ground abductive goals. We present an extension for temporal reasoning based on Abductive Event Calculus. We show the power of the approach by applying it to planning and solving well-known temporal reasoning problems. Interestingly, the procedure generates partial plans; the order of events is left unspeciied when they do not interfere.
The Use of Show and Tell (S&T) Method in Teaching Vocabulary at the Second Year Students of Junior High School (SMP) Negeri 4 Galesong Selatan Kabupaten Takalar

The result of the data indicated that there was a significant difference between students' post-test in experimental class and controlled class. The mean score of post test (9.02) in experimental class was higher than the mean score of post-test (5.63) in controlled class. Through t-test (14.2) was higher than t-tabel (2.042) at the level of significance 0.05 with degree of freedom (df) = 36. Form the result of the research, the researcher concluded that the hypothesis was accepted. It means that using Show & Tell (S&T) method was effective towards the students vocabulary mastery at the second Year Student of Junior High School (SMP) Negeri 4 Galesong Selatan Kabupaten Takalar. Therefore, English teacher may use Show & Tell (S&T) Method in teaching English process. Because it can make the English learning process more enjoyable, fun and effective.
XANADUE: a system for detecting changes to XML data in tree-unaware relational databases

Recently, a number of main memory algorithms for detecting the changes to XML data have been proposed. These approaches are not suitable for detecting changes to large XML document as it requires a lot of memory to keep the two versions of XML documents in the memory. We have developed a novel XML change detection system, called XANADUE that uses traditional relational database engines for detecting changes to large XML data. In this approach, we store the XML documents in the relational database and issue SQL queries (whenever appropriate) to detect the changes. This demonstration will showcase the functionality of our system and the effectiveness of XML change detection in relational environment.
The VPN Problem with Concave Costs

Only recently Goyal, Olver, and Shepherd [Proc. STOC, ACM, New York, 2008] proved that the symmetric virtual private network design (sVPN) problem has the tree routing property, namely, that there always exists an optimal solution to the problem whose support is a tree. Combining this with previous results by Fingerhut, Suri, and Turner [J. Algorithms, 24 (1997), pp. 287-309] and Gupta et al. [Proc. STOC, ACM, New York, 2001], sVPN can be solved in polynomial time. In this paper we investigate an APX-hard generalization of sVPN, where the contribution of each edge to the total cost is proportional to some non-negative, concave, and nondecreasing function of the capacity reservation. We show that the tree routing property extends to the new problem and give a constant-factor approximation algorithm for it. We also show that the undirected uncapacitated single-source minimum concave-cost flow problem has the tree routing property when the cost function has some property of symmetry.
Production and immunogenicity of chimeric virus-like particles containing the spike glycoprotein of infectious bronchitis virus

Infectious bronchitis virus (IBV) poses a severe threat to the poultry industry and causes heavy economic losses worldwide. Vaccination is the most effective method of preventing infection and controlling the spread of IBV, but currently available inactivated and attenuated virus vaccines have some disadvantages. We developed a chimeric virus-like particle (VLP)-based candidate vaccine for IBV protection. The chimeric VLP was composed of matrix 1 protein from avian influenza H5N1 virus and a fusion protein neuraminidase (NA)/spike 1 (S1) that was generated by fusing IBV S1 protein to the cytoplasmic and transmembrane domains of NA protein of avian influenza H5N1 virus. The chimeric VLPs elicited significantly higher S1-specific antibody responses in intramuscularly immunized mice and chickens than inactivated IBV viruses. Furthermore, the chimeric VLPs induced significantly higher neutralization antibody levels than inactivated H120 virus in SPF chickens. Finally, the chimeric VLPs induced significantly higher IL-4 production in mice. These results demonstrate that chimeric VLPs have the potential for use in vaccines against IBV infection.
Spirituality/Religiosity: A Cultural and Psychological Resource among Sub-Saharan African Migrant Women with HIV/AIDS in Belgium

Spirituality/religion serves important roles in coping, survival and maintaining overall wellbeing within African cultures and communities, especially when diagnosed with a chronic disease like HIV/AIDS that can have a profound effect on physical and mental health. However, spirituality/religion can be problematic to some patients and cause caregiving difficulties. The objective of this paper was to examine the role of spirituality/religion as a source of strength, resilience and wellbeing among sub-Saharan African (SSA) migrant women with HIV/AIDS. A qualitative study of SSA migrant women was conducted between April 2013 and December 2014. Participants were recruited through purposive sampling and snowball techniques from AIDS Reference Centres and AIDS workshops in Belgium, if they were 18 years and older, French or English speaking, and diagnosed HIV positive more than 3 months beforehand. We conducted semi-structured interviews with patients and did observations during consultations and support groups attendances. Thematic analysis was used to analyse the data. 44 women were interviewed, of whom 42 were Christians and 2 Muslims. None reported religious/spiritual alienation, though at some point in time many had felt the need to question their relationship with God by asking “why me? ” A majority reported being more spiritual/religious since being diagnosed HIV positive. Participants believed that prayer, meditation, regular church services and religious activities were the main spiritual/religious resources for achieving connectedness with God. They strongly believed in the power of God in their HIV/AIDS treatment and wellbeing. Spiritual/religious resources including prayer, meditation, church services, religious activities and believing in the power of God helped them cope with HIV/AIDS. These findings highlight the importance of spirituality in physical and mental health and wellbeing among SSA women with HIV/AIDS that should be taken into consideration in providing a caring and healthy environment.
Comparison of clinical and cognitive characteristics of a Mexican adult clinical population with and without ADHD

Introduction. Attention deficit hyperactivity disorder (ADHD) is a neurodevelopmental disorder affecting approximately 5% of the world population, with symptoms that may persist into adulthood. Despite the findings on the clinical course of this disorder, information regarding comorbidity patterns, psychosocial and executive functioning in adult life in those with and without ADHD in Latin American samples is scarce. Objective. The aim of this study is to compare the comorbidity pattern, psychosocial, and executive functioning of adults with and without ADHD from a clinical sample. Method. One hundred and fifty-one patients between 20 and 45 years, with screened positively on ASRS-V1.1, were invited to continue an evaluation process as part of clinical research program (PROMETEO): 1) K-SADS-PL Mx interview, 2) MINI-Plus interview, ASRS-V1-1 18 item version, BRIEF self-reported questionnaire, SCQA-ADHD, and 3) Individual case review by clinical expert in ADHD. Results. Individuals in the ADHD group had a higher average of comorbid disorders (2.5 SD 1.1 vs. 1.3 SD 1.0 respectively, F = .439; t = -6.621; df = 149; p < .001), more likelihood of procrastinating (OR = 6.5; 95% CI[2.6, 16.2]; z = 4.0) and were more likely to present difficulties in both the behavior regulation index (OR = 104.9; 95% CI[31.8, 345.7]; z = 7.65) and the metacognitive index (OR = 94.79; 95% CI[29.10, 308.76]; z = 7.56) compared to the non-ADHD group, regardless of gender. Discussion and conclusions. Our results indicate that the ADHD adult group presented with more comorbidity, and worse psychosocial and executive functioning than non-ADHD adults.
Managing Traceability Links with MaTraca

Traceability links are used to ensure co-evolution among related software artefacts. That is, to ensure that changes to the application are correctly and completely propagated. Much emphasis has been put on reverse engineering and co-evolution of vertical traceability links (i.e., across artefacts of the different levels of abstraction like UML, requirements documents, source code). However, today's applications require automatic support to deal with complex dependencies across heterogeneous source code entities (e.g., it is not uncommon for web applications to require multi-language and multi-paradigm programming). This paper introduces MaTraCa, an Eclipse plugin to maintain traceability links among entities of the same level of abstraction (i.e., code) in complex applications. MaTraCa stands for Managing Traceability Changes. MaTraCa focuses on horizontal links, that is, relations across software artefacts of the same level of abstraction such as source code, config files, html forms, etc.
Fused DTI/HARDI Visualization

High-angular resolution diffusion imaging (HARDI) is a diffusion weighted MRI technique that overcomes some of the decisive limitations of its predecessor, diffusion tensor imaging (DTI), in the areas of composite nerve fiber structure. Despite its advantages, HARDI raises several issues: complex modeling of the data, nonintuitive and computationally demanding visualization, inability to interactively explore and transform the data, etc. To overcome these drawbacks, we present a novel, multifield visualization framework that adopts the benefits of both DTI and HARDI. By applying a classification scheme based on HARDI anisotropy measures, the most suitable model per imaging voxel is automatically chosen. This classification allows simplification of the data in areas with single fiber bundle coherence. To accomplish fast and interactive visualization for both HARDI and DTI modalities, we exploit the capabilities of modern GPUs for glyph rendering and adopt DTI fiber tracking in suitable regions. The resulting framework, allows user-friendly data exploration of fused HARDI and DTI data. Many incorporated features such as sharpening, normalization, maxima enhancement and different types of color coding of the HARDI glyphs, simplify the data and enhance its features. We provide a qualitative user evaluation that shows the potentials of our visualization tools in several HARDI applications.
Optimal Diversity–Multiplexing Tradeoff and Code Constructions of Some Constrained Asymmetric MIMO Systems

In multiple-input-multiple-output (MIMO) communications, the notion of asymmetric channel refers to the situation when the number of transmit antennas is strictly larger than the number of receive antennas. Such channels can often be found in MIMO downlink transmissions. While existing cyclic-division-algebra (CDA)-based codes can still be employed to achieve the optimal diversity-multiplexing tradeoff (DMT) at high signal-to-noise ratio (SNR) regime, such codes cannot be directly decoded using, for example, the pure sphere decoding method. Although other means of decoding methods such as minimum mean square error generalized decision feedback equalizer (MMSE-GDFE) with lattice search and regularized lattice decoding are available, an alternative approach is to constrain the number of active transmit antennas in each channel use to be no larger than the number of receive antennas. The resulting system is coined constrained asymmetric MIMO system. Two general types of asymmetrical channels are considered in this paper, namely, 1) when there are two receive antennas and the number of transmit antennas is arbitrary, and 2) when the number of transmit antennas is one larger than the number of receive antennas. Explicit optimal transmission schemes as well as the corresponding code constructions for such constrained asymmetric MIMO channels are presented, and are shown to achieve the same DMT performance as their unconstrained counterparts.
On the planning of a hybrid IT infrastructure

With the emergence of utility computing and the continuous search for reducing the cost of running information technology (IT) infrastructures, we will soon experience an important change on the way these infrastructures are assembled, configured and managed. In this paper we consider the problem of managing a hybrid high-performance computing infrastructure whose processing elements comprise in-house dedicated machines, a utility computing service provider, and idle machines from a best-effort peer-to-peer grid. This infrastructure supports the execution of both best-effort and real-time applications. Realtime applications use primarily computing power from the in- house machines and any processing power that can be attained from the best-effort grid. Extra capacity required to meet deadlines is purchased from the utility computing service provider. This extra capacity is reserved for future use through short term contracts which are negotiated with no human intervention. We take a business-driven approach for the management of this hybrid infrastructure and propose heuristics that can be used by a contract planner agent to reduce the cost of running the applications at the same time that guarantees that deadlines are met. In particular, we show that constructing an estimation for the behavior of the grid is essential for making contracts that lead to high efficiency in the use of the hybrid infrastructure.
A Distance Scan Algorithm for Spatial Access Structures

In geographic information systems it is often useful to select an object located closest to a given point or to scan the objects with respect to their distance to a given point in ascending order. An example for a query of this type would be to retrieve ten hotels with at least three stars lying closest to the venue of a conference. Various subtypes of similar queries exist. On the other hand, research in geometric access structures has concentrated mainly on range queries. We present an e cient algorithm for closestand distance-scan-queries of various kinds. Our algorithm is based on the nearest neighbour algorithm for k-d-trees given by Friedman et al. [FBF77] and re ned by Sproull [Spr91]. We adapt this algorithm to external access structures and extend it to process a broader class of queries. Furthermore we show that the algorithm can be applied to point objects as well as to non-point objects, and that it can be used with all spatial access structures using a hierarchical directory. Analytical and experimental results show the outstanding performance of the algorithm.
Fast and accurate molecular Hartree-Fock with a finite-element multigrid method

We present a multigrid scheme for the solution of finite-element Hartree-Fock equations for diatomic molecules. It is shown to be fast and accurate, the time effort depending linearly on the number of variables. Results are given for the molecules LiH, BH, N_2 and for the Be atom in our molecular grid which agrees very well with accurate values from an atomic code. Highest accuracies were obtained by applying an extrapolation scheme; we compare with other numerical methods. For N_2 we get an accuracy below 1 nHartree.
There Is Nobody to Rely on: Cracks in the Intergenerational Contract Among the Elders in Arab Society in Israel

This study aims to examine the ways that old Palestinian Arabs in Israel experience and talk about ageing. Semistructured in-depth interviews were conducted among 25 Arab men and women, Muslims and Christians, aged 65 to 85 years. Using the concepts of “intergenerational contract” and “gender contract,” the study reveals a new discourse reflecting a complex relationship between the elders and their families, characterized by ambivalence and internal conflict. The findings indicate that the intergenerational contract has not disappeared and that family loyalty still exists, but the cracks are gradually widening. The gender contract, which remains stable in the perception of the elders, is changing as well, while the young women are struggling to comply with their part in the contract. The elders are therefore, aware of the possibility that the intergenerational contract will not be implemented in the traditional way and that there is no one to rely on.
Optical Imaging of Long-Term Depression in the Mouse Cerebellar Cortex In Vivo

Conjunctive stimulation of climbing fiber and parallel fiber inputs results in long-term depression (LTD) at parallel fiber–Purkinje cell synapses. Although hypothesized to play a major role in cerebellar motor learning, there has been no characterization of the cellular and molecular mechanisms of LTD in the whole animal, let alone its spatial properties, both of which are critical to understanding the role of LTD in cerebellar function. Neutral red optical imaging of the cerebellar cortex in the anesthetized mouse was used to visualize the spatial patterns of activation. Stimulation of the parallel fibers evoked a transverse beam of optical activity, and stimulation of the contralateral inferior olive evoked parasagittal bands. Conjunctive stimulation of parallel fibers and climbing fibers induced a long-term decrease (at least 1 hr) in the optical response to subsequent parallel fiber activation confined to the region of interaction between these two inputs. Activation of climbing fibers alone failed to induce the long-term decrease. Field potential recordings confirmed that the depression is postsynaptic and restricted to the interaction site. The long-term depression in the beam was prevented by a group 1 metabotropic glutamate receptor (mGluR1) antagonist and was absent in transgenic mice selectively expressing an inhibitor of protein kinase C (PKC) in Purkinje cells. Conversely, the long-term depression occurred in the mGluR4 knock-out mouse, consistent with its postsynaptic origin. In addition to providing the first visualization of parallel fiber–Purkinje cell LTD in the cerebellar cortex, this study demonstrates the spatial specificity of LTD and its dependence on mGluR1 and PKC in vivo.
Word-Based or Morpheme-Based? Annotation Strategies for Modern Hebrew Clitics

Morphologically rich languages pose a challenge to the annotators of treebanks with respect to the status of orthographic (space-delimited) words in the syntactic parse trees. In such languages an orthographic word may carry various, distinct, sorts of information and the question arises whether we should represent such words as a sequence of their constituent morphemes (i.e., a Morpheme-Based annotation strategy) or whether we should preserve their special orthographic status within the trees (i.e., a Word-Based annotation strategy). In this paper we empirically address this challenge in the context of the development of Language Resources for Modern Hebrew. We compare and contrast the Morpheme-Based and Word-Based annotation strategies of pronominal clitics in Modern Hebrew and we show that the Word-Based strategy is more adequate for the purpose of training statistical parsers as it provides a better PP-attachment disambiguation capacity and a better alignment with initial surface forms. Our findings in turn raise new questions concerning the interaction of morphological and syntactic processing of which investigation is facilitated by the parallel treebank we made available.