Miracle-dz/UniFAR-FTUs huggingface dataset:
Agile game: a project management game for agile methods

Since mid-1990s, companies have adopted agile methods and incorporated them in their development methodologies. For this reason, future project managers and developers need to have a full understanding of these methods. At present, the university’s approach to agile methods is theoretical and is not reflected during the development of a product and their practical use. The purpose of this project is the creation of a software system in the form of a game, named Agile Game, which simulates their use. The system is designed for use as supplementary material in lectures, to help students understand agile methods, to present their use within a project, and to demonstrate how they differ from traditional project management methodologies. The final system, which is web based, was implemented using PHP, MySQL and JavaScript. It was fully tested against the requirements and evaluated by peer students. The evaluation showed that the majority of users were satisfied with the system but they thought that it should contain more detailed information at every step of the game. For this reason, some parts of the design and the content were reviewed to meet user requirements.
Levetiracetam and lamotrigine effects as mono- and polytherapy on bone mineral density in epileptic patients

ABSTRACT The purpose of this study was to determine the effect of lamotrigine (LTG) and levetiracetam (LEV) as mono- and polytherapy on biochemical markers of bone turnover and bone mineral density in Egyptian adult patients with epilepsy. Methods Forty-eight patients were divided into four groups: two received monotherapy of either LTG or LEV, and the other two groups received polytherapy comprising (valproate [VPA] + LTG or VPA + LEV). Thirty matched healthy participants were included in the study. Participants completed a nutritional and physical activity questionnaire. Biochemical markers of bone and mineral metabolism and bone mineral density of the lumbar spine were measured at baseline and at six months. Results In the LEV monotherapy group, the bone formation markers showed a significant decrease in serum alkaline phosphatase and serum osteocalcin levels while the bone resorption marker showed a significant increase in urinary deoxypyridinoline levels. After six months of treatment, bone mineral density showed a significant decrease in all treated groups, while among monotherapy groups, this significant decrease was more prevalent in the LEV monotherapy group compared with the LTG monotherapy group. Furthermore, there was significant negative correlation between urinary deoxypyridinoline levels and bone mineral density in the LEV monotherapy group. Conclusion Using new generation antiepileptics, LEV monotherapies and polytherapy showed harmful effects on bone but LTG did not.
Comparison of endoplasmic reticulum stress and mitochondrial biogenesis responses after 12 weeks of treadmill running and ladder climbing exercises in the cardiac muscle of middle-aged obese rats

The purpose of the present study was to compare the influence of aerobic exercise (AE) lasting 12 weeks to that of resistance exercise (RE) of the same duration on endoplasmic reticulum (ER) stress and mitochondrial biogenesis in the cardiac muscle of middle-aged obese rats. Obesity was induced in thirty 50-week-old male Sprague Dawley rats over 6 weeks by administration of a high-fat diet. The rats were then subjected to treadmill-running (AE) and ladder-climbing (RE) exercises 3 times per week for 12 weeks. Rats in the AE group showed significantly lower increases in body weight and intraperitoneal fat than those in the sedentary control (SC) group (P<0.05). The 12-week exercise regimes resulted in a significant increase in expression of mitochondrial biogenesis markers and levels of peroxisome proliferator-activated receptor gamma coactivator 1α in the cardiac muscle (P<0.05). Phosphorylation of PKR-like ER kinase, an ER stress marker, decreased significantly (P<0.05) after the exercise training. Although a trend for decreased C/EBP homologous protein (CHOP) expression was observed in both exercise groups, only the AE group had a statistically significant decrease (P<0.05). Levels of GRP78, an ER stress marker that protects cardiac muscle, did not significantly differ among the groups. Although only the AE group decreased body weight and fat mass, the two exercise regimes had similar effects on cardiac muscle with the exception of CHOP. Therefore, we suggest that both AE, which results in weight loss, and high-intensity RE, though not accompanied by weight loss, protect obese cardiac muscle effectively.
Statistical performance guarantees in large-scale cross-path packet switch

Recently, a quasi-static routing scheme called path switching was proposed for large-scale packet switch systems. The path-switched Clos network is called a cross-path switch. The cross-path switch is capable of supporting multirate and multicast traffic. In this paper, we develop a general framework for it to handle multimedia traffic. We study the statistical behavior of the cross-path switch using exponential bounded burstiness (EBB) processes as source session traffic models. With characterizing the service guarantees by service curves, we derive a set of statistical bounds on the delay, backlog and departure processes at the switch on a per-session basis. These bounds are necessary for providing per-session statistical quality of service (QoS) guarantees in the cross-path switch and achieving high system utilization.
Generating guitar solos by integer programming

In this paper, we present a framework for computer-aided composition (CAC) that uses exact combinatorial optimisation methods to generate guitar solos from a newly proposed data-set of licks over an accompaniment based on the 12-bar blues chord progression. An integer programming formulation, which can be solved to optimality by a branch-and-cut algorithm, was developed for this problem whose objective is to determine an optimal sequence of a set of licks given a matrix of transition costs derived from user preferences. The generated solos are displayed in tablature format. Outputs of the system were evaluated in an empirical experiment with 173 participants. The results show that the solos whose licks were optimally sequenced were significantly more enjoyed than those randomly sequenced. We project that the developed framework could be of potential use to guitarists looking for original material; as an educational tool for future composers; and to support composers in discovering unique and novel compositional ideas.
Descriptive complexity of constraint problems

Constraint problems are a powerful framework in which many common combinatorial problems can be expressed. Examples include graph colouring problems, Boolean satisfaction, graph cut problems, systems of equations, and many more. One typically distinguishes between constraint satisfaction problems (CSPs), which model strictly decision problems, and so-called valued constraint satisfaction problems (VCSPs), which also include optimisation problems. A key open problem in this field is the long-standing dichotomy conjecture by Feder and Vardi. It claims that CSPs only fall into two categories: Those that are NP-complete, and those that are solvable in polynomial time. This stands in contrast to Ladner’s theorem, which, assuming P 6= NP, guarantees the existence of problems that are neither NP-complete, nor in P, making CSPs an exceptional class of problems. While the Feder-Vardi conjecture is proven to be true in a number of special cases, it is still open in the general setting. (Recent claims affirming the conjecture are not considered here, as they have not been peer-reviewed yet.) In this thesis, we approach the complexity of constraint problems from a descriptive complexity perspective. Namely, instead of studying the computational resources necessary to solve certain constraint problems, we consider the expressive power necessary to define these problems in a logic. We obtain several results in this direction. For instance, we show that Schaefer’s dichotomy result for the case of CSPs over the Boolean domain can be framed as a definability result: Either a CSP is definable in fixed-point logic with rank (FPR), or it is NP-hard. Furthermore, we show that a dichotomy exists also in the general case. For VCSPs over arbitrary domains, we show that a VCSP is either definable in fixed-point logic with counting (FPC), or it is not definable in infinitary logic with counting (C). We show that these definability dichotomies also have algorithmic implications. In particular, using our results on the definability of VCSPs, we prove a dichotomy on the number of levels in the Lasserre hierarchy necessary to obtain an exact solution: For a finite-valued VCSP, either it is solved by the first level of the hierarchy, or one needs Ω(n) levels. Finally, we explore how other methods from finite model theory can be useful in the context of constraint problems. We consider pebble games for finite variable logics in this context, and expose new connections between CSPs, pebble games, and homomorphism preservation results.
Rank and rate: multi-task learning for recommender systems

The two main tasks in the Recommender Systems domain are the ranking and rating prediction tasks. The rating prediction task aims at predicting to what extent a user would like any given item, which would enable to recommend the items with the highest predicted scores. The ranking task on the other hand directly aims at recommending the most valuable items for the user. Several previous approaches proposed learning user and item representations to optimize both tasks simultaneously in a multi-task framework. In this work we propose a novel multi-task framework that exploits the fact that a user does a two-phase decision process - first decides to interact with an item (ranking task) and only afterward to rate it (rating prediction task). We evaluated our framework on two benchmark datasets, on two different configurations and showed its superiority over state-of-the-art methods.
Activated ATF6 Induces Intestinal Dysbiosis and Innate Immune Response to Promote Colorectal Tumorigenesis.

BACKGROUND & AIMS Activating transcription factor 6 (ATF6) regulates endoplasmic reticulum stress. We studied whether ATF6 contributes to the development of colorectal cancer (CRC) using tissue from patients and transgenic mice. METHODS We analyzed data from 541 patients with CRC in The Cancer Genome Atlas database for genetic variants and aberrant expression levels of unfolded protein response genes. Findings were validated in a cohort of 83 patients with CRC in Germany. We generated mice with intestinal epithelial cell-specific expression of the active form of Atf6 (nATF6IEC) from 2 alleles (homozygous), mice with expression of nATF6IEC from 1 allele (heterozygous), and nATF6IECfl/fl mice (controls). All nATF6IEC mice were housed under either specific-pathogen-free or germ-free conditions. Cecal microbiota from homozygous nATF6IEC mice or control mice was transferred into homozygous nATF6IEC mice or control mice. nATF6IEC mice were crossed with mice with disruptions in the myeloid differentiation primary response gene 88 and toll-like receptor adaptor molecule 1 gene (Myd88/Trif-knockout mice). Intestinal tissues were collected from mice and analyzed by histology, immunohistochemistry, immunoblots, gene expression profiling of unfolded protein response and inflammatory genes, array-based comparative genome hybridization, and 16S ribosomal RNA gene sequencing. RESULTS Increased expression of ATF6 was associated with reduced disease-free survival times of patients with CRC. Homozygous nATF6IEC mice developed spontaneous colon adenomas at 12 weeks of age. Compared with controls, homozygous nATF6IEC mice had changes in the profile of their cecal microbiota, increased proliferation of intestinal epithelial cells, and loss of the mucus barrier-all preceding tumor formation. These mice had increased penetration of bacteria into the inner mucus layer and activation of signal transducer and activator of transcription 3, yet inflammation was not observed at the pretumor or tumor stages. Administration of antibiotics to homozygous nATF6IEC mice greatly reduced tumor incidence, and germ-free housing completely prevented tumorigenesis. Analysis of nATF6IEC MyD88/TRIF-knockout mice showed that tumor initiation and growth required MyD88/TRIF-dependent activation of signal transducer and activator of transcription 3. Transplantation of cecal microbiota from nATF6IEC mice and control mice, collected before tumor formation, caused tumor formation in ex-germ-free nATF6IEC mice. CONCLUSIONS In patients with CRC, ATF6 was associated with reduced time of disease-free survival. In studies of nATF6IEC mice, we found sustained intestinal activation of ATF6 in the colon to promote dysbiosis and microbiota-dependent tumorigenesis.
Structural basis for prolidase deficiency disease mechanisms

Prolidase is a metallopeptidase that cleaves iminodipeptides containing a proline (Pro) or hydroxyproline (Hyp) residue at their C‐terminal end. The disease prolidase deficiency (PD) is a rare recessive human disorder characterized by reduced prolidase activity. PD manifests itself by a wide range of severe clinical symptoms, most commonly as skin ulceration, recurrent infections of the respiratory tract, and mental retardation. Several mutations in the PEPD gene have been identified that are responsible for the loss or the reduction of prolidase activity. In contrast, the structural basis of enzyme inactivation has so far remained elusive. In this study, we present high resolution crystal structures of a number of human prolidase (HsProl) variants, in which single amino acids are either substituted by others or deleted. The observed implications of the mutations on the three‐dimensional structure of HsProl are reported and discussed and related to their enzymatic activity. The resulting structures may be divided into four groups depending on the presumed effect of the corresponding mutations on the reaction mechanism. The four possible inactivation mechanisms, which could be elucidated, are disruption of the catalytic Mn2(OH−)‐center, introduction of chain disorder along with the displacement of important active site residues, rigidification of the active site, and flexibilization of the active site.
Fabrication of novel tubular scaffold for tendon repair from chitosan in combination with zinc oxide nanoparticles

Chitosan bears numerous properties, such as biocompatibility, biodegradability and non-toxicity making it suitable for use in different biomedical fields. Zinc (Zn) is required for fibroblasts proliferation and collagen synthesis as essential elements of wound healing. Its nanoparticles are well known for their capability to enhance wound healing by cell adhesion and migration improvement through growth factors-mediated mechanisms. Poor blood supply and unique histological characteristics of tendon make its regeneration always slow. Also, adhesion formation between tendon and its surrounding tissues is another problem for neotendon to return to its normal structure and functional activities. In this study, a novel tubular scaffold of zinc oxide (ZnO) nanoparticles loaded chitosan has been fabricated for tendon repair. Experimental complete tenotomy of deep digital flexor tendon in a rabbit model was done and scaffolds were placed in the transected area after two ends suturing. After four and eight weeks, adhesion formation around the tendons and tissue reaction to the scaffolds were evaluated macroscopically. Inflammation, angiogenesis and collagen fibers arrangement were also analyzed in histopathological evaluations. After eight weeks, the scaffolds were absorbed completely, adhesions around the tendon were decreased and there was no sign of significant tissue reaction and/or infection in histopathological analyses. The reduced adhesion formation, improved gliding function and better histopathological characteristics suggest this scaffold application as a potential therapy in treatment of tendon acute injuries.
Are Sovereigns Entitled to the Benefit of the International Rule of Law? An Introduction

In this symposium, we publish Jeremy Waldron's article, �Are Sovereigns Entitled to the Benefit of the Rule of Law? � together with four responses, by Samantha Besson, David Dyzenhaus, Thomas Poole and Alexander Somek. Waldron is justifiably renowned as a jurisprude and theorist of the concept of the rule of law. His engagement with international law is more recent, but no less significant. In this article, he takes a familiar (perhaps even tired) question among international lawyers � can there be something akin to a rule of law in international affairs? � and recasts how we ought to think about it. With characteristically deft and plain-speaking arguments, Waldron burrows to the heart of the issue: What might it mean to speak of an �international rule of law,� and who or what are properly understood as its beneficiaries?
Immunolocalization of enamel matrix protein-like proteins in the tooth enameloid of spotted gar, Lepisosteus oculatus, an actinopterygian bony fish

ABSTRACT Enameloid is a well-mineralized tissue covering the tooth surface in fish and it corresponds to the outer-most layer of dentin. It was reported that both dental epithelial cells and odontoblasts are involved in the formation of enameloid. Nevertheless, the localization and timing of secretion of ectodermal enamel matrix proteins in enameloid are unclear. In the present study, the enameloid matrix during the stages of enameloid formation in spotted gar, Lepisosteus oculatus, an actinopterygian, was examined mainly by transmission electron microscopy-based immunohistochemistry using an anti-mammalian amelogenin antibody and antiserum. Positive immunoreactivity with the antibody and antiserum was found in enameloid from the surface to the dentin-enameloid junction just before the formation of crystallites. This immunoreactivity disappeared rapidly before the full appearance of crystallites in the enameloid during the stage of mineralization. Immunolabelling was usually found along the collagen fibrils but was not seen on the electron-dense fibrous structures, which were probably derived from matrix vesicles in the previous stage. In inner dental epithelial cells, the granules in the distal cytoplasm often showed positive immunoreactivity, suggesting that the enamel matrix protein-like proteins originated from inner dental epithelial cells. Enamel matrix protein-like proteins in the enameloid matrix might be common to the enamel matrix protein-like proteins previously reported in the collar enamel of teeth and ganoine of ganoid scales, because they exhibited marked immunoreactivity with the same anti-mammalian amelogenin antibodies. It is likely that enamel matrix protein-like proteins are involved in the formation of crystallites along collagen fibrils in enameloid.
Genetic and Common Environmental Contributions to Familial Resemblances in Plasma Carotenoid Concentrations in Healthy Families

Carotenoids have shown an interindividual variability that may be due to genetic factors. The only study that has reported heritability of serum α- and β-carotene has not considered the environmental component. This study aimed to estimate the contribution of both genetic and common environmental effects to the variance of carotenoid concentrations and to test whether their phenotypic correlations with cardiometabolic risk factors are explained by shared genetic and environmental effects. Plasma carotenoid concentrations (α-carotene, β-carotene, β-cryptoxanthin, lutein, lycopene, zeaxanthin, and total carotenoids) of 48 healthy subjects were measured. Heritability estimates of carotenoid concentrations were calculated using the variance component method. Lutein and lycopene showed a significant familial effect (p = 6 × 10−6 and 0.0043, respectively). Maximal heritability, genetic heritability, and common environmental effect were computed for lutein (88.3%, 43.8%, and 44.5%, respectively) and lycopene (45.2%, 0%, and 45.2%, respectively). Significant phenotypic correlations between carotenoid concentrations and cardiometabolic risk factors were obtained for β-cryptoxanthin, lycopene, and zeaxanthin. Familial resemblances in lycopene concentrations were mainly attributable to common environmental effects, while for lutein concentrations they were attributable to genetic and common environmental effects. Common genetic and environmental factors may influence carotenoids and cardiometabolic risk factors, but further studies are needed to better understand the potential impact on disease development.
On Approximating (Sparse) Covering Integer Programs

We consider approximation algorithms for covering integer programs of the form min $\langle c, x \rangle $ over $x \in \mathbb{N}^n $ subject to $A x \geq b $ and $x \leq d$; where $A \in \mathbb{R}_{\geq 0}^{m \times n}$, $b \in \mathbb{R}_{\geq 0}^m$, and $c, d \in \mathbb{R}_{\geq 0}^n$ all have nonnegative entries. We refer to this problem as $\operatorname{CIP}$, and the special case without the multiplicity constraints $x \le d$ as $\operatorname{CIP}_{\infty}$. These problems generalize the well-studied Set Cover problem. We make two algorithmic contributions. First, we show that a simple algorithm based on randomized rounding with alteration improves or matches the best known approximation algorithms for $\operatorname{CIP}$ and $\operatorname{CIP}_{\infty}$ in a wide range of parameter settings, and these bounds are essentially optimal. As a byproduct of the simplicity of the alteration algorithm and analysis, we can derandomize the algorithm without any loss in the approximation guarantee or efficiency. Previous work by Chen, Harris and Srinivasan [12] which obtained near-tight bounds is based on a resampling-based randomized algorithm whose analysis is complex. Non-trivial approximation algorithms for $\operatorname{CIP}$ are based on solving the natural LP relaxation strengthened with knapsack cover (KC) inequalities [5,24,12]. Our second contribution is a fast (essentially near-linear time) approximation scheme for solving the strengthened LP with a factor of $n$ speed up over the previous best running time [5]. Together, our contributions lead to near-optimal (deterministic) approximation bounds with near-linear running times for $\operatorname{CIP}$ and $\operatorname{CIP}_{\infty}$.