Miracle-dz/UniFAR-FTUs huggingface dataset:
Microswimming in complex fluids

Many microorganisms have the ability to propel themselves through their fluid environments by periodically actuating their body. The biological fluid environments surrounding these microswimmers are typically complex fluids containing many high-molecular weight protein molecules, which give the fluid non-Newtonian rheological properties. In this thesis, we investigate the effect that one such rheological property, viscoelasticity, has on microswimming. We consider a classical model of a microswimmer, the so-called Taylor’s waving sheet and generalise it to arbitrary shapes. We employ the Oldroyd-B model to study its swimming analytically and numerically. We attempt to develop a mechanistic understanding of the swimmer’s behaviour in viscoelastic fluids. It has recently been suggested that continuum models of complex biological fluids might not be appropriate for studying the swimming of flagellated microorganisms as the size of biological macromolecules is comparable to the typical width of a microorganism’s flagellum. A part of this thesis is devoted to exploring this scenario. We propose an alternative method for modelling complex fluids using a two-fluid depletion region model and we have developed a numerical solver to find the swimming speed and rate of work for the generalised Taylor’s waving sheet model swimmer using this alternate depletion region model. This thesis is organised as follows. In the first chapter, we outline a physical mechanism for the slowing down of Taylor’s sheet in an Oldroyd-B fluid as the Deborah number increases. We demonstrate how a microswimmer can be designed to avoid this. In the second chapter, we investigate swimming in an Oldroyd-B fluid near a solid boundary and show that, at large amplitudes and low polymer concentrations, the swimming speed of Taylor’s sheet increases with De. In the third chapter, we show how the Oldroyd-B model can be adapted using depletion regions. In the final chapter, we investigate optimal swimming in a Newtonian fluid. We show that while the organism’s energetics are important,
Purification of complement-fixing antigens of Rickettsia sennetsu by ether treatment

Soluble and particulate complement-fixing antigens of Rickettsia sennetsu were prepared from spleen suspensions of mice infected with the rickettsia and treated with cyclophosphamide. The medium used during purification of antigens, a solution consisting of equal volumes of phosphate-glutamate-sucrose buffer and veronal-buffered saline, was suitable for obtaining antigens with high titers and no anti-complementary activity. By heat treatment, it was demonstrated that the soluble antigen was heat labile and the particulate antigen was heat stable. The soluble antigen was precipitated by 80% saturation with ammonium sulfate. Cross-complement fixation tests using both soluble and particulate antigens revealed that there was no antigenic difference among strains of R. Sennetsu. On the other hand, no cross-activity was observed between R. sennetsu and R. orientalis.
Identification of determinants for weight reduction in overweight and obese children and adolescents

We conducted a pilot trial of electronic technology integrated into the treatment of children and adolescents who are overweight or obese. A total of 30 patients (mean age 14 years, mean BMI 32.7 kg/m2) were admitted to our hospital to participate in a structured treatment and teaching programme (STTP). To assess physical activity and eating habits, a mobile motion sensor board (MoSeBo) or a sensor for physical activity, integrated into a mobile phone with digital camera (DiaTrace) was used. Over an average period of four days of monitoring, the mean intensity (15.4 activity units) and duration of physical activity (267 min/d) were recorded with the mobile sensors. The mean time spent walking was 64 min/d, running 11 min/d, cycling 24 min/d and car driving 21 min/d. There were significant differences (P < 0.001) between self-reported physical activity and objective assessment: in general the duration of physical activity documented by children and adolescents was much higher than the objective assessment. Similarly, the real caloric intake was higher than the self-estimates (P = 0.085). A multivariate analysis showed that the following variables were significantly associated with weight reduction in the hospital STTP (R-squared = 0.59): high motivation, intrafamilial conflicts, duration of physical activity assessed with the MoSeBo/DiaTrace system, and the body fat mass at onset of therapy. All children and adolescents included in the trial completed it. Although the MoSeBo/DiaTrace system was used for a relatively short period in each patient, the high acceptance demonstrated that it could be integrated into therapy easily.
SeDMiD for Confusion Detection: Uncovering Mind State from Time Series Brain Wave Data

Understanding how brain functions has been an intriguing topic for years. With the recent progress on collecting massive data and developing advanced technology, people have become interested in addressing the challenge of decoding brain wave data into meaningful mind states, with many machine learning models and algorithms being revisited and developed, especially the ones that handle time series data because of the nature of brain waves. However, many of these time series models, like HMM with hidden state in discrete space or State Space Model with hidden state in continuous space, only work with one source of data and cannot handle different sources of information simultaneously. In this paper, we propose an extension of State Space Model to work with different sources of information together with its learning and inference algorithms. We apply this model to decode the mind state of students during lectures based on their brain waves and reach a significant better results compared to traditional methods.
Altering TET dioxygenase levels within physiological range affects DNA methylation dynamics of HEK293 cells

The TET family of dioxygenases (TET1/2/3) can convert 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC) and has been shown to be involved in active and passive DNA demethylation. Here, we demonstrate that altering TET dioxygenase levels within physiological range can affect DNA methylation dynamics of HEK293 cells. Overexpression of TET1 increased global 5hmC levels and was accompanied by mild DNA demethylation of promoters, gene bodies and CpG islands. Conversely, the simultaneous knockdown of TET1, TET2, and TET3 led to decreased global 5hmC levels and mild DNA hypermethylation of above-mentioned regions. The methylation changes observed in the overexpression and knockdown studies were mostly non-reciprocal and occurred with different preference depending on endogenous methylation and gene expression levels. Single-nucleotide 5hmC profiling performed on a genome-wide scale revealed that TET1 overexpression induced 5mC oxidation without a distribution bias among genetic elements and structures. Detailed analysis showed that this oxidation was related to endogenous 5hmC levels. In addition, our results support the notion that the effects of TET1 overexpression on gene expression are generally unrelated to its catalytic activity.
Synchronous Tree Adjoining Machine Translation

Tree Adjoining Grammars have well-known advantages, but are typically considered too difficult for practical systems. We demonstrate that, when done right, adjoining improves translation quality without becoming computationally intractable. Using adjoining to model optionality allows general translation patterns to be learned without the clutter of endless variations of optional material. The appropriate modifiers can later be spliced in as needed. In this paper, we describe a novel method for learning a type of Synchronous Tree Adjoining Grammar and associated probabilities from aligned tree/string training data. We introduce a method of converting these grammars to a weakly equivalent tree transducer for decoding. Finally, we show that adjoining results in an end-to-end improvement of +0.8 Bleu over a baseline statistical syntax-based MT model on a large-scale Arabic/English MT task.
Reengineering Web applications based on cloned pattern analysis

Web applications are subject to continuous and rapid evolution. Often it happens that programmers indiscriminately duplicate Web pages without considering systematic development and maintenance methods. This practice creates code clones that make Web applications hard to maintain and reuse. This paper presents an approach for reengineering Web applications based on clone analysis that aims at identifying and generalizing static and dynamic pages and navigational patterns of a Web application. Clone analysis is also helpful for identifying literals that can be generated from a database. A case study is described which shows how the proposed approach can be used for restructuring the navigational structure of a Web application by removing redundant code.
Human Exposure to Endocrine-Disrupting Chemicals and Prenatal Risk Factors for Cryptorchidism and Hypospadias: A Nested Case–Control Study

Background Exposure to xenoestrogens during pregnancy may disturb the development and function of male sexual organs. Objective In this study we aimed to determine whether the combined effect of environmental estrogens measured as total effective xenoestrogen burden (TEXB) is a risk factor for male urogenital malformations. Methods In a case–control study, nested in a mother–child cohort (n = 702) established at Granada University Hospital, we compared 50 newborns with diagnosis of cryptorchidism and/or hypospadias with 114 boys without malformations matched by gestational age, date of birth, and parity. Controls did not differ from the total cohort in confounding variables. TEXB and levels of 16 organochlorine pesticides were measured in placenta tissues. Characteristics of parents, pregnancy, and birth were gathered by questionnaire. We used conditional and unconditional regression models to estimate odds ratios (ORs) and 95% confidence intervals (CIs). Results TEXB from organohalogenated compounds was detectable in 72% and 54% of case and control placentas, respectively. Compared with controls, cases had an OR for detectable versus non-detectable TEXB of 2.82 (95% CI, 1.10–7.24). More pesticides were detected in cases than in controls (9.34 ± 3.19 vs. 6.97 ± 3.93). ORs for cases with detectable levels of pesticides, after adjusting for potential confounders in the conditional regression analysis, were o,p′-DDT (OR = 2.25; 95% CI, 1.03–4.89), p,p′-DDT (OR = 2.63; 95% CI, 1.21–5.72), lindane (OR = 3.38; 95% CI, 1.36–8.38), mirex (OR = 2.85; 95% CI, 1.22–6.66), and endosulfan alpha (OR = 2.19; 95% CI, 0.99–4.82). Engagement of mothers in agriculture (OR = 3.47; 95% CI, 1.33–9.03), fathers’ occupational exposure to xenoestrogens (OR = 2.98; 95% CI, 1.11–8.01), and history of previous stillbirths (OR = 4.20; 95% CI, 1.11–16.66) were also associated with risk of malformations. Conclusions We found an increased risk for male urogenital malformations related to the combined effect of environmental estrogens in placenta.
The shortest vector in a lattice is hard to approximate to within some constant

We show the shortest vector problem in the l/sub 2/ norm is NP-hard (for randomized reductions) to approximate within any constant factor less than /spl radic/2. We also give a deterministic reduction under a reasonable number theoretic conjecture. Analogous results hold in any l/sub p/ norm (p/spl ges/1). In proving our NP-hardness result, we give an alternative construction satisfying Ajtai's probabilistic variant of Sauer's lemma, that greatly simplifies Ajtai's original proof.
From HOT to COOL: transforming higher-order typed languages to concept-constrained object-oriented languages

In this paper, we present a transformation that maps type-level expressions from functional higher-order, typed (HOT) languages to type-level expressions in object-oriented HOT languages by mapping higher-order types to type parameters of generics that are constrained with appropriate concepts. We introduce a novel form of "defunctionalization" and a correctness criterion based on the kind structure of the transformed expression, and show that our transformation preserves kind structure. The transformation is retargetable, based on two new kernel languages that can be bound to different functional and object-oriented languages; we already provide bindings to Haskell as front end and C++ concepts and Scala traits in the back ends. The transformational approach presents an alternative to a language extension and is useful in particular if functional features are employed at specification time. We motivate the approach and illustrate it using three sizable functional libraries in C++ that have signatures that are automatically generated from the corresponding Haskell signatures.
Research on Community Division Algorithm with Directed and Weighted Network in Pervasive Sensing Environment

In view of the existing community network division algorithm without considering the weight and direction of the edge, we propose a novel algorithm in Pervasive Sensing Environment. Based on the node optimal path, the algorithm calculates the optimal path tree of mobile nodes, similarity index and community dispersion index and so on parameters to realize the reasonable division for directed weighted community network. The experimental results show that the accuracy of the algorithm is to achieve an average of 95%, higher than existing models about 10.9%. In addition, the algorithm still has good accuracy for other different types of network data, further demonstrated the efficiency and scalability of the algorithm.
Therapeutic Reference Range for Plasma Concentrations of Paroxetine in Patients With Major Depressive Disorders

Background: We investigated the relationship between plasma concentrations of paroxetine and the therapeutic effect of the drug, and we evaluated the therapeutic reference range for plasma concentration of paroxetine in patients with major depressive disorders (MDD). Methods: In this study, 120 patients with MDD were treated with 10–40 mg/d of paroxetine for 6 weeks, and 89 patients completed the protocol. The Montgomery–Asberg Depression Rating Scale (MADRS) was used to evaluate the patients at 0, 1, 2, 4, and 6 weeks. At the 6-week treatment time point, the patients were divided into 7 groups according to their paroxetine plasma concentrations in increments of 20 ng/mL. We used an analysis of variance and a &khgr;2 test to define the therapeutic reference range for plasma paroxetine concentrations. Results: We used 50% as the cutoff values for the percentage of MADRS improvement to determine the responder rates, and we defined remitters as patients with MADRS scores <10 at the 6-week treatment time point. We analyzed the responder and remitter rates of the patients according to their plasma paroxetine concentrations: 20 ng/mL, 40 ng/mL, and 60 ng/mL using the &khgr;2 test. According to the results of the &khgr;2 test in the responder rates, the 20–60 ng/mL plasma paroxetine group showed the highest effect size. Conclusions: The results of this study suggested that a range of 20–60 ng/mL is the therapeutic reference range for concentrations of paroxetine in plasma in patients with MDD.
Cosimulation for Smart Grid Communications

Migration from today's power systems to future smart grids is a necessity as the energy demand continues to grow and an increasing amounts of renewable energies need to be accommodated in the grid. One of the key enablers of the smart grid is the integration of information and communication technology (ICT) into the grids in order to monitor and control power generation, distribution, and demand. Considering the close interdependence of future smart grids and communication networks, there is a need for numerical simulation to thoroughly understand the impact of the communication networks on the performance of power system dynamics, and vice versa. This paper provides an overview of available simulation techniques for smart grid communications with a focus on cosimulation frameworks and their enabling technologies. A decision tree comparing relative advantages of available cosimulation platforms and providing guidelines on how to select from them for a given application is presented. A case study analyzing agent-based shipboard smart grid protections with VPNET is presented.
Human Computer Collaboration to Improve Annotations in Semantic Wikis

Semantic wikis are very promising tools for producing structured and unstructured data. However, they suffer from a lack of user provided semantic annotations, resulting in a loss of efficiency, despite of their high potential. This paper focuses on an original way to encourage users to annotate semantically pages. We propose a system that suggests automatically computed annotations to users. Users thus only have to validate, complete, modify, refuse or ignore these suggested annotations. We assume that as the annotation task becomes easier, more users will provide annotations. The system we propose is based on collaborative filtering recommender systems, it does not exploit the content of the pages but the usage made on these pages by the users: annotations are deduced from the usage of the pages and the annotations previously provided. The resulting semantic wikis contain several kinds of annotations that are differentiated by their status: human provided annotations, computer provided annotations (suggested by the system), human-computed interactions (suggested by the system and validated by the users) and refused annotations (suggested by the system and refused by the user). Navigation and (semantic) search will thus be facilitated and more efficient.
Oxidative and Electrophilic Stresses Activate Nrf2 through Inhibition of Ubiquitination Activity of Keap1

ABSTRACT The Keap1-Nrf2 system is the major regulatory pathway of cytoprotective gene expression against oxidative and/or electrophilic stresses. Keap1 acts as a stress sensor protein in this system. While Keap1 constitutively suppresses Nrf2 activity under unstressed conditions, oxidants or electrophiles provoke the repression of Keap1 activity, inducing the Nrf2 activation. However, the precise molecular mechanisms behind the liberation of Nrf2 from Keap1 repression in the presence of stress remain to be elucidated. We hypothesized that oxidative and electrophilic stresses induce the nuclear accumulation of Nrf2 by affecting the Keap1-mediated rapid turnover of Nrf2, since such accumulation was diminished by the protein synthesis inhibitor cycloheximide. While both the Cys273 and Cys288 residues of Keap1 are required for suppressing Nrf2 nuclear accumulation, treatment of cells with electrophiles or mutation of these cysteine residues to alanine did not affect the association of Keap1 with Nrf2 either in vivo or in vitro. Rather, these treatments impaired the Keap1-mediated proteasomal degradation of Nrf2. These results support the contention that Nrf2 protein synthesized de novo after exposure to stress accumulates in the nucleus by bypassing the Keap1 gate and that the sensory mechanism of oxidative and electrophilic stresses is closely linked to the degradation mechanism of Nrf2.
Refractive Development in the “ROP Rat”

Although retinopathy of prematurity (ROP) is clinically characterized by abnormal retinal vessels at the posterior pole of the eye, it is also commonly characterized by vascular abnormalities in the anterior segment, visual dysfunction which is based in retinal dysfunction, and, most commonly of all, arrested eye growth and high refractive error, particularly (and paradoxically) myopia. The oxygen-induced retinopathy rat model of ROP presents neurovascular outcomes similar to the human disease, although it is not yet known if the “ROP rat” also models the small-eyed myopia characteristic of ROP. In this study, magnetic resonance images (MRIs) of albino (Sprague-Dawley) and pigmented (Long-Evans) ROP rat eyes, and age- and strain-matched room-air-reared (RAR) controls, were examined. The positions and curvatures of the various optical media were measured and the refractive state (℞) of each eye estimated based on a previously published model. Even in adulthood (postnatal day 50), Sprague-Dawley and Long-Evans ROP rats were significantly myopic compared to strain-matched controls. The myopia in the Long-Evans ROP rats was more severe than in the Sprague-Dawley ROP rats, which also had significantly shorter axial lengths. These data reveal the ROP rat to be a novel and potentially informative approach to investigating physiological mechanisms in myopia in general and the myopia peculiar to ROP in particular.
Measuring the Quality of Approximated Clusterings

Clustering has become an increasingly important task in modern applica- tion domains. In many areas, e.g. when clustering complex objects, in distributed clustering, or when clustering mobile objects, due to technical, security, or efficiency reasons it is not possible to compute an "optimal" clustering. Recently a lot of re- search has been done on efficiently computing approximated clusterings. Here, the crucial question is, how much quality has to be sacrificed for the achieved gain in ef- ficiency. In this paper, we present suitable quality measures allowing us to compare approximated clusterings with reference clusterings. We first introduce a quality measure for clusters based on the symmetric set difference. Using this distance func- tion between single clusters, we introduce a quality measure based on the minimum weight perfect matching of sets for comparing partitioning clusterings, as well as a quality measure based on the degree-2 edit distance for comparing hierarchical clus- terings.