Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantum diffusion with disorder, noise and interaction

Disorder, noise and interaction play a crucial role in the transport properties of real systems, but they are typically hard to control and study, both theoretically and experimentally, especially in the quantum case. Here, we explore a paradigmatic problem, the diffusion of a wavepacket, by employing ultra-cold atoms in a quasi-periodic lattice with controlled noise and tunable interaction. The presence of quasi-disorder leads to Anderson localization, while both interaction and noise tend to suppress localization and restore transport, although with completely different mechanisms. When only noise or interaction is present, we observe a diffusion dynamics that can be explained by existing microscopic models. When noise and interaction are combined, we observe instead a complex anomalous diffusion. By combining experimental measurements with numerical simulations, we show that such anomalous behavior can be modeled with a generalized diffusion equation in which the noise- and interaction-induced diffusions enter in an additive manner. Our study reveals also a more complex interplay between the two diffusion mechanisms in the regimes of strong interaction or narrowband noise.
Isolated Focal Dystonia as a Disorder of Large‐Scale Functional Networks

Abstract Isolated focal dystonias are a group of disorders with diverse symptomatology but unknown pathophysiology. Although recent neuroimaging studies demonstrated regional changes in brain connectivity, it remains unclear whether focal dystonia may be considered a disorder of abnormal networks. We examined topology as well as the global and local features of large‐scale functional brain networks across different forms of isolated focal dystonia, including patients with task‐specific (TSD) and nontask‐specific (NTSD) dystonias. Compared with healthy participants, all patients showed altered network architecture characterized by abnormal expansion or shrinkage of neural communities, such as breakdown of basal ganglia‐cerebellar community, loss of a pivotal region of information transfer (hub) in the premotor cortex, and pronounced connectivity reduction within the sensorimotor and frontoparietal regions. TSD were further characterized by significant connectivity changes in the primary sensorimotor and inferior parietal cortices and abnormal hub formation in insula and superior temporal cortex, whereas NTSD exhibited abnormal strength and number of regional connections. We suggest that isolated focal dystonias likely represent a disorder of large‐scale functional networks, where abnormal regional interactions contribute to network‐wide functional alterations and may underline the pathophysiology of isolated focal dystonia. Distinct symptomatology in TSD and NTSD may be linked to disorder‐specific network aberrations.
Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins

ABSTRACT Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia.
The radio field as a sensor — A segmentation based soil moisture sensing approach

Soil moisture sensing is important for many different monitoring applications. Especially for a dam monitoring system, soil moisture is one of the most safety-critical parameters. The coverage area of spot based soil moisture sensors is very limited and they mostly provide insignificant benefits, if the area of interest is not largely known. The developed Soil Moisture Sensing system uses the radio field as a sensor and covers a larger area with minimum invasion, even at locations difficult to reach. The radio field between buried nodes provides information about the channel conditions allowing assessments to be made of the soil characteristics within the communication channel. Long Range packet radio modules, originate from the Internet of Things, ensure a robust communication with a high receiver sensitivity enabling an application as Wireless Underground Sensors. In this paper, the sensing system is used for a long-term evaluation of the soil moisture at the airside of the Bever dam near to Wuppertal in Germany. It is shown that the measured Received Signal Strength Indicator variation of the underground communication link quality enables a classification of precipitation events. Further, the experimental setup of a sensor field in the laboratory performs a segmentation based soil moisture sensing and visualizes the moisture with a higher resolution. This concept is transferred to the Long Range approach while ensuring a reasonable trade-off between evaluation accuracy and battery lifetime.
Doxorubicin Cardiomyopathy

Established doxorubicin cardiomyopathy is a lethal disease. When congestive heart failure develops, mortality is approximately 50%. Extensive research has been done to understand the mechanism and pathophysiology of doxorubicin cardiomyopathy, and considerable knowledge and experience has been gained. Unfortunately, no effective treatment for established doxorubicin cardiomyopathy is presently available. Extensive research has been done and is being done to discover preventive treatments. However an effective and clinically applicable preventive treatment is yet to be discovered.
Vika/vox, a novel efficient and specific Cre/loxP-like site-specific recombination system

Targeted genome engineering has become an important research area for diverse disciplines, with site-specific recombinases (SSRs) being among the most popular genome engineering tools. Their ability to trigger excision, integration, inversion and translocation has made SSRs an invaluable tool to manipulate DNA in vitro and in vivo. However, sophisticated strategies that combine different SSR systems are ever increasing. Hence, the demand for additional precise and efficient recombinases is dictated by the increasing complexity of the genetic studies. Here, we describe a novel site-specific recombination system designated Vika/vox. Vika originates from a degenerate bacteriophage of Vibrio coralliilyticus and shares low sequence similarity to other tyrosine recombinases, but functionally carries out a similar type of reaction. We demonstrate that Vika is highly specific in catalyzing vox recombination without recombining target sites from other SSR systems. We also compare the recombination activity of Vika/vox with other SSR systems, providing a guideline for deciding on the most suitable enzyme for a particular application and demonstrate that Vika expression does not cause cytotoxicity in mammalian cells. Our results show that Vika/vox is a novel powerful and safe instrument in the ‘genetic toolbox’ that can be used alone or in combination with other SSRs in heterologous hosts.
Asynchronous and Selective Transmission for DeWiring of Building Management Systems

In this paper, we show a design and implementation of a (partial) wireless building management system (BMS). Compared to the existing wired BMS, a wireless system can be much cheaper and more flexible in deployment. There are existing studies on smart and wireless BMS. Our design differs from others as the latter usually takes a re-arch approach and develops a brand new suite of protocols. However, it can take a considerably long time for re-standardization and adoption by vendors. Our design does not intend to tear down the full suite of upper layer protocols. We thus face difficulties as we need to maintain the upper layer protocols in operation and support their data traffic. The key ideas of our approach are an asynchronous-response framework to maintain the control plane of the upper layer protocols intact, and a modular design to prioritize and schedule data flow to handle link quality and throughput variations. We implemented the proposed design into a real system and evaluated the system by comprehensive experiments with real BMS controllers and software. In addition, we conducted a field deployment by integrating our system with the BMS in FG-building of The Hong Kong Polytechnic University. The system operated smoothly during 5-h deployment.
Medium-chain TAG improve intestinal integrity by suppressing toll-like receptor 4, nucleotide-binding oligomerisation domain proteins and necroptosis signalling in weanling piglets challenged with lipopolysaccharide

Abstract This study was conducted to evaluate whether medium-chain TAG (MCT) could alleviate Escherichia coli lipopolysaccharide (LPS)-induced intestinal injury by regulating intestinal epithelial inflammatory response, as well as necroptosis. A total of twenty-four weanling piglets were randomly allotted to one of four treatments in a 2×2 factorial arrangement including diet type (5 % maize oil v. 4 % MCT+1 % maize oil) and immune stress (saline v. E. coli LPS). The piglets were fed diets containing maize oil or MCT for 21 d. On 21 d, piglets were injected intraperitoneally with saline or LPS. The blood and intestinal samples were collected at 4 h post injection. Supplementation with MCT improved intestinal morphology, digestive and barrier function, indicated by increased jejunal villus height, increased jejunal and ileal disaccharidases (sucrase and maltase) activities, as well as enhanced protein expression of claudin-1. Furthermore, the protein expression of heat-shock protein 70 in jejunum and the concentration of TNF-α in plasma were reduced in the piglets fed diets supplemented with MCT. In addition, MCT down-regulated the mRNA expression of toll-like receptor 4 (TLR4) and nucleotide-binding oligomerisation domain proteins (NOD) signalling-related genes in jejunum and ileum. Finally, MCT inhibited jejunal and ileal enterocyte necroptosis indicated by suppressed mRNA expression of the receptor-interacting protein 3 and mixed-lineage kinase domain-like protein. These results indicate that MCT supplementation may be closely related to inhibition of TLR4, NOD and necroptosis signalling pathways and concomitant improvement of intestinal integrity under an inflammatory condition.
Forecasting using incomplete models

We consider the task of forecasting an infinite sequence of future observations based on some number of past observations, where the probability measure generating the observations is "suspected" to satisfy one or more of a set of incomplete models, i.e. convex sets in the space of probability measures. This setting is in some sense intermediate between the realizable setting where the probability measure comes from some known set of probability measures (which can be addressed using e.g. Bayesian inference) and the unrealizable setting where the probability measure is completely arbitrary. We demonstrate a method of forecasting which guarantees that, whenever the true probability measure satisfies an incomplete model in a given countable set, the forecast converges to the same incomplete model in the (appropriately normalized) Kantorovich-Rubinstein metric. This is analogous to merging of opinions for Bayesian inference, except that convergence in the Kantorovich-Rubinstein metric is weaker than convergence in total variation.
Glutathione and immune function

The immune system works best if the lymphoid cells have a delicately balanced intermediate level of glutathione. Even moderate changes in the intracellular glutathione level have profound effects on lymphocyte functions. Certain functions, such as the DNA synthetic response, are exquisitely sensitive to reactive oxygen intermediates and, therefore, are favoured by high levels of the antioxidant glutathione. Certain signal pathways, in contrast, are enhanced by oxidative conditions and favoured by low intracellular glutathione levels. The available evidence suggests that the lymphocytes from healthy human subjects have, on average, an optimal glutathione level. There is no indication that immunological functions such as resistance to infection or the response to vaccination may be enhanced in healthy human subjects by administration of glutathione or its precursor amino acid cysteine. However, immunological functions in diseases that are associated with a cysteine and glutathione deficiency may be significantly enhanced and potentially restored by cysteine supplementation. This factor has been studied most extensively in the case of human immunodeficiency virus (HIV)-infected patients who were found to experience, on average, a massive loss of S equivalent to a net loss of approximately 4 g cysteine/d. Two randomized placebo-controlled trials have shown that treatment of HIV-infected patients with N-acetyl-cysteine caused in both cases a significant increase in all immunological functions under test, including an almost complete restoration of natural killer cell activity. It remains to be tested whether cysteine supplementation may be useful also in other diseases and conditions that are associated with a low mean plasma cystine level and impaired immunological functions.
1 2 N ov 2 01 2 Clipping of Arbitrary Polygons with Degeneracies

Polygon clipping is a frequent operation in Arbitrary LagrangianEulerian methods, Computer Graphics, GIS, and CAD. In fact, clipping algorithms are said to be one of the most important operations in computer graphics. [7, 1] Thus, efficient and general polygon clipping algorithms are of great importance. Greiner et al.[3] developed a time efficient algorithm which could clip arbitrary polygons, including concave and self intersecting polygons. However, the Greiner-Hormann algorithm does not properly handle degenerate cases, without the undesirable need for perturbing vertices. [5] We present an extension to the Greiner-Hormann polygon clipping algorithm which properly deals with degenerate cases. We combine the method proposed by Kim et al.[5] and the method mentioned by Liu et al.[6] to remove or properly label degenerate cases. Additionally, the algorithm presented avoids the need for calculating midpoints, doesn’t require additional entry/exit flags, and avoids changing the vertex data structure used in the original Greiner-Hormann algorithm, which was required by the extension presented by Kim et al.[5]
Preventing Dementia: Why We Should Focus on Health Promotion Now

The world's older population has been growing at a rate of 2.4% per year during the past decade, and in the year 2000 there were 580 million people aged 60 years or older (World Health Organization, 1998). With the 85 years and older group being the fastest growing segment of the population, age-related diseases and disabilities are rapidly increasing. Psychiatric morbidity is common in later life; 15% of older adults have clinically significant mental health disorders, with neurodegenerative conditions such as dementia taking the lead (Regier et al., 1998). Substantial progress has been made in the quest to unravel the pathophysiological mechanisms leading to dementia, improve the accuracy of early diagnosis, and develop dementia treatment-specific compounds. However, such developments may take decades to have a significant impact on clinical practice.
Advancing Patient Care Through Specialty Pharmacy Services in an Academic Health System.

BACKGROUND With the rapid growth of specialty pharmacies, including those within academic health systems, pharmacists have the opportunity to improve patient care through the management of specialty medications. Specialty pharmacists within academic health systems are uniquely positioned to overcome restrictions to medication access, financial constraints, and provider burdens that often lead to obstacles for patients to start and maintain necessary treatments. The Vanderbilt Specialty Pharmacy (VSP) model at Vanderbilt University Medical Center (VUMC) provides an example of a patient-centered, collaborative care prototype that places pharmacists directly into specialty clinics to assist with comprehensive management of patients on specialty medications. PROGRAM DESCRIPTION VSP integrates specialty pharmacy services within existing specialty clinics based on the needs of each individual clinic. Each clinic is staffed with at least 1 clinical pharmacist and 1 pharmacy technician. The pharmacist is integrally involved in medication selection, initiation, and monitoring. The specialty pharmacy team ensures appropriate medication access and cost, provides extensive medication education, ensures patients are adherent to treatment, and coordinates care between patients and providers using the electronic medical record. OBSERVATIONS Integration of pharmacists within specialty clinics at VUMC benefits providers, the health system, and patient care. This model has demonstrated decreased provider and clinic burden, decreased time to medication approval and initiation, excellent patient and provider satisfaction, substantial patient cost savings, optimal medication adherence, and overall improved continuity of care for patients on specialty medications. Since its inception in 2011, VSP has integrated 24 clinical pharmacists and 17 pharmacy technicians into 20 specialty clinics, with continued quarterly growth. IMPLICATIONS The VSP model advances the role of pharmacists in managing patients on specialty medications in collaboration with providers. The integrated collaborative approach as presented by VSP represents a best practices model for those establishing and advancing specialty pharmacy services within academic health systems. DISCLOSURES No outside funding supported this study. The authors have nothing to disclose. Study concept and design were principally contributed by Bagwell and Newman, along with the other authors. Lee took the lead in data collection, along with Carver, Bagwell, Kelley, and Newman. Data interpretation was performed by Carver, Kelley, Lee, and Bagwell, with assistance from Newman. The manuscript was written by Bagwell, Carver, Kelley, and Lee and revised primarily by Bagwell, along with the other authors.
Dose-dependent control of proliferation and sperm specification by FOG-1/CPEB

RNA-binding proteins control germline development in metazoans. This work focuses on control of the C. elegans germline by two RNA-binding proteins: FOG-1, a CPEB homolog; and FBF, a PUF family member. Previous studies have shown that FOG-1 specifies the sperm fate and that FBF promotes proliferation. Here, we report that FOG-1 also promotes proliferation. Whereas fbf-1 fbf-2 double mutants make ∼120 germ cells, fog-1; fbf-1 fbf-2 triple mutants make only ∼10 germ cells. The triple mutant germline divides normally until early L2, when germ cells prematurely enter meiosis and begin oogenesis. Importantly, fog-1/+; fbf-1 fbf-2 animals make more germ cells than fbf-1 fbf-2 double mutants, demonstrating that one dose of wild-type fog-1 promotes proliferation more effectively than two doses – at least in the absence of FBF. FOG-1 protein is barely detectable in proliferating germ cells, but abundant in germ cells destined for spermatogenesis. Based on fog-1 dose effects, together with the gradient of FOG-1 protein abundance, we suggest that low FOG-1 promotes proliferation and high FOG-1 specifies spermatogenesis. FBF binds specifically to regulatory elements in the fog-1 3′UTR, and FOG-1 increases in animals lacking FBF. Therefore, FBF represses fog-1 expression. We suggest that FBF promotes continued proliferation, at least in part, by maintaining FOG-1 at a low level appropriate for proliferation. The dose-dependent control of proliferation and cell fate by FOG-1 has striking parallels with Xenopus CPEB, suggesting a conserved mechanism in animal development.
Composite Generation and Transmission Reliability Evaluation in Large Hydroelectric Systems

This paper describes the CONFTRA model developed for composite generation/transmission reliability evaluation in the Brazilian system. The network is represented by a linearized power flow model. , Generation; rescheduling and load shedding are calculated by a fast linear programming algorithm. The dependence of generating capacity on the system hydrological conditions is explicitly represented. Monte-Carlo methods are used to select system states. The number of samplings is reduced by the use of "importance sampling" techniques. Sensitivity analysis with regard to both generation and line reinforcement is provided. A case study with the Brazilian Southeast system is presented and discussed.
Model-based development of security requirements

We present a model-based approach using two dimensions to propagate security restrictions: along the lifecycle and along the architectural levels. We apply security patterns to perform this propagation. We believe that this double propagation can be very effective for security and reliability. This approach can also facilitate the security analysis of the system and can be used to verify compliance with regulations. We have developed a methodology to apply these ideas and we are extending it to make it more powerful, in particular to increase its level of security and to add to it also reliability concerns. The extensions include two new metamodels for security requirements and a validation approach.
Generating kernel matrix for rotation forest through genetic programming

Classification is one of the most important issues in real world. Recent researches advocate combining multiple classifiers, e.g, ensemble learning methods. These methods are the common approaches for classification that create a set of classifiers and then classify new data points by majority voting. Also, evolutionary algorithms have been used for finding optimal parameters and classifiers in classification issues, e.g, Genetic Programming (GP). In this paper, a new RF method is proposed and called Rotation Kernel Forest (RKF). In RKF method: first, some equations are generated by GP that are employed as the feature function φ(χ). In the second step, kernel matrix is constructed based on φ(χ) and at the end, projection matrix is achieved. RKF method generates not only a new kernel matrix but also a new projection matrix. The experimental results show apparently the efficiency of RKF comparing to the advanced ensemble methods in terms of accuracy of classification. Wilcoxon signed-ranks test confirms the superiority of RKF in comparison to the other methods.