Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficiency and Robustness Issues in Complex Statistical Designs for Two-Color Microarray Experiments

Identifying differentially expressed genes is one of the common goals of microarray experiments. The use of an efficient design in microarray experiments can improve the power of the inferential procedure. Besides efficiency, robustness considerations should also be considered in selecting good microarray designs because missing observations often occur in the microarray experiments. In this dissertation, $E$--optimality criterion is used as the efficiency criterion and three robustness criteria are proposed to quantify the robustness of a microarray design.For a given number of available arrays and number of treatment conditions, different microarray designs can be considered. The number of possible designs could be very large and thus a complete analysis of efficiency and robustness considerations could be computationally infeasible. A genetic algorithm based method is suggested for selecting good microarray designs for a set of given research questions. This method can be used to find good designs for both the one--way and two--factor factorial experiments. The use of both the efficiency and robustness criteria in the search procedure is also proposed. As an example, efficient and robust designs for the factorial experiments are reported for different numbers of arrays.
Joint Trust for Belief Revision

The process of belief revision is impacted by trust relationships between agents. In the simplest case, information is reported from a single source and the belief change that occurs is dependent on the extent to which that source is trusted over a particular domain. In this paper, we are concerned with the more complicated case where the new information is reported by a set of agents. We ﬁrst introduce a simple model of trust in an agent, and show how it inﬂuences the process of belief revision. We then deﬁne an joint notion of trust that is built by combining the trust held in each individual agent in the reporting set. We use this formal framework to deﬁne precisely when a collection of agents can be seen as a trusted authority over a particular formula for revision. While our framework is based on a particular model of trust, we argue that this approach can be used to deﬁne a suitable notion of joint trust in a wide range of settings.
Recent Advances in Metaphotonic Biosensors

Metaphotonic devices, which enable light manipulation at a subwavelength scale and enhance light–matter interactions, have been emerging as a critical pillar in biosensing. Researchers have been attracted to metaphotonic biosensors, as they solve the limitations of the existing bioanalytical techniques, including the sensitivity, selectivity, and detection limit. Here, we briefly introduce types of metasurfaces utilized in various metaphotonic biomolecular sensing domains such as refractometry, surface-enhanced fluorescence, vibrational spectroscopy, and chiral sensing. Further, we list the prevalent working mechanisms of those metaphotonic bio-detection schemes. Furthermore, we summarize the recent progress in chip integration for metaphotonic biosensing to enable innovative point-of-care devices in healthcare. Finally, we discuss the impediments in metaphotonic biosensing, such as its cost effectiveness and treatment for intricate biospecimens, and present a prospect for potential directions for materializing these device strategies, significantly influencing clinical diagnostics in health and safety.
KRAS and NRAS Translation Is Increased upon MEK Inhibitors-Induced Processing Bodies Dissolution

Simple Summary Cancer therapies directly targeting the mitogen-activated protein kinase (MAPK) pathway lead to cancer drug resistance. Resistance has been linked to compensatory RAS overexpression, but the mechanisms underlying this overexpression remain unclear. Here, we find that MEK inhibitors (MEKi) increases translation of the KRAS and NRAS oncogenes through a mechanism involving liquid–liquid phase separation (LLPS), and more particularly processing body (P-body) dissolution. Overall, we describe a new feedback loop mechanism involving P-bodies and phase separation that regulates RAS translation. Identification of key components that regulate LLPS will be important for future targeted therapeutic strategies. Abstract Overactivation of the mitogen-activated protein kinase (MAPK) pathway is a critical driver of many human cancers. However, therapies directly targeting this pathway lead to cancer drug resistance. Resistance has been linked to compensatory RAS overexpression, but the mechanisms underlying this response remain unclear. Here, we find that MEK inhibitors (MEKi) are associated with an increased translation of the KRAS and NRAS oncogenes through a mechanism involving dissolution of processing body (P-body) biocondensates. This effect is seen across different cell types and is extremely dynamic since removal of MEKi and ERK reactivation result in reappearance of P-bodies and reduced RAS-dependent signaling. Moreover, we find that P-body scaffold protein levels negatively impact RAS expression. Overall, we describe a new feedback loop mechanism involving biocondensates such as P-bodies in the translational regulation of RAS proteins and MAPK signaling.
Quality of Life and Kidney Function in Older Adults: Prospective Data of the SCOPE Study

A longitudinal alteration in health-related quality of life (HRQoL) over a two-year period and its association with early-stage chronic kidney disease (CKD) progression was investigated among 1748 older adults (>75 years). HRQoL was measured by the Euro-Quality of Life Visual Analog Scale (EQ-VAS) at baseline and at one and two years after recruitment. A full comprehensive geriatric assessment was performed, including sociodemographic and clinical characteristics, the Geriatric Depression Scale-Short Form (GDS-SF), Short Physical Performance Battery (SPPB), and estimated glomerular filtration rate (eGFR). The association between EQ-VAS decline and covariates was investigated by multivariable analyses. A total of 41% of the participants showed EQ-VAS decline, and 16.3% showed kidney function decline over the two-year follow-up period. Participants with EQ-VAS decline showed an increase in GDS-SF scores and a greater decline in SPPB scores. The logistic regression analyses showed no contribution of a decrease in kidney function on EQ-VAS decline in the early stages of CKD. However, older adults with a greater GDS-SF score were more likely to present EQ-VAS decline over time, whereas an increase in the SPPB scores was associated with less EQ-VAS decline. This finding should be considered in clinical practice and when HRQoL is used to evaluate health interventions among older adults.
IMPLEMENTING ARTIFICIAL NEURAL NETWORK BASED DVR TO IMPROVE POWER QUALITY OF RUMUOLA-RUMUOMOI 11kV DISTRIBUTION NETWORK

The most vexing problem plaguing Rumuomoi's 11kV distribution network is voltage sag and swell, which degrades power quality. There has been no effective mitigation control implemented. The purpose of this research is to address the issue of power quality by implementing artificial neural network (ANN) control with an embedded dynamic voltage restorer (DVR). To begin, the artificial neural network is trained using the input and desired data obtained during simulation using a proportional integral (PI) controller. To limit the amount of data obtained during training, the Levenberg-Marquardt feed forward back method is utilized, and the result for each iteration is determined in Matlab software. The desired dynamic voltage restorer system was tested using a replicated model of Rumuomoi 11kV and it was determined that Bus 7 is 0.938p. u, Bus 8 is 0.9244p. u, Bus 9 is 0.9148p. u, Bus 10 is 0.9035p. u, Bus 11 is 0.8912p. u, and Bus 12 is 0.8811p. u, all of which exceeded the statutory limit condition of 0.95-1.01p. u. There were no bus voltage violations after network optimization with DVR, demonstrating that DVR is effective at enhancing power quality by removing voltage sag and swell in the distribution network.
Head positioning control for low sampling rate systems based on two degree-of-freedom control

To enhance formatting efficiency in high density hard disk drives, it is desirable to decrease the number of embedded servo signals. As a consequence, the sampling rate of servo systems has been becoming lower. In this situation, it is difficult to attain fast track seeking by using only a feedback controller. This paper presents a high-speed track seek technique, based on two degree-of-freedom control. A new reference model is developed by focusing on the attainment of fast track seeking through the effective use of a voice coil motor, which functions as a disk head actuator. The model generates reference trajectories, allowing high-speed movement. Also, in order to quickly settle the disk head to a target track under various disturbances, an initial value compensation (IVC) method to minimize a quadratic performance index is developed. Experimental results, using a 3-1/2 inch hard disk drive, confirm the validity of the proposed method.
Investigation of the Tendency of Carbon Fibers to Disintegrate into Respirable Fiber-Shaped Fragments

Recent reports of the release of large numbers of respirable and critically long fiber-shaped fragments from mesophase pitch-based carbon fiber polymer composites during machining and tensile testing have raised inhalation toxicological concerns. As carbon fibers and their fragments are to be considered as inherently biodurable, the fiber pathogenicity paradigm motivated the development of a laboratory test method to assess the propensity of different types of carbon fibers to form such fragments. It uses spallation testing of carbon fibers by impact grinding in an oscillating ball mill. The resulting fragments were dispersed on track-etched membrane filters and morphologically analyzed by scanning electron microscopy. The method was applied to nine different carbon fiber types synthesized from polyacrylonitrile, mesophase or isotropic pitch, covering a broad range of material properties. Significant differences in the morphology of formed fragments were observed between the materials studied. These were statistically analyzed to relate disintegration characteristics to material properties and to rank the carbon fiber types according to their propensity to form respirable fiber fragments. This tendency was found to be lower for polyacrylonitrile-based and isotropic pitch-based carbon fibers than for mesophase pitch-based carbon fibers, but still significant. Although there are currently only few reports in the literature of increased respirable fiber dust concentrations during the machining of polyacrylonitrile-based carbon fiber composites, we conclude that such materials have the potential to form critical fiber morphologies of WHO dimensions. For safe-and-sustainable carbon fiber-reinforced composites, a better understanding of the material properties that control the carbon fiber fragmentation is imperative.
Caffeine content and acidity levels of some non-alcoholic water-based beverages sold in Banda zone, Kampala, Uganda

Background:The consumption of has gained attention due to its ability to promote acute benefits such as improved attention, cognitive performance, reduction of fatigue, increased wakefulness, and analgesia. However, the result of caffeine consumption is a concern, it is important to inform consumers about the caffeine content and acidity levels of all non-alcoholic water-based beverages.Methods:The samples were sonicated and subjected to analysis by high-performance liquid chromatography-ultraviolet method and pH meter method for acidity content. Results: The highest concentration of caffeine was found in energy drink, ED; with 64.01±0.07 mg/L as compared to soft drinks, SD1; 20.20±0.02 mg/L, SD2; 23.14±0.08 mg/L, and SD3; 29.88±0.02 mg/L. All obtained concentrations were below the permissible levels for caffeine (200 mg/L) intake by the United States Food and Drug Administration. The study also showed that all the non-alcoholic beverages were acidic except bottled water in the sequence BW < ED < SD. The categorical range was bottled water; BW2; 8.01±0.03, BW1; 7.5±0.10, BW3; 7.5±0.11, BW4 6.85±1.38, and Energy drink; ED; 3.17±0.01, and finally, soft drinks; SD2; 2.82±0.02, SD1; 2.61±0.02, and SD3; 2.59±0.05. Conclusions: The results obtained in this study provide satisfactory information on the caffeine and acidity contents of the commonly consumed non-alcoholic water-based beverages in Banda, Kampala-Uganda. This in the future could pose serious health risks, since some individuals consume multiple servings of the drinks in a short time, which could result in intoxication/overdose.Keywords: caffeine, soft drinks, energy drinks, public health, Banda
Dementia Risk Models in an Australian First Nations Population: Cross-Sectional Associations and Preparation for Follow-Up

Background: Reducing the burden of dementia in First Nations populations may be addressed through developing population specific methods to quantify future risk of dementia. Objective: To adapt existing dementia risk models to cross-sectional dementia prevalence data from a First Nations population in the Torres Strait region of Australia in preparation for follow-up of participants. To explore the diagnostic utility of these dementia risk models at detecting dementia. Methods: A literature review to identify existing externally validated dementia risk models. Adapting these models to cross-sectional data and assessing their diagnostic utility through area under the receiver operating characteristic curve (AUROC) analyses and calibration using Hosmer-Lemeshow Chi2. Results: Seven risk models could be adapted to the study data. The Aging, Cognition and Dementia (AgeCoDe) study, the Framingham Heart Study (FHS), and the Brief Dementia Screening Indicator (BDSI) had moderate diagnostic utility in identifying dementia (i.e., AUROC >0.70) before and after points for older age were removed. Conclusion: Seven existing dementia risk models could be adapted to this First Nations population, and three had some cross-sectional diagnostic utility. These models were designed to predict dementia incidence, so their applicability to identify prevalent cases would be limited. The risk scores derived in this study may have prognostic utility as participants are followed up over time. In the interim, this study highlights considerations when transporting and developing dementia risk models for First Nations populations.
An efficient method to sample Musca domestica (Linnaeus, 1758) (Diptera: Muscidae) using coloured pan-traps in a cage poultry facility

When houseflies find optimal conditions to develop, they rapidly increase their population size negatively impacting both humans and animals through nuisance and the transmission of pathogens. Musca domestica Linnaeus, 1758 (Diptera: Muscidae) shows a preference for animal faeces and for this reason it is a serious pest in animal breeding facilities. To prevent proliferation of houseflies and to evaluate the efficiency of the control methods, it is important to routinely monitor the activity of this dipteran in such facilities. There are several types of traps for sampling houseflies in breeding sites, here we used colored pan-traps to evaluate the efficiency of the trap and its color in sampling M. domestica in a cage poultry facility located in the city of Nepomuceno, Minas Gerais, Brazil. To do so, we set up yellow, white, blue and red pan-traps next to the cages of poultries and collected flies once a week for a period of a year. Although the density of M. domestica was high during the entire period of sampling, more flies were collected in white (monthly average of 470.83 flies) than in yellow (327.55), blue (267.14) and red traps (199.63). Hence, we argue that this poultry farm needs to improve its housefly monitoring program and we suggest a continuous use of white pan-traps to monitor the efficiency of the pest control methods implemented in the facility.
Analyzing Data from a Regression Discontinuity Study: A Research Note.

The Chow Test (Chow, 1960) is a method well known in econometrics. It was originally designed to analyze the same variables obtained in two different data sets to determine if they were similar enough to be pooled together. The method, however, could be used to determine if two regression lines are different from one another. This article discusses the use of the Chow Test on data obtained in a regression discontinuity study.
A Discussion of: "Process Consistency for AdaBoost" by Wenxin Jiang "On the Bayes-risk consistency of regularized boosting methods" by G´ abor Lugosi and Nicolas Vayatis "Statistical Behavior and Consistency of Classification Methods based on Convex Risk Minimization" by Tong Zhang

The notion of a boosting algorithm was originally introduced by Valiant in the context of the “probably approximately correct” (PAC) model of learnability [19]. In this context boosting is a method for provably improving the accuracy of any “weak” classification learning algorithm. The first boosting algorithm was invented by Schapire [16] and the second one by Freund [2]. These two algorithms were introduced for a specific theoretical purpose. However, since the introduction of AdaBoost [5], quite a number of perspectives on boosting have emerged. For instance, AdaBoost can be understood as a method for maximizing the “margins” or “confidences” of the training examples [17]; as a technique for playing repeated matrix games [4, 6]; as a linear or convex programming method [15]; as a functional gradient-descent technique [8, 13, 14, 3]; as a technique for Bregman-distance optimization in a broader framework that includes logistic regression [1, 10, 12]; and finally as a stepwise model-fitting method for minimization of the exponential loss function, an approximation of the negative log binomial likelihood [7]. The current papers add to this list of perspectives, giving a view of boosting that is very different from its original interpretation and analysis as an algorithm for improving the accuracy of a weak learner. These many different points of view add to the richness of the theory of boosting, and are enormously helpful in the practical design of new or better algorithms for machine learning and statistical inference. Originally, boosting algorithms were designed expressly for classification. The goal in this setting is to accurately predict the classification of a new example. Either the prediction is correct, or it is not. There is no attempt made to estimate the conditional probability of each class. In practice, this sometimes is not enough since we may want to have some sense of how likely our prediction is to be correct, or we may want to incorporate numbers that look like probabilities into a larger system. Later, Friedman, Hastie and Tibshirani [7] showed that AdaBoost can in fact be used to estimate such probabilities, arguing that AdaBoost approximates a form of logistic regression. They and others [1] subsequently modified AdaBoost to explicitly minimize the loss function associated with logistic regression, with the intention of computing such estimated probabilities. In one of the current papers, Zhang vastly generalizes this approach showing that conditional probability estimates P{y|x} can be obtained when minimizing any smooth convex loss function,
The Role of Weather System Changes and Catchment Characteristics in the Rainfall‐Runoff Relationship Shift in Victoria, Australia

Many Victorian catchments experienced a rainfall‐runoff relationship (RRR) shift during the Millennium Drought (1997–2009). Less annual streamflow was generated from annual rainfall during the drought than would have been expected for the same rainfall before the drought. Changes in weather systems, such as cyclones, fronts, and thunderstorms, were also observed during this period. In this study, we assess the role that changes in weather systems played in the RRR shift. We find that catchments that experienced a RRR shift tended to receive less of their rainfall from frontal weather systems, and more of their rainfall from thunderstorm‐enhanced cyclone and cyclone‐front hybrid systems during the drought than catchments that showed little change in RRR. Overall, changes in the proportion of rainfall from weather systems alone explained up to 43% of the variance in the RRR shift between catchments. Including parameters that quantify catchment processes and physiographic features indicated that weather system changes are not the primary indicator of a RRR shift. Catchment mean slope, aridity and valley confinement, together with proportional rainfall change of cyclone‐thunderstorms and cyclone‐front‐thunderstorms, explained 60% of the variance in the RRR shift between catchments. Focusing on streamflow availability, we find the importance of different weather systems and catchment characteristics varies depending on warm or cool season, eastern or western Victoria, and before or during the drought. Following the drought, some catchments largely maintained the RRR shift that occurred during the drought, and also experienced less of their rainfall from fronts and cyclones compared to the other catchments.
Phosphorylcholine and KR12-Containing Corneal Implants in HSV-1-Infected Rabbit Corneas

Severe HSV-1 infection can cause blindness due to tissue damage from severe inflammation. Due to the high risk of graft failure in HSV-1-infected individuals, cornea transplantation to restore vision is often contraindicated. We tested the capacity for cell-free biosynthetic implants made from recombinant human collagen type III and 2-methacryloyloxyethyl phosphorylcholine (RHCIII-MPC) to suppress inflammation and promote tissue regeneration in the damaged corneas. To block viral reactivation, we incorporated silica dioxide nanoparticles releasing KR12, the small bioactive core fragment of LL37, an innate cationic host defense peptide produced by corneal cells. KR12 is more reactive and smaller than LL37, so more KR12 molecules can be incorporated into nanoparticles for delivery. Unlike LL37, which was cytotoxic, KR12 was cell-friendly and showed little cytotoxicity at doses that blocked HSV-1 activity in vitro, instead enabling rapid wound closure in cultures of human epithelial cells. Composite implants released KR12 for up to 3 weeks in vitro. The implant was also tested in vivo on HSV-1-infected rabbit corneas where it was grafted by anterior lamellar keratoplasty. Adding KR12 to RHCIII-MPC did not reduce HSV-1 viral loads or the inflammation resulting in neovascularization. Nevertheless, the composite implants reduced viral spread sufficiently to allow stable corneal epithelium, stroma, and nerve regeneration over a 6-month observation period.
Strongly-coupled systems in gauge/gravity duality

As an introduction, we present the original formulation of the AdS/CFT correspondence, between N = 4 Super Yang-Mills theory with gauge group SU(N) and type IIB string theory on AdS5 x S5. In a first part, we show how the ingredients of the AdS/CFT correspondence can be applied in a phenomenological way to study strongly correlated systems of fermions and present two fundamental models, the electron star and the holographic superconductor. We construct a holographic model for the study of Bose-Fermi systems at finite density and show that the simultaneous presence of bosonic and fermionic degrees of freedom is favoured at zero temperature. By solving the field equation of a probe spinor field in these solutions, we show that the system admits a large number of electron-like and/or hole-like Fermi surfaces and a charged scalar condensate. In a second part, we study asymptotically-AdS4 BPS black hole solutions in the N = 2 gauged supergravity theory. Using the duality transformations in a simple STU model, we find new static and rotating BPS black hole solutions.