Miracle-dz/UniFAR-FTUs huggingface dataset:
Blood DNA methylation and Type 2 Diabetes Mellitus: a protocol for systematic review and meta-analysis

Background: This research aims to evaluate the efficacy and safety of synbiotics for treating chronic kidney disease. Methods: Related articles written in English were sourced from EMBASE, PubMed, Cochrane Library, and China National Knowledge Infrastructure. These articles were used in the evaluation of the effect of synbiotics for treating chronic kidney disease. The extent of the relationship was assessed by calculating the pooled risk ratio, mean differences or standardized mean difference along with the equivalent 95% confidence intervals. The risk of bias introduced through each study was considered by adopting the Cochrane Risk of Bias Tool. Suitable statistical researchmethods were utilized for the synthesis of the data. The RevMan 5.3 software was used to conduct all statistical analysis. Results: The final results of the current study is due to be included in a peer-reviewed journal. Conclusion:The final remarks of the current study will be useful evidence for determining whether synbiotics is an effective and safe therapeutic method for treating chronic kidney disease. OSF registration number: DOI 10.17605/OSF.IO/UASF4 (https://osf.io/uasf4/). Abbreviation: CKD = chronic kidney disease.
Phylogenetics, genome diversity and origin of modern leopard, Panthera pardus

Leopards, Panthera pardus, are widely distributed across southern Asia and sub‐Saharan Africa. The extent and phylogeographic patterns of molecular genetic diversity were addressed in a survey of 77 leopards from known geographical locales representing 13 of the 27 classical trinomial subspecies. Phylogenetic analysis of mitochondrial DNA sequences (727 bp of NADH5 and control region) and 25 polymorphic microsatellite loci revealed abundant diversity that could be partitioned into a minimum of nine discrete populations, tentatively named here as revised subspecies: P. parduspardus, P. p. nimr, P. p. saxicolor, P. p. fusca, P. p. kotiya, P. p. delacouri, P. p. japonensis, P. p. orientalis and P. p. melas. However, because of limited sampling of African populations, this may be an underestimate of modern phylogeographic population structure. Combined phylogeographic and population diversity estimates support an origin for modern leopard lineages 470 000–825 000 years ago in Africa followed by their migration into and across Asia more recently (170 000–300 000 years ago). Recent demographic reductions likely have led to genetic impoverishment in P. p. orientalis and in the island subspecies P. p. kotiya.
Moving Toward Patient-Centered Care in Africa: A Discrete Choice Experiment of Preferences for Delivery Care among 3,003 Tanzanian Women

Objective In order to develop patient-centered care we need to know what patients want and how changing socio-demographic factors shape their preferences. Methods We fielded a structured questionnaire that included a discrete choice experiment to investigate women’s preferences for place of delivery care in four rural districts of Pwani Region, Tanzania. The discrete choice experiment consisted of six attributes: kind treatment by the health worker, health worker medical knowledge, modern equipment and medicines, facility privacy, facility cleanliness, and cost of visit. Each woman received eight choice questions. The influence of potential supply- and demand- side factors on patient preferences was evaluated using mixed logit models. Results 3,003 women participated in the discrete choice experiment (93% response rate) completing 23,947 choice tasks. The greatest predictor of health facility preference was kind treatment by doctor (β = 1.13, p<0.001), followed by having a doctor with excellent medical knowledge (β = 0.89 p<0.001) and modern medical equipment and drugs (β = 0.66 p<0.001). Preferences for all attributes except kindness and cost were changed with changes to education, primiparity, media exposure and distance to nearest hospital. Conclusions Care quality, both technical and interpersonal, was more important than clinic inputs such as equipment and cleanliness. These results suggest that while basic clinic infrastructure is necessary, it is not sufficient for provision of high quality, patient-centered care. There is an urgent need to build an adequate, competent, and kind health workforce to raise facility delivery and promote patient-centered care.
Using hidden non-Markovian Models to reconstruct system behavior in partially-observable systems

Many complex technical systems today have some basic protocol capability, which is used for example to monitor the quality of production output or to keep track of oil pressure in a modern car. The recorded protocols are usually used to detect deviations from some predefined standards and issue warnings. However, the information in such a protocol is not sufficient to determine the source or cause of the problem, since only part of the system is being observed. In this paper we present an approach to reconstruct missing information in only partially-observable stochastic systems based only on recorded system output. The approach uses Hidden non-Markovian Models to model the partially-observable system and Proxel-based simulation to analyze the recorded system output. Experiments were conducted using a production line example. The result of the analysis is a set of possible system behaviors that could have caused the recorded protocol, including their probabilities. We will show that our approach is able to reconstruct the relevant information to determine the source of non-standard system behavior. The combination of Hidden non-Markovian Models and Proxel-based simulation holds the potential to reconstruct unobserved information from partial or even noisy output protocols of a system. It adds value to the information already recorded in many production systems today and opens new possibilities in the analysis of inherently only partially-observable systems.
From Early Contraction to Post-Folding Fluid Evolution in the Frontal Part of the Bóixols Thrust Sheet (Southern Pyrenees) as Revealed by the Texture and Geochemistry of Calcite Cements

Structural, petrological and geochemical (δ13C, δ18O, clumped isotopes, 87Sr/86Sr and ICP-MS) analyses of fracture-related calcite cements and host rocks are used to establish a fluid-flow evolution model for the frontal part of the Bóixols thrust sheet (Southern Pyrenees). Five fracture events associated with the growth of the thrust-related Bóixols anticline and Coll de Nargó syncline during the Alpine orogeny are distinguished. These fractures were cemented with four generations of calcite cements, revealing that such structures allowed the migration of different marine and meteoric fluids through time. During the early contraction stage, Lower Cretaceous seawater circulated and precipitated calcite cement Cc1, whereas during the main folding stage, the system opened to meteoric waters, which mixed with the connate seawater and precipitated calcite cement Cc2. Afterwards, during the post-folding stages, connate evaporated marine fluids circulated through newly formed NW-SE and NE-SW conjugate fractures and later through strike-slip faults and precipitated calcite cements Cc3 and Cc4. The overall paragenetic sequence reveals the progressive dewatering of Cretaceous marine host sediments during progressive burial, deformation and fold tightening and the input of meteoric waters only during the main folding stage. This study illustrates the changes of fracture systems and the associated fluid-flow regimes during the evolution of fault-associated folds during orogenic growth.
Probing the timescale of the exchange interaction in a ferromagnetic alloy

The underlying physics of all ferromagnetic behavior is the cooperative interaction between individual atomic magnetic moments that results in a macroscopic magnetization. In this work, we use extreme ultraviolet pulses from high-harmonic generation as an element-specific probe of ultrafast, optically driven, demagnetization in a ferromagnetic Fe-Ni alloy (permalloy). We show that for times shorter than the characteristic timescale for exchange coupling, the magnetization of Fe quenches more strongly than that of Ni. Then as the Fe moments start to randomize, the strong ferromagnetic exchange interaction induces further demagnetization in Ni, with a characteristic delay determined by the strength of the exchange interaction. We can further enhance this delay by lowering the exchange energy by diluting the permalloy with Cu. This measurement probes how the fundamental quantum mechanical exchange coupling between Fe and Ni in magnetic materials influences magnetic switching dynamics in ferromagnetic materials relevant to next-generation data storage technologies.
The Modulation Scale Spectrum and its Application to Rhythm-Content Description

In this paper, we propose the Modulation Scale Spectrum as an extension of the Modulation Spectrum through the Scale domain. The Modulation Spectrum expresses the evolution over time of the amplitude content of various frequency bands by a second Fourier Transform. While its use has been proven for many applications, it is not scale-invariant. Because of this, we propose the use of the Scale Transform instead of the second Fourier Transform. The Scale Transform is a special case of the Mellin Transform. Among its properties is "scale-invariance". This implies that two timestretched version of a same music track will have (almost) the same Scale Spectrum. Our proposed Modulation Scale Spectrum therefore inherits from this property while describing frequency content evolution over time. We then propose a specific implementation of the Modulation Scale Spectrum in order to represent rhythm content. This representation is therefore tempo-independent. We evaluate the ability of this representation to catch rhythm characteristics on a classification task. We demonstrate that for this task our proposed representation largely exceeds results obtained so far while being highly tempo-independent.
Evaluation of CBT for increasing threat detection performance in X-ray screening

The relevance of aviation security has increased dramatically in recent years. Airport security technology has evolved remarkably over the last decade, which is especially evident for state-of-the-art X-ray screening systems. However, such systems will be only as effective as the people who operate them. Recognizing all kinds of prohibited items in X-ray images of passenger bags is a challenging object recognition task. In this article we present a method to measure screener detection performance based on signal detection theory. This method is applied to measure training effects resulting from individually adaptive computer based training (CBT). We have found large increases of detection performance and substantial reductions in response time suggesting that CBT is a very effective tool for increasing effectiveness and efficiency in aviation security screening.
EVITA-RAD : an Extensible Enterprise VoIce PorTAl – Rapid Application Development tool

Speech interactivity and call automation technology has reached a point of reliability sufficient for deployment at the enterprise level. Even though Voice User Interface (VUI) applications are growing in popularity, the development process remains a bottleneck to its widespread adoptation. Currently available development tools are meant for either professionals or programmers experienced in VoiceXML, speech recognition, dialogue design, and platform specific languages. We present a web-based tool, EVITA-RAD, driven by an extensible and modular design paradigm for building dialogues. By incorporating database access and abstracting many issues of programming in VoiceXML into modules, our tool allows users to focus on designing dynamic and useful dialogue applications. Thus, EVITA-RAD lowers the barrier of entry for VUI application development, and helps promote widespread adoption of VUI applications.
Node Failure Time and Coverage Loss Time Analysis for Maximum Stability Vs Minimum Distance Spanning Tree based Data Gathering in Mobile Sensor Networks

A mobile sensor network is a wireless network of sensor nodes that move arbitrarily. In this paper, we explore the use of a maximum stability spanning tree -based data gathering (Max.Stability -DG) algorithm and a minimum-distance spanning tree-based data gathering (MST -DG) algorithm for mobile sensor networks. We analyze the impact of these two algorithms onthe node failure times and the resulting coverage loss due to node failures. Both the Max.Stability -DG and MST-DG algorithms are based on a greedy strategy of determining a data gathering tree when one is needed and using that tree as long as it exists. The Max.Stability-DG algorithm assumes the availability of the complete knowledge of future topology changes and determines a data gathering tree whose corresponding spanning tree would exist for the longest time since the current time instant; whereas, theMST-DG algorithm determines a data gathering tree whose corresponding spanning tree is the minimum distance tree at the current time instant. We observe the Max.Stability-DG trees to incur a longer network lifetime (time of disconnection of the network of live sensor nodes due to node failures), a larger coverage loss time for a particular fraction of loss of coverage as well as a lower fraction of coverage loss at any time. The tradeoff is that the Max.Stability-DG trees incur a lower node lifetime (the t ime of first node failure) due to repeated use of a data gathering tree for a longer time .
Firefixia: an accessibility web browser customization toolbar for people with dyslexia

People with dyslexia often face difficulties on consuming written content at the Web. This occurs mainly because websites' designs do not consider the barriers faced by them, since dyslexia is not taken into account as often as other functional limitations. Guidelines for designing accessible Web pages are being consolidated and studied. Meanwhile, people with dyslexia face barriers and develop workarounds to overcome these difficulties. This work presents a customization toolbar called Firefixia, especially designed to support people with dyslexia to adapt the presentation of Web content according to their preferences. Firefixia was tested by 4 participants with diagnosed dyslexia. The participants evaluated and provided us feedback regarding the toolbar most/least useful features. From the presented results, one expects to highlight the need for end-user customization features that are easy to access, easy to use, and easy to explore. Participants reported that the most useful customization features are the text size, the text alignment, and the link color. Finally, this work indicates promising directions for end-user customization tools such as Firefixia.
A budget and deadline aware scientific workflow resource provisioning and scheduling mechanism for cloud

Currently in large-scale scientific experiments, scientists often submit scientific workflow jobs at different time. From the view of system, the entire workload is a stream of jobs submitted at an unpredictable time and different job has different priority and deadline. Moreover the cost of performing these jobs cannot exceed a certain budget constraint. Therefore how to perform scientific workflow applications efficiently in cloud has become the urgent problem. However most of existing work didn't consider unpredictable submission time of jobs, as well as budget and deadline constrains. In this paper, we design an elastic resource provisioning and task scheduling mechanism to perform scientific workflows in cloud. Our goal is to complete as many high-priority workflows as possible under budget and deadline constrains. This mechanism consists of three phases: workflow preprocessing, elastic resource provisioning and task scheduling. We perform evaluation with real AMS experiment scientific computing data under different budget constraints. We also consider inaccurate task execution time, VM provisioning delays and task failures in evaluation. The results show that our mechanism achieves a better performance than these reference mechanisms. In addition, the inaccurate task execution time, VM provisioning delays, and task failures do not bring significant impact to mechanism's performance.
Still doing evolutionary algorithms with Perl

Algorithm::Evolutionary (A::E from now on) was introduced in 2002, after a talk in YAPC::EU in Munich. 7 years later, A::E is in its 0.67 version (past its "number of the beast" 0.666), and has been used extensively, to the point of being the foundation of much of the (computer) science being done by our research group (and, admittedly, not many others). All is not done, however; now A::E is being integrated with POE so that evolutionary algorithms (EAs) can be combined with all kinds of servers and used in client, servers, and anything in between. In this companion to the talk I will explain what evolutionary algorithms are, what they are being used for, how to do them with Perl (using these or other fine modules found in CPAN) and what evolutionary algorithms can do for Perl at large.
Population structure, fecundity and morphological characteristics of M. vollenhovenii (Herklots, 1857) on lower volta river basin channel, Ghana

Population structure, fecundity and morphological characteristics of M. vollenhovenii were studied around Lower Volta River, Ghana subject to dirt of information on this prawn species around the study location. The most prominent morphological characteristics already documented for identification of this species was rostrum bearing 13-15 continuous teeth dorsally and 4-5 teeth on its ventral part. These morphological traits formed the principal components for identification in this study. Results showed that morphological traits on second pereiopods such as presence of spines, spinules, teeth borne within the fingers, and dense projections of setae-like features on telson and uropod were observed relevant for identification purposes. Other results revealed that maximum total length recorded in this study (150-155mm) was higher than total length ranges (≤125mm) documented for this species in earlier studies. Consequently, two adult’s classes of prawns were identified (old adult class 81-120mm; and young adults 31-80mm) and older class was observed to be more in catches than the younger prawns. Absolute fecundity revealed that oocytes estimation varied with respect to seasons, ages of prawns and body sizes of specimens examined. In conclusion, this study observed that M. vollenhovenii fishery is operating in a sustainable manner at the time of this study around the study location.
Haustoria Segmentation in Microscope Colour Images of Barley Cells

Dyed barley cells in microscope colour images of biological experi- ments are analysed for the occurrence of haustoria of the powdery mildew fungus by a fully automated screening system. The region of interest in the images is found by applying Canny's edge detector to the hue channel of the HSV colour space. For the segmentation of potential haustoria within the dyed cells, two dif- ferent methods are considered: A clustering in RGB colour space using the Ex- pectation Maximisation (EM) algorithm, and morphological contrast enhance- ment of the colour image with subsequent hysteresis thresholding in the satura- tion channel of the enhanced images. The second approach seems to be more viable because of its robustness and more promising results. Automating the screening and the analysis of biological experiments is a challenging research area in the field of bioinformatics and engineering. This paper is related to a project studying resistance mechanisms of crop plants against the powdery mildew fungus from the genetical point of view. In the experiments, young barley leaves are bombarded with DNA-coated particles to "switch on or off" desired genes in cells. For analysis purposes, an additional reporter gene 1 is expressed in cells that were hit by a particle. This dyes the affected genetically transformed cells greenish blue and allows their identification by bright field microscopy (7). The task is to evaluate the susceptibility of the genetically transformed cells to the powdery mildew fungus under the impact of different test genes. A successful penetration of the fungus into the cell is indicated by the development of a haustorium - a dark object consisting of a "waist" with "fingers" that is located between the cell wall and the cell membrane and feeds the fungus by leaching the cell (see Figure 2). These objects have to be counted in an automatic analysis procedure. Since there are many genes to be considered for a potential resistance of the plant against pathogens, a big number of experiments has to be performed to obtain a suffi- cient statistical confidence. Therefore, an automated image acquisition system and an
Supervised single-channel speech dereverberation and denoising using a two-stage processing

In many acoustic conditions, a single-channel recorded speech signal may be severely affected by reverberation and noise, leading to a reduced speech quality and intelligibility. This paper focuses on proposing a novel two-stage processing scheme for single-channel speech dereverberation and denoising to enhance the spectrum of the noisy reverberant signal. Similar as previous methods, the proposed method uses a non-negative approximation of the convolutive transfer function (N-CTF) to simultaneously estimate the magnitude spectrograms of the speech signal and the room impulse response (RIR). What's the novelty of proposed algorithm is decomposing the RIRs into two parts to build a two-stage processing scheme for enhancing speech from the noisy environments. The proposed algorithm is iteratively updated to estimate a less reverberant speech signal and a short RIR at first stage, then the clean speech signal and another short RIR are estimated by iteratively updating at the second stage. There are always denosing process steps within both stages. The advantages of our proposed algorithm are more capable to enhance the speech and more time-saving by decomposing the long RIRs into two parts. Additionally, the optimal estimator is derived based on temporal stacking to utilize speech temporal dynamics. Experiments are performed on two simulated RIRs to compare the performances of the proposed method with a state-of-the-art method and the results show that the proposed method has significantly improved the enhanced speech quality and intelligibility.
Self-Reported Inability to Cry as a Symptom of Anhedonic Depression in Outpatients with a Major Depressive Disorder

To ascertain whether self-reported inability to cry would be associated with symptoms of anhedonic depression, the 21-item Beck Depression Inventory-II was administered to 1,050 outpatients diagnosed with a DSM-IV-TR major depressive disorder. 219 (21%) patients reported on the BDI-II Crying item that they were unable to cry, and 831 (79%) patients reported they were able to cry. Only BDI-II Loss of Interest was significantly associated with the inability to cry after the other BDI-II symptoms were controlled for using a multiple logistic-regression analysis. The inability to cry was discussed as an indicator of anhedonic depression.