Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Mass Spectrometry Data Using Bayesian Wavelet-Based Functional Mixed Models

In this chapter, we demonstrate how to analyze MALDI-TOF/SELDITOF mass spectrometry data using the wavelet-based functional mixed model introduced by Morris and Carroll (2006), which generalizes the linear mixed models to the case of functional data. This approach models each spectrum as a function, and is very general, accommodating a broad class of experimental designs and allowing one to model nonparametric functional effects for various factors, which can be conditions of interest (e.g. cancer/normal) or experimental factors (blocking factors). Inference on these functional effects allows us to identify protein peaks related to various outcomes of interest, including dichotomous outcomes, categorical outcomes, continuous outcomes, and any interactions among factors. Functional random effects make it possible to account for correlation between spectra from the same individual or block in a flexible manner. After fitting this model using an MCMC, the output can be used to perform peak detection and identify the peaks that are related to factors of interest, while automatically adjusting for nonlinear block effects that are characteristic of these data. We apply this method to mass spectrometry data from an University of Texas MD Anderson Cancer Center experiment studying the serum proteome of mice injected with one of two cell lines in one of two organs. This methodology ap-
Costing of National STI Program Implementation for the Global STI Control Strategy for the Health Sector, 2016-2021

Introduction In 2016 the World Health Assembly adopted the global strategy on Sexually Transmitted Infections (STI) 2016–2021 aiming to reduce curable STIs by 90% by 2030. We costed scaling-up priority interventions to coverage targets. Methods Strategy-targeted declines in Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum and Trichomonas vaginalis were applied to WHO-estimated regional burdens at 2012. Syndromic case management was costed for these curable STIs, symptomatic Herpes Simplex Virus 2 (HSV-2), and non-STI vaginal syndromes, with incrementally expanding etiologic diagnosis. Service unit costs were multiplied with clinic attendances and people targeted for screening or prevention, by income tier. Human papilloma virus (HPV) vaccination and screening were costed for coverage increasing to 60% of 10-year-old girls for vaccination, and 60% of women 30–49 years for twice-lifetime screening (including clinical follow-up for positive screens), by 2021. Results Strategy implementation will cost an estimated US$ 18.1 billion over 2016–2021 in 117 low- and middle-income countries. Cost drivers are HPV vaccination ($3.26 billion) and screening ($3.69 billion), adolescent chlamydia screening ($2.54 billion), and antenatal syphilis screening ($1.4 billion). Clinical management—of 18 million genital ulcers, 29–39 million urethral discharges and 42–53 million vaginal discharges annually—will cost $3.0 billion, including $818 million for service delivery and $1.4 billion for gonorrhea and chlamydia testing. Global costs increase from $2.6 billion to $ 4.0 billion over 2016–2021, driven by HPV services scale-up, despite vaccine price reduction. Sub-Saharan Africa, bearing 40% of curable STI burdens, covers 44% of global service needs and 30% of cost, the Western Pacific 15% of burden/need and 26% of cost, South-East Asia 20% of burden/need and 18% of cost. Conclusions Costs of global STI control depend on price trends for HPV vaccines and chlamydia tests. Middle-income and especially low-income countries need increased investment, innovative financing, and synergizing with other health programs.
Optimisation of Multipurpose Reservoir Operation by coupling SWAT and Genetic Algorithm for Optimal Operating Policy (Case Study: Ganga River basin)

Reservoirs are recognized as one of the most efficient infrastructure components in integrated water resources management and development. At present, with the ongoing advancement of social economy and requirement of water, the water resources shortage problem has worsened, and the operation of reservoirs, in terms of consumption of flood water, has become significantly important. Reservoirs perform both regulation of flood and integrated water resources management, in which the flood limited water level is considered as the most important parameter for trade-off between regulation of flood and conservation. To achieve optimal operating policies for reservoirs, large numbers of simulation and optimization models have been developed in the course of recent decades, which vary notably in their applications and working. Since each model has their own limitations, the determination of fitting model for derivation of reservoir operating policies is challenging and most often there is always a scope for further improvement as the selection of model depends on availability of data. Subsequently, assessment and evaluation associated with the operation of reservoir stays conventional. In the present study, the Soil and Water Assessment Tool (SWAT) models and a Genetic Algorithm model has been developed and applied to two reservoirs in Ganga River basin, India to derive the optimal operational policies. The objective function is set to minimize the annual sum of squared deviation form desired irrigation release and desired storage volume. The decision variables are release for irrigation and other demands (industrial and municipal demands), from the reservoir. As a result, a simulation-based optimization model was recommended for optimal reservoir operation, such as allocation of water, flood regulation, hydropower generation, irrigation demands and navigation and e-flows using a definite combination of decision variables. Since the rule curves are derived through random search it is found that the releases are same as that of demand requirements. Hence based on simulated result, in the present case study it is concluded that GA-derived policies are promising and competitive and can be effectively used operation of the reservoir.
Biopsychosocial factors in chronic spine -related pain: Contributions to pain intensity and perceived disability

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Sanitation sustainability, seasonality and stacking: Improved facilities for how long, where and whom?

Despite high-profile efforts to ‘reinvent the toilet’ (Gates Foundation, 2014) and ‘end open defecation’ (UNICEF, 2016a), WHO/UNICEF, (2017) estimated that in 2015, 2.3 billion lacked access to improved sanitation and 892 million practised open defecation (OD). This has been associated with severe environmental and health impacts (Coffey, 2014; Rees, 2014; UNICEF, 2016a) which could worsen if climate change-induced flooding or extreme events facilitate the spread of water-borne disease (McMichael, et al. 2006; Papworth, et al. 2015). Although an estimated 2.1 billion gained access to improved sanitation between 1990 and 2015 (WHO/UNICEF, 2015a), the extent to which this translated into ‘an improvement in the adequacy of provision’ (Satterthwaite 2015,5) varies greatly over space, by season and between user groups. In 2015, 56% of India’s population lacked basic sanitation and 40% practised open defecation although rural-urban and socio-economic variations were significant (WHO/UNICEF, 2017). These figures almost certainly over-estimate sanitation coverage as most household-level census, Demographic and Health Survey (DHS) and Multiple Indicator Cluster Survey (MICS) data used to inform sanitation tracking do ‘not include informal urban settlements or slums, which are often not considered in official data collection’ (WSSCC, 2015:3). Dry season bias in household survey data collection (Pullum, 2008; Wright et al., 2012) coupled with seasonal shifts in sanitation practices (Routray et al 2015; Sahoo et al 2015) are likely to create further distortion. Focus on the presence of particular sanitation technologies (as proxies for sanitation access), meanwhile, can conceal significant health threats in the absence of checks on whether their quality or use is sufficient to reduce health risks (Gine et al., 2011).
Mineralogy and magnetic properties of the 1999 Chi-Chi earthquake (Mw 7.6) slip zone and their implications

During an earthquake, the physical and the chemical transformations along a slip zone lead to alteration and formation of minerals within the gouge layer of a mature fault zone. The gouge contains magnetic minerals, which could be formed under the combined action of friction heat and fluid. Thus, gouge has the capacity to behave as a magnetic recorder during an earthquake. This constitutes a conceivable way to identify earthquakes slip zones. Besides, altered and neoformed magnetic minerals can be used as tracers of some earthquake processes. In this study, we investigate the rock magnetism and paleomagnetism of the Chelungpu fault gouge that hosts the principal slip zone of the Chi-Chi earthquake (Mw 7.6, 1999, Taiwan) using Taiwan Chelungpu-fault Drilling Project (TCDP) hole-B core samples. We also took a Chelungpu fault outcrop sample for identification of nanoparticle, which associated with fracture energy estimation in fault gouge.
High-efficiency watt-level MASMOS® power amplifier for LTE applications

This paper reports for the first time a power amplifier (PA) based on the recently proposed MASMOS® transistor. This PA complies with the long-term evolution (LTE) power level requirements while offering a high efficiency. The MASMOS® transistor, available in low-cost 180-nm standard CMOS process, provides a higher breakdown voltage compared to conventional CMOS transistors. Therefore, the MASMOS® transistor is of high interest as it is able to generate a Watt-level output power with high efficiency in the highest LTE-bands. A reconfigurable power cell, implementing resizable MASMOS® transistors and offering a discrete control of both the output power and the dc consumption is introduced. Based on this reconfigurable cell, a two-stage PA is designed. This PA exhibits a measured 30.2 dBm output power at 2.5 GHz with a gain and power-added efficiency (PAE) of 21.8 dB and 54% respectively.
Development of SyReC based expandable reversible logic circuits

Reversible computing is gaining high interest from researchers due to its various promises. One of the prominent advantages perceived from reversible logic is that of reduced power dissipation with many reversible gates at hand, designing a reversible circuit (combinational) has received due attention and achievement. A proposed language for description of reversible circuit, namely SyReC, is also in place. What remain are the software tools which would help in reversible circuit synthesis through simulation. Beginning with the smallest reversible circuit realizations the SyReC statements and expressions, we employ a hierarchal approach to develop a complete reversible circuit, entirely from its SyReC code. We implement this as a software tool. The tool allows a user to expand a reversible circuit of choice in terms of bit width of its inputs. The background approach of expansion of a reversible circuit has also been proposed as a part of this dissertation. Also, a user can use the tool to observe the effect of expansion on incurred costs, in terms of increase in number of lines, number of gates and quantum cost. The importance of observing the change in costs with respect to scale of expansion is important not only from analysis point of view, but also because the cost depends on the approach used for expansion. This dissertation also proposes a reversible circuit design for elevator controller (combinational) and the related costs. The aim is to emphasize use of the proposed approach is designing customized circuits.
Effects of 99mTc-MIBI and 99mTc-MDP administration on dual-energy X-ray absorptiometry bone mineral density measurements

ObjectiveNuclear medicine procedures are often performed in close-time proximity to bone densitometry studies. The purpose of this study was to determine the effects of 99mTc-hexakis-2-methoxyisobutyl isonitrile (MIBI) and 99mTc-methylene diphosphonate (MDP) on the accuracy of bone mineral density (BMD) measurements performed using dual-energy X-ray density. MethodsThe effect of a diagnostic dose of 99mTc-MIBI on BMD estimations in the lumbar spine and the left total hip was assessed in 30 patients (19 female, 11 male; mean age: 55.5±10.5 years) by using a Lunar DPX-NT scanner. Thirty patients, admitted to the nuclear medicine department for bone scintigraphy (15 female, 15 male; mean age: 56±15.92 years), were included into the study. Each patient underwent dual-energy X-ray density assessment for which a Lunar DPX-NT scanner was used before and 2 h after intravenous injection of 99mTc-MDP (925 MBq) and 99mTc-MIBI (1110 MBq). BMD measurements were calculated from lumbar spine (including L2–4) and left hip (including femoral neck, trochanter, and total hip). For statistical analysis, the Wilcoxon test was used and a P value of less than 0.05 was accepted as statistically significant. ResultsAccording to Wilcoxon's statistical test, we found extremely significant changes on the measured BMD, T-score, before and 2 h after the injection of 99mTc-MIBI for lumbar spine and left hip in 30 patients. We found statistically significant decrement on measured BMD from lumbar spine and trochanter before and 2 h after the injection of 99mTc-MDP. Although MDP BMD values in femoral neck and total hip were decreased after the injection of Tc-99m, they did not reach a statistically significant value. The comparison of pre-T-score and post-T-score values showed a statistically significant decrease after the injection for only L2–4 lumbar spine (P = 0.002), but left hip of pre-T-score and post-T-score values did not reach a statistically significant value. ConclusionIn this study, it was determined that measured BMD values are decreased in lumbar spine for all patients. The magnitude of the effect is dependent on the location of the activity. We assume that some radioactivity from 99mTc is counted by the densitometer's detector, thus resulting in a decrease in the measured BMD. Scintigraphy and bone densitometry should be performed on different days to avoid artifactual reduction in BMD measurements.
Application and standardization of turbo codes in third-generation high-speed wireless data services

This paper addresses the application of turbo codes for third-generation wireless services. It describes the specific characteristics of high-rate data applications in third-generation wide-band code-division multiple-access (CDMA) systems that make turbo codes superior to convolutional codes. In particular, it shows the positive effect of fast power control employed in these systems on the relative performance of turbo codes with respect to convolutional codes. It also shows how turbo and convolutional codes behave differently when the figure of merit is changed to frame error rate from bit error rate for high-speed data services. Furthermore, it describes in detail how and why the standardized turbo code has been selected in the presence of other candidates, which were also based on iterative decoding. Details of turbo interleaving and trellis termination as specified in the standards are explained. Performance of turbo codes under wide-band CDMA operating conditions are presented. The suitability of turbo codes for low-rate data applications is discussed. Finally it is shown that the performance loss as a result of internal decoder parameter quantization is negligible.
A Language for Construction of Belief Networks

A method for incrementally constructing belief networks, which are directed acyclic graph representations for probability distributions, is described. A network-construction language, FRAIL3, which is similar to a forward-chaining language using data dependencies but has additional features for specifying distributions, was developed. A particularly important feature of this language is that is allows the user to conveniently specify conditional probability matrices using stereotyped models of intercausal interaction. Using FRAIL3, one can define parmeterized classes of probabilistic models. These parameterized models make it possible to apply probabilistic reasoning to problems for which it is impractical to have a single large, static model. >
Extensional Models of Untyped Lambda-mu Calculus

This paper proposes new mathematical models of the untyped Lambda-mu calculus. One is called the stream model, which is an extension of the lambda model, in which each term is interpreted as a function from streams to individual data. The other is called the stream combinatory algebra, which is an extension of the combinatory algebra, and it is proved that the extensional equality of the Lambda-mu calculus is equivalent to equality in stream combinatory algebras. In order to define the stream combinatory algebra, we introduce a combinatory calculus SCL, which is an abstraction-free system corresponding to the Lambda-mu calculus. Moreover, it is shown that stream models are algebraically characterized as a particular class of stream combinatory algebras.
Occurrence of Sooty Blotch and Flyspeck Disease on Sweet Persimmon in Korea

Sooty blotch and flyspeck (SBFS), a disease caused by a complex of fungi, results in substantial economic losses for commercial growers of sweet persimmon (Diospyros kaki L.) in Korea. However, many species causing SBFS in Korea have not been identified and sources of inoculum are uncertain. Based on mycological characteristics, pathogenicity, and molecular data, the causal fungi were identified as Dissoconium sp. and Zygophiala wisconsinensis. This is the first report of SBFS of sweet persimmon in Korea.
Gene Targeting Study Reveals Unexpected Expression of Brain-expressed X-linked 2 in Endocrine and Tissue Stem/Progenitor Cells in Mice*

Background: The role and precise expression pattern of individual brain-expressed X-linked genes in vivo were unknown. Results: Bex2-EGFP knock-in–knock-out mice were viable and fertile. Outside the brain, EGFP was expressed in specific cell populations. Conclusion: Bex2 plays redundant roles in vivo but is specifically expressed in endocrine and stem/progenitor cells. Significance: Bex2 is a novel marker for endocrine and stem/progenitor cells. Identification of genes specifically expressed in stem/progenitor cells is an important issue in developmental and stem cell biology. Genome-wide gene expression analyses in liver cells performed in this study have revealed a strong expression of X-linked genes that include members of the brain-expressed X-linked (Bex) gene family in stem/progenitor cells. Bex family genes are expressed abundantly in the neural cells and have been suggested to play important roles in the development of nervous tissues. However, the physiological role of its individual members and the precise expression pattern outside the nervous system remain largely unknown. Here, we focused on Bex2 and examined its role and expression pattern by generating knock-in mice; the enhanced green fluorescence protein (EGFP) was inserted into the Bex2 locus. Bex2-deficient mice were viable and fertile under laboratory growth conditions showing no obvious phenotypic abnormalities. Through an immunohistochemical analysis and flow cytometry-based approach, we observed unique EGFP reporter expression patterns in endocrine and stem/progenitor cells of the liver, pyloric stomach, and hematopoietic system. Although Bex2 seems to play redundant roles in vivo, these results suggest the significance and potential applications of Bex2 in studies of endocrine and stem/progenitor cells.
Dynamic simulation of constrained mechanical systems using recursive projection algorithm

In this paper, the dynamic simulation of constrained mechanical systems that are interconnected of rigid bodies is studied using projection recursive algorithm. The method uses the concepts of linear and angular momentums to generate the rigid body equations of motion in terms of the Cartesian coordinates of a dynamically equivalent constrained system of particles, without introducing any rotational coordinates and the corresponding rotational transformation matrix. Closed-chain system is transformed to open-chain by cutting suitable kinematical joints and introducing cut-joint constraints. For the resulting open-chain system, the equations of motion are generated recursively along the serial chains. An example is chosen to demonstrate the generality and simplicity of the developed formulation.
Integrating heterogeneous reatures for efficient content based music retrieval

In this paper, we present a novel feature extraction method facilitating efficient content-based music retrieval and classification, called <i>InMAF</i>. The goal of our approach is to allow straightforward incorporation of multiple musical features, such as timbral texture, pitch and rhythm structure, into a single low dimensional vector that is effective for retrieval and classification. Unlike earlier approaches that used only acoustic properties as the basis for retrieval, our approach can easily incoporate human music perception to improve accuracy of retrieval and classification process. The superiority of our method is demonstrated by comparing it with state-of-the-art approaches in the areas of music classification (using a variety of machine learning algorithms), query effectiveness and robustness against audio distortion.
Development and evaluation of a DNA detection kit on authentication of Zaocys dhumnades based on a bioinformatics method and PCR technology

The aim of the study was to investigate the characteristics of Zaocys dhumnades cytochrome b (cyt b) gene. Bioinformatics technology was used to design primers, sequence and blast, in conjunction with PCR technology. A kind of Zaocys dhumnades DNA test kit was developed, and it's indexes including specificity, sensitivity and stability were evaluated. Results by kit method were in accordance with the ones by China Pharmacopoeia method (2012 edition). The sensitivity was 0.025g of each tested specimen in the lowest amount. The stability of kit assay proved effective after repeated thawing 20 times, and specificity got to 100% in identification of authentic and fake samples. The developed DNA kit is accurate, effective in identification of Zaocys dhumnades authentication. It had simple, fast properties, and demonstrated the broad prospect in quality control of Zaocys dhumnades in the medicine field.
Feature facial image recognition using VQ histogram in the DCT domain

In this paper, a novel algorithm using vector quantization (VQ) method for facial image recognition in DCT domain is presented. Firstly, feature vectors of facial image are generated by using DCT (Discrete Cosine transform) coefficients in low frequency domains. Then codevector referred count histogram, which is utilized as a very effective personal feature value, is obtained by Vector Quantization (VQ) processing. Publicly available AT&T database of 40 subjects with 10 images per subject containing variations in lighting, posing, and expressions, is used to evaluate the performance of the proposed algorithm. Experimental results show face recognition using proposed feature vector is very efficient. The highest average recognition rate of 94.8% is obtained.