Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional brain imaging of cognitive dysfunction in Parkinson's disease

Multiple factors are involved in the development of cognitive impairment in Parkinson's disease (PD) and related disorders. Notably, several underlying factors, such as monoaminergic dysfunction, Lewy body pathology, Alzheimer disease-like pathology and cerebrovascular disease are implied in the PD pathophysiology of cognitive impairment. The mesocortical dopaminergic system is associated with executive functions which are frequently affected in PD and are influenced by local levodopa concentration, dopamine metabolism and baseline performance status. The ventral striatum and frontal cortex are associated with impulse control disorders reported in PD patients treated with dopamine replacement therapy. Cholinergic impairment in PD plays a cardinal role in the development of dementia. Acetylcholinesterase positron emission tomography demonstrates that posterior brain areas are related to cognitive decline in PD patients. Amyloid radiotracer illustrates that patients with PD with severe cognitive impairment were prone to accompanied cortical amyloid deposition. Metabolism/perfusion change associated with cognitive impairment in PD, so-called PD related cognitive pattern, is characterised by reduced frontoparietal activity and is an effective way to differentiate and monitor cognitive function of individual PD patients. Cognitive impairment in PD cannot be explained by a single mechanism and is entangled by multiple factors. Imaging studies can unravel each pathological domain, further shed light on the interrelation between different pathomechanisms, not only in PD but also in other dementia related disorders, and thereby integrate its interpretation to apply to therapeutics in individual patients.
Live imaging of root–bacteria interactions in a microfluidics setup

Significance Microbial interactions in the rhizosphere, the microenvironment surrounding plant roots, are a major research area for both plant biologists and microbial ecologists. A significant obstacle in this field is the difficulty in studying root–bacteria interactions in real time. Here, we developed a microfluidics-based device that allows dynamic imaging of root–bacterial interactions at previously unattainable spatiotemporal resolutions. The intimate interaction of Bacillus subtilis with plant roots is accurately traced in high resolution to the root elongation zone. We further reveal how bacterial behavior leads to rapid root colonization and exclusion of competing bacteria. Hence, this approach has the potential to transform our understanding of root–bacteria interactions and the modulation of bacterial communities colonizing the root surface. Plant roots play a dominant role in shaping the rhizosphere, the environment in which interaction with diverse microorganisms occurs. Tracking the dynamics of root–microbe interactions at high spatial resolution is currently limited because of methodological intricacy. Here, we describe a microfluidics-based approach enabling direct imaging of root–bacteria interactions in real time. The microfluidic device, which we termed tracking root interactions system (TRIS), consists of nine independent chambers that can be monitored in parallel. The principal assay reported here monitors behavior of fluorescently labeled Bacillus subtilis as it colonizes the root of Arabidopsis thaliana within the TRIS device. Our results show a distinct chemotactic behavior of B. subtilis toward a particular root segment, which we identify as the root elongation zone, followed by rapid colonization of that same segment over the first 6 h of root–bacteria interaction. Using dual inoculation experiments, we further show active exclusion of Escherichia coli cells from the root surface after B. subtilis colonization, suggesting a possible protection mechanism against root pathogens. Furthermore, we assembled a double-channel TRIS device that allows simultaneous tracking of two root systems in one chamber and performed real-time monitoring of bacterial preference between WT and mutant root genotypes. Thus, the TRIS microfluidics device provides unique insights into the microscale microbial ecology of the complex root microenvironment and is, therefore, likely to enhance the current rate of discoveries in this momentous field of research.
Optimization Criteria for Effort Estimation using Fuzzy Technique

Effective cost estimation is the most challenging activity in software development. Software cost estimation is not an exact science. Cost estimation process involves a series of systematic steps that provide estimate with acceptable risk. Some prevalent LOC based models areBailey Basili model, Alaa F. Sheta G.E. Model, and Alaa F. Sheta, Model 2 [1] . Two new models, based on fuzzy logic sizing, are presented in this paper. Rather than using a single number, the software size is regarded as a triangular fuzzy number. We can optimize the estimated effort for any application by varying arbitrary constants for these models. The developed models are tested on 10 NASA software projects [2], on the basis of four criterions for assessment of software cost estimation models. Comparison of all the models, cited above, is done and it is found that the developed models provide better estimation.
Next-Generation Sequencing Reveals Frequent Opportunities for Exposure to Hepatitis C Virus in Ghana

Globally, hepatitis C Virus (HCV) infection is responsible for a large proportion of persons with liver disease, including cancer. The infection is highly prevalent in sub-Saharan Africa. West Africa was identified as a geographic origin of two HCV genotypes. However, little is known about the genetic composition of HCV populations in many countries of the region. Using conventional and next-generation sequencing (NGS), we identified and genetically characterized 65 HCV strains circulating among HCV-positive blood donors in Kumasi, Ghana. Phylogenetic analysis using consensus sequences derived from 3 genomic regions of the HCV genome, 5'-untranslated region, hypervariable region 1 (HVR1) and NS5B gene, consistently classified the HCV variants (n = 65) into genotypes 1 (HCV-1, 15%) and genotype 2 (HCV-2, 85%). The Ghanaian and West African HCV-2 NS5B sequences were found completely intermixed in the phylogenetic tree, indicating a substantial genetic heterogeneity of HCV-2 in Ghana. Analysis of HVR1 sequences from intra-host HCV variants obtained by NGS showed that three donors were infected with >1 HCV strain, including infections with 2 genotypes. Two other donors share an HCV strain, indicating HCV transmission between them. The HCV-2 strain sampled from one donor was replaced with another HCV-2 strain after only 2 months of observation, indicating rapid strain switching. Bayesian analysis estimated that the HCV-2 strains in Ghana were expanding since the 16th century. The blood donors in Kumasi, Ghana, are infected with a very heterogeneous HCV population of HCV-1 and HCV-2, with HCV-2 being prevalent. The detection of three cases of co- or super-infections and transmission linkage between 2 cases suggests frequent opportunities for HCV exposure among the blood donors and is consistent with the reported high HCV prevalence. The conditions for effective HCV-2 transmission existed for ~ 3–4 centuries, indicating a long epidemic history of HCV-2 in Ghana.
Quantifying Freshwater Mass Balance in the Central Tibetan Plateau by Integrating Satellite Remote Sensing, Altimetry, and Gravimetry

The Tibetan Plateau (TP) has been observed by satellite optical remote sensing, altimetry, and gravimetry for a variety of geophysical parameters, including water storage change. However, each of these sensors has its respective limitation in the parameters observed, accuracy and spatial-temporal resolution. Here, we utilized an integrated approach to combine remote sensing imagery, digital elevation model, and satellite radar and laser altimetry data, to quantify freshwater storage change in a twin lake system named Chibuzhang Co and Dorsoidong Co in the central TP, and compared that with independent observations including mass changes from the Gravity Recovery and Climate Experiment (GRACE) data. Our results show that this twin lake, located within the Tanggula glacier system, remained almost steady during 1973–2000. However, Dorsoidong Co has experienced a significant lake level rise since 2000, especially during 2000–2005, that resulted in the plausible connection between the two lakes. The contemporary increasing lake level signal at a rate of 0.89 ± 0.05 cm·yr−1, in a 2° by 2° grid equivalent water height since 2002, is higher than the GRACE observed trend at 0.41 ± 0.17 cm·yr−1 during the same time span. Finally, a down-turning trend or inter-annual variability shown in the GRACE signal is observed after 2012, while the lake level is still rising at a consistent rate.
Control of the orientational characteristics of disk-like hematite particles by a simple shear flow

We discuss the behavior of oblate spheroidal hematite particles in a simple shear flow. Magneto-rheological properties are strongly dependent on the magnetic field direction. For instance, a rod-like hematite particle suspension exhibits negative viscosity characteristics in a certain direction of an applied magnetic field. From this background, we here consider the case of an external magnetic field applied in the direction of the angular velocity vector of a simple shear flow. If the magnetic field is much more dominant than the thermal motion, the particle can almost freely rotate about the direction of the angular velocity vector. This characteristic rotational motion is suppressed or controlled by the shear flow more significantly with increasing shear rate.
Copy-move forgery detection in digital images

The ready availability of image-editing software makes it important to ensure the authenticity of images. This thesis concerns the detection and localization of cloning, or Copy-Move Forgery (CMF), which is the most common type of image tampering, in which part(s) of the image are copied and pasted back somewhere else in the same image. Post-processing can be used to produce more realistic doctored images and thus can increase the difficulty of detecting forgery. This thesis presents three novel methods for CMF detection, using feature extraction, surface fitting and segmentation. The Dense Scale Invariant Feature Transform (DSIFT) has been improved by using a different method to estimate the canonical orientation of each circular block. The Fitting Function Rotation Invariant Descriptor (FFRID) has been developed by using the least squares method to fit the parameters of a quadratic function on each block curvatures. In the segmentation approach, three different methods were tested: the SLIC superpixels, the Bag of Words Image and the Rolling Guidance filter with the multi-thresholding method. We also developed the Segment Gradient Orientation Histogram (SGOH) to describe the gradient of irregularly shaped blocks (segments). The experimental results illustrate that our proposed algorithms can detect forgery in images containing copy-move objects with different types of transformation (translation, rotation, scaling, distortion and combined transformation). Moreover, the proposed methods are robust to post-processing (i.e. blurring, brightness change, colour reduction, JPEG compression, variations in contrast and added noise) and can detect multiple duplicated objects. In addition, we developed a new method to estimate the similarity threshold for each image by optimizing a cost function based probability distribution. This method can detect CMF better than using a fixed threshold for all the test images, because our proposed method reduces the false positive and the time required to estimate one threshold for different images in the dataset. Finally, we used the hysteresis to decrease the number of false matches and produce the best possible result.
Interactive Co-Design of Form and Function for Legged Robots using the Adjoint Method

Our goal is to make robotics more accessible to casual users by reducing the domain knowledge required in designing and building robots. Towards this goal, we present an interactive computational design system that enables users to design legged robots with desired morphologies and behaviors by specifying higher level descriptions. The core of our method is a design optimization technique that reasons about the structure, and motion of a robot in coupled manner in order to achieve user-specified robot behavior, and performance. We are inspired by the recent works that also aim to jointly optimize robot's form and function. However, through efficient computation of necessary design changes, our approach enables us to keep user-in-the-loop for interactive applications. We evaluate our system in simulation by automatically improving robot designs for multiple scenarios. Starting with initial user designs that are physically infeasible or inadequate to perform the user-desired task, we show optimized designs that achieve user-specifications, all while ensuring an interactive design flow.
Gas phase hydrogen permeation in alpha titanium and carbon steels

Commercially pure titanium and heats of Armco ingot iron and steels containing from 0.008-1.23 w/oC were annealed or normalized and machined into hollow cylinders. Coefficients of diffusion for alpha-Ti and alpha-Fe were determined by the lag-time technique. Steady state permeation experiments yield first power pressure dependence for alpha-Ti and Sievert's law square root dependence for Armco iron and carbon steels. As in the case of diffusion, permeation data confirm that alpha-titanium is subject to at least partial phase boundary reaction control while the steels are purely diffusion controlled. The permeation rate in steels also decreases as the carbon content increases. As a consequence of Sievert's law, the computed hydrogen solubility decreases as the carbon content increases. This decreases in explained in terms of hydrogen trapping at carbide interfaces. Oxidizing and nitriding the surfaces of alpha-titanium membranes result in a decrease in the permeation rate for such treatment on the gas inlet surfaces but resulted in a slight increase in the rate for such treatment on the gas outlet surfaces. This is explained in terms of a discontinuous TiH2 layer.
Wideband six-port reflectometer

In this paper a wideband six-port reflectometer, composed of coupled-line directional couplers is proposed. It is shown that modifications applied to the classic solution have allowed for increasing the operational bandwidth. In addition, the obtained structure is easily scalable for further bandwidth broadening. For the experimental verification, the performance of two manufactured versions of proposed six-port has been verified by measuring their S-parameters with a VNA. The results have confirmed the expected performance improvement comparing to the well-known solution.
Highly Variable Patterns of Linkage Disequilibrium in Multiple Soybean Populations

Prospects for utilizing whole-genome association analysis in autogamous plant populations appear promising due to the reported high levels of linkage disequilibrium (LD). To determine the optimal strategies for implementing association analysis in soybean (Glycine max L. Merr.), we analyzed the structure of LD in three regions of the genome varying in length from 336 to 574 kb. This analysis was conducted in four distinct groups of soybean germplasm: 26 accessions of the wild ancestor of soybean (Glycine soja Seib. et Zucc.); 52 Asian G. max Landraces, the immediate results of domestication from G. soja; 17 Asian Landrace introductions that became the ancestors of North American (N. Am.) cultivars, and 25 Elite Cultivars from N. Am. In G. soja, LD did not extend past 100 kb; however, in the three cultivated G. max groups, LD extended from 90 to 574 kb, likely due to the impacts of domestication and increased self-fertilization. The three genomic regions were highly variable relative to the extent of LD within the three cultivated soybean populations. G. soja appears to be ideal for fine mapping of genes, but due to the highly variable levels of LD in the Landraces and the Elite Cultivars, whole-genome association analysis in soybean may be more difficult than first anticipated.
A Qualitative Assessment of Alcohol Consumption and Sexual Risk Behaviors Among Men Who Have Sex With Men and Transgender Women in Peru

ABSTRACT Background: Peruvian men who have sex with men (MSM) and transgender women (TGW) experience the double burden of a highly concentrated HIV epidemic with a high prevalence of alcohol use disorders (AUDs). Recent research has associated both with risky sexual behaviors, including unprotected sex, having multiple sexual partners, engaging in sex work, having recent sexually transmitted infections, and having HIV-infected partners. AUDs have also been associated in MSM/TGW with being unaware of HIV+ status. Objectives: This study aims to further examine issues associated with alcohol consumption, HIV infection, and risk behaviors in a qualitative analysis of focus groups conducted with MSM/TGW in Peru. Methods: A total of 26 MSM/TGW participants with AUDs participated in three semi-structured focus groups in Lima, Peru. Content analysis was facilitated by software, and specific themes were elucidated. Results: Participants described their drinking patterns, including the types of alcoholic drinks they consumed. They depicted drinking frequently and over multiple-day sessions. Problematic drinking behaviors were described, as well as the perceived characteristics of alcohol dependence. Interestingly, HIV-infected participants who were prescribed antiretroviral therapy did not believe that their drinking affected their medication adherence. These insights can aid in the design of future interventions aiming to reduce problematic drinking as well as HIV-related risk behaviors and, subsequently, HIV incidence. Conclusions: Peruvian MSM/TGW exhibit problematic drinking, which may be associated with risky sexual behaviors and HIV transmission. Interest in reducing alcohol consumption was high, suggesting the need for targeted behavioral and pharmacological interventions.
Coding-theorem like behaviour and emergence of the universal distribution from resource-bounded algorithmic probability

ABSTRACT Previously referred to as ‘miraculous’ in the scientific literature because of its powerful properties and its wide application as optimal solution to the problem of induction/inference, (approximations to) Algorithmic Probability (AP) and the associated Universal Distribution are (or should be) of the greatest importance in science. Here we investigate the emergence, the rates of emergence and convergence, and the Coding-theorem like behaviour of AP in Turing-subuniversal models of computation. We investigate empirical distributions of computing models in the Chomsky hierarchy. We introduce measures of algorithmic probability and algorithmic complexity based upon resource-bounded computation, in contrast to previously thoroughly investigated distributions produced from the output distribution of Turing machines. This approach allows for numerical approximations to algorithmic (Kolmogorov-Chaitin) complexity-based estimations at each of the levels of a computational hierarchy. We demonstrate that all these estimations are correlated in rank and that they converge both in rank and values as a function of computational power, despite fundamental differences between computational models. In the context of natural processes that operate below the Turing universal level because of finite resources and physical degradation, the investigation of natural biases stemming from algorithmic rules may shed light on the distribution of outcomes. We show that up to 60% of the simplicity/complexity bias in distributions produced even by the weakest of the computational models can be accounted for by Algorithmic Probability in its approximation to the Universal Distribution.
STUDY ON COMPOSITE HONEYCOMB SANDWICH STRUCTURE FORMED T-JOINTS UNDER TENSILE LOAD

The tensile behavior of T-joints consisting of integral composite honeycomb sandwich structure is studied by experiment. The strength and failure modes of such elements are both obtained. An FEM model of the joint is then established. The classified damage criterion, failure criterion, and stiffness degradation rules are applied in order to simulate the damage and the tensile properties of the joint. The result of the FEM model shows good correlation with those from experiments. Results have shown that the weak point of the structure is on the end of web panel near to the skin panel. Out-of-plane fracture of the honeycomb in this area leads to the final failure of the structure. Tensile load on the web panel is transmitted to the skin panel mainly through the transition area, while the lapping zone between the web panel and the skin panel contributes less to the transmission. Parameter studies show that the length of the lapping zone has marginal effects on the strength of the structure, while thickening the skin`s honeycomb or employing honeycombs with a lower modulus can increase the strength.
Experimental dispersal reveals characteristic scales of biodiversity in a natural landscape

Significance Biological communities differ dramatically in numbers and identities of species, a pattern that could be explained by many mechanisms that each vary with spatial scale. Testing how ecological mechanisms transition among scales is key to understanding the maintenance of diversity but is infeasible in most systems. In a natural plant community, we experimentally enhanced seed dispersal over scales ranging from 1 m to 10 km using a seed vacuum. Our results indicate that pervasive dispersal limitation constrains local communities at and above 100 m, causing communities to contain half as many species as the environment is capable of supporting. Our results suggest that many species at risk for extirpation in this global biodiversity hotspot could be restored through managed dispersal. Ecological theory posits that dispersal among habitat patches links local communities and is a key “regional” process that maintains biological diversity. However, manipulations required to experimentally test regional processes are infeasible for most systems, and thus more work is needed to detect the scales at which regional processes manifest and their overall effect on diversity. In a Californian grassland, a hotspot for global biodiversity, we used a seed vacuum to increase dispersal at spatial scales varying from 1 m to 10 km while maintaining a realistic spatial structure of species pools and environmental conditions. We found that dispersal limitation has a profound influence on diversity; species richness increased with the spatial scale of seed mixing, doubling in plots that received seed from large (≥5 km) compared with small (≤5 m) scales. This increase in diversity corresponded to an increase in how well species distributions were explained by environmental conditions, from modest at small scales (R2 = 0.34) to strong at large scales (R2 = 0.52). Responses to the spatial scale of seed mixing were nonlinear, with no differences below 5 m or above 5 km. Nonlinearities were explained by homogeneity of environmental conditions below 5 m and by a lack of additional variation in the species pool above 5 km. Our approach of manipulating natural communities at different spatial scales reveals (i) nonlinear transitions in the importance of environmental sorting and dispersal, and (ii) the negative effects of dispersal limitation on local diversity, consistent with previous research suggesting that large numbers of species are headed toward regional extinction.