Miracle-dz/UniFAR-FTUs huggingface dataset:
MIGRAINE: MRI Graph Reliability Analysis and Inference for Connectomics

Currently, connectomes (e.g., functional or structural brain graphs) can be estimated in humans at ≈ 1 mm3 scale using a combination of diffusion weighted magnetic resonance imaging, functional magnetic resonance imaging and structural magnetic resonance imaging scans. This manuscript summarizes a novel, scalable implementation of open-source algorithms to rapidly estimate magnetic resonance connectomes, using both anatomical regions of interest (ROIs) and voxel-size vertices. To assess the reliability of our pipeline, we develop a novel non-parametric non-Euclidean reliability metric. Here we provide an overview of the methods used, demonstrate our implementation, and discuss available user extensions. We conclude with results showing the efficacy and reliability of the pipeline over previous state-of-the-art.
Adaptive Fuzzy Sliding Mode Control of Underwater Robotic Vehicles

Abstract: Sliding mode control is a very attractive control scheme because of its robustness against modelling imperfections and external disturbances. It has been successfully employed to the dynamic positioning of remotely operated underwater vehicles. In such situations, the discontinuities in the control law must be smoothed out to avoid the undesirable chattering effects. The adoption of properly designed boundary layers have proven effective in completely eliminating chattering, however, leading to an inferior tracking performance. This work describes the development of a dynamic positioning system for underwater robotic vehicles. The adopted approach is based on the sliding mode control strategy and enhanced by an adaptive fuzzy algorithm for uncertainty/disturbance compensation. Numerical results are presented in order to demonstrate the control system’s performance.
The aroQ-encoded monofunctional chorismate mutase (CM-F) protein is a periplasmic enzyme in Erwinia herbicola

Enteric bacteria possess two species of chorismate mutase which exist as catalytic domains on the amino termini of the bifunctional PheA and TyrA proteins. In addition, some of these organisms possess a third chorismate mutase, CM-F, which exists as a small monofunctional protein. The CM-F gene (denoted aroQ) from Erwinia herbicola was cloned and sequenced for the first time. A strategy for selection by functional complementation in a chorismate mutase-free Escherichia coli background was devised by using a recombinant plasmid derivative of pUC18 carrying a Zymomonas mobilis tyrC insert which encodes cyclohexadienyl dehydrogenase. The aroQ gene is 543 bp in length, predicting a 181-residue protein product having a calculated molecular mass of 20,299 Da. The E. herbicola aroQ promoter is recognized by E. coli, and a putative sigma-70 promoter region was identified. N-terminal amino acid sequencing of the purified CM-F protein indicated cleavage of a 20-residue signal peptide. This was consistent with the monomeric molecular mass determined for the enzyme of about 18,000 Da. The native enzyme is a homodimer. The implied translocation of CM-F was confirmed by osmotic shock experiments which demonstrated a periplasmic location. Immunogold electron microscopy indicated a polar localization within the periplasm. Polyclonal antibody raised against E. herbicola CM-F did not cross-react with the CM-F protein from the closely related Serratia rubidaea, as well as from a number of other gram-negative bacteria. Furthermore, when the E. herbicola aroQ gene was used as a probe in Southern blot hybridizations with EcroRI digests of chromosomal DNA from S. rubidaea and other enteric organisms, no hybridization was detected at low stringency. Thus, the aroQ gene appears to be unusually divergent among closely related organisms. The deduced CM-F amino acid sequence did not exhibit compelling evidence for homology with the monofunctional chorismate mutase protein of Bacillus subtilis.
Macroeconomic implications of relative price distortions: Seigniorage, output and welfare ∗

We compare macroeconomic models of sticky-prices (Calvo and Costsof-adjustment) with flexible price models in terms of optimal seigniorage. This sheds light on the importance of relative price distortions. Sticky-price models with no price dispersion terms have unattractive implications, we argue, when it comes to the derivation of optimal policies. We provide examples where they may imply very high inflation as part of the optimal plan, or that inflation does not matter for the ranking of alternatove policies.
A recognition safety net: bi-level threshold recognition for mobile motion gestures

Designers of motion gestures for mobile devices face the difficult challenge of building a recognizer that can separate gestural input from motion noise. A threshold value is often used to classify motion and effectively balances the rates of false positives and false negatives. We present a bi-level threshold recognition technique designed to lower the rate of recognition failures by accepting either a tightly thresholded gesture or two consecutive possible gestures recognized by a relaxed model. Evaluation of the technique demonstrates that the technique can aid in recognition for users who have trouble performing motion gestures. Lastly, we suggest the use of bi-level thresholding to scaffold the learning of gestures.
Approximating the Evolution History of Software from Source Code

SUMMARY Once a software product has been released, a large number of software products may be derived from an original single product. Management and maintenance of product variants are important, but those are hardly cared because developers do not make efforts for the further maintainability in the initial phase of software development. However, history of products would be lost in typical cases and developers have only source code of products in the worst case. In this paper, we approximate the evolution history of software products using source code of them. Our key idea is that two successive products are the most similar pair of products in evolution history, and have many similar source files. We did an experiment to compare the analysis result with actual evolution history. The result shows 78% (on average) of edges in the extracted trees are consistent with the actual evolution history of the products.
A Narrative Perspective on the Effect of Depo-Provera on Libido

Few studies have explored women's subjective experiences with Depo-Provera, in particular its impact on their sexual selves and everyday lives. Thirty-four (34) women were interviewed about their experiences using Depo-Provera and other methods of contraception, with interviews analyzed using a thematic narrative analysis approach. A key theme emerging in interviews was decrease in libido (sexual desire) in taking Depo-Provera, which was linked with emotions, body image, and had social ramifications. Four participants' stories serve as exemplars for exploring subjective complexity. "Lived" accounts of user experiences are essential for overcoming a reductive focus on contraceptive side effects, which elides connections and obscures user understanding. A narrative perspective provides an empirical basis for developing family planning programs and sexual health policies that acknowledge more experientially grounded conceptualiza- tions of women's sexual and reproductive health and wellbeing.
Clinical Performance and Management Outcomes with the DecisionDx-UM Gene Expression Profile Test in a Prospective Multicenter Study

Uveal melanoma management is challenging due to its metastatic propensity. DecisionDx-UM is a prospectively validated molecular test that interrogates primary tumor biology to provide objective information about metastatic potential that can be used in determining appropriate patient care. To evaluate the continued clinical validity and utility of DecisionDx-UM, beginning March 2010, 70 patients were enrolled in a prospective, multicenter, IRB-approved study to document patient management differences and clinical outcomes associated with low-risk Class 1 and high-risk Class 2 results indicated by DecisionDx-UM testing. Thirty-seven patients in the prospective study were Class 1 and 33 were Class 2. Class 1 patients had 100% 3-year metastasis-free survival compared to 63% for Class 2 (log rank test p = 0.003) with 27.3 median follow-up months in this interim analysis. Class 2 patients received significantly higher-intensity monitoring and more oncology/clinical trial referrals compared to Class 1 patients (Fisher's exact test p = 2.1 × 10−13 and p = 0.04, resp.). The results of this study provide additional, prospective evidence in an independent cohort of patients that Class 1 and Class 2 patients are managed according to the differential metastatic risk indicated by DecisionDx-UM. The trial is registered with Clinical Application of DecisionDx-UM Gene Expression Assay Results (NCT02376920).
An online hierarchical supervoxel segmentation algorithm based on Uniform Entropy Slice

Supervoxel plays a significant role in video segmentation task in which moving objects in the video are detected and their external boundaries are obtained. This is due to the observation that hierarchies of supervoxel can process the video into a multiscale decomposition with more information for later analysis than other approaches using the concept of supervoxels to video segmentation. Most available supervoxel video segmentation methods require the whole voxels in the video to be loaded into memory first before processing can occur which is impossible even for medium sized videos containing 100 frames, of reasonable complex background and foreground of moving objects. The results of deploying these more traditional approaches show that they tend to under-segment at lower levels and over-segment at high levels, so it is a challenge to use the results to analyze the video, e.g., in detection of objects. In this paper, we present an algorithm to overcome these limitations. Our method, called StreamUES, is based on the Uniform Entropy Slice (UES). It not only can seek a selection of supervoxels by using the post hoc feature criterion such as optical flow, but also can work on streaming modem use a clip of frames at one time until the end of the video clip is reached. Our results indicate the StreamUES can work very well with a challenging dataset viz., VSB 100, which we used to evaluate the proposed StreamUES technique.
Perturbations of the Ink4a/Arf gene locus in aflatoxin B1-induced mouse lung tumors.

Lung tumors from AC3F1 mice treated with aflatoxin B(1) (AFB(1)), were examined for loss of alleles, point mutations and hypermethylation of CpG sites within the promoters of the two genes in the Ink4a/Arf gene locus. Loss of microsatellite alleles in the Ink4a/Arf region occurred in 22 of 74 (30%) AFB(1)-induced lung tumors. Fifty-one of 61 (83%) tumors had at least partial methylation of CpG sites within the p16Ink4a promoter-exon 1alpha region. At least partial methylation of CpG sites was observed in 43 of 49 (88%) tumors analyzed for p19Arf promoter hypermethylation, with methylation of identified transcription factor binding sites or consensus sequences occurring in 21 tumors (DMP1/Ets in two tumors, CTCF in four tumors, E2F in three tumors, Sp1 in 16 tumors). Two tumors contained point mutations in the p19Arf promoter. Nuclear staining for p19(Arf) was decreased by 80-100% in 41 of 71 (58%) tumors. The concordance between p19Arf molecular perturbations and altered protein expression was 63%. However, upon comparing p19Arf promoter perturbations (i.e. methylation of functional transcription factor binding sites and point mutations) and altered p19(Arf) expression, the concordance was 86%, suggesting a mechanism for changes in protein expression in some tumors. There was an absence of a mutually exclusive relationship between disruption of p53 and p19(Arf), since the concordance was 62%. Similarly, no evidence was found of inverse relationships between perturbation of p16Ink4a and p19(Arf) (43% concordance) or p16Ink4(a) and p53 (37% concordance), suggesting that inactivation of these genes occurs independently and provides evidence that, although these genes may participate in cooperative cellular pathways, they also have functions in independent pathways that are important in mouse lung tumorigenesis.
Fossilization of melanosomes via sulfurization

Fossil melanin granules (melanosomes) are an important resource for inferring the evolutionary history of colour and its functions in animals. The taphonomy of melanin and melanosomes, however, is incompletely understood. In particular, the chemical processes responsible for melanosome preservation have not been investigated. As a result, the origins of sulfur‐bearing compounds in fossil melanosomes are difficult to resolve. This has implications for interpretations of original colour in fossils based on potential sulfur‐rich phaeomelanosomes. Here we use pyrolysis gas chromatography mass spectrometry (Py‐GCMS), fourier transform infrared spectroscopy (FTIR) and time of flight secondary ion mass spectrometry (ToF‐SIMS) to assess the mode of preservation of fossil microstructures, confirmed as melanosomes based on the presence of melanin, preserved in frogs from the Late Miocene Libros biota (NE Spain). Our results reveal a high abundance of organosulfur compounds and non‐sulfurized fatty acid methyl esters in both the fossil tissues and host sediment; chemical signatures in the fossil tissues are inconsistent with preservation of phaeomelanin. Our results reflect preservation via the diagenetic incorporation of sulfur, i.e. sulfurization (natural vulcanization), and other polymerization processes. Organosulfur compounds and/or elevated concentrations of sulfur have been reported from melanosomes preserved in various invertebrate and vertebrate fossils and depositional settings, suggesting that preservation through sulfurization is likely to be widespread. Future studies of sulfur‐rich fossil melanosomes require that the geochemistry of the host sediment is tested for evidence of sulfurization in order to constrain interpretations of potential phaeomelanosomes and thus of original integumentary colour in fossils.
Fault-Tolerant Associative Memories Based on $c$-Partite Graphs

Associative memories allow the retrieval of previously stored messages given a part of their content. In this paper, we are interested in associative memories based on c-partite graphs that were recently introduced. These memories are almost optimal in terms of the amount of storage they require (efficiency) and allow retrieving messages with low complexity. We propose a generic implementation model for the retrieval algorithm that can be readily mapped to an integrated circuit and study the retrieval performance when hardware components are affected by faults. We show using analytical and simulation results that these associative memories can be made resilient to circuit faults with a minor modification of the retrieval algorithm. In one example, the memory retains 88% of its efficiency when 1% of the storage cells are faulty, or 98% when 0.1% of the binary outputs of the retrieval algorithm are faulty. When considering storage faults, the fault tolerance exhibited by the proposed associative memory can be comparable to using a capacity-achieving error correction code for protecting the stored information.
Liver Preservation With Machine Perfusion and a Newly Developed Cell‐Free Oxygen Carrier Solution Under Subnormothermic Conditions

We describe a new preservation modality combining machine perfusion (MP) at subnormothermic conditions (21°C) with a new hemoglobin‐based oxygen carrier (HBOC) solution. MP (n = 6) was compared to cold static preservation (CSP; n = 6) in porcine orthotopic liver transplants after 9 h of cold ischemia and 5‐day follow‐up. Recipients' peripheral blood, serial liver biopsies, preservation solutions and bile specimens were collected before, during and after liver preservation. Clinical laboratorial and histological analyses were performed in addition to mitochondrial functional assays, transcriptomic, metabolomic and inflammatory mediator analyses. Compared with CSP, MP animals had: (1) significantly higher survival (100% vs. 33%; p < 0.05); (2) superior graft function (p < 0.05); (3) eight times higher hepatic O2 delivery than O2 consumption (0.78 mL O2/g/h vs. 0.096 mL O2/g/h) during MP; and (4) significantly greater bile production (MP = 378.5 ± 179.7; CS = 151.6 ± 116.85). MP down‐regulated interferon (IFN)‐α and IFN‐γ in liver tissue. MP allografts cleared lactate, produced urea, sustained gluconeogenesis and produced hydrophilic bile after reperfusion. Enhanced oxygenation under subnormothermic conditions triggers regenerative and cell protective responses resulting in improved allograft function. MP at 21°C with the HBOC solution significantly improves liver preservation compared to CSP.
Age-Related Differences in Plasma Proteins: How Plasma Proteins Change from Neonates to Adults

The incidence of major diseases such as cardiovascular disease, thrombosis and cancer increases with age and is the major cause of mortality world-wide, with neonates and children somehow protected from such diseases of ageing. We hypothesized that there are major developmental differences in plasma proteins and that these contribute to age-related changes in the incidence of major diseases. We evaluated the human plasma proteome in healthy neonates, children and adults using the 2D-DIGE approach. We demonstrate significant changes in number and abundance of up to 100 protein spots that have marked differences in during the transition of the plasma proteome from neonate and child through to adult. These proteins are known to be involved in numerous physiological processes such as iron transport and homeostasis, immune response, haemostasis and apoptosis, amongst others. Importantly, we determined that the proteins that are differentially expressed with age are not the same proteins that are differentially expressed with gender and that the degree of phosphorylation of plasma proteins also changes with age. Given the multi-functionality of these proteins in human physiology, understanding the differences in the plasma proteome in neonates and children compared to adults will make a major contribution to our understanding of developmental biology in humans.
Practical Issues in Imaging Hydraulic Conductivity through Hydraulic Tomography

Hydraulic tomography has been developed as an alternative to traditional geostatistical methods to delineate heterogeneity patterns in parameters such as hydraulic conductivity (K) and specific storage (Ss). During hydraulic tomography surveys, a large number of hydraulic head data are collected from a series of cross‐hole tests in the subsurface. These head data are then used to interpret the spatial distribution of K and Ss using inverse modeling. Here, we use the Sequential Successive Linear Estimator (SSLE) of Yeh and Liu (2000) to interpret synthetic pumping test data created through numerical simulations and real data generated in a laboratory sandbox aquifer to obtain the K tomograms. Here, we define “K tomogram” as an image of K distribution of the subsurface (or the inverse results) obtained via hydraulic tomography. We examine the influence of signal‐to‐noise ratio and biases on results using inverse modeling of synthetic and real cross‐hole pumping test data. To accomplish this, we first show that the pumping rate, which affects the signal‐to‐noise ratio, and the order of data included into the SSLE algorithm both have large impacts on the quality of the K tomograms. We then examine the role of conditioning on the K tomogram and find that conditioning can improve the quality of the K tomogram, but can also impair it, if the data are of poor quality and conditioning data have a larger support volume than the numerical grid used to conduct the inversion. Overall, these results show that the quality of the K tomogram depends on the design of pumping tests, their conduct, the order in which they are included in the inverse code, and the quality as well as the support volume of additional data that are used in its computation.
Fundamental bounds on RSS-based wireless localization in passive UHF RFID systems

Radio-Frequency IDentification (RFID) systems carry critical importance for reaping the benefits of a diverse set of applications that will be enabled by the emerging Internet of Things (IoT). In particular, RFID based position estimation and tracking will facilitate a wide array of location based services. Considering a monostatic RFID configuration with a three dimensional antenna radiation pattern, this paper investigates the limits of localization accuracy for received signal strength (RSS) based wireless localization using passive UHF RFID systems. The Cramer-Rao Lower Bound (CRLB) for the localization accuracy are derived, and are compared with the localization accuracy of maximum likelihood estimators for various RFID antenna topologies. Numerical results show that due to the directional antenna pattern used in RFID systems, the localization accuracy can degrade at blind locations that remain outside of the RFID readers' main beam patterns.Cramer-Rao Lower Bound (CRLB) for the localization accuracy are derived, and are compared with the localization accuracy of maximum likelihood estimators for various RFID antenna topologies. Numerical results show that due to the directional antenna
Morphological Features for Parsing Morphologically-rich Languages: A Case of Arabic

We investigate how morphological features in the form of part-of-speech tags impact parsing performance, using Arabic as our test case. The large, fine-grained tagset of the Penn Arabic Treebank (498 tags) is difficult to handle by parsers, ultimately due to data sparsity. However, ad-hoc conflations of treebank tags runs the risk of discarding potentially useful parsing information. The main contribution of this paper is to describe several automated, language-independent methods that search for the optimal feature combination to help parsing. We first identify 15 individual features from the Penn Arabic Treebank tagset. Either including or excluding these features results in 32,768 combinations, so we then apply heuristic techniques to identify the combination achieving the highest parsing performance. Our results show a statistically significant improvement of 2.86% for vocalized text and 1.88% for unvocalized text, compared with the baseline provided by the Bikel-Bies Arabic POS mapping (and an improvement of 2.14% using product models for vocalized text, 1.65% for unvocalized text), giving state-of-the-art results for Arabic constituency parsing.
Superposition codes for mismatched decoding

An achievable rate is given for discrete memoryless channels with a given (possibly suboptimal) decoding rule. The result is obtained using a refinement of the superposition coding ensemble. The rate is tight with respect to the ensemble average, and can be weakened to the LM rate of Hui and Csiszár-Körner, and to Lapidoth's rate based on parallel codebooks.
MULTISCALE RECURRENT PATTERNS AND GENERALISED SIDE-MATCH APPLIED TO IMAGE COMPRESSION

The Side-Match Multidimensional Multiscale Parser (SMMMP) is a coding method based on the approximate multiscale pattern matching concept, where the dictionary is bui lt considering smoothness constraints around block boundari es. This assumption can favor the coding of smooth signals, resulting in superior-quality reconstructed representatio ns. In this work, a generalised framework for side-match is presented, in which the match attempt with neighboring blocks is performed in a hierarchical way and with a greater degree of restriction. An improved dictionary usage strategy is al so presented, which employs elements from the causal neighborhood of the input block. The simulations performed on gray-scale images show that the proposed method is effective, presenting superior performance when compared to its predecessor.