Miracle-dz/UniFAR-FTUs huggingface dataset:
Longitudinal structural and molecular neuroimaging in agrammatic primary progressive aphasia

The agrammatic variant of primary progressive aphasia affects normal grammatical language production, often occurs with apraxia of speech, and is associated with left frontal abnormalities on cross-sectional neuroimaging studies. We aimed to perform a detailed assessment of longitudinal change on structural and molecular neuroimaging to provide a complete picture of neurodegeneration in these patients, and to determine how patterns of progression compare to patients with isolated apraxia of speech (primary progressive apraxia of speech). We assessed longitudinal structural MRI, diffusion tensor imaging and 18F-fluorodeoxyglucose PET in 11 agrammatic aphasia subjects, 20 primary progressive apraxia of speech subjects, and 62 age and gender-matched controls with two serial assessments. Rates of change in grey matter volume and hypometabolism, and white matter fractional anisotropy, mean diffusivity, radial diffusivity and axial diffusivity were assessed at the voxel-level and for numerous regions of interest. The greatest rates of grey matter atrophy in agrammatic aphasia were observed in inferior, middle, and superior frontal gyri, premotor and motor cortices, as well as medial temporal lobe, insula, basal ganglia, and brainstem compared to controls. Longitudinal decline in metabolism was observed in the same regions, with additional findings in medial and lateral parietal lobe. Diffusion tensor imaging changes were prominent bilaterally in inferior and middle frontal white matter and superior longitudinal fasciculus, as well as right inferior fronto-occipital fasciculus, superior frontal and precentral white matter. More focal patterns of degeneration of motor and premotor cortex were observed in primary progressive apraxia of speech. Agrammatic aphasia showed greater rates of grey matter atrophy, decline in metabolism, and white matter degeneration compared to primary progressive apraxia of speech in the left frontal lobe, predominantly inferior and middle frontal grey and white matter. Correlations were also assessed between rates of change on neuroimaging and rates of clinical decline. Progression of aphasia correlated with rates of degeneration in frontal and temporal regions within the language network, while progression of parkinsonism and limb apraxia correlated with degeneration of motor cortex and brainstem. These findings demonstrate that disease progression in agrammatic aphasia is associated with widespread neurodegeneration throughout regions of the language network, as well as connecting white matter tracts, but also with progression to regions outside of the language network that are responsible for the development of motor symptoms. The fact that patterns of progression differed from primary progressive apraxia of speech supports the clinical distinction of these syndromes.
Universal Fractional-Order Design of Linear Phase Lead Compensation Multirate Repetitive Control for PWM Inverters

Repetitive control (RC) with linear phase lead compensation provides a simple but very effective control solution for any periodic signal with a known period. Multirate repetitive control (MRC) with a downsampling rate can reduce the need of memory size and computational cost, and then leads to a more feasible design of the plug-in RC systems in practical applications. However, with fixed sampling rate, both MRC and its linear phase lead compensator are sensitive to the ratio of the sampling frequency to the frequency of interested periodic signals: 1) MRC might fails to exactly compensate the periodic signal in the case of a fractional ratio; 2) linear phase lead compensation might fail to enable MRC to achieve satisfactory performance in the case of a low ratio. In this paper, a universal fractional-order design of linear phase lead compensation MRC is proposed to tackle periodic signals with high accuracy, fast dynamic response, good robustness, and cost-effective implementation regardless of the frequency ratio, which offers a unified framework for housing various RC schemes in extensive engineering application. An application example of programmable ac power supply is explored to comprehensively testify the effectiveness of the proposed control scheme.
On Clustering Induced Voronoi Diagrams

In this paper, we study a generalization of the classical Voronoi diagram, called clustering induced Voronoi diagram (CIVD). Different from the traditional model, CIVD takes as its sites the power set U of an input set P of objects. For each subset C of P, CIVD uses an influence function F(C, q) to measure the total (or joint) influence of all objects in C on an arbitrary point q in the space ℝd, and determines the influence-based Voronoi cell in ℝd for C. This generalized model offers a number of new features (e.g., simultaneous clustering and space partition) to Voronoi diagram which are useful in various new applications. We investigate the general conditions for the influence function which ensure the existence of a small-size (e.g., nearly linear) approximate CIVD for a set P of n points in ℝd for some fixed d. To construct CIVD, we first present a standalone new technique, called approximate influence (AI) decomposition, for the general CIVD problem. With only O(n log n) time, the AI decomposition partitions the space ℝd into a nearly linear number of cells so that all points in each cell receive their approximate maximum influence from the same (possibly unknown) site (i.e., a subset of P). Based on this technique, we develop assignment algorithms to determine a proper site for each cell in the decomposition and form various (1-ε)-approximate CIVDs for some small fixed € > 0. Particularly, we consider two representative CIVD problems, vector CIVD and density-based CIVD, and show that both of them admit fast assignment algorithms; consequently, their (1 - €)-approximate CIVDs can be built in O(n logd+1 n) and O(n log2 n) time, respectively.
Low‐cost Kinect Version 2 imaging system for breath hold monitoring and gating: Proof of concept study for breast cancer VMAT radiotherapy

Abstract Voluntary inspiration breath hold (VIBH) for left breast cancer patients has been shown to be a safe and effective method of reducing radiation dose to the heart. Currently, VIBH protocol compliance is monitored visually. In this work, we establish whether it is possible to gate the delivery of radiation from an Elekta linac using the Microsoft Kinect version 2 (Kinect v2) depth sensor to measure a patient breathing signal. This would allow contactless monitoring during VMAT treatment, as an alternative to equipment–assisted methods such as active breathing control (ABC). Breathing traces were acquired from six left breast radiotherapy patients during VIBH. We developed a gating interface to an Elekta linac, using the depth signal from a Kinect v2 to control radiation delivery to a programmable motion platform following patient breathing patterns. Radiation dose to a moving phantom with gating was verified using point dose measurements and a Delta4 verification phantom. 60 breathing traces were obtained with an acquisition success rate of 100%. Point dose measurements for gated deliveries to a moving phantom agreed to within 0.5% of ungated delivery to a static phantom using both a conventional and VMAT treatment plan. Dose measurements with the verification phantom showed that there was a median dose difference of better than 0.5% and a mean (3% 3 mm) gamma index of 92.6% for gated deliveries when using static phantom data as a reference. It is possible to use a Kinect v2 device to monitor voluntary breath hold protocol compliance in a cohort of left breast radiotherapy patients. Furthermore, it is possible to use the signal from a Kinect v2 to gate an Elekta linac to deliver radiation only during the peak inhale VIBH phase.
Region-based Memory Management in Prolog Master's Thesis March 2000

This thesis investigates whether region-based memory management can successfully be applied to Prolog programs. The answer is affirmative. It is shown how region-based memory management can be extended to work with backtracking and logical variables. Experiments with a prototype region-based Prolog implementation show that the time efficiency of the extended region-based model compares favorably with garbage collection and is not prohibitively worse than a purely stack-based Prolog implementation. The thesis also describes a method for translating a subset of Prolog into C programs that use the extended region-based memory manager. The translation involves several typed and untyped intermediate languages with rigorously defined semantics. Informal arguments for the correctness of most of the individual transformation phases are provided; they are meant to be expandable into fully rigorous proofs.
Development of a Humanized HLA-A2.1/DP4 Transgenic Mouse Model and the Use of This Model to Map HLA-DP4-Restricted Epitopes of HBV Envelope Protein

A new homozygous humanized transgenic mouse strain, HLA-A2.1+/+HLA-DP4+/+ hCD4+/+mCD4−/−IAβ−/−β2m−/− (HLA-A2/DP4), was obtained by crossing the previously characterized HLA-A2+/+β2m−/− (A2) mouse and our previously created HLA-DP4+/+ hCD4+/+mCD4−/−IAβ−/− (DP4) mouse. We confirmed that the transgenes (HLA-A2, HLA-DP4, hCD4) inherited from the parental A2 and DP4 mice are functional in the HLA-A2/DP4 mice. After immunizing HLA-A2/DP4 mice with a hepatitis B DNA vaccine, hepatitis B virus-specific antibodies, HLA-A2-restricted and HLA-DP4-restricted responses were observed to be similar to those in naturally infected humans. Therefore, the present study demonstrated that HLA-A2/DP4 transgenic mice can faithfully mimic human cellular responses. Furthermore, we reported four new HLA-DP4-restricted epitopes derived from HBsAg that were identified in both vaccinated HLA-A2/DP4 mice and HLA-DP4-positive human individuals. The HLA-A2/DP4 mouse model is a promising preclinical animal model carrying alleles present to more than a quarter of the human population. This model should facilitate the identification of novel HLA-A2- and HLA-DP4-restricted epitopes and vaccine development as well as the characterization of HLA-DP4-restricted responses against infection in humans.
Complete mitochondrial genome of Australian spiny lobster, Panulirus cygnus (George, 1962) (Crustacea: Decapoda: Palinuridae) from coast of Australia

Abstract We characterized the total mitochondrial genome of Australian spiny lobster, Panulirus cygnus (George, 1962), which is found along the western coast of Australia. Total mitochondrial genome length of P. cygnus was 15 724 bp, in which 13 proteins, 2 ribosomal RNAs, 22 transfer RNAs, and a putative control region were encoded. Nine and four protein-coding genes are encoded on the H-strand and on the L-strand, respectively. According to the phylogenetic analysis, P. cygnus was most closely related to Panulirus japonicus among the compared six species belonging to Palinuridae. Although overall gene organization was the same, the putative control region (between SrRNA gene and tRNAIlel) is least similar to one another among mitochondrial genomes from the compared six species belonging to Palinuridae
The Effect of the Tsetse Fly on African Development

The TseTse fly is unique to Africa and transmits a parasite harmful to humans and lethal to livestock. This paper tests the hypothesis that the TseTse reduced the ability of Africans to generate an agricultural surplus historically. Ethnic groups inhabiting TseTse-suitable areas were less likely to use domesticated animals and the plow, less likely to be politically centralized, and had a lower population density. These correlations are not found in the tropics outside of Africa, where the fly does not exist. The evidence suggests current economic performance is affected by the TseTse through the channel of precolonial political centralization. (JEL I12, N57, O13, O17, Q12, Q16, Q18)
Comparative Study of Sentiment Classification for Automated Translated Latin Reviews Into Arabic

The majority of available sentiment analysis systems treat English text, which resulted in a significant number of resources to assist researchers in this field. Unfortunately, this is not the case for other languages and, in particular, for the Arabic language. Few serious research attempts are reported to build necessary resources such as datasets to serve Arabic sentiment analysis research efforts. In order to expedite building necessary huge datasets in Arabic or any other dataset-poor language, automatic translation from a rich source-language can make a viable alternative to generate the required resources for a target language. This is mainly driven by the assumption that translation usually preserves the sentiment upto certain degree. In this work, we study the viability of this approach to automatically translate a huge dataset from English to Arabic for sentiment analysis purposes. Experimental results show that sentiment analysis of both original (English) dataset and the translated one (Arabic) produce comparable results. As a result, automatically translated English datasets shall add to the required resources for building robust Arabic sentiment analysis systems. Although automated translation may yield poor translations in terms of readability and comprehension by humans, sentiment analysis systems can still predict the majority of correct sentiments. Such sentiment is preserved by key words. We believe automated translation may be considered as a viable option to produce rich and well represented datasets in order to develop robust and efficient Arabic sentiment analyzers.
Revisiting Parole Decision Making: Testing for the Punitive Hypothesis in a Large U.S. Jurisdiction

The decision to grant conditional release from prison (aka the parole decision) has been largely neglected in the contemporary criminological literature, despite its critical implications. The current study, conducted in Pennsylvania, United States, tests for punitive themes in parole decision making by examining the impact of several measures reflective of punishment satisfaction on the decision to grant release to eligible parole candidates. The results indicate that the amount of time served in relation to the original punishment does not predict parole decisions but the nature of the original offense does. Moreover, inmates eligible for parole have to experience at least one parole denial to increase their chances of release, suggesting that parole decision makers use the parole process as a punitive means. The implications of the findings are discussed.
Sparsity-Based cholesky factorization and its application to hyperspectral anomaly detection

Estimating large covariance matrices has been a longstanding important problem in many applications and has attracted increased attention over several decades. This paper deals with two methods based on pre-existing works to impose sparsity on the covariance matrix via its unit lower triangular matrix (aka Cholesky factor) T. The first method serves to estimate the entries of T using the Ordinary Least Squares (OLS), then imposes sparsity by exploiting some generalized thresholding techniques such as Soft and Smoothly Clipped Absolute Deviation (SCAD). The second method directly estimates a sparse version of T by penalizing the negative normal log-likelihood with L1 and SCAD penalty functions. The resulting covariance estimators are always guaranteed to be positive definite. Some Monte-Carlo simulations as well as experimental data demonstrate the effectiveness of our estimators for hyperspectral anomaly detection using the Kelly anomaly detector.
Hydrodynamic fluctuations and instabilities in ordered suspensions of self-propelled particles.

We construct the hydrodynamic equations for suspensions of self-propelled particles (SPPs) with spontaneous orientational order, and make a number of striking, testable predictions: (i) Nematic SPP suspensions are always absolutely unstable at long wavelengths. (ii) SPP suspensions support novel propagating modes at long wavelengths, coupling orientation, flow, and concentration. (iii) In a wave number regime accessible only in low Reynolds number systems such as bacteria, polar-ordered suspensions are invariably convectively unstable. (iv) The variance in the number N of particles, divided by the mean , diverges as (2/3 ) in polar-ordered SPP suspensions.
PhaseU: Real-time LOS identification with WiFi

WiFi technology has fostered numerous mobile computing applications, such as adaptive communication, finegrained localization, gesture recognition, etc., which often achieve better performance or rely on the availability of Line-Of-Sight (LOS) signal propagation. Thus the awareness of LOS and Non-Line-Of-Sight (NLOS) plays as a key enabler for them. Realtime LOS identification on commodity WiFi devices, however, is challenging due to limited bandwidth of WiFi and resulting coarse multipath resolution. In this work, we explore and exploit the phase feature of PHY layer information, harnessing both space diversity with antenna elements and frequency diversity with OFDM subcarriers. On this basis, we propose PhaseU, a real-time LOS identification scheme that works in both static and mobile scenarios on commodity WiFi infrastructure. Experimental results in various indoor scenarios demonstrate that PhaseU consistently outperforms previous approaches, achieving overall LOS and NLOS detection rates of 94.35% and 94.19% in static cases and both higher than 80% in mobile contexts. Furthermore, PhaseU achieves real-time capability with millisecond-level delay for a connected AP and 1-second delay for unconnected APs, which is far beyond existing approaches.
Changes of Serum Glycoproteins in Lung Cancer Patients

Lung cancer (LC) is one of the leading causes of cancer deaths worldwide and approximately 3 million individuals die from this disease each year. Therefore, detecting LC at its early stages is very important to achieve decreased LC mortality. While gene expression profiling has been successfully used to classify various tumors and assess tumor stages, the gene-based prediction for LC is not yet entirely dependable. In serum, glycosylation is one of the most common post-translational modifications, and glycoproteins play a core role in a diversity of biological processes and pathogenesis. The development of an analytical approach for the study of variations of human serum glycoproteins has been limited by the structural heterogeneity of the post-translational modifications and the complexity of glycomics. Thus, in this report we present a strategy of using Concavanalin A (Con A) as an affinity agent combined with twodimensional electrophoresis (2-DE) and nanoLC ESI-MS/MS to enrich and characterize the N-linked glycoproteins that are the most common glycosylation motifs in serum. By comparison of serum samples between LC patients and the healthy, we found that 8 glycoproteins were significantly up regulated in LC serum and 3 glycoproteins were down regulated. The useful information related to LC was discovered while we investigated changes of glycosylation in LC serum. The results suggested that the combination of proteomic techniques could be used for mining protein biomarkers for LC.
Clinical Evaluation of a Polyherbal Nutritional Supplement in Dyslipidemic Volunteers

ABSTRACT Ten important plant parts routinely used in South Indian ethnic food preparation as spices and condiments were investigated for their potential antidyslipidemic properties. The aim of the study was to characterize the biochemical properties of the polyherbal formulation (nutritional supplement) and evaluate its use to control dyslipidemia in patients. Phytochemical evaluation, in vitro α-amylase inhibitory assay, and high performance thin layer chromatography (HPTLC) fingerprinting were carried out with alcoholic extracts of all 10 individual plants and with the nutritional supplement. Investigation in human volunteers was conducted to evaluate the effect on dyslipidemia as measured by serum lipid biomarkers. Sixty-five volunteers were recruited for this study. Biomarker values at baseline and at 6th visit (end of review, 8/9 months) were compared to assess the usefulness of the nutritional supplement in the normalization of lipid biomarkers. In the qualitative analysis of metabolites, the results revealed the presence of various bioactive primary and secondary metabolites that might be responsible for their medicinal attributes. In human volunteers, after supplement intake along with standard therapy, we observed significant decrease in serum cholesterol, triglyceride, low-density lipoprotein (LDL), and very low-density lipoprotein (VLDL) levels. High-density lipoprotein (HDL) level did not change in test patient volunteers. Reductions in hemoglobin A1C (HBA1C) and postprandial blood sugar levels were observed; the difference was not statistically significant. We believe that the polyherbal formulation of 10 medicinal plants has potent antidyslipidemic activity. Our results contribute for the first time toward documentation of augmented dyslipidemia control by use of the formulation.
Performance Analysis of Three Text-Join Algorithms

When a multidatabase system contains textual database systems (i.e., information retrieval systems), queries against the global schema of the multidatabase system may contain a new type of joins-joins between attributes of textual type. Three algorithms for processing such a type of joins are presented and their I/O costs are analyzed in this paper. Since such a type of joins often involves document collections of very large size, it is very important to find efficient algorithms to process them. The three algorithms differ on whether the documents themselves or the inverted files on the documents are used to process the join. Our analysis and the simulation results indicate that the relative performance of these algorithms depends on the input document collections, system characteristics, and the input query. For each algorithm, the type of input document collections with which the algorithm is likely to perform well is identified. An integrated algorithm that automatically selects the best algorithm to use is also proposed.
The Hexameric Structures of Human Heat Shock Protein 90

Background The human 90-kDa heat shock protein (HSP90) functions as a dimeric molecular chaperone. HSP90 identified on the cell surface has been found to play a crucial role in cancer invasion and metastasis, and has become a validated anti-cancer target for drug development. It has been shown to self-assemble into oligomers upon heat shock or divalent cations treatment, but the functional role of the oligomeric states in the chaperone cycle is not fully understood. Principal Findings Here we report the crystal structure of a truncated HSP90 that contains the middle segment and the carboxy-terminal domain, termed MC-HSP90. The structure reveals an architecture with triangular bipyramid geometry, in which the building block of the hexameric assembly is a dimer. In solution, MC-HSP90 exists in three major oligomer states, namely dimer, tetramer and hexamer, which were elucidated by size exclusion chromatography and analytical ultracentrifugation. The newly discovered HSP90 isoform HSP90N that lacks the N-terminal ATPase domain also exhibited similar oligomerization states as did MC-HSP90. Conclusions While lacking the ATPase domain, both MC-HSP90 and HSP90N can self-assemble into a hexameric structure, spontaneously. The crystal structure of MC-HSP90 reveals that, in addition to the C-terminal dimerization domain, the residue W320 in the M domain plays a critical role in its oligomerization. This study not only demonstrates how the human MC-HSP90 forms a hexamer, but also justifies the similar formation of HSP90N by using 3D modeling analysis.