Miracle-dz/UniFAR-FTUs huggingface dataset:
Symbol-driven compression of Burrows Wheeler transformed text

Despite the enormous growth in storage capacity in recent years, the search for fast and efficient text compression algorithms continues. As processor speed is increasing at a higher rate than disk access time is decreasing, there is now even more reason to store information in a compressed form than there was previously. Prediction by Partial Matching (PPM), first published in 1984, was a significant step forward in the quest for efficient text compression. The Burrows Wheeler transform (BWT), introduced ten years later, has been the next significant breakthrough; its best implementations rank alongside those of PPM. In most BWT implementations, transformed text is converted to a string of ranks with a move-to-front (MTF) or similar mechanism before being compressed. Ranks are then encoded with an Ordermodel or a hierarchy of such models, with some substrings of repeated ranks encoded as run lengths. Although these rank based methods perform very well, the transformation to MTF numbers blurs the distinction between individual symbols and is a possible cause of ineffectiveness. Instead of relying on symbol ranking, we examine the problem of modelling the transformed text as a sequence of segments with iid symbols, using three different techniques. First, methods of segmentation that use only the transformed text, ignoring the sort contexts, are investigated. Segments may be of uniform length or they may be identified as having the same number of distinct symbols. Alternatively, segment boundaries may be inserted whenever a small number of symbols is predicted poorly by the symbols already assigned to the segment. In all of these approaches, encoding a segment involves encoding the number of distinct symbols in the segment and the subalphabet of symbols. The segment substring is described either by encoding the symbol frequencies and then applying enumerative probability estimation, or by encoding the segment length and applying adaptive probability estimation. In both cases arithmetic coding is employed to maximize compression effectiveness. The distributions of the segment parameters are determined adaptively from the text already compressed. In some of the programs, we weaken the notion of segmentation, by employing a number of sliding windows with different degrees of
Optimizing the Predictive Value of Diagnostic Decision Rules

An approach to finding an optimal solution for an important diagnostic problem is described. Examples are taken from laboratory medicine, where the problem can be stated as finding the best combination of tests for making a diagnosis. These tests are typically numerical with unknown decision thresholds. Because of uncertainty in classification, the solution is described in terms of maximizing measures of decision rule performance on a data base of cases, for example maximizing positive predictive value, subject to a constraint of a minimum sensitivity. The resultant rules are quite similar to classifi cation production rules, and the procedures described should be valid for many knowledge acquisition and refinement tasks. The solution is found by a heuristic search procedure, and empirical results for several data bases and published studies are described.
A Disaggregated Analysis of Wealth Status and Educational Attainment in Nigeria Using the Multinomial Logit Approach

For most studies that have been carried out, a country’s level of income and aggregate wealth go a long way in shaping the overall welfare of citizens therein. This study seeks to investigate the relationship between wealth status and educational attainment, as a manifestation of income inequality, especially when the wealth status is disaggregated. With data obtained from the National Demographic and Health Survey (DHS) 2013 and the adoption of the multinomial logit model, this study captured exogenous variables such as wealth index, the core variable; household sex preference, a dummy variable that takes the value of 1 if a household prefers a male child and 0 otherwise; and place, another control variable. This study finds that there is a very significant relationship between wealth status and educational attainment, especially for the individual categories of wealth index, hence, educational inequality hinders the quest to achieve higher educational levels for individuals from low wealth families. This study therefore recommends that the government should engender state-based subsidized education cost programs that will be targeted at poor households, as well as intensify efforts in solidifying the overall educational framework in the country, especially in the rural areas bereft of facilities.
Lemmatization of Multi-word Common Noun Phrases and Named Entities in Polish

In the paper we present a tool for lemmatization of multi-word common noun phrases and named entities for Polish called LemmaPL. The tool is based on a set of manually crafted rules and heuristics utilizing a set of dictionaries (including morphological, named entities and inflection patterns). The accuracy of lemmatization obtained by the tool reached 97.99% on a dataset with multi-word common noun phrases and 86.17% for case-sensitive evaluation on a dataset with named entities.
Technical specification and requirements of static VAr compensation (SVC) protection consist of TCR, TSC and combined TCR/TSC

One of the most important disturbances in power systems is variation of voltage. SVC is used as a tool for compensating disturbances. SVC protection requirements are very important in application. The equipment in a SVC must be protected from disadvantage due to all types of system jeopardizes. In this paper a perfect protection system is designed and relevant technical specifications for only a TCR,only TSC or combined TCR/TSC is presented.
Regulatory phosphorylation of the p34cdc2 protein kinase in vertebrates.

The p34cdc2 protein kinase is a conserved regulator of the eukaryotic cell cycle. Here we show that residues Thr14 and Tyr15 of mouse p34cdc2 become phosphorylated as mouse fibroblasts proceed through the cell cycle. We have mutated these residues and measured protein kinase activity of the p34cdc2 variants in a Xenopus egg extract. Phosphorylation of residues 14 and 15, which lie within the presumptive ATP‐binding region of p34cdc2, normally restrains the protein kinase until it is specifically dephosphorylated and activated at the G2/M transition. Regulation by dephosphorylation of Tyr15 is conserved from fission yeast to mammals, while an extra level of regulation of mammalian p34cdc2 involves Thr14 dephosphorylation. In the absence of phosphorylation on these two residues, the kinase still requires cyclin B protein for its activation. Inhibition of DNA synthesis inhibits activation of wild‐type p34cdc2 in the Xenopus system, but a mutant which cannot be phosphorylated at residues 14 and 15 escapes this inhibition, suggesting that these phosphorylation events form part of the pathway linking completion of DNA replication to initiation of mitosis.
Analysis of samples based on a polarization microscope technique

The aim of this paper is to study a transparent birefringent sample with a polarizer microscope, we measure orientation of optic axis of the sample and phase retardation. We make a polarizer microscope using a generated polarized beam. With a Mach-Zehnder setup we control polarized state of the beam. We use a Spatial Light Modulator to modulate X and Y components independently. The polarized beam illuminates the birefringent samples and passes through a circular polarizer. Intensity values captured with a CCD camera show us the sample information. We obtain the orientation of fast axis of birefringent sample.
Neural response during attentional control and emotion processing predicts improvement after cognitive behavioral therapy in generalized social anxiety disorder

Background Individuals with generalized social anxiety disorder (gSAD) exhibit attentional bias to salient stimuli, which is reduced in patients whose symptoms improve after treatment, indicating that mechanisms of bias mediate treatment success. Therefore, pre-treatment activity in regions implicated in attentional control over socio-emotional signals (e.g. anterior cingulate cortex, dorsolateral prefrontal cortex) may predict response to cognitive behavioral therapy (CBT), evidence-based psychotherapy for gSAD. Method During functional magnetic resonance imaging, 21 participants with gSAD viewed images comprising a trio of geometric shapes (circles, rectangles or triangles) alongside a trio of faces (angry, fearful or happy) within the same field of view. Attentional control was evaluated with the instruction to ‘match shapes’, directing attention away from faces, which was contrasted with ‘match faces’, whereby attention was directed to emotional faces. Results Whole-brain voxel-wise analyses showed that symptom improvement was predicted by enhanced pre-treatment activity in the presence of emotional face distractors in the dorsal anterior cingulate cortex and dorsal medial prefrontal cortex. Additionally, CBT success was foretold by less activity in the amygdala and/or increased activity in the medial orbitofrontal gyrus during emotion processing. Conclusions CBT response was predicted by pre-treatment activity in prefrontal regions and the amygdala. The direction of activity suggests that individuals with intact attentional control in the presence of emotional distractors, regulatory capacity over emotional faces and/or less reactivity to such faces are more likely to benefit from CBT. Findings indicate that baseline neural activity in the context of attentional control and emotion processing may serve as a step towards delineating mechanisms by which CBT exerts its effects.
Adaptación de un instrumento de evaluación de la insatisfacción corporal

In this article we present an assessment instrument for body image dissatisfaction: The Body Shape Questionnaire (Cooper, Taylor, Cooper & Fairburn, 1987). We apport the data obtained in five different studies in order to provide information about its reliability and validity in our society, The studies hove being done on universitary and eating disorders patients samples, We compare the results in this questionnaire with others obtained in adopted or not body dissatisfaction instruments. Our final goal is to provide with assessment instruments of body image because in our society there are very few of them
Clinical respiratory scales: which one should we use?

ABSTRACT Introduction: There are countless clinical respiratory scales for acute dyspnoea. Most healthcare professionals choose one based on previous personal experience or following local practice, unaware of the implications of their choice. The lack of critical comparisons between those different tools has been a widespread problem that only recently has begun to be addressed via score validation studies. Here we try to assess and compare the quality criteria of measurement properties of acute dyspnoea scores. Areas covered: A literature review was conducted by searching the PubMed database. Forty-five documents were deemed eligible as they reported the use or building of clinical scales, using at least two parameters, and applied these to an acute episode of respiratory dyspnoea. Our primary focus was the description of the validity, reliability and utility of 41 suitable scoring instruments. Differences in sample selection, study design, rater profiles and potential methodological shortcomings were also addressed. Expert commentary: All acute dyspnoea scores lack complete validation. In particular, the areas of measurement error and interpretability have not been addressed correctly by any of the tools reviewed. Frequent modification of pre-existing scores (in items composition and/or name), differences in study design and discrepancies in reviewed sources also hinder the search for an adequate tool.
Estuarine Fish Communities along a Spatial Urbanization Gradient

ABSTRACT Valenti, J.L. ; Grothues, T.M. , and Able, K.W. , 2017. Estuarine fish communities along a spatial urbanization gradient. In: Buchanan, G.A. ; Belton, T.J., and Paudel, B. (eds.), A Comprehensive Assessment of Barnegat Bay–Little Egg Harbor, New Jersey. The human population surrounding Barnegat Bay, New Jersey, has increased dramatically in recent decades. Consequently, urbanization (anthropogenic development) of the watershed has occurred, resulting in shoreline hardening and habitat destruction. A resulting gradient of urbanization increases from the southern to the northern portion of the bay's watershed. The objective of this study was to investigate cumulative impacts of urbanization in Barnegat Bay by assessing species composition, abundance, and diversity of fish communities in relation to the large-scale urbanization gradient in the watershed. Otter trawl surveys occurred in April, June, August, and October for 3 years (2012–2014) at 40 sampling sites stratified along the urbanization gradient. The sampling sites included four different representative, subtidal subhabitats: open bay (soft bottom), submerged aquatic vegetation beds, upper marsh creek, and marsh creek mouth. Analyses did not reveal strong differences in fish communities among strata that could be solely attributed to the urbanization gradient. Fish species composition was similar among strata, whereas species abundances and diversity differed among strata. Many of the observed differences in abundance and diversity were attributed to ecological variables unassociated with the urbanization gradient. Further study on potential urbanization effects should include investigations at the species level and at smaller scales.
Subfemtosecond pulse generation by molecular modulation

This Letter suggests and analyzes a technique for producing subfemtosecond pulses of radiation. We will show that two laser beams whose frequency difference is slightly offset from a molecular transition will, for an appropriate choice of gas pressure and cell length, generate a spectrum of Raman sidebands whose Fourier transform is a periodic train of subfemtosecond pulses. The essence of the technique is the concurrent generation of a frequency modulated (FM) waveform and the use of group velocity dispersion to temporally compress this waveform. By numerically modeling this process in molecular deuterium sD2d, we calculate a generated train of pulses with a pulse spacing of 11.1 fs and a pulse length of 0.21 fs. The coherence rab (Fig. 1) of the driven molecular transition is central to this work. This coherence is established by driving the molecular transition slightly off resonance with driving lasers of sufficient intensity that the product of their Rabi frequencies exceeds the product of the detuning from the molecular electronic states and the detuning from the Raman transition. With the linewidth of the applied laser pulses small as compared to the Raman detuning, the magnitude of the molecular coherence approaches 0.5, and its sign is determined by the sign of the Raman detuning. For the conditions of the previous paragraph, the generation and phase-slip lengths are of the same order, and Raman sideband generation proceeds collinearly and very differently than in the conventional low coherence regime. In essence, the molecular motion now modulates the electronic refractive index much in the same way that a low frequency electric field modulates the refractive index of a polar crystal. Incident optical frequencies become frequency modulated with peak (sinusoidal) frequency deviations and spectral bandwidths that substantially exceed the width of the visible spectrum. This allows the extension of compression techniques, such as the use of group velocity dispersion as described here, to a new regime of short pulse compression. In pertinent prior work, (1) the authors have noted how an electromagnetically induced transparency (EIT)-like excitation may be used to generate a broad comb of coherent sidebands, but the Bessel-function nature of the spectrum and the possibility of pulse compression were not
A new low-cost non intrusive platform for injecting soft errors in SRAM-based FPGAs

SRAM-based Field Programmable Gate Arrays (FPGAs) are becoming more and more popular among aerospace devices. Radiation effects have to be investigated in order to measure the fault tolerance degree of the applications and to validate new mitigation techniques. Fault injection is one of the possible evaluation methods. Several platforms have been developed in the past years in order to inject soft errors within FPGAs, however they have their greater drawbacks in intrusiveness and high-costs. In this paper we propose a new, low-cost and not-intrusive, fault injection platform to emulate soft errors within the configuration memory of SRAM-based FPGAs. In particular, radiation effects can be evaluated without modifying neither the circuit implemented in the FPGA nor the application it executes, thus allowing to study the real system that will take part to the mission. Experimental results on several test circuits are reported and commented, demonstrating the feasibility of the presented approach.
Effects of ovariectomy and estrogen therapy on type II collagen degradation and structural integrity of articular cartilage in rats: implications of the time of initiation.

OBJECTIVE To investigate how the time of initiation influences the effects of estrogen therapy on type II collagen (CII) turnover and the structural integrity of articular cartilage in ovariectomized rats and to determine whether estrogen exerts direct effects on the catabolic function of chondrocytes ex vivo. METHODS A total of 46 Sprague-Dawley rats were distributed into 1 of the following treatment groups: 1) ovariectomy, 2) ovariectomy plus early estrogen therapy, 3) ovariectomy plus delayed estrogen therapy, or 4) sham operation. Cartilage turnover was estimated by measuring the serum levels of C-telopeptide of type II collagen (CTX-II). Cartilage lesions at week 9 were quantified using a published scoring technique. The presence of the CTX-II epitope in articular cartilage was assessed by immunohistochemistry. The effects of estrogen (1-100 nM) on chondrocytes were investigated in bovine cartilage explants subjected to catabolic cytokines (tumor necrosis factor alpha [TNFalpha] and oncostatin M [OSM]). RESULTS In ovariectomized rats, estrogen therapy evoked significant decreases in serum CTX-II independently of the time of initiation; yet, delayed initiation resulted in diminished efficacy in terms of preventing cartilage lesions. CTX-II fragments were present in articular cartilage, colocalizing with early lesions at the cartilage surface. In untreated animals, the early relative increases in serum CTX-II were proportional to the severity of cartilage lesions at week 9 (r = 0.73, P < 0.01). Estrogen significantly and dose-dependently countered CTX-II release from TNFalpha plus OSM-stimulated cartilage explants ex vivo. CONCLUSION Our results suggest that estrogen counters the acceleration of CII degradation and related structural alterations, and these benefits can be maximized by early initiation after menopause. The protective effect of estrogen seems to involve direct inhibition of the catabolic function of chondrocytes.
DISA: A Scientific Writing Advisor with Deep Information Structure Analysis

This paper demonstrates DISA, a higher-level writing assistant system, which analyzes the information structure of abstracts, and retrieves the knowledge according to the research goals from the related work. By incorporating the latest neural-network technologies including linguistically-informed neural-network and autoencoder, we construct an intelligent system which extends the scope of computeraided writing.
Epilepsy imaging in adults: getting it right.

OBJECTIVE The purpose of this article is to describe an MRI protocol optimized for epilepsy evaluation, common causes of epilepsy visualized on MR images of patients evaluated for medically intractable partial epilepsy, and the basic concepts of advanced imaging techniques in the evaluation of epilepsy. CONCLUSION Epilepsy is one of the most common neurologic disorders in the United States. The long-term seizure-free success of epilepsy surgery is related to the ability to define and completely resect the epileptogenic zone. Detection of structural lesions at preoperative imaging requires not only a dedicated epilepsy protocol but also meticulous examination of the images by the interpreting radiologist with particular attention to subtle abnormalities that might otherwise go unreported.
A patient with a 20‐year lag phase between JAK2‐V617F+ myeloproliferation and NPM1‐mutated AML arguing against a common origin of disease

We have sought to unravel the molecular biology of a female patient who in 1985 at the age of 55 was diagnosed with a chronic myeloproliferative neoplasm (MPN) and in whom overt acute myeloid leukemia (AML) developed in 2005. To this end, DNA and RNA (extracted from either paraffin‐embedded bone marrow (BM) or from BM and/or peripheral blood stored in an RNA/DNA‐preserving buffer) were analyzed by qPCR and by capillary gel electrophoresis of PCR products. We found the patient to be JAK2‐V617F mutation positive throughout the course of disease, while a mutation of the nucleophosmin (NPM1) gene emerged at AML diagnosis and relapse. The 20‐yr lag phase between the polycythemia vera and the AML adds indirect evidence to the growing realization that the leukemic transformation in patients with MPN occurs from in a JAK2 wild‐type stem cell.
Changes in non-linear and time-domain heart rate variability indices between critically ill COVID-19 and all-cause sepsis patients -a retrospective study

Objective: To measure heart rate variability metrics in critically ill COVID-19 patients with comparison to all-cause critically ill sepsis patients. Design and patients: Retrospective analysis of COVID-19 patients admitted to an ICU for at least 24h at any of Emory Healthcare ICUs between March and April 2020. The comparison group was a cohort of all-cause sepsis patients prior to COVID-19 pandemic. Interventions: none. Measurements: Continuous waveforms were captured from the patient monitor. The EKG was then analyzed for each patient over a 300 second (s) observational window, that was shifted by 30s in each iteration from admission till discharge. A total of 23 HRV metrics were extracted in each iteration. We use the Kruskal-Wallis and Steel-Dwass tests (p < 0.05) for statistical analysis and interpretations of HRV multiple measures. Results: A total of 141 critically-ill COVID-19 patients met inclusion criteria, who were compared to 208 patients with all-cause sepsis. Demographic parameters were similar apart from a high proportion of African-Americans in the COVID-19 cohort. Three non-linear markers, including SD1:SD2, sample entropy, approximate entropy and four linear features mode of Beat-to-Beat interval (NN), Acceleration Capacity (AC), Deceleration Capacity (DC), and pNN50, were statistical significance between more than one binary combinations of the sub-groups (comparing survivors and non-survivors in both the COVID-19 and sepsis cohorts). The three nonlinear features and AC, DC, and NN (mode) were statistically significant across all four combinations. Temporal analysis of the main markers showed low variability across the 5 days of analysis, compared with sepsis patients. Conclusions: Heart rate variability is broadly implicated across patients infected with SARS-CoV-2, and admitted to the ICU for critical illness. Comparing these metrics to patients with all-cause sepsis suggests a unique set of expressions that differentiate this viral phenotype. This finding could be investigated further as a potential biomarker to predict poor outcome in this patient population, and could also be a starting point to measure potential autonomic dysfunction in COVID-19.