Miracle-dz/UniFAR-FTUs huggingface dataset:
On codes that avoid specified differences

We study the number of binary sequences whose differences do not include certain disallowed patterns. We show that the number of such sequences increases exponentially with their length and that the exponent, or capacity, is the logarithm of the joint spectral radius of an appropriately defined set of matrices. We derive a new algorithm for determining the joint spectral radius of sets of nonnegative matrices and combine it with existing algorithms to determine the capacity of several sets of disallowed differences that arise in practice.
Role of the protein tyrosine phosphatase SHP‐1 in Interleukin‐6 regulation of prostate cancer cells

Interleukin‐6 (IL‐6) is a multifunctional cytokine that has been implicated in the modulation of growth and progression of prostate cancer. Decreased expression of the tyrosine phosphatase SHP‐1, involved in regulation of cytokine and tyrosine kinase receptor signaling, has been shown to be associated with less favorable outcome among prostate cancer patients.
Pyramidal displacement mapping: a GPU based artifacts-free ray tracing through an image pyramid

Displacement mapping enables us to details to polygonal meshes. We present a real-time artifacts-free inverse displacement mapping method using per-pixel ray tracing through an image pyramid on the GPU. In each pixel, we make a ray and trace the ray through a displacement map to find an intersection. To skip empty-regions safely, we use the quad-tree image pyramid of a displacement map in top-down order. For magnification we estimate an intersection between a ray and a bi-linearly interpolated displacement. For minification we perform a mipmap-like prefiltering to improve quality of result images and rendering performance. Results show that our method produces correct images even at steep grazing angles. Rendering speed of test scenes were over hundreds of frames per second and less influence to the resolution of the map. Our method is simple enough to add to existing virtual reality systems easily.
Discriminative Non-blind Deblurring

Non-blind deblurring is an integral component of blind approaches for removing image blur due to camera shake. Even though learning-based deblurring methods exist, they have been limited to the generative case and are computationally expensive. To this date, manually-defined models are thus most widely used, though limiting the attained restoration quality. We address this gap by proposing a discriminative approach for non-blind deblurring. One key challenge is that the blur kernel in use at test time is not known in advance. To address this, we analyze existing approaches that use half-quadratic regularization. From this analysis, we derive a discriminative model cascade for image deblurring. Our cascade model consists of a Gaussian CRF at each stage, based on the recently introduced regression tree fields. We train our model by loss minimization and use synthetically generated blur kernels to generate training data. Our experiments show that the proposed approach is efficient and yields state-of-the-art restoration quality on images corrupted with synthetic and real blur.
A Maximum Entropy Chinese Character-Based Parser

The paper presents a maximum entropy Chinese character-based parser trained on the Chinese Treebank ("CTB" henceforth). Word-based parse trees in CTB are first converted into character-based trees, where word-level part-of-speech (POS) tags become constituent labels and character-level tags are derived from word-level POS tags. A maximum entropy parser is then trained on the character-based corpus. The parser does word-segmentation, POS-tagging and parsing in a unified framework. An average label F-measure 81.4% and word-segmentation F-measure 96.0% are achieved by the parser. Our results show that word-level POS tags can improve significantly word-segmentation, but higher-level syntactic strutures are of little use to word segmentation in the maximum entropy parser. A word-dictionary helps to improve both word-segmentation and parsing accuracy.
The Prevalence of Blinding Trachoma in Northern States of Sudan

Background Despite historical evidence of blinding trachoma, there have been no widespread contemporary surveys of trachoma prevalence in the northern states of Sudan. We aimed to conduct district-level surveys in this vast region in order to map the extent of the problem and estimate the need for trachoma control interventions to eliminate blinding trachoma. Methods and Findings Separate, population based cross-sectional surveys were conducted in 88 localities (districts) in 12 northern states of Sudan between 2006 and 2010. Two-stage cluster random sampling with probability proportional to size was used to select the sample. Trachoma grading was done using the WHO simplified grading system. Key prevalence indicators were trachomatous inflammation-follicular (TF) in children aged 1–9 years and trachomatous trichiasis (TT) in adults aged 15 years and above. The sample comprised 1,260 clusters from which 25,624 households were surveyed. A total of 106,697 participants (81.6% response rate) were examined for trachoma signs. TF prevalence was above 10% in three districts and between 5% and 9% in 11 districts. TT prevalence among adults was above 1% in 20 districts (which included the three districts with TF prevalence >10%). The overall number of people with TT in the population was estimated to be 31,072 (lower and upper bounds = 26,125–36,955). Conclusion Trachoma mapping is complete in the northern states of Sudan except for the Darfur States. The survey findings will facilitate programme planning and inform deployment of resources for elimination of trachoma from the northern states of Sudan by 2015, in accordance with the Sudan Federal Ministry of Health (FMOH) objectives.
A Validation Study of a Smartphone-Based Finger Tapping Application for Quantitative Assessment of Bradykinesia in Parkinson’s Disease

Background Most studies of smartphone-based assessments of motor symptoms in Parkinson’s disease (PD) focused on gait, tremor or speech. Studies evaluating bradykinesia using wearable sensors are limited by a small cohort size and study design. We developed an application named smartphone tapper (SmT) to determine its applicability for clinical purposes and compared SmT parameters to current standard methods in a larger cohort. Methods A total of 57 PD patients and 87 controls examined with motor UPDRS underwent timed tapping tests (TT) using SmT and mechanical tappers (MeT) according to CAPSIT-PD. Subjects were asked to alternately tap each side of two rectangles with an index finger at maximum speed for ten seconds. Kinematic measurements were compared between the two groups. Results The mean number of correct tapping (MCoT), mean total distance of finger movement (T-Dist), mean inter-tap distance, and mean inter-tap dwelling time (IT-DwT) were significantly different between PD patients and controls. MCoT, as assessed using SmT, significantly correlated with motor UPDRS scores, bradykinesia subscores and MCoT using MeT. Multivariate analysis using the SmT parameters, such as T-Dist or IT-DwT, as predictive variables and age and gender as covariates demonstrated that PD patients were discriminated from controls. ROC curve analysis of a regression model demonstrated that the AUC for T-Dist was 0.92 (95% CI 0.88–0.96). Conclusion Our results suggest that a smartphone tapping application is comparable to conventional methods for the assessment of motor dysfunction in PD and may be useful in clinical practice.
Relationship between exacerbation frequency and lung function decline in chronic obstructive pulmonary disease

Background: Chronic obstructive pulmonary disease (COPD) is characterised by both an accelerated decline in lung function and periods of acute deterioration in symptoms termed exacerbations. The aim of this study was to investigate whether these are related. Methods: Over 4 years, peak expiratory flow (PEF) and symptoms were measured at home daily by 109 patients with COPD (81 men; median (IQR) age 68.1 (63–74) years; arterial oxygen tension (Pao2) 9.00 (8.3–9.5) kPa, forced expiratory volume in 1 second (FEV1) 1.00 (0.7–1.3) l, forced vital capacity (FVC) 2.51 (1.9–3.0) l); of these, 32 (29 men) recorded daily FEV1. Exacerbations were identified from symptoms and the effect of frequent or infrequent exacerbations (> or < 2.92 per year) on lung function decline was examined using cross sectional, random effects models. Results: The 109 patients experienced 757 exacerbations. Patients with frequent exacerbations had a significantly faster decline in FEV1 and peak expiratory flow (PEF) of –40.1 ml/year (n=16) and –2.9 l/min/year (n=46) than infrequent exacerbators in whom FEV1 changed by –32.1 ml/year (n=16) and PEF by –0.7 l/min/year (n=63). Frequent exacerbators also had a greater decline in FEV1 if allowance was made for smoking status. Patients with frequent exacerbations were more often admitted to hospital with longer length of stay. Frequent exacerbations were a consistent feature within a patient, with their number positively correlated (between years 1 and 2, 2 and 3, 3 and 4). Conclusions: These results suggest that the frequency of exacerbations contributes to long term decline in lung function of patients with moderate to severe COPD.
The interplay of cholinergic function, attention, and falls in Parkinson's disease

Dopamine loss in the substantia nigra causes several of the motor signs seen in Parkinson's disease, but there is now increasing evidence highlighting the importance of cholinergic loss in the pathophysiology of nonmotor symptoms. The nucleus basalis of Meynert supplies the majority of the cholinergic input to the cerebral cortex, with the pedunculopontine nucleus providing many subcortical structures with acetylcholine. Both these structures undergo degeneration in Parkinson's disease (PD), with more severe loss associated with cognitive impairment. The risk of dementia in PD is greater than that in control subjects, with impairments in attention, visuospatial function, and executive control dominating. Imaging studies have demonstrated degeneration of the cholinergic system in PD, Parkinson's disease dementia, and dementia with Lewy bodies, with improvements in attention seen following the introduction of cholinesterase inhibitors. Conversely, anticholinergic drugs are associated with cognitive decline, with neuropathology studies indicating the presence of increased neurofibrillary tangles and senile plaque formation. In addition, these drugs are also known to precipitate visual hallucinations, lending support to a cholinergic basis for visual hallucinations in PD. Gait, falls, and cognition may also be related, as evidenced by the findings that fallers perform less well on test of attention than nonfallers and that greater postural instability is associated with worse scores on attention and executive function. It is therefore feasible that cognition (namely, attention), visual hallucinations, falls, and gait are subserved by acetylcholine, and this is further explored in this clinically orientated review. © 2011 Movement Disorder Society
Nocturnal activity in the cathemeral red‐fronted lemur (Eulemur fulvus rufus), with observations during a lunar eclipse

Several ecological and physiological factors have been suggested to structure circadian activity in cathemeral primates, i.e., those that are regularly active both day and night, but their relative importance remains controversial. We studied the nocturnal activity of a group of cathemeral redfronted lemurs (Eulemur fulvus rufus) in Kirindy Forest in Western Madagascar to examine its relationship with one environmental factor, ambient light levels, in detail. To this end, nightly travel distances and moon luminosity were determined between March and June 1996. During this transitional period between the wet and dry seasons these red‐fronted lemurs were regularly active at night, and traveled significantly larger distances during full‐moon nights compared to new‐moon nights. The importance of ambient luminosity for nocturnal activity was highlighted by observations during a total lunar eclipse (i.e., during a full‐moon night), which caused abrupt cessation of the animal’s activity. Our results support the hypothesis that nocturnal activity of these cathemeral lemurs is regulated also by changes in ambient light levels. Am. J. Primatol. 53:69–78, 2001. © 2001 Wiley‐Liss, Inc.
Time-Course of Neuromuscular Changes during and after Maximal Eccentric Contractions

This study tested the relationship between the magnitude of muscle damage and both central and peripheral modulations during and after eccentric contractions of plantar flexors. Eleven participants performed 10 sets of 30 maximal eccentric contractions of the plantar flexors at 45°·s−1. Maximal voluntary torque, evoked torque (peripheral component) and voluntary activation (central component) were assessed before, during, immediately after (POST) and 48 h after (48 h) the eccentric exercise. Voluntary eccentric torque progressively decreased (up to −36%) concomitantly to a significant alteration of evoked torque (up to −34%) and voluntary activation (up to −13%) during the exercise. Voluntary isometric torque (−48 ± 7%), evoked torque (−41 ± 14%) and voluntary activation (−13 ± 11%) decreased at POST, but only voluntary isometric torque (−19 ± 6%) and evoked torque (−10 ± 18%) remained depressed at 48 h. Neither changes in voluntary activation nor evoked torque during the exercise were related to the magnitude of muscle damage markers, but the evoked torque decrement at 48 h was significantly correlated with the changes in voluntary activation (r = −0.71) and evoked torque (r = 0.77) at POST. Our findings show that neuromuscular responses observed during eccentric contractions were not associated with muscle damage. Conversely, central and peripheral impairments observed immediately after the exercise reflect the long-lasting reduction in force-generating capacity.
Rheology, Mechanical and Thermal Properties of C18-CNT/LDPE Nanocomposites

Abstract Nanocomposites of low density polyethylene (LDPE)/C18 modified multi wall carbon nanotubes (C18-CNT) were prepared by melt blending. The effect of C18-CNT loading and compatibilizer (maleic anhydride modified polyethylene, MAPE) on the morphology, mechanical, thermal and rheological properties of LDPE was studied. FE-SEM images of nanocomposites show reduced agglomeration of the in LDPE/C18-CNT in comparison with uncompatibilized C18-CNT. For uncompatibilized nanocomposites, yield strength and Young's modulus increased with loading of C18-CNT. Ultimate strength, show improvement up to 2 wt% loading. However, percent elongation and toughness were reduced for C18-CNT at all loadings. Apart from elongation and toughness, addition of compatibilizer improved all mechanical properties as compared to pure LDPE and nanocomposites without compatibilizer. Percent crystallinity shows a correlation with Young's modulus. Both, Young's modulus and total crystallinity increased with C18-CNT loading and further increase with the incorporation of compatibilizer was observed. Results of phase angle suggest no presence of network. Also, addition of C18-CNT did not increase strain hardening, maintained extensional viscosity and time of break up to 1.5 s−1 Hencky rate. The C18 modifier is viewed to act similar to a long chain branching on linear polymers. The C18 modification of CNT resulted in reduced viscous and elastic properties of the composites. In turn, this is expected to lead to enhancement in the processing of these composites. Overall, compatibilized C18-CNT resulted in improved mechanical properties and better processing behavior.
Progressive tricuspid valve disease in patients with congenitally corrected transposition of the great arteries.

BACKGROUND The outcome of patients with corrected transposition of the great arteries (CTGA) is variably affected by associated intracardiac defects, tricuspid valve competence, and systemic right ventricular (RV) function. The relative importance of these factors in long-term outcome has not been evaluated. METHODS AND RESULTS Since 1958, 40 patients with CTGA were studied to determine risk factors for poor outcome, including age, open heart surgery, tricuspid insufficiency (TI), cardiac rhythm, pulmonary overcirculation, and RV dysfunction. Follow-up ranged from 7 to 36 years (mean 20 years). Intracardiac repair was performed in 21 patients; 19 were unoperated or had closed heart procedures. For the purposes of this study the designation TI(S) refers to at least moderately severe TI as delineated by echocardiogram and/or angiography. TI(s) was the only independently significant factor for death (P=0.01), and in turn, only the presence of a morphologically abnormal TV predicted TI(s)(P=0.03). Twenty-year survival without TI(S)was 93%, but only 49% with TI(S). Poor long-term postoperative outcome was due to TI(S) in all but 1 patient; 20-year survival rates for operated patients with and without TI(s)were 34% and 90%, respectively (P=0.002). Similarly, 20-year survival rates for unoperated patients with and without TI(s)were 60% and 100%, respectively, whether or not attempts to repair the TI were made (P=0.08). CONCLUSIONS TI(S)represents the major risk factor for CTGA patients; RV dysfunction appears to be almost always secondary to long-standing TI. Decisions related to surgical interventions with or without associated lesions must be strongly influenced by the status of the tricuspid valve.
Genomics, the origins of agriculture, and our changing microbe‐scape: Time to revisit some old tales and tell some new ones

ABSTRACT Though agriculture is often viewed as one of humanity's crowning achievements, skeletal evidence indicates that dependence on domesticated plants and animals was accompanied by an increase in infectious disease. Scientists have proposed that many important infections emerged in the period following the advent of agriculture, as a result of newly dense populations and novel proximity to domestic animals that served as reservoirs for novel pathogens. Here, we review genomic evidence regarding pathogen origins, analyzing these data using the epidemiological transition framework. Genetic information has forced us to reconsider how and when many important pathogens emerged; it appears that a number of infections thought to result from contact with domesticated animals arose much earlier than agriculture was adopted. We also consider the broader effect of agriculture upon the microbiome, exploring potential consequences for human health. We end by discussing the changes in the human microbe‐scape we are likely to see in the future. Am J Phys Anthropol 57:135–152, 2013. © 2013 Wiley Periodicals, Inc.
Growth state‐dependent regulation of plasminogen activator inhibitor type‐1 gene expression during epithelial cell stimulation by serum and transforming growth factor‐β1

Transcription of the plasminogen activator inhibitor type‐1 (PAI‐1) gene appears to be growth state regulated in several cell types (e.g., Ryan and Higgins, 1993, J Cell Physiol 155:376–384; Mu et al., 1998, J Cell Physiol 174:90–98). Transit of serum‐stimulated normal rat kidney (NRK) epthelial cells through the first division cycle after release from quiescence (G0) provided a model system to assess the kinetics and mechanisms underlying PAI‐1 expression in a growth “activated” phenotype. PAI‐1 mRNA transcripts increased by more than 20‐fold during the G0→G1 transition; induced expression had immediate‐early response characteristics and abruptly declined prior to the onset of DNA synthesis. Transcriptional activity of the PAI‐1 gene paralleled the steady‐state mRNA abundance profile during this first synchronized growth cycle after release from quiescence. Although PAI‐1 mRNA levels were up‐regulated (approximately threefold) upon exposure to several different growth factors, neutralizing antibodies to transforming growth factor‐β1 (TGF‐β1) effectively attenuated the more than ninefold serum‐associated PAI‐1 inductive response by more than 70% (at both the mRNA transcript and protein levels). Similar to the metabolic requirements for serum‐mediated PAI‐1 transcription, PAI‐1 induction upon addition of TGF‐β1 to quiescent NRK cell cultures was actinomycin D sensitive and resistant to cyclohexamide and puromycin, suggesting a primary mode of transcript control. The response to protein synthesis inhibitors, however, was complex. While cyclohexamide appeared to stabilize, or at least maintain, fetal bovine serum (FBS)‐ or TGF‐β1‐stimulated PAI‐1 mRNA levels, puromycin had no such affect. The amplitude and duration of induced PAI‐1 expression were the same in either the presence or absence of puromycin. Cyclohexamide when used alone (i.e., in non‐FBS‐ or TGF‐β1‐treated cultures), moreover, effectively stimulated PAI‐1 induction whereas puromycin was ineffective. Although TGF‐β1 was not a complete mitogen in the NRK cell system, incubation of quiescent renal cell cultures with TGF‐β1, prior to serum stimulation, resulted in a 10‐ to 12‐fold increase in PAI‐1 expression coincident with exit out of G0. These data support a model in which PAI‐1 gene expression is closely associated with creation of the growth‐activated state and that cell cycle controls appear to be superimposed on the time course of the serum‐induced expression of the PAI‐1 gene. J. Cell. Physiol. 181:96–106, 1999. © 1999 Wiley‐Liss, Inc.
Artificial Skin Ridges Enhance Local Tactile Shape Discrimination

One of the fundamental requirements for an artificial hand to successfully grasp and manipulate an object is to be able to distinguish different objects’ shapes and, more specifically, the objects’ surface curvatures. In this study, we investigate the possibility of enhancing the curvature detection of embedded tactile sensors by proposing a ridged fingertip structure, simulating human fingerprints. In addition, a curvature detection approach based on machine learning methods is proposed to provide the embedded sensors with the ability to discriminate the surface curvature of different objects. For this purpose, a set of experiments were carried out to collect tactile signals from a 2 × 2 tactile sensor array, then the signals were processed and used for learning algorithms. To achieve the best possible performance for our machine learning approach, three different learning algorithms of Naïve Bayes (NB), Artificial Neural Networks (ANN), and Support Vector Machines (SVM) were implemented and compared for various parameters. Finally, the most accurate method was selected to evaluate the proposed skin structure in recognition of three different curvatures. The results showed an accuracy rate of 97.5% in surface curvature discrimination.
Systematicity in sentence processing with a recursive self-organizing neural network

As potential candidates for human cognition, connection- ist models of sentence processing must learn to behave systematically by generalizing from a small traning set. It was recently shown that Elman networks and, to a greater extent, echo state networks (ESN) possess lim- ited ability to generalize in artificial language learning tasks. We study this capacity for the recently introduced recursive self-organizing neural network model and show that its performance is comparable with ESNs.