Miracle-dz/UniFAR-FTUs huggingface dataset:
Testing Dependence Among Serially Correlated Multicategory Variables

The contingency table literature on tests for dependence among discrete multicategory variables is extensive. Standard tests assume, however, that draws are independent and only limited results exist on the effect of serial dependency—a problem that is important in areas such as economics, finance, medical trials, and meteorology. This article proposes new tests of independence based on canonical correlations from dynamically augmented reduced rank regressions. The tests allow for an arbitrary number of categories as well as multiway tables of arbitrary dimension and are robust in the presence of serial dependencies that take the form of finite-order Markov processes. For three-way or higher order tables we propose new tests of joint and marginal independence. Monte Carlo experiments show that the proposed tests have good finite sample properties. An empirical application to microeconomic survey data on firms' forecasts of changes to their production and prices demonstrates the importance of correcting for serial dependencies in predictability tests.
Ventricular arrhythmias and the autonomic tone in patients with mitral valve prolapse

The aim of this study was to evaluate a possible relation between the autonomic tone determined by daily urine catecholamine excretion and the incidence of ventricular arrhythmias (VA) in patients with mitral valve prolapse (MVP). The study included 53 patients (31 women and 22 men) aged 19–52 years (mean age 32.7). The diagnosis of MVP was based on medical history, physical examination, and echocardiography. Cardiac arrhythmias were detected by Holter monitoring and classified according to Lown grades. Daily heart rate and duration of corrected QT interval using Basett's formula were also analyzed. Daily urine adrenaline and noradrenaline levels were determined fluorometrically by Von Euler and Lishajko's method. The patients with Lown's grade III‐V VA were evaluated with particular consideration. Student's t‐test was used for statistical analysis. On Holter monitoring 26 patients showed VA, including 6 with grade I, 11 with grade II, 2 with grade III, 4 with grade IV, and 3 with grade V according to Lown's classification. The remaining 27 patients were free of cardiac arrhythmias. Mean daily heart rate ranged from 54–93 beats/min (73±8.44, mean±SD) and corrected QT from 336–494 ms (411±37.17). Daily adrenaline and noradrenaline excretion for the whole group of patients were 0.01–16.2 μg (2.1±2.38) and 1.6–31.0 μg (13.1±7.27), respectively, which was within normal range. However, the patients with serious ventricular arrhythmias showed significantly higher daily adrenaline excretion. Individual analysis of two‐thirds of patients with ventricular arrhythmias grade III‐V showed daily urine noradrenaline levels exceeding mean values for the whole group. Our results suggest that in patients with MVP and serious VA, increased autonomic tone may be of great importance.
Investigating the role of body shape on the perception of emotion

In order to analyze the emotional content of motions portrayed by different characters, we created real and virtual replicas of an actor exhibiting six basic emotions: sadness, happiness, surprise, fear, anger, and disgust. In addition to the video of the real actor, his actions were applied to five virtual body shapes: a low- and high-resolution virtual counterpart, a cartoon-like character, a wooden mannequin, and a zombie-like character (Figures 1 and 2). In a point light condition, we also tested whether the absence of a body affected the perceived emotion of the movements. Participants were asked to rate the actions based on a list of 41 more complex emotions. We found that the perception of emotional actions is highly robust and to the most part independent of the character's body, so long as form is present. When motion alone is present, emotions were generally perceived as less intense than in the cases where form was present.
Comparative Histological Study of Caecum in Cattle, Sheep and Goat

Comparative histology of the caecum of adult cattle,sheep and goat was studied. Caecum of all three animals consisted of four layers namely tunica mucosa, tela submucosa,tunica muscularis and tunica serisa. Intestinal glands were mostly located at base region of tunica mucosa. In caecum of goat mucus secreting intestional glands were present in the close vicinity of lamina muscularis and serous secreting glands were present at apical end of tunica mucosa. Tela submucosa was largest in cattle as compared to sheep and goat. Aggregated lymphatic nodules are present in caecum of sheep in the vicinity of lamina muscularis. In caecum of goat tunica serosa was a loose connective tissue.
Interferon-gamma, macrophages, and virus spread after HSV-1 injection.

PURPOSE After uniocular anterior chamber (AC) injection of HSV-1, the anterior segment of BALB/c mice becomes inflamed and infected; however, virus does not spread from the anterior segment to cause retinitis in the injected eye. The purpose of these studies was to determine whether interferon (IFN-)-γ and Mac-1(+) cells play a role in preventing direct anterior-to-posterior spread of HSV-1 in the injected eye. METHODS One AC of adult female BALB/c mice was injected with HSV-1 (KOS). The location of IFN-α, IFN-β, and IFN-γ in the injected eye was determined by immunofluorescence, and mRNA expression was quantified by qPCR. Injected eyes of IFN-γ knockout or clodronate-treated macrophage-depleted mice were examined to determine whether the absence of IFN-γ or Mac-1(+) macrophages affected the sites or timing of virus spread. RESULTS IFN-α, IFN-β, and IFN-γ were observed in the anterior segment of injected eyes through 72 hours and mRNA levels of IFN-β and IFN-γ were increased in virus-infected eyes 48 to 120 hours after infection. However, the absence of IFN-γ or macrophages did not affect either the sites or the timing of HSV-1 infection in injected eyes. CONCLUSIONS Protection of the retina of the injected eye does not depend on a single cell type or cytokine. In addition, in the eye, as in other sites of the body, there are redundancies in the innate response to virus infection.
Exploring Eye Movements in Patients with Glaucoma When Viewing a Driving Scene

Background Glaucoma is a progressive eye disease and a leading cause of visual disability. Automated assessment of the visual field determines the different stages in the disease process: it would be desirable to link these measurements taken in the clinic with patient's actual function, or establish if patients compensate for their restricted field of view when performing everyday tasks. Hence, this study investigated eye movements in glaucomatous patients when viewing driving scenes in a hazard perception test (HPT). Methodology/Principal Findings The HPT is a component of the UK driving licence test consisting of a series of short film clips of various traffic scenes viewed from the driver's perspective each containing hazardous situations that require the camera car to change direction or slow down. Data from nine glaucomatous patients with binocular visual field defects and ten age-matched control subjects were considered (all experienced drivers). Each subject viewed 26 different films with eye movements simultaneously monitored by an eye tracker. Computer software was purpose written to pre-process the data, co-register it to the film clips and to quantify eye movements and point-of-regard (using a dynamic bivariate contour ellipse analysis). On average, and across all HPT films, patients exhibited different eye movement characteristics to controls making, for example, significantly more saccades (P<0.001; 95% confidence interval for mean increase: 9.2 to 22.4%). Whilst the average region of ‘point-of-regard’ of the patients did not differ significantly from the controls, there were revealing cases where patients failed to see a hazard in relation to their binocular visual field defect. Conclusions/Significance Characteristics of eye movement patterns in patients with bilateral glaucoma can differ significantly from age-matched controls when viewing a traffic scene. Further studies of eye movements made by glaucomatous patients could provide useful information about the definition of the visual field component required for fitness to drive.
Transcriptional regulation of the Escherichia coli oxyR gene as a function of cell growth

The oxyR regulon plays a central role in the defense of Escherichia coli against the endogenous oxidative damage associated with active aerobic growth. Here we have studied the transcriptional regulation of oxyR in E. coli growing aerobically in rich medium. Expression of a single-copy oxyR'::lacZ reporter construct varied sixfold along the growth curve, with the highest value at 4 to 6 h of growth (approximately 14 x 10(8) cells x ml(-1)). Direct measurements of oxyR mRNA by primer extension showed the same biphasic expression but with a peak somewhat earlier in cell growth (2 to 3 h; approximately 3.5 x 10(8) cells x ml(-1)). The results of immunoblotting experiments demonstrated that the level of OxyR protein exhibits the same biphasic expression. Mutant strains lacking adenylate cyclase (cya) or Crp protein (crp) failed to increase oxyR expression during exponential growth. On the other hand, an rpoS mutation allowed oxyR expression to continue increasing as the cells entered stationary phase. Consistent with a biological role for increased levels of OxyR during exponential growth, the crp cya strain had lower activities of catalase hydroperoxidase I and glutathione reductase and an increased sensitivity to exogenously added hydrogen peroxide. These results suggest that the Crp-dependent upregulation of oxyR in exponential phase is a component of a multistep strategy to counteract endogenous oxidative stress in actively growing E. coli cells.
Dental implant failure rates and associated risk factors.

PURPOSE To guide treatment planning by analyzing the rates of dental implant failure to determine associated risk factors. MATERIALS AND METHODS All consecutively treated patients from January 1982 until January 2003 were included in a retrospective cohort study, as defined in the hierarchy of evidence for dental implant literature. Data regarding gender, age, implant location, bone quality, bone volume, and medical history were recorded. Correlations between these data and implant survival were calculated to establish relative risk (RR) ratios. RESULTS Increasing age was strongly associated with the risk of implant failure. Compared to patients younger than 40 years, patients in the 60-to-79 age group had a significantly higher risk of implant failure (RR = 2.24; P < .05). Gender, hypertension, coronary artery disease, pulmonary disease, steroid therapy, chemotherapy, and not being on hormone replacement therapy for postmenopausal women were not associated with a significant increase in implant failure. Smoking (RR = 1.56), diabetes (RR = 2.75), head and neck radiation (RR = 2.73), and postmenopausal estrogen therapy (RR = 2.55) were correlated with a significantly increased failure rate. Overall, implant failure was 8.16% in the maxilla and 4.93% in the mandible (P < .001). DISCUSSION Patients who were over age 60, smoked, had a history of diabetes or head and neck radiation, or were postmenopausal and on hormone replacement therapy experienced significantly increased implant failure compared with healthy patients. CONCLUSION Overall, dental implant failure is low and there are no absolute contraindications to implant placement. Conditions that were found to be correlated with an increased risk of failure should be considered during treatment planning and factored into the informed consent process.
AVACS – Automatic Verification and Analysis of Complex Systems REPORTS of SFB / TR 14 AVACS Editors : Board of SFB / TR 14 AVACS Logic and Model Checking for Hidden Markov Models by

The branching-time temporal logic PCTL has been introduced to specify quantitative properties over probability systems, such as discrete-time Markov chains. Until now, however, no logics have been defined to specify properties over hidden Markov models (HMMs). In HMMs the states are hidden, and the hidden processes produce a sequence of observations. In this paper we extend the logic PCTL to POCTL. With our logic one can state properties such as “there is at least a 90 percent probability that the model produces a given sequence of observations” over HMMs. Subsequently, we give model checking algorithms for POCTL over HMMs. This report is the full version of a paper which appeared in FORTE’05 [25].
Program complexity metrics and programmer opinions

Various program complexity measures have been proposed to assess maintainability. Only relatively few empirical studies have been conducted to back up these assessments through empirical evidence. Researchers have mostly conducted controlled experiments or correlated metrics with indirect maintainability indicators such as defects or change frequency. This paper uses a different approach. We investigate whether metrics agree with complexity as perceived by programmers. We show that, first, programmers' opinions are quite similar and, second, only few metrics and in only few cases reproduce complexity rankings similar to human raters. Data-flow metrics seem to better match the viewpoint of programmers than control-flow metrics, but even they are only loosely correlated. Moreover we show that a foolish metric has similar or sometimes even better correlation than other evaluated metrics, which raises the question how meaningful the other metrics really are. In addition to these results, we introduce an approach and associated statistical measures for such multi-rater investigations. Our approach can be used as a model for similar studies.
The Role of Patents in Information and Communication Technologies: A Survey of the Literature

During the last decades, the number of ICT related patents has increased considerably. In association with a great fragmentation in IP rights, the increasing number of patents has generated a series of potentially problematic consequences. Patent thickets, royalty stacking, the emergence of patent assertion entities, increased patent litigation – in particular around standard essential patents – and the difficulties in the definition of fair, reasonable and non-discriminatory (FRAND) licensing terms are among the most debated issues in the literature that we review in this paper. We devote a specific section of our survey to patents involving software products, where the above problems are amplified by the high level of abstraction of computer algorithms. In our analysis we mix theoretical and empirical arguments with a more policy-oriented reasoning. This allows us to better position the different issues in the relevant political and economic context.
Costs and financial burden of care and support services to PLHA and households in South India

Abstract The objective of this study is to estimate the medical and non-medical out-of-pocket expenditure on care and support services to PLHA, the financial burden on households, the indirect costs and coping strategies to meet the financial burden. A structured pre-tested questionnaire was used to collect data from a cohort of 153 clients of YRG CARE, a leading Chennai based NGO, who had completed the first and third waves of interview during 2000/01 and 2001/02 respectively. The results show that the median out-of-pocket medical and non-medical expenditures (direct cost) for treatment and services are Rs. 6,000 (US $ 122) in a reference period of six months. Clients on antiretroviral (ARV) drugs spend five times more than those not on ARV. The median direct cost significantly increases with stage of disease, household income, and poverty level. The financial burden of treatment, measured as the ratio of direct cost to household income, is greater on lower income (82%) than on higher income (28%) households. 31% and 45% of the clients reported loss of income and workdays respectively. In conclusion, the direct costs and financial burden of care and support services increase with the stage of disease. The financial burden is disproportionately more on low-income households. HIV/AIDS leads to depletion of savings and increases the indebtedness of households.
Unreinforced spatial (latent) learning is mediated by a circuit that includes dorsal entorhinal cortex and fimbria fornix

The relationship of the entorhinal cortex (EC) and fimbria‐fornix (FF) in unreinforced spatial (latent) learning was studied using the conditioned‐cue‐preference task on an eight‐arm radial maze. The maze was turned before every trial to eliminate the use of local cues. During three pre‐exposure sessions, food‐deprived rats explored the center platform and two adjacent arms of the maze. Since most of the same cues were visible from both arm locations, discriminating them required spatial learning. The rats were then alternately confined to the end of each arm over several days: one arm always contained food, the other was empty. Finally, the rats were allowed free access to both arms with no food present. Normal rats spent more time in their food‐paired than in their unpaired arms showing that they learned to discriminate between the arm locations. Bilateral micro‐injections of muscimol into the dorsal, but not into the ventral EC, given before the pre‐exposure sessions only, impaired the discrimination. The discrimination was also impaired in rats with unilateral lesions of FF and contralateral injections of muscimol into the dorsal EC given before the pre‐exposure sessions. Ipsilateral FF lesions and entorhinal inactivation had no effect. These results indicate that the acquisition of information during unreinforced exploration of a novel environment requires an intact circuit involving the dorsal EC and fimbria fornix. Together with previous reports, that this form of learning does not require a functional hippocampus, (Gaskin et al. (2005) Hippocampus 15:1085–1093) the findings also suggest that the acquisition of certain kinds of unreinforced information by this circuit is independent of the hippocampus. © 2007 Wiley‐Liss, Inc.
Alteration of Political Belief by Non-invasive Brain Stimulation

People generally have imperfect introspective access to the mechanisms underlying their political beliefs, yet can confidently communicate the reasoning that goes into their decision making process. An innate desire for certainty and security in ones beliefs may play an important and somewhat automatic role in motivating the maintenance or rejection of partisan support. The aim of the current study was to clarify the role of the DLPFC in the alteration of political beliefs. Recent neuroimaging studies have focused on the association between the DLPFC (a region involved in the regulation of cognitive conflict and error feedback processing) and reduced affiliation with opposing political candidates. As such, this study used a method of non-invasive brain simulation (tRNS) to enhance activity of the bilateral DLPFC during the incorporation of political campaign information. These findings indicate a crucial role for this region in political belief formation. However, enhanced activation of DLPFC does not necessarily result in the specific rejection of political beliefs. In contrast to the hypothesis the results appear to indicate a significant increase in conservative values regardless of participant's initial political orientation and the political campaign advertisement they were exposed to.
The CDK7-cycH-p36 complex of transcription factor IIH phosphorylates p53, enhancing its sequence-specific DNA binding activity in vitro

Phosphorylation is believed to be one of the mechanisms by which p53 becomes activated or stabilized in response to cellular stress. Previously, p53 was shown to interact with three components of transcription factor IIH (TFIIH): excision repair cross-complementing types 2 and 3 (ERCC2 and ERCC3) and p62. This communication demonstrates that p53 is phosphorylated by the TFIIH-associated kinase in vitro. The phosphorylation was found to be catalyzed by the highly purified kinase components of TFIIH, the CDK7-cycH-p36 trimeric complex. The phosphorylation sites were mapped to the C-terminal amino acids located between residues 311 and 393. Serines 371, 376, 378, and 392 may be the potential sites for this kinase. Phosphorylation of p53 by this kinase complex enhanced the ability of p53 to bind to the sequence-specific p53-responsive DNA element as shown by gel mobility shift assays. These results suggest that the CDK7-cycH-p36 trimeric complex of TFIIH may play a role in regulating p53 functions in cells.
Epidemiology of Invasive Early-Onset Neonatal Sepsis, 2005 to 2014

BACKGROUND: Group B Streptococcus (GBS) and Escherichia coli have historically dominated as causes of early-onset neonatal sepsis. Widespread use of intrapartum prophylaxis for GBS disease led to concerns about the potential adverse impact on E coli incidence. METHODS: Active, laboratory, and population-based surveillance for culture-positive (blood or cerebrospinal fluid) bacterial infections among infants 0 to 2 days of age was conducted statewide in Minnesota and Connecticut and in selected counties of California and Georgia during 2005 to 2014. Demographic and clinical information were collected and hospital live birth denominators were used to calculate incidence rates (per 1000 live births). We used the Cochran–Amitage test to assess trends. RESULTS: Surveillance identified 1484 cases. GBS was most common (532) followed by E coli (368) and viridans streptococci (280). Eleven percent of cases died and 6.3% of survivors had sequelae at discharge. All-cause (2005: 0.79; 2014: 0.77; P = .05) and E coli (2005: 0.21; 2014: 0.18; P = .25) sepsis incidence were stable. GBS incidence decreased (2005: 0.27; 2014: 0.22; P = .02). Among infants <1500 g, incidence was an order of magnitude higher for both pathogens and stable. The odds of death among infants <1500 g were similar for both pathogens but among infants ≥1500 g, the odds of death were greater for E coli cases (odds ratio: 7.0; 95% confidence interval: 2.7–18.2). CONCLUSIONS: GBS prevention efforts have not led to an increasing burden of early-onset E coli infections. However, the stable burden of E coli sepsis and associated mortality underscore the need for interventions.
Ultracontractivity and the Heat Kernel for Schrijdinger Operators and Dirichlet Laplacians

connections between integral kernels of positivity preserving semigroups and suitable Lp contractivity properties are established. Then these questions are studied for the semigroups generated by -A + V and H,, the Dirichlet Laplacian for an open, connected region Q. As an application under a suitable hypothesis, Sobolev estimates are proved valid up to 352, of the form /n(x)1 ,< coo(x) lJHk,nllZ, where o0 is the unique positive L2 eigenfunction of H, .
bz-rates: A Web Tool to Estimate Mutation Rates from Fluctuation Analysis

Fluctuation analysis is the standard experimental method for measuring mutation rates in micro-organisms. The appearance of mutants is classically described by a Luria-Delbrück distribution composed of two parameters: the number of mutations per culture (m) and the differential growth rate between mutant and wild-type cells (b). A precise estimation of these two parameters is a prerequisite to the calculation of the mutation rate. Here, we developed bz-rates, a Web tool to calculate mutation rates that provides three useful advances over existing Web tools. First, it allows taking into account b, the differential growth rate between mutant and wild-type cells, in the estimation of m with the generating function. Second, bz-rates allows the user to take into account a deviation from the Luria-Delbrück distribution called z, the plating efficiency, in the estimation of m. Finally, the Web site provides a graphical visualization of the goodness-of-fit between the experimental data and the model. bz-rates is accessible at http://www.lcqb. upmc.fr/bzrates.