Miracle-dz/UniFAR-FTUs huggingface dataset:
Probabilistic Arithmetic Automata and Their Applications

We present a comprehensive review on probabilistic arithmetic automata (PAAs), a general model to describe chains of operations whose operands depend on chance, along with two algorithms to numerically compute the distribution of the results of such probabilistic calculations. PAAs provide a unifying framework to approach many problems arising in computational biology and elsewhere. We present five different applications, namely 1) pattern matching statistics on random texts, including the computation of the distribution of occurrence counts, waiting times, and clump sizes under hidden Markov background models; 2) exact analysis of window-based pattern matching algorithms; 3) sensitivity of filtration seeds used to detect candidate sequence alignments; 4) length and mass statistics of peptide fragments resulting from enzymatic cleavage reactions; and 5) read length statistics of 454 and IonTorrent sequencing reads. The diversity of these applications indicates the flexibility and unifying character of the presented framework. While the construction of a PAA depends on the particular application, we single out a frequently applicable construction method: We introduce deterministic arithmetic automata (DAAs) to model deterministic calculations on sequences, and demonstrate how to construct a PAA from a given DAA and a finite-memory random text model. This procedure is used for all five discussed applications and greatly simplifies the construction of PAAs. Implementations are available as part of the MoSDi package. Its application programming interface facilitates the rapid development of new applications based on the PAA framework.
Diversity of Retinal Ganglion Cells Identified by Transient GFP Transfection in Organotypic Tissue Culture of Adult Marmoset Monkey Retina

The mammalian retina has more diversity of neurons than scientists had once believed in order to establish complicated vision processing. In the monkey retina, morphological diversity of retinal ganglion cells (RGCs) besides dominant midget and parasol cells has been suggested. However, characteristic subtypes of RGCs in other species such as bistratified direction-selective ganglion cells (DSGC) have not yet been identified. Increasing interest has been shown in the common marmoset (Callithrix jacchus) monkey as a “super-model” of neuroscientific research. Here, we established organotypic tissue culture of the adult marmoset monkey retina with particle-mediated gene transfer of GFP to survey the morphological diversity of RGCs. We successfully incubated adult marmoset monkey retinas for 2 to 4 days ex vivo for transient expression of GFP. We morphologically examined 121 RGCs out of more than 3240 GFP-transfected cells in 5 retinas. Among them, we identified monostratified or broadly stratified ganglion cells (midget, parasol, sparse, recursive, thorny, and broad thorny ganglion cells), and bistratified ganglion cells (recursive, large, and small bistratified ganglion cells [blue-ON/yellow-OFF-like]). By this survey, we also found a candidate for bistratified DSGC whose dendrites were well cofasciculated with ChAT-positive starburst dendrites, costratified with ON and OFF ChAT bands, and had honeycomb-shaped dendritic arbors morphologically similar to those in rabbits. Our genetic engineering method provides a new approach to future investigation for morphological and functional diversity of RGCs in the monkey retina.
Zero defect manufacturing: state-of-the-art review, shortcomings and future directions in research

This paper provides a literature review on zero defect manufacturing based on the content analysis performed for 280 research articles published from 1987 to 2018 in a variety of academic journals and conference proceedings. The review summarises the state-of-the-art, highlights shortcomings and further directions in research. Accordingly, we investigated how zero defect manufacturing was implemented and evaluated the main research patterns in the sample by analysing key factors. Based on the extensive review of the zero defect manufacturing literature, we identified and highlighted four distinctive strategies based on overarching themes for zero defect manufacturing, i.e. detection, repair, prediction, and prevention. Evaluation of current research and descriptive analysis highlighted six major shortcomings of current research in zero defect manufacturing: (i) focus on a single strategy instead of a holistic approach for global optima; (ii) certain industries are under-researched; (iii) full potential of industry-academia collaboration is not achieved; (iv) not enough focus on the beginning of manufacturing lifecycle; (v) cost–benefit comparative analysis is not evident; (vi) standard and clear definition of terms are missing. Finally, we presented four further directions in which an advance of the topic would stimulate scholarly and practical needs: (i) shift from local to global solutions; (ii) investigate pros and cons; (iii) role of people and human activities in manufacturing; (iv) new business models for zero defect manufacturing.
End-to-End Driving in a Realistic Racing Game with Deep Reinforcement Learning

We address the problem of autonomous race car driving. Using a recent rally game (WRC6) with realistic physics and graphics we train an Asynchronous Actor Critic (A3C) in an end-to-end fashion and propose an improved reward function to learn faster. The network is trained simultaneously on three very different tracks (snow, mountain, and coast) with various road structures, graphics and physics. Despite the more complex environments the trained agent learns significant features and exhibits good performance while driving in a more stable way than existing end-to-end approaches.
Positive Definite $\ell_1$ Penalized Estimation of Large Covariance Matrices

The thresholding covariance estimator has nice asymptotic properties for estimating sparse large covariance matrices, but it often has negative eigenvalues when used in real data analysis. To simultaneously achieve sparsity and positive definiteness, we develop a positive definite $\ell_1$-penalized covariance estimator for estimating sparse large covariance matrices. An efficient alternating direction method is derived to solve the challenging optimization problem and its convergence properties are established. Under weak regularity conditions, non-asymptotic statistical theory is also established for the proposed estimator. The competitive finite-sample performance of our proposal is demonstrated by both simulation and real applications.
Use of dietary supplements in Denmark is associated with health and former smoking

Abstract Objectives: To describe the use of dietary supplements in a group of Danish adults and to investigate the differences between users and non-users with respect to age, gender, health and lifestyle factors. Design: Cross-sectional study in two Danish cities. Setting: The Danish Investigation on Iodine Intake and Thyroid Diseases, 1997–1998. Subjects: Participants were 3707 women (selected age groups between 18 and 65 years) and 942 men (60–65 years). Participation rate was 50%. Supplement data were collected in a personal interview. Data on education, smoking, alcohol intake, physical activity, use of medication and self-perceived health were derived from a self-administered questionnaire. Multiple logistic regression was used for the statistical analysis. Results: Participants were asked about all kinds of supplements, ranging from products containing vitamins and minerals, to fish oils and products of herbal origin. On average 59% reported use of some kind of dietary supplement. Most common were combined multivitamin/mineral products (48%) followed by single vitamin C products (10%). Twelve per cent used three or more different supplements. Supplement use was strongly associated with age and gender, being highest among elderly women (78%). Ex-smokers were more likely to use supplements than subjects who had never smoked (odds ratio (OR) 1.36, 95% confidence interval (CI) 1.09–1.76). Supplement use was more likely among subjects who had many days of illness (OR = 1.37, 95% CI 1.12–1.66) and among users of medication (OR = 1.22, 95% CI 1.04–1.42). Subjects who perceived their health as poor were more likely to use supplements other than just a multivitamin/mineral tablet (OR = 2.2, 95% CI 1.31–3.77). Conclusions: Use of dietary supplements was related to age, gender and smoking, but also to poor self-perceived health status and absence from work. This indicates that a group of people use supplements as a form of self-medication.
Inhibition of a spliceosome turnover pathway suppresses splicing defects

Defects in assembly are suggested to signal the dissociation of faulty splicing complexes. A yeast genetic screen was performed to identify components of the putative discard pathway. Weak mutant alleles of SPP382 (also called NTR1) were found to suppress defects in two proteins required for spliceosome activation, Prp38p and Prp8p. Spp382p is shown necessary for cellular splicing, with premRNA and, for some alleles, excised intron, accumulating after inactivation. Like spp382-1, a mutant allele of AAR2 was identified in this suppressor screen. Like Spp382p, Aar2p has a reported role in spliceosome recycling and is found with Spp382p in a complex recovered with a mutant version of the spliceosomal core protein Prp8p. Possible insight into to the spp382 suppressor phenotype is provided by the observation that defective splicing complexes lacking the 5′ exon cleavage intermediate are recovered by a tandem affinity purification-tagged Spp382 derivative. Stringent proteomic and two-hybrid analyses show that Spp382p also interacts with Cwc23p, a DNA J-like protein present in the spliceosome and copurified with the Prp43p DExD/H-box ATPase. Spp382p binds Prp43p and Prp43p requires Spp382p for intron release from the spliceosome. Consistent with a related function in the removal of defective complexes, three prp43 mutants are also shown to suppress splicing defects, with efficiencies inversely proportionate to the measured ATPase activities. These and related genetic data support the existence of a Spp382p-dependent turnover pathway acting on defective spliceosomes.
Hierarchical multilabel classification trees for gene function prediction (Extended abstract)

Prediction of gene function is a so-called hierarchical multilabel classification (HMC) task: a single instance can be labelled with multiple classes rather than just one (i.e., a gene can have multiple functions), and these classes are organized in a hierarchy. Many machine learning methods focus on learning predictive models with a single target variable. One can then learn to predict all classes separately and combine the predictions afterwards. An alternative is to upgrade these methods towards the HMC context. In this paper we explore this alternative for classification trees. A comparison of learning HMC trees with learning normal classification trees shows that the former has clear advantages with respect to accuracy, efficiency, and interpretability. It seems worth investigating to what extent these results carry over to other machine learning methods.
Pore‐Filling of Spiro‐OMeTAD in Solid‐State Dye Sensitized Solar Cells: Quantification, Mechanism, and Consequences for Device Performance

In this paper, the pore filling of spiro‐OMeTAD (2,2′,7,7′‐tetrakis‐(N,N‐di‐p‐methoxyphenylamine)9,9′‐spirobifluorene) in mesoporous TiO2 films is quantified for the first time using XPS depth profiling and UV–Vis absorption spectroscopy. It is shown that spiro‐OMeTAD can penetrate the entire depth of the film, and its concentration is constant throughout the film. We determine that in a 2.5‐µm‐thick film, the volume of the pores is 60–65% filled. The pores become less filled when thicker films are used. Such filling fraction is much higher than the solution concentration because the excess solution on top of the film can act as a reservoir during the spin coating process. Lastly, we demonstrate that by using a lower spin coating speed and higher spiro‐OMeTAD solution concentration, we can increase the filling fraction and consequently the efficiency of the device.
Effects of S 6-Strain Mycoplasma gallisepticum Inoculation at 10 , 22 , or 45 Weeks of Age on the Digestive and Reproductive Organ Characteristics of Commercial Egg-Laying Hens 1

Experimental inoculation of commercial laying hens with the S6-strain of Mycoplasma gallisepticum (S6MG) at 20 wk of age, while being maintained under ideal conditions, has previously been shown to affect the lengths and weights of various portions of the reproductive tract. Two trials were conducted in the current study to compare the effects of S6MG inoculation prior to lay at 10 wk of age, during onset of lay at 22 wk of age, and during lay at 45 wk of age on the digestive and reproductive organs of commercial layers similarly housed and maintained under ideal conditions. In each trial, liver weight, liver moisture and lipid concentration,
Implementation of single precision floating point square root on FPGAs

The square root operation is hard to implement on FPGAs because of the complexity of the algorithms. In this paper, we present a non-restoring square root algorithm and two very simple single precision floating point square root implementations based on the algorithm on FPGAs. One is low-cost iterative implementation that uses a traditional adder/subtracter. The operation latency is 25 clock cycles and the issue rate is 24 clock cycles. The other is high-throughput pipelined implementation that uses multiple adder/subtracters. The operation latency is 15 clock cycles and the issue rate is one clock cycle. It means that the pipelined implementation is capable of accepting a square root instruction on every clock cycle.
Energy intake and expenditure in elderly patients admitted to hospital with acute illness

Studies on hospitalized elderly subjects have demonstrated that negative energy balance is common during hospitalization, but have concentrated primarily on long-stay and psychogeriatric patients. There is little information on energy balance in elderly patients admitted with acute illness from the community, despite the importance of this patient group and the presence of a number of factors likely to predispose such patients to negative energy balance. In the present study energy balance was quantified in twenty patients (eight males, mean age 82 (SD 05) years; twelve females, mean age 84 (SD 6) years) admitted from the community with acute illness, and predicted basal metabolic rate (BMR) was compared with measured resting metabolic rate (RMR). Most patients were in negative energy balance during hospitalization, and median measured energy intake (El):measured RMR ratio was 1·0 (range 0·7–1·8). The mean difference between measured El and estimated total energy expenditure was −1·3 MJ/d (range -3·4 to +2·5 MJ/d). Estimated total energy expenditure exceeded measured El in fifteen of the patients and there was a significant decline in mid-arm muscle circumference (paired t, P < 0·05) during hospitalization. We conclude that moderate negative energy balance is common in this patient group, and that these patients are at risk of undernutrition during their hospital stay.
Theory of Mind and Reading Comprehension in Deaf and Hard-of-Hearing Signing Children

Theory of Mind (ToM) is related to reading comprehension in hearing children. In the present study, we investigated progression in ToM in Swedish deaf and hard-of-hearing (DHH) signing children who were learning to read, as well as the association of ToM with reading comprehension. Thirteen children at Swedish state primary schools for DHH children performed a Swedish Sign Language (SSL) version of the Wellman and Liu (2004) ToM scale, along with tests of reading comprehension, SSL comprehension, and working memory. Results indicated that ToM progression did not differ from that reported in previous studies, although ToM development was delayed despite age-appropriate sign language skills. Correlation analysis revealed that ToM was associated with reading comprehension and working memory, but not sign language comprehension. We propose that some factor not investigated in the present study, possibly represented by inference making constrained by working memory capacity, supports both ToM and reading comprehension and may thus explain the results observed in the present study.
Using Retweets to Shape our Online Persona: a Topic Modeling Approach

Online social networking technologies have given rise to new social behaviors, with the like on Facebook being a prominent example. We study on a specific type of social behavior: the ability to reiterate a friend’s activity, that is, to redistribute an exact copy of content that he or she has posted online (e.g., words, videos, or pictures). Such reiteration tools enable the user to leverage someone else’s self-expression to enhance his or her own image as reflected by the online platform. We focus on the effects of such reiteration tools on the way users present themselves online. Specifically, using data from Twitter we ask: (1) Do users utilize retweets to expand the breadth of topics they discuss, by adding topics not discussed in their self-tweets, or do they use it to enhance their self-produced persona, adding further content relating to the topics they already discuss in their self-tweets? (2) Do users utilize the retweet option to change the distribution of the topics they discuss in their self-tweets? (3) We focus on users' heterogeneity by asking whether the behaviors we analyze differ between expert users and non-expert users.We analyzed data taken from Twitter over a period of 3 weeks in 2015, with regard to 2,435 non-expert core users (defined as users who tweet regularly and are likely to use the platform for personal rather than professional purposes), 415 expert users and the users whom they followed. We find that users rarely add new topics to their profile when retweeting; instead, they enrich their persona by deepening the discussion of topics that they address in their self-tweets. Furthermore, we find that a user's retweets do remarkably little to alter the distribution of topics she discusses in her self-tweets. Finally, we find that both non-expert and expert users tend to add few new topics via retweets, and that this tendency is stronger among expert users. Specifically, on average, experts retweet less often and add fewer topics per tweet, indicating that they rely more on their own words when engaging in impression management.
What Predicts an Advanced-Stage Diagnosis of Breast Cancer? Sorting Out the Influence of Method of Detection, Access to Care, and Biologic Factors

Background: Multiple studies have yielded important findings regarding the determinants of an advanced-stage diagnosis of breast cancer. We seek to advance this line of inquiry through a broadened conceptual framework and accompanying statistical modeling strategy that recognize the dual importance of access-to-care and biologic factors on stage. Methods: The Centers for Disease Control and Prevention–sponsored Breast and Prostate Cancer Data Quality and Patterns of Care Study yielded a seven-state, cancer registry–derived population-based sample of 9,142 women diagnosed with a first primary in situ or invasive breast cancer in 2004. The likelihood of advanced-stage cancer (American Joint Committee on Cancer IIIB, IIIC, or IV) was investigated through multivariable regression modeling, with base-case analyses using the method of instrumental variables (IV) to detect and correct for possible selection bias. The robustness of base-case findings was examined through extensive sensitivity analyses. Results: Advanced-stage disease was negatively associated with detection by mammography (P < 0.001) and with age < 50 (P < 0.001), and positively related to black race (P = 0.07), not being privately insured [Medicaid (P = 0.01), Medicare (P = 0.04), uninsured (P = 0.07)], being single (P = 0.06), body mass index > 40 (P = 0.001), a HER2 type tumor (P < 0.001), and tumor grade not well differentiated (P < 0.001). This IV model detected and adjusted for significant selection effects associated with method of detection (P = 0.02). Sensitivity analyses generally supported these base-case results. Conclusions: Through our comprehensive modeling strategy and sensitivity analyses, we provide new estimates of the magnitude and robustness of the determinants of advanced-stage breast cancer. Impact: Statistical approaches frequently used to address observational data biases in treatment-outcome studies can be applied similarly in analyses of the determinants of stage at diagnosis. Cancer Epidemiol Biomarkers Prev; 25(4); 613–23. ©2016 AACR.
The Observed Growth of Massive Galaxy Clusters II: X-ray Scaling Relations

This is the second in a series of papers in which we derive simultaneous constraints on cosmology and X-ray scaling relations using observations of massive, X-ray flux-selected galaxy clusters. The data set consists of 238 clusters with 0.1-2.4keV luminosities >2.5 x 10 44 h -2 70 erg s -1 , and incorporates follow-up observations of 94 of those clusters using the Chandra X-ray Observatory or ROSAT (11 were observed with both). The clusters are drawn from three samples based on the ROSAT All-Sky Survey: the ROSAT Brightest Cluster Sample (78/37 clusters detected/followed-up), the ROSAT-ESO Flux-Limited X-ray sample (126/25) and the bright sub-sample of the Massive Cluster Survey (34/32). Our analysis accounts self-consistently for all selection effects, covariances and systematic uncertainties. Here we describe the reduction of the follow-up X-ray observations, present results on the cluster scaling relations, and discuss their implications. Our constraints on the luminosity-mass and temperature-mass relations, measured within r 500 , lead to three important results. First, the data support the conclusion that excess heating of the intracluster medium (or a combination of heating and condensation of the coldest gas) has altered its thermodynamic state from that expected in a simple, gravitationally dominated system; however, this excess heat is primarily limited to the central regions of clusters (r < 0.15r 500 ). Secondly, the intrinsic scatter in the centre-excised luminosity-mass relation is remarkably small, being bounded at the < 10 per cent level in current data; for the hot, massive clusters under investigation, this scatter is smaller than in either the temperature-mass or Y x -mass relations (10-15 per cent). Thirdly, the evolution with redshift of the scaling relations is consistent with the predictions of simple, self-similar models of gravitational collapse, indicating that the mechanism responsible for heating the central regions of clusters was in operation before redshift 0.5 (the limit of our data) and that its effects on global cluster properties have not evolved strongly since then. Our results provide a new benchmark for comparison with numerical simulations of cluster formation and evolution.