Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary Analysis of Inter-Farm Transmission Dynamics in a Highly Pathogenic Avian Influenza Epidemic

Phylogenetic studies have largely contributed to better understand the emergence, spread and evolution of highly pathogenic avian influenza during epidemics, but sampling of genetic data has never been detailed enough to allow mapping of the spatiotemporal spread of avian influenza viruses during a single epidemic. Here, we present genetic data of H7N7 viruses produced from 72% of the poultry farms infected during the 2003 epidemic in the Netherlands. We use phylogenetic analyses to unravel the pathways of virus transmission between farms and between infected areas. In addition, we investigated the evolutionary processes shaping viral genetic diversity, and assess how they could have affected our phylogenetic analyses. Our results show that the H7N7 virus was characterized by a high level of genetic diversity driven mainly by a high neutral substitution rate, purifying selection and limited positive selection. We also identified potential reassortment in the three genes that we have tested, but they had only a limited effect on the resolution of the inter-farm transmission network. Clonal sequencing analyses performed on six farm samples showed that at least one farm sample presented very complex virus diversity and was probably at the origin of chronological anomalies in the transmission network. However, most virus sequences could be grouped within clearly defined and chronologically sound clusters of infection and some likely transmission events between farms located 0.8–13 Km apart were identified. In addition, three farms were found as most likely source of virus introduction in distantly located new areas. These long distance transmission events were likely facilitated by human-mediated transport, underlining the need for strict enforcement of biosafety measures during outbreaks. This study shows that in-depth genetic analysis of virus outbreaks at multiple scales can provide critical information on virus transmission dynamics and can be used to increase our capacity to efficiently control epidemics.
Forensic automatic speaker recognition

Automatic speaker recognition technology appears to have reached a sufficient level of maturity for realistic application in the field of forensic science. However, there are key issues to be solved before the forensic community will accept its use as an investigative assistant or as evidence in actual criminal cases. To assess the state of the technology, the Federal Bureau of Investigation (FBI) built a speech corpus that included multiple levels of increasing difficulty based on text-independence, channelindependence, speaking mode, and speech duration. An evaluation of multiple automatic speaker recognition programs indicated that a large GMM model-based recognition algorithm operating with features that are robust with respect to channel variations had the best performance. In this paper we describe (1) the results of evaluations of the recognition performance produced by multiple participating research organizations, (2) The FBI’s initial Forensic Automatic Speaker Recognition (FASR) program based on these concepts, and (3) a confidence measurement method to indicate the probabilistic certainty level of correctness of each recognition decision. We will also discuss the need and justification for input speech screening and pre-processing to improve the recognition performance of the FASR as applied in a real forensic environment.
dILA neurons in the dorsal spinal cord are the product of terminal and non-terminal asymmetric progenitor cell divisions, and require Mash1 for their development

dILA and dILB neurons comprise the major neuronal subtypes generated in the dorsal spinal cord, and arise in a salt-and-pepper pattern from a broad progenitor domain that expresses the bHLH factor Mash1. In this domain, Mash1-positive and Mash1-negative cells intermingle. Using a Mash1GFP allele in mice, we show here that Mash1+ progenitors give rise to dILA and dILB neurons. Using retroviral tracing in the chick, we demonstrate that a single progenitor can give rise to a dILA and a dILB neuron, and that dILA neurons are the product of asymmetric progenitor cell divisions. In Mash1-null mutant mice, the development of dILA, but not of dILB neurons is impaired. We provide evidence that a dual function of Mash1 in neuronal differentiation and specification accounts for the observed changes in the mutant mice. Our data allow us to assign to Mash1 a function in asymmetric cell divisions, and indicate that the factor coordinates cell cycle exit and specification in the one daughter that gives rise to a dILA neuron.
A Direct Differential Approach to Photometric Stereo with Perspective Viewing

Shape from shading and photometric stereo are two fundamental problems in computer vision aimed at reconstructing surface depth given either a single image taken under a known light source or multiple images taken under different illuminations from the same viewing angle. Whereas the former uses partial differential equation techniques to solve the image irradiance equation, the latter can be expressed as a linear system of equations in surface derivatives when three or more images are given. Therefore, it seems that current photometric stereo techniques do not extract all possible depth information from each image by itself. Extending our previous results on this problem, we consider the more realistic perspective projection of surfaces during the photographic process. Under this assumption, there is a unique weak solution (Lipschitz continuous) to the problem at hand, solving the well-known convex/concave ambiguity of the shape from shading problem. The main contribution of this paper is based on a new .
Representation of Linguistic Form and Function in Recurrent Neural Networks

We present novel methods for analyzing the activation patterns of recurrent neural networks from a linguistic point of view and explore the types of linguistic structure they learn. As a case study, we use a standard standalone language model, and a multi-task gated recurrent network architecture consisting of two parallel pathways with shared word embeddings: The Visual pathway is trained on predicting the representations of the visual scene corresponding to an input sentence, and the Textual pathway is trained to predict the next word in the same sentence. We propose a method for estimating the amount of contribution of individual tokens in the input to the final prediction of the networks. Using this method, we show that the Visual pathway pays selective attention to lexical categories and grammatical functions that carry semantic information, and learns to treat word types differently depending on their grammatical function and their position in the sequential structure of the sentence. In contrast, the language models are comparatively more sensitive to words with a syntactic function. Further analysis of the most informative n-gram contexts for each model shows that in comparison with the Visual pathway, the language models react more strongly to abstract contexts that represent syntactic constructions.
Relationship between space-vector modulation and three-phase carrier-based PWM: a comprehensive analysis [three-phase inverters]

This paper comprehensively analyzes the relationship between space-vector modulation and three-phase carrier-based pulse width modulation (PWM). The relationships involved, such as the relationship between modulation signals (including zero-sequence component and fundamental components) and space vectors, the relationship between the modulation signals and the space-vector sectors, the relationship between the switching pattern of space-vector modulation and the type of carrier, and the relationship between the distribution of zero vectors and different zero-sequence signal are systematically established. All the relationships provide a bidirectional bridge for the transformation between carrier-based PWM modulators and space-vector modulation modulators. It is shown that all the drawn conclusions are independent of the load type. Furthermore, the implementations of both space-vector modulation and carrier-based PWM in a closed-loop feedback converter are discussed.
Applications of high and low fidelity prototypes in researching intuitive interaction

This paper addresses some of the issues involved in incorporating use of prototypes into a research program. Definitions, merits and uses of both low and high-fidelity prototypes are discussed and then the applications of prototypes in our research program into intuitive interaction are explored. It has previously been established that intuitive interaction is based on past experience, and can be encouraged by designing interfaces that contain familiar features (Blackler, 2006; Blackler, Popovic, & Mahar, 2007b). Two aspects of the research program which are relevant to prototyping are: researching the issues of how intuitive use happens and how it can be better facilitated; and developing ways to help designers include investigations about users and their existing knowledge into their design processes in order to make interfaces more intuitive. The current and future planned applications of high and low-fidelity prototypes in each of these areas are explored. Then experiences with using high-fidelity touchscreen prototypes for experimental research into intuitive interaction are discussed, including problems with the prototypes, how they were addressed and what we have learned from the process. Next the potential for low-fidelity prototypes to elicit users’ tacit knowledge during the design process is explored. This has exciting possibilities due to the link between intuitive interaction and tacit knowledge. Finally, the challenges of developing prototype-based design tools for use by older people are discussed and future directions for using prototypes in our research program are considered. Keywords: Prototypes; intuitive interaction; experimental methodology; implicit or tacit knowledge
Exploiting Linked Open Data in Cold-start Recommendations with Positive-only Feedback

In recommender systems, user preferences can be acquired either explicitly by means of ratings, or implicitly --e.g., by processing text reviews, and by mining item browsing and purchasing records. Most existing collaborative filtering approaches have been designed to deal with numerical ratings, such as the 5-star ratings in Amazon and Netflix, for both rating prediction and item ranking (a.k.a. top-N recommendation) tasks. In many e-commerce and social network sites, however, user preferences are usually expressed in the form of binary and unary (positive-only) ratings, such as the thumbs up/down in YouTube and the likes in Facebook, respectively. Moreover, in these cases, the well-known problem of cold-start --i.e., the scarcity of user preferences-- is highly remarkable. To address this situation, we explore a number of graph-based and matrix factorization recommendation models that jointly exploit user ratings and item metadata. In this work, such metadata are automatically obtained from DBpedia --the queriable and structured version of Wikipedia which is considered as the core knowledge repository of the Linked Open Data initiative--, and the models are evaluated with a Facebook dataset covering three distinct domains, namely books, movies and music. The results achieved in our experiments show that the proposed hybrid recommendation models, which exploit rating and semantic data, outperform content-based and collaborative filtering baselines.
Cardiac function in spontaneously diabetic BB rats treated with low and high dose insulin.

Cardiac abnormalities observed in animals with drug-induced diabetes may be due to the direct cardiotoxic effect of the drugs or factors not related to the diabetic state. The purpose of this investigation was to examine cardiac sarcoplasmic reticular (SR) calcium transport and heart function in the BB rat, a strain in which diabetes occurs spontaneously and clearly resembles insulin-dependent diabetes in humans. Complete insulin withdrawal for 2 or 4 days from BB diabetic rats leads to a spectrum of metabolic derangements including a loss of body weight, hyperglycemia, and elevated triglyceride levels confirming the insulin dependence of this model. The present study involved treating BB diabetic rats with a low (hyperglycemic) and high (normoglycemic) insulin dose for 12 weeks after the detection of glycosuria. The hearts from these animals were then isolated, and SR Ca2+ transport and heart function (using isolated perfused working hearts) were examined and compared with BB nondiabetic littermates or Wistar controls. Strain-related differences were found in ATP-dependent SR Ca2+ transport between the Wistar and BB rats. There were, however, no significant diabetes-related differences in SR Ca2+ transport between the low dose insulin treated diabetic group (LD) and the high dose insulin treated diabetic group (HD) or the nondiabetic littermates. Plasma lipid concentrations of the LD and HD BB rats and nondiabetic littermates were also generally higher than those of control Wistar rats indicating strain-related but not diabetes-related differences. In addition, there were no differences in cardiac function between the LD and BB nondiabetic littermates or Wistar controls. (ABSTRACT TRUNCATED AT 250 WORDS)
Spatial Patterns, Longitudinal Development, and Hemispheric Asymmetries of Cortical Thickness in Infants from Birth to 2 Years of Age

Cortical thickness (CT) is related to normal development and neurodevelopmental disorders. It remains largely unclear how the characteristic patterns of CT evolve in the first 2 years. In this paper, we systematically characterized for the first time the detailed vertex-wise patterns of spatial distribution, longitudinal development, and hemispheric asymmetries of CT at 0, 1, and 2 years of age, via surface-based analysis of 219 longitudinal magnetic resonance images from 73 infants. Despite the dynamic increase of CT in the first year and the little change of CT in the second year, we found that the overall spatial distribution of thin and thick cortices was largely present at birth, and evolved only modestly during the first 2 years. Specifically, the precentral gyrus, postcentral gyrus, occipital cortex, and superior parietal region had thin cortices, whereas the prefrontal, lateral temporal, insula, and inferior parietal regions had thick cortices. We revealed that in the first year thin cortices exhibited low growth rates of CT, whereas thick cortices exhibited high growth rates. We also found that gyri were thicker than sulci, and that the anterior bank of the central sulcus was thicker than the posterior bank. Moreover, we showed rightward hemispheric asymmetries of CT in the lateral temporal and posterior insula regions at birth, which shrank gradually in the first 2 years, and also leftward asymmetries in the medial prefrontal, paracentral, and anterior cingulate cortices, which expanded substantially during this period. This study provides the first comprehensive picture of early patterns and evolution of CT during infancy.
STARCH DIGESTION IN THE HORSE

The rate and extent of starch digestion is determined by: 1. properties of the starch granule; 2. the effect of processing; 3. associated food structures (plant cell walls); 4. transit time through the small intestine; 5. the availability and concentration of enzymes. These factors will affect the glycemic response of the horse to feeding and the subsequent production of insulin. Resistant starch, together with undigested starch, will pass into the large intestine of the horse where it may be fermented to short chain fatty acids. Resistant starch may escape digestion in the small intestine of the horse because: 1. of physical entrapment within a food, such as in partly-milled grains and seeds (RS 1 starch); 2. starch granules have a B or C crystalline structure which is highly resistant to digestion (RS 2 starch); 3. retrogradation through food processing, mainly in the form of retro-graded amylose (RS 3 starch). RS 3 starch is entirely resistant to digestion by pancreatic amylase in man (Englyst and Macfarlane, 1986) and this starch is commonly found in peas. RS 1 and RS 2 are quantitatively the most important forms of resistant starch found in horse feeds.
Treatment of Ulcerative Colitis With Clonidine

In the present 30‐week, double‐blind study of 45 ulcerative colitis (UC) patients treated with prednisone, sulfasalazine, clonidine, or placebo, we found that clonidine (an alpha2 agonist) and prednisone were effective in treating idiopathic UC. Both drugs were more effective than sulfasalazine. Furthermore, clonidine potentiated prednisone and sulfasalazine effects. Clonidine was chosen because its effect on distal colon motility is similar to thioproperazine, an antipsychotic drug that despite many adverse effects, possesses powerful anti‐UC properties. Rating scales were outlined in order to evaluate clinical, endoscopic, histologic, and radiologic changes. Plasma cortisol levels, sedimentation rate, serum glutamic‐oxaloacetic transaminase, serum glutamic‐pyruvic transaminase, and other biochemical parameters were determined to assess the efficacy of each drug. Distal colon motility changes were also assessed. All our UC patients showed raised cortisol plasma levels and low sigmoidal tone during relapse periods. These parameters were reversed during remission periods. Peripheral and central mechanisms are discussed.
Search for Transcriptional and Metabolic Markers of Grape Pre-Ripening and Ripening and Insights into Specific Aroma Development in Three Portuguese Cultivars

Background Grapes (Vitis species) are economically the most important fruit crop worldwide. However, the complexity of molecular and biochemical events that lead to ripening of berries as well as how aroma is developed are not fully understood. Methodology/Principal Findings In an attempt to identify the common mechanisms associated with the onset of ripening independently of the cultivar, grapes of Portuguese elite cultivars, Trincadeira, Aragonês, and Touriga Nacional, were studied. The mRNA expression profiles corresponding to veraison (EL35) and mature berries (EL36) were compared. Across the three varieties, 9,8% (2255) probesets corresponding to 1915 unigenes were robustly differentially expressed at EL 36 compared to EL 35. Eleven functional categories were represented in this differential gene set. Information on gene expression related to primary and secondary metabolism was verified by RT-qPCR analysis of selected candidate genes at four developmental stages (EL32, EL35, EL36 and EL 38). Gene expression data were integrated with metabolic profiling data from GC-EI-TOF/MS and headspace GC-EI-MS platforms. Conclusions/Significance Putative molecular and metabolic markers of grape pre-ripening and ripening related to primary and secondary metabolism were established and revealed a substantial developmental reprogramming of cellular metabolism. Altogether the results provide valuable new information on the main metabolic events leading to grape ripening. Furthermore, we provide first hints about how the development of a cultivar specific aroma is controlled at transcriptional level.
Multiple Exposure Time Based Laser Speckle Contrast Analysis: Demonstration of Applicability in Skin Perfusion Measurements

The applicability of multiple exposure time based LASCA was demonstrated on skin blood perfusion monitoring. The method was compared to β-corrected and non-corrected single exposure time measurements while the data simultaneously recorded by a laser Doppler system were used as reference. The skin of the forearm was illuminated with the light of an 808 nm laser diode. Speckle images were recorded in the exposure time range of 1-100 ms and relative perfusion changes caused by ischemia were determined. The results showed an obvious nonlinear relationship between the data of the non-corrected single exposure time LASCA method and the laser Doppler system, while a good linearity was observed for the multiple exposure time method with a correlation factor of 0.83. Keywords-LASCA; Multiple Exposure Times; Skin Perfusion; Laser Doppler Flowmetry
Assessment of the arrowtooth flounder stock in the Gulf of Alaska

1. The 2019 NMFS Gulf of Alaska bottom-trawl survey biomass estimates, standard error, and survey length composition data were added. 2. Survey age data were included for the 2017 NMFS Gulf of Alaska bottom-trawl survey. 3. Fishery catch was updated for 2017 and 2018, and was extrapolated through the end of 2019 for an estimate of 20,554 t. Catch of 24,186 t was assumed for 2020 in the projections, which was based on the 5 year average 2014-2018. 4. Fishery length composition data was updated for 2017, 2018, and 2019.
SafeChoice: A Novel Approach to Hypergraph Clustering for Wirelength-Driven Placement

This paper presents a completely new approach to the problem of hypergraph clustering for wirelength-driven placement. The novel algorithm we propose is called SafeChoice (SC). Different from all previous approaches, SC is proposed based on a fundamental theorem, safe condition which guarantees that clustering would not degrade the placement wirelength. To mathematically derive such a theorem, we first introduce the concept of safe clustering, i.e., do clustering without degrading the placement quality. To efficiently check the safe condition for pair-wise clustering, we propose a technique called selective enumeration. SafeChoice maintains a global priority queue based on the safeness and area of potential clusters. Using a simple heuristic, it automatically stops clustering when generating more clusters would degrade the placement wirelength. Moreover, we extend SafeChoice to do clustering while considering the object physical locations, i.e., physical clustering. Finally, we apply SafeChoice into a two-phase placement framework and propose a high-quality analytical placement algorithm called SCPlace. Comprehensive experimental results show that the clusters produced by SC consistently help the placer to achieve the best wirelength among all other clustering algorithms, and SCPlace generates the best half-perimeter wirelength compared with all other state-of-the-art placers.