Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Selection Signatures and Candidate Genes Related to Environmental Adaptation and Economic Traits in Tibetan Pigs

Simple Summary Modern agricultural methods have led to the introduction of normally highland Tibetan pigs to lowland areas because of their high-quality meat. Similar to humans, indigenous Tibetan pigs residing in high-altitude regions may develop high-altitude de-acclimatization syndrome when exposed to low-altitude environments. Thus, it is important to better understand the low-altitude adaptation mechanisms of Tibetan pigs. We performed a comparative analysis between highland and lowland Tibetan pigs using genotyping data to investigate their genetic differences. Our results showed that immune-related genes were selected in highland Tibetan pigs, whereas genes associated with reproduction, growth and development, and blood pressure regulation were selected in lowland Tibetan pigs. These findings will contribute to research into the genetic basis of environmental adaptation and important economic traits in Tibetan pigs and provide genetic targets for breeding programs to improve Tibetan pigs. Abstract Tibetan pigs are indigenous to the Qinghai–Tibet Plateau and have been the subject of extensive genomic research primarily focused on their adaptation to high altitudes. However, genetic modifications associated with their response to low-altitude acclimation have not been thoroughly explored. To investigate the genetic basis underlying the low-altitude acclimation of Tibetan pigs, we generated and analyzed genotyping data of Tibetan pigs that inhabit high-altitude regions (average altitude 4000 m) and Tibetan pigs that have inhabited nearby low-altitude regions (average altitude 500 m) for approximately 20 generations. We found that the highland and lowland Tibetan pigs have distinguishable genotype and phenotype variations. We identified 46 and 126 potentially selected SNPs associated with 29 and 56 candidate genes in highland and lowland Tibetan pigs, respectively. Candidate genes in the highland Tibetan pigs were involved in immune response (NFYC and STAT1) and radiation (NABP1), whereas candidate genes in the lowland Tibetan pigs were related to reproduction (ESR2, DMRTA1, and ZNF366), growth and development (NTRK3, FGF18, and MAP1B), and blood pressure regulation (CARTPT). These findings will help to understand the mechanisms of environmental adaptation in Tibetan pigs and offer valuable information into the genetic improvement of Tibetan pigs pertaining to low-altitude acclimation and economic traits.
The Normalized Cut criterion and algorithm

We present a new view of image segmentation by pairwise similarities. We interpret the similarities as edge flows in a Markov random walk and study the eigenvalues and eigenvectors of the walk's transition matrix. This interpretation shows that spectral methods for clustering and segmentation have a probabilistic foundation. In particular, we prove that the Normalized Cut method arises naturally from our framework. Finally, the framework provides a principled method for learning the similarity function as a combination of features.
Learning Segmentation by Random Walks

We present a new view of image segmentation by pairwise similarities. We interpret the similarities as edge ows in a Markov random walk and study the eigenvalues and eigenvectors of the walk's transition matrix. This interpretation shows that spectral methods for clustering and segmentation have a probabilistic foundation. In particular, we prove that the Normalized Cut method arises naturally from our framework. Finally, the framework provides a principled method for learning the similarity function as a combination of features.
Multiple Lines of Evidence Support 199 SARS-CoV-2 Positively Selected Amino Acid Sites

SARS-CoV-2 amino acid variants that contribute to an increased transmissibility or to host immune system escape are likely to increase in frequency due to positive selection and may be identified using different methods, such as codeML, FEL, FUBAR, and MEME. Nevertheless, when using different methods, the results do not always agree. The sampling scheme used in different studies may partially explain the differences that are found, but there is also the possibility that some of the identified positively selected amino acid sites are false positives. This is especially important in the context of very large-scale projects where hundreds of analyses have been performed for the same protein-coding gene. To account for these issues, in this work, we have identified positively selected amino acid sites in SARS-CoV-2 and 15 other coronavirus species, using both codeML and FUBAR, and compared the location of such sites in the different species. Moreover, we also compared our results to those that are available in the COV2Var database and the frequency of the 10 most frequent variants and predicted protein location to identify those sites that are supported by multiple lines of evidence. Amino acid changes observed at these sites should always be of concern. The information reported for SARS-CoV-2 can also be used to identify variants of concern in other coronaviruses.
Modelling intra-salt layers when building velocity models for depth migration. Examples of the Santos Basins, Brazilian offshore

Building seismic velocity models honouring complexities evident from seismic data is fundamental to generate inputs for several applications in seismic modeling and imaging. This is particularly important for complex areas, such as the Pre-Salt section of Santos Basin, in the Brazilian offshore. We present a methodology to build velocity models incorporating the geological features identified in legacy seismic data for this basin. Of particular interest is, the internal stratification within the salt section. To characterize a geological layer we propose the use of model-based impedance that combines the geological knowledge from wells and seismic interpretations using rock property relationships. The results are shown in both gathers and stacked migrated sections with improvements in the flattening and the focusing of target reflectors. This approach can also be extended to generate an input velocity model for FWI migration process.
The Development of a Symptom Questionnaire for Assessing Virtual Reality Viewing Using a Head-Mounted Display

Purpose. Virtual reality devices, including virtual reality head-mounted displays, are becoming increasingly accessible to the general public as technological advances lead to reduced costs. However, there are numerous reports that adverse effects such as ocular discomfort and headache are associated with these devices. To investigate these adverse effects, questionnaires that have been specifically designed for other purposes such as investigating motion sickness have often been used. The primary purpose of this study was to develop a standard questionnaire for use in investigating symptoms that result from virtual reality viewing. In addition, symptom duration and whether priming subjects elevates symptom ratings were also investigated. Methods. A list of the most frequently reported symptoms following virtual reality viewing was determined from previously published studies and used as the basis for a pilot questionnaire. The pilot questionnaire, which consisted of 12 nonocular and 11 ocular symptoms, was administered to two groups of eight subjects. One group was primed by having them complete the questionnaire before immersion; the other group completed the questionnaire postviewing only. Postviewing testing was carried out immediately after viewing and then at 2-min intervals for a further 10 min. Results. Priming subjects did not elevate symptom ratings; therefore, the data were pooled and 16 symptoms were found to increase significantly. The majority of symptoms dissipated rapidly, within 6 min after viewing. Frequency of endorsement data showed that approximately half of the symptoms on the pilot questionnaire could be discarded because <20% of subjects experienced them. Conclusions. Symptom questionnaires to investigate virtual reality viewing can be administered before viewing, without biasing the findings, allowing calculation of the amount of change from pre- to postviewing. However, symptoms dissipate rapidly and assessment of symptoms needs to occur in the first 5 min postviewing. Thirteen symptom questions, eight nonocular and five ocular, were determined to be useful for a questionnaire specifically related to virtual reality viewing using a head-mounted display.
Game-theoretical analysis of deep neural networks

In recent years, deep learning has imposed itself as the state of the art ML method in many real-world tasks, such as computer vision or natural language processing to name a few [1]. While achieving impressive performance in practice, training DNNs requires optimizing a non-convex non-concave objective function even in the case of linear activation functions and can potentially lead to local minima that are arbitrary far from global minimum. This, however, is not the typical behaviour observed in practice, as several works [2, 3] showed empirically that even in the case of training the state-of-the-art convolutional or fully-connected feedforward neural networks one does not converge to suboptimal local minima. Such a mysterious behaviour made studying the loss surface of DNNs and characterizing their local minima one of the topics of high scientific importance for the ML community.
Historical Nankai-Suruga megathrust earthquakes recorded by tsunami and terrestrial mass movement deposits on the Shirasuka coastal lowlands, Shizuoka Prefecture, Japan

Geological investigations of coastal sediment sequences play a key role in verifying earthquake and tsunami characteristics inferred from historical records. In this paper, we present a multi-proxy investigation of a coastal lowland site facing the Nankai-Suruga megathrust and appraise evidence for tsunamis and earthquake-triggered terrestrial mass movements occurring over the last 800 years. Combining a high-resolution chronology with X-ray computed tomography and analyses of particle size, diatoms, pollen, non-pollen palynomorphs and aerial photographs, we present the most compelling geological evidence of the 1361 CE Kōan (also known as Shōhei) tsunami reported to date from any site along the megathrust. This finding is consistent with either of two recent hypotheses: a single larger rupture of both the Nankai and Tōnankai regions or two smaller ruptures separated by a few days. Enhancing the site chronology using Bayesian age modelling, we verify evidence for inundation during the 1498 CE Meiō tsunami. While previous investigations identified evidence for historically recorded tsunamis in 1605, 1707 and 1854 CE and a storm surge in 1680 or 1699 CE, we encountered a thick sand layer rather than discrete extreme wave deposits in this interval. The overprinting of evidence highlights the potential for geological records to underestimate the frequency of these events. A terrestrial mass movement also deposited a sand layer at the site; radionuclide dating and aerial photographs provide independent confirmation that this may have been triggered by intense shaking in 1944 CE during the most recent great Nankai-Suruga megathrust earthquake.
Sparsity-based Recovery of Finite Alphabet Solutions of Underdetermined Linear System

We consider the problem of estimating a deterministic finite alphabet vector f from underdetermined measurements y = Af where A is a given (random) matrix. Two new methods are introduced for the recovery of finite alphabet signals via `1 minimization through convex optimization. The first method is based on regularization, whereas in the second approach, the problem is formulated as the recovery of sparse signals after a suitable sparse transform. The regularization-based method is less complex than the transformation-based one. When p = 2 and (n,N) grows proportionally, it is proved that the same conditions are necessary and sufficient for each method to perform signal recovery. According to these necessary and sufficient conditions, the two methods yield similar performance results. When p > 2, the existence of necessary and sufficient conditions for signal recovery remains an open problem. However, a conjecture on the behaviour of the transform-based method can be given and is supported by experimental results. In addition, these experimental results show that the transform-based approach performs better than the regularization-based one.
Effect of Sel-Plex and Bioplex substitution of inorganic trace mineral sources on performance, feathering, and hock condition of broilers.

A trial was conducted to compare performance, footpad, gait and feathering responses in broilers fed diets in which inorganic trace minerals were replaced by increasing levels of organic sources. There were 8 replicate pens of 75 mixed-sex Hubbard JV broilers for each of 4 treatments: 1) inorganic forms (CuSO4, ZnOxide, FeSO4, MnOxide, NaSelenite) at 15 ppm Cu, 60 ppm Zn, Mn and Fe, and 0.3 ppm Se; 2) organic minerals: 5 ppm Cu and 15 ppm Zn, Mn and Fe in Bioplex (Alltech Inc.) form, and 0.1 ppm Se as Sel-Plex (Alltech Inc.); while treatments 3 and 4 contained the same organic mineral sources as trt 2 and respectively 2 and 3-fold higher levels. Diets were based on corn and soy. Birds were housed on straw litter for the 42 day trial with performance parameters measured at 21 and 42 days. Gait score was measured at day 21 and 42 (70 birds at day 21 and 100 birds per treatment at day 42). Hock burn scores, gait scores (21 and 42 days) and feather scores (42 days) were determined on the same birds. Data were subjected to ANOVA followed by a Duncan’s post hoc test. Arcsine transformation of percentage data occurred prior to analysis. Increasing amounts of dietary Bioplex trace minerals tended to improve (NS) body weight at 42 days ( 2053, 2068, 2092 and 2084 g for trts 14, respectively). FCR (1.88-1.90) was unaffected. No effect on gait, footpad or hock scores was observed. Feather scores at 21 days increased with dietary Bioplex levels from 22.9 in trt 1 to 24.5 in trt 4 (not significant). At 42 days there was also a trend toward increased feathering. It can be concluded that inorganic trace mineral levels in broiler feed can be reduced to at least 1/3 of the standard levels when replace with organic forms (Bioplex, Sel-Plex) without compromising performance. __________________________________________________________________________________
Evaluation of Mobility Models For Vehicular Ad-Hoc Network Simulations

There is a growing interest in deployment and evaluation of routing protocols for Vehicular Ad-Hoc Wireless Networks (VANETs) in urban contexts. The mobility model of nodes is one of the most important factors that impacts the evaluation of any wireless ad-hoc routing protocol using simulations. In this paper we make the case that the state-of-the-art simulation techniques do not effectively model many important factors that come into play in urban mobile environment. We present two new simple mobility models for VANETs that account for constrained movement pattern of vehicles on urban streets. Using traffic patterns and street maps, we perform a comprehensive comparison of the impact of our two new mobility models against two earlier mobility models. Unlike prior results in this area, our results demonstrate that the mobility model used in simulation does significantly impact the delivery ratio and packet delays in VANETs. With plenty of room for further improvement, our models provide a sound starting point for the development of more realistic and accurate mobility and obstacle models for VANET simulations.
Istituto Di Analisi Dei Sistemi Ed Informatica Consiglio Nazionale Delle Ricerche

Any institution that disseminates data in aggregated form has the duty to ensure that individual confidential information is not disclosed, either by not releasing data or by perturbing the released data, while maintaining data utility. Controlled tabular adjustment (CTA) is a promising technique of the second type where a protected table that is close to the original one in some chosen distance is constructed. We attempt, for the first time, to solve CTA with Euclidean distances; this gives rise to difficult Mixed Integer Quadratic Problems (MIQPs) with pairs of linked semi-continuous variables. We provide a novel analysis of Perspective Reformulations (PRs) for this special structure; in particular, we devise a Projected PR (P2R) which is piecewise-conic but simplifies to a (nonseparable) MIQP when the instance is symmetric. We then compare different formulations of the CTA problem, showing that the ones based on P2R most often obtain better computational results.
A Precise High-Dimensional Asymptotic Theory for Boosting and Min-L1-Norm Interpolated Classifiers

This paper establishes a precise high-dimensional asymptotic theory for boosting on separable data, taking statistical and computational perspectives. We consider the setting where the number of features (weak learners) $p$ scales with the sample size $n$, in an over-parametrized regime. Under a broad class of statistical models, we provide an exact analysis of the generalization error of boosting, when the algorithm interpolates the training data and maximizes the empirical $\ell_1$-margin. The relation between the boosting test error and the optimal Bayes error is pinned down explicitly. In turn, these precise characterizations resolve several open questions raised in \cite{breiman1999prediction, schapire1998boosting} surrounding boosting. On the computational front, we provide a sharp analysis of the stopping time when boosting approximately maximizes the empirical $\ell_1$ margin. Furthermore, we discover that the larger the overparametrization ratio $p/n$, the smaller the proportion of active features (with zero initialization), and the faster the optimization reaches interpolation. At the heart of our theory lies an in-depth study of the maximum $\ell_1$-margin, which can be accurately described by a new system of non-linear equations; we analyze this margin and the properties of this system, using Gaussian comparison techniques and a novel uniform deviation argument. Variants of AdaBoost corresponding to general $\ell_q$ geometry, for $q > 1$, are also presented, together with an exact analysis of the high-dimensional generalization and optimization behavior of a class of these algorithms.
Methane emission through ebullition from an estuarine mudflat: 2. Field observations and modeling of occurrence probability

Ebullition can transport methane (CH4) at a much faster rate than other pathways, albeit over limited time and area, in wetland soils and sediments. However, field observations present large uncertainties in ebullition occurrences and statistic models are needed to describe the function relationship between probability of ebullition occurrence and water level changes. A flow‐through chamber was designed and installed in a mudflat of an estuarine temperate marsh. Episodic increases in CH4 concentration signaling ebullition events were observed during ebbing tides (15 events over 456 ebbing tides) and occasionally during flooding tides (4 events over 455 flooding tides). Ebullition occurrence functions were defined using logistic regression as the relative initial and end water levels, as well as tidal amplitudes were found to be the key functional variables related to ebullition events. Ebullition of methane was restricted by a surface frozen layer during winter; melting of this layer during spring thaw caused increases in CH4 concentration, with ebullition fluxes similar to those associated with large fluctuations in water level around spring tides. Our findings suggest that initial and end relative water levels, in addition to tidal amplitude, partly regulate ebullition events in tidal wetlands, modulated by the lunar cycle, storage of gas bubbles at different depths and seasonal changes in the surface frozen layer. Maximum tidal strength over a few days, rather than hourly water level, may be more closely associated with the possibility of ebullition occurrence as it represents a trade‐off time scale in between hourly and lunar periods.
Aalborg Universitet Bounds on information combining Land

When the same data sequence is transmitted over two independent channels, or when a data sequence is transmitted twice but independently over the same channel, the independent observations can be combined at the receiver side. From an information-theory point of view, the overall mutual information between the data sequence and the received sequences represents a combination of the mutual information of the two channels. This concept is termed information combining. In this paper, a lower bound and an upper bound on the combined information is presented, and it is proved that these bounds are tight. Furthermore, this principle is extended to the computation of extrinsic information on single code bits for a repetition code and for a single parity-check code of length three, respectively. For illustration of the concept and the bounds on information combining, two applications are considered. First, bounds on the information processing characteristic (IPC) of a parallel concatenated code are derived from its extrinsic information transfer (EXIT) chart. Second, bounds on the EXIT chart for an outer repetition code and for an outer single parity-check code of a serially concatenated coding scheme are computed.
In-situ measurement of objective lens data of a high-resolution electron microscope.

Bragg-reflex images of small individual crystallites in the size range of 20-100 A diameter with known crystallographic orientation were used in a transmission electron microscope to determine in-situ: (a) the relationship between objective lens current (or accelerating voltage) changes in discrete steps and corresponding defocus, (b) the spherical aberration coefficient, and (c) the axial chromatic aberration coefficient of the objective lens. The accuracy of the described method is better than 5%. The same specimen can advantageously be used to properly aline the illuminating beam with respect to the optical axis.
Investigation of Activated Sludge Properties under Different Electrical Field and in the Presence of Calcium

The purpose of this research was to study the impact of direct current (DC) application on activated sludge (AS) properties. A control reactor without an electrical field and a series of 1.5L batch reactors were filled with activated sludge at two levels of mixed liquor suspended solid concentrations (LR MLSS: 5000-7000 mg/L and HR MLSS: 10000-12000 mg/L) and were subjected to four electrical modes (continuous, 5ON:5OFF, 5ON:10OFF and 5ON:15OFF) for 48 hours. Experiments were performed for both AS alone and AS mixed with different concentrations of calcium salt (250 and 750 mg/L). The sludge volume index (SVI), time to filtration (TTF), particle sizes, specific oxygen consumption rate, soluble microbial products (SMP) and phosphate concentrations were measured before and after the experiments. Designed reactors’ parameters permitted the microorganisms to preserve their bioactivity. Results showed that the continuous electrical mode achieved the highest reduction in SVI. At all electrical modes, over 75% reduction in phosphate concentration was achieved. For most of the AS properties, the impact of EC at LR MLSS was higher than that at HR MLSS. A longer exposure time to DC resulted in smaller particle sizes. As the exposure time to DC decreased, the amount of SMP deposited on the anode surface increased. More calcium was deposited on the cathode surface at a longer exposure time. Furthermore, the addition of 250 mg Ca2+/L to AS, in the absence of an electrical field, resulted in 33% and 63 % higher SMP and phosphate removal efficiency. The results can be applied to better control electrocoagulation processes within various wastewater treatment system including MBR and SMEBR.