Miracle-dz/UniFAR-FTUs huggingface dataset:
Go with the flow—biology and genetics of the lactation cycle

Lactation is a dynamic process, which evolved to meet dietary demands of growing offspring. At the same time, the mother's metabolism changes to meet the high requirements of nutrient supply to the offspring. Through strong artificial selection, the strain of milk production on dairy cows is often associated with impaired health and fertility. This led to the incorporation of functional traits into breeding aims to counteract this negative association. Potentially, distributing the total quantity of milk per lactation cycle more equally over time could reduce the peak of physiological strain and improve health and fertility. During lactation many factors affect the production of milk: food intake; digestion, absorption, and transportation of nutrients; blood glucose levels; activity of cells in the mammary gland, liver, and adipose tissue; synthesis of proteins and fat in the secretory cells; and the metabolic and regulatory pathways that provide fatty acids, amino acids, and carbohydrates. Whilst the endocrine regulation and physiology of the dynamic process of milk production seems to be understood, the genetics that underlie these dynamics are still to be uncovered. Modeling of longitudinal traits and estimating the change in additive genetic variation over time has shown that the genetic contribution to the expression of a trait depends on the considered time-point. Such time-dependent studies could contribute to the discovery of missing heritability. Only very few studies have estimated exact gene and marker effects at different time-points during lactation. The most prominent gene affecting milk yield and milk fat, DGAT1, exhibits its main effects after peak production, whilst the casein genes have larger effects in early lactation. Understanding the physiological dynamics and elucidating the time-dependent genetic effects behind dynamically expressed traits will contribute to selection decisions to further improve productive and healthy breeding populations.
Real-time Tracking in Image Sequences based-on Parameters Updating with Temporal and Spatial Neighborhoods Mixture Gaussian Model

— Gaussian mixture background model is widely used in moving target detection of the image sequences. However, traditional Gaussian mixture background model usually considers the time continuity of the pixels, and establishes background through statistical distribution of pixels without taking into account the pixels’ spatial similarity, which will cause noise, imperfection and other problems. This paper proposes a new Gaussian mixture modeling approach, which combines the color and gradient of the spatial information, and integrates the spatial information of the pixel sequences to establish Gaussian mixture background. The experimental results show that the movement background can be extracted accurately and efficiently, and the algorithm is more robust, and can work in real time in tracking applications.
The NtrC Family Regulator AlgB, Which Controls Alginate Biosynthesis in Mucoid Pseudomonas aeruginosa, Binds Directly to the algD Promoter

ABSTRACT Alginate production in mucoid (MucA-defective) Pseudomonas aeruginosa is dependent upon several transcriptional regulators, including AlgB, a two-component response regulator belonging to the NtrC family. This role of AlgB was apparently independent of its sensor kinase, KinB, and even the N-terminal phosphorylation domain of AlgB was dispensable for alginate biosynthetic gene (i.e., algD operon) activation. However, it remained unclear whether AlgB stimulated algD transcription directly or indirectly. In this study, microarray analyses were used to examine a set of potential AlgB-dependent, KinB-independent genes in a PAO1 mucA background that overlapped with genes induced by d-cycloserine, which is known to activate algD expression. This set contained only the algD operon plus one other gene that was shown to be uninvolved in alginate production. This suggested that AlgB promotes alginate production by directly binding to the algD promoter (PalgD). Chromosome immunoprecipitation revealed that AlgB bound in vivo to PalgD but did not bind when AlgB had an R442E substitution that disrupted the DNA binding domain. AlgB also showed binding to PalgD fragments in an electrophoretic mobility shift assay at pH 4.5 but not at pH 8.0. A direct systematic evolution of ligands by exponential enrichment approach showed AlgB binding to a 50-bp fragment located at bp −224 to −274 relative to the start of PalgD transcription. Thus, AlgB belongs to a subclass of NtrC family proteins that can activate promoters which utilize a sigma factor other than σ54, in this case to stimulate transcription from the σ22-dependent PalgD promoter.
Metal–Organic Frameworks as Promising Photosensitizers for Photoelectrochemical Water Splitting

Ti‐based metal‐organic frameworks (MOFs) are demonstrated as promising photosensitizers for photoelectrochemical (PEC) water splitting. Photocurrents of TiO2 nano wire photoelectrodes can be improved under visible light through sensitization with aminated Ti‐based MOFs. As a host, other sensitizers or catalysts such as Au nanoparticles can be incorporated into the MOF layer thus further improving the PEC water splitting efficiency.
The hydrogen peroxide-sensitive proteome of the chloroplast in vitro and in vivo

Hydrogen peroxide (H2O2) evolves during cellular metabolism and accumulates under various stresses causing serious redox imbalances. Many proteomics studies aiming to identify proteins sensitive to H2O2 used concentrations that were above the physiological range. Here the chloroplast proteins were subjected to partial oxidation by exogenous addition of H2O2 equivalent to 10% of available protein thiols which allowed for the identification of the primary targets of oxidation. The chosen redox proteomic approach employed differential labeling of non-oxidized and oxidized thiols using sequential alkylation with N-ethylmaleimide and biotin maleimide. The in vitro identified proteins are involved in carbohydrate metabolism, photosynthesis, redox homeostasis, and nitrogen assimilation. By using methyl viologen that induces oxidative stress in vivo, mostly the same primary targets of oxidation were identified and several oxidation sites were annotated. Ribulose-1,5-bisphosphate (RubisCO) was a primary oxidation target. Due to its high abundance, RubisCO is suggested to act as a chloroplast redox buffer to maintain a suitable redox state, even in the presence of increased reactive oxygen species release. 2-cysteine peroxiredoxins (2-Cys Prx) undergo redox-dependent modifications and play important roles in antioxidant defense and signaling. The identification of 2-Cys Prx was expected based on its high affinity to H2O2 and is considered as a proof of concept for the approach. Targets of Trx, such as phosphoribulokinase, glyceraldehyde-3-phosphate dehydrogenase, transketolase, and sedoheptulose-1,7-bisphosphatase have at least one regulatory disulfide bridge which supports the conclusion that the identified proteins undergo reversible thiol oxidation. In conclusion, the presented approach enabled the identification of early targets of H2O2 oxidation within the cellular proteome under physiological experimental conditions.
Design of antisense oligonucleotides stabilized by locked nucleic acids.

The design of antisense oligonucleotides containing locked nucleic acids (LNA) was optimized and compared to intensively studied DNA oligonucleotides, phosphorothioates and 2'-O-methyl gapmers. In contradiction to the literature, a stretch of seven or eight DNA monomers in the center of a chimeric DNA/LNA oligonucleotide is necessary for full activation of RNase H to cleave the target RNA. For 2'-O-methyl gapmers a stretch of six DNA monomers is sufficient to recruit RNase H. Compared to the 18mer DNA the oligonucleotides containing LNA have an increased melting temperature of 1.5-4 degrees C per LNA depending on the positions of the modified residues. 2'-O-methyl nucleotides increase the T(m) by only <1 degree C per modification and the T(m) of the phosphorothioate is reduced. The efficiency of an oligonucleotide in supporting RNase H cleavage correlates with its affinity for the target RNA, i.e. LNA > 2'-O-methyl > DNA > phosphorothioate. Three LNAs at each end of the oligonucleotide are sufficient to stabilize the oligonucleotide in human serum 10-fold compared to an unmodified oligodeoxynucleotide (from t(1/2) = approximately 1.5 h to t(1/2) = approximately 15 h). These chimeric LNA/DNA oligonucleotides are more stable than isosequential phosphorothioates and 2'-O-methyl gapmers, which have half-lives of 10 and 12 h, respectively.
Tears for girls and teeth for boys: the influence of gender on children’s depiction of sadness and anger in their drawings

Abstract Up to now, very few studies investigated the influence of gender on the depiction of emotions in children’s drawings. However, the literature on emotions reveals differences between boys and girls in various kinds of tasks (e.g. recognising emotional facial expressions, understanding an emotional situation, etc.). Therefore, we examined the impact of gender on the depiction of sadness and anger. We took into account children’s gender but also the gender of the character expressing the target emotion. Forty-four boys and forty-seven girls aged 7–8 and thirty-six boys and fifty-three girls aged 9–10 were asked to listen to stories where the main character (either a male or a female) was feeling sad or angry and then to draw the facial cues corresponding to the target emotion. Two methods were used to rate the drawings: judges assessed the correct vs. incorrect depiction of the two target emotions and a content analysis was then conducted on the correct drawings so as to reveal the type of facial cues used by children. By showing the major influence of children’s gender on their depiction of sadness and anger, our findings offer promising lines of research in educational and clinical settings.
Time-Discrete Geodesics in the Space of Shells Time-Discrete Geodesics in the Space of Shells

Based on a paper from Heeren et al. this report presents a method of finding a natural deformation between two shapes with a given correspondence. It is based on minimizing an energy function derived from results of elasticity theory. Different than other algorithms this energy has only parameters with concrete physical meanings. Furthermore proper discretization methods are presented. The resulting algorithm is a nonlinear optimization in R3M(K−1) depending on the number of vertices of the input shapes and the number of the calculated intermediate shapes of the deformation. The computation can be sped up by a multi-level optimization approach.
Application of ℓp-regularized least squares for 0≤p≤1 in estimating discrete spectrum of relaxations for electromagnetic induction responses

The EMI response of a target can be accurately modeled by a sum of real exponentials. However, it is difficult to obtain the model parameters from measurements when the number of exponentials in the sum is unknown and the summands are highly correlated. Traditionally, the time constants and residues are estimated by nonlinear iterative search. Most of these methods, however, often suffer from (a) sub-optimal solutions that are far from the truth and (b) complex parameters that do not have physical meaning. In this paper, the estimation problem is reformulated into a linear system by enumerating the relaxation parameter space. The model parameters are then estimated through a modified Lp-regularized least squares algorithm for 0 <= p <= 1. Using tests on synthetic data and laboratory measurement of known targets the proposed method is shown to provide satisfactory and stable estimates of the model parameters. From the lab data, we demonstrate that the proposed method can correctly estimate the relaxation time constants of a target, which is of great value as the time constants are position and orientation invariant and can be used as features in target discrimination. We also propose an empirical method to select the regularization parameter to the Lp-regularization problem. The resulting selection rule has the logged regularization parameter in a linear relationship with the noise level. This simple relationship allows the proposed method be applied in practice with short computation time while being robust.
“How to Do Things With Words”: Mechanisms Bridging Language and Action in Management Research

We review the past quarter century of literature linking language and action in management research published from 1993 through 2017. Different from recent in-depth reviews that focus narrowly on particular forms that words take, we look across these different kinds of word assemblages to uncover broad themes and mechanisms that link words with action outcomes in organizational settings. Classifying common conceptual approaches and prominent outcomes, we systematize and synthesize existing work on how to do things with words, identifying points of tension or contradiction as well as consistencies or overlaps across areas of research and methodologies. In addition, we go beyond typologies of how words are constructed to unearth how words function in the service of action; in so doing, we articulate three underlying mechanisms that connect words to action—resonance, enactment, and power—and discuss each. We end with a discussion of promising avenues for future research.
Tropomyosin-like seven residue periodicity in three immunologically distinct streptococal M proteins and its implications for the antiphagocytic property of the molecule

Partial sequences of three immunologically distinct group A streptococcal M proteins (M5, M6, and M24) revealed significant homology with each other, certain amino acid residues being conserved within the three molecules. In addition, a common feature of the sequenced regions of these M proteins was their high alpha-helical potential and the presence of a repeating seven residue periodicity that is characteristic of the double helical coiled-coil molecule, tropomyosin. The existence of a tropomyosin-like seven residue periodicity strongly suggests that regions of these three M proteins may participate in intra- and/or intermolecular coiled-coil interactions. Because of the constraints imposed by such a repeating periodicity, certain conserved residues within the M proteins would occupy spatially equivalent positions in the tertiary structure of these molecules. This common characteristic could play an important role in the common antiphagocytic property of the immunologically diverse M molecules. In addition to similarities in the secondary structure of M proteins and tropomyosin, significant sequence homology has also been observed between certain regions of these molecules with up to 50% identical residues. As a result of the striking structural similarity with tropomyosin, M proteins may play a regulatory role in the contractile mechanisms involved in phagocytosis.
Nucleotide Diversity and Selection Signature in the Domesticated Silkworm, Bombyx mori, and Wild Silkworm, Bombyx mandarina

Abstract To investigate the patterns of nucleotide diversity in domesticated silkworm, Bombyx mori L. (Lepidoptera: Bombycidae) and its wild relative, Chinese wild silkworm, Bombyx mandarina Moore, we sequenced nine nuclear genes. Neutrality test and coalescent simulation for these genes were performed to look at bottleneck intensity and selection signature; linkage disequilibrium (LD) within and between loci was employed to investigate allele association. As a result, B. mori lost 33–49% of nucleotide diversity relative to wild silkworm, which is similar to the loss levels found in major cultivated crops. Diversity of B. mori is significantly lower than that of B. mandarina measured as &pgr;total (0.01166 vs. 0.1741) or &thgr;W(0.01124 vs. 0.02206). Bottleneck intensity of domesticated silkworm is 1.5 (in terms of k = Nb /d, Nb -bottleneck population size; d-bottleneck duration) with different durations. Gene DefA showed signature of artificial selection by all analysis methods and might experience strong artificial selection in B. mori during domestication. For nine loci, both curves of LD decay rapidly within 200 bp and drop slowly when distance is > 200 bp, although that of B. mori decays slower than B. mandarina at loci investigated. However, LD could not be estimated at DefA in B. mori and at ER in both silkworms. Elevated LD observed in B. mori may be indicator of selection and demographic events.
Matrix transformations and application to perturbed problems of some sequence spaces equations with operators

Given any sequence z = (zn)n≥1 of positive real numbers and any set E of complex sequences, we write Ez for the set of all sequences y = (yn)n≥1 such that y/z = (yn/zn)n≥1 ∈ E; in particular, cz = s z denotes the set of all sequences y such that y/z converges. Starting with the equation Fx = Fb we deal with some perturbed equation of the form E+ Fx = Fb, where E is a linear space of sequences. In this way we solve the previous equation where E = (Ea)T and (E,F) ∈ {(`∞, c) , (c0, `∞) , (c0, c) , (`p, c) , (`p, `∞) , (w0, `∞)} with p ≥ 1, and T is a triangle.
Prevalence of Non-Tuberculosis Mycobacterial Infections among Tuberculosis Suspects in Iran: Systematic Review and Meta-Analysis

Introduction The infections due to Non-Tuberculosis Mycobacteria (NTM) are becoming an important health problem in many countries in the world. Globally, an increase in NTM infections has been reported from many countries around the world. However, limited information is available about the prevalence of NTM infections in Iran. Material and Methods The data of the prevalence of NTM infections were collected from databases such as PubMed, Web of science, Cochrane Library, Embase, Scopus, Iranmedex, and Scientific Information Database. Comprehensive Meta-Analysis (V2.0, Biostat) software was used to analyze the data. Results The meta-analyses showed that the prevalence of NTM infections was 10.2% (95% confidence interval [95% CI] 6.3-15.9) among culture-positive cases of tuberculosis (TB) in Iran. The further stratified analyses indicated that the prevalence of NTM was higher in studies that were done after year 2000. Additionally, M. simiae (43.3% [95% CI 36.8-50.0]), M. intracellucar (27.3% [95% CI 0.7-95.5]) and M. fortuitum (22.7% [95% CI 16.1-30.9]) were the most prevalent NTM species, respectively. Discussion The relatively high prevalence of NTM infections (10.2%) among culture positive cases for TB underlines the need for greater enforcement of infection control strategies. Establishment of appropriate diagnostic criteria and management guidelines for NTM diseases and expanding the number and quality of regional reference laboratories may facilitate more accurate action for prevention and control of NTM infections in Iran.
A missing link in root-to-frontier tree pattern matching

Abstra t. Tree pattern mat hing (tpm) algorithms play an important role in pra ti al appli ations su h as ompilers and XML do ument validation. Many tpm algorithms based on tree automata have appeared in the literature. For reasons of eÆ ien y, these automata are preferably deterministi . Deterministi root-to-frontier tree automata (drftas) are less powerful than nondeterministi ones, and no root-to-frontier tpm algorithm using drftas has appeared so far. Ho mann & O'Donnell [HO82℄ presented a root-to-frontier tpm algorithm based on an Aho-Corasi k automaton re ognizing tree stringpaths, but no relationship between this algorithm and algorithms using tree automata has been des ribed. In this paper, we show that a spe i drfta an be used for stringpath mat hing in a root-to-frontier tpm algorithm. This algorithm has not appeared in the literature before, and provides a missing link between tpm algorithms using stringpath automata and those using tree automata.
基於相依詞向量的剖析結果重估與排序(N-best Parse Rescoring Based on Dependency-Based Word Embeddings)

Rescoring approaches for parsing aim to re-rank and change the order of parse trees produced by a general parser for a given sentence. The re-ranking quality depends on the precision of the rescoring function. However it is a challenge to design an appropriate function to determine the qualities of parse trees. No matter which method is used, Treebank is a widely used resource in parsing task. Most approaches utilize complex features to re-estimate the tree structures of a given sentence [1, 2, 3]. Unfortunately, sizes of treebanks are generally small and insufficient, which results in a common problem of data sparseness. Learning knowledge from analyzing large-scaled unlabeled data is compulsory and proved useful in the previous works [4, 5, 6]. How to extract useful information from unannotated large scale corpus has been a research issue. Word embeddings have become increasingly popular lately, proving to be valuable as a source of features in a broad range of NLP tasks [7, 8, 9].
A model for the metallicity evolution of damped Lyman α systems

We apply a physically motivated stellar feedback model to analyse the statistical properties of damped Lyman a systems (DLAs) expected in the concordance cold dark matter (CDM) model. Our feedback model produces extended low-metallicity cold gaseous discs around small galaxies. Since the space density of galaxies with low circular speeds is high, these discs dominate the cross-section for the identification of DLAs at all redshifts. The combined effects of star formation, outflows and infall in our models result in mild evolution of the N H I weighted metallicity content in DLAs with redshift, consistent with observations. According to our model, DLAs contribute only a small fraction of the volume averaged star formation rate at redshifts 7$5. Our model predicts weak evolution in Ω H I over the redshift range z = 0-5. Furthermore, we show that the cosmological evolution of Ω H I and the cosmic star formation rate are largely disconnected and conclude that the evolution of Ω H I as a function of redshift is more likely to tell us about feedback processes and the evolution of the outer gaseous components of small galaxies than about the cosmic history of star formation.
New Attestation Based Security Architecture for In-Vehicle Communication

This paper presents a novel security architecture for in-vehicle communication. The ratio of electronics to vehicle equipment is steadily increasing. And novel vehicles will also have connectibility to public networks to provide many kinds of services. Therefore, they are expected to suffer from a wide variety of threats and the electronic control units (ECUs) embedded in them may execute execute malicious programs because of tampering. The remote attestation scheme with the trusted platform module (TPM) has been attracting a great deal of attention to cope with such issues. However, it is not feasible for vehicle systems because the conventional attestation process cannot adapt to in-vehicle communication and TPM cannot adapt to time-constrained vehicle systems. We propose an attestation based security architecture that is suitable for novel vehicles.
Multilinear Isometric Embedding for visual pattern analysis

This paper proposes a novel tensor based dimensionality reduction algorithm called Multilinear Isometric Embedding (MIE) based on a representative manifold learning algorithm Isomap. Unlike Isomap that unfolds input data to the vector form, MIE directly works on more general tensor representation and utilizes iterative strategy to seek the low-dimensional equivalence, which best preserves the global geometry. By avoiding the problems caused by data vectorization, MIE reduces the data analysis difficulty and computational cost. More importantly, MIE keeps the intrinsic tensor structure of the data in low-dimensional representation. Meanwhile, MIE inherits the merits of Isomap, i.e., the ability of uncovering the global geometry of high-dimensional observations. By providing explicit embedding function, MIE makes the embedding of new data points to the low-dimensional space straightforward. Experiments on various datasets validate the effectiveness of proposed method.