Miracle-dz/UniFAR-FTUs huggingface dataset:
Erasing gametes to write blastocysts: metabolism as the new player in epigenetic reprogramming

Abstract Understanding preimplantation embryonic development is crucial for the improvement of assisted reproductive technologies and animal production. To achieve this goal, it is important to consider that gametes and embryos are highly susceptible to environmental changes. Beyond the metabolic adaptation, the dynamic status imposed during follicular growth and early embryogenesis may create marks that will guide the molecular regulation during prenatal development, and consequently impact the offspring phenotype. In this context, metaboloepigenetics has gained attention, as it investigates the crosstalk between metabolism and molecular control, i.e., how substrates generated by metabolic pathways may also act as players of epigenetic modifications. In this review, we present the main metabolic and epigenetic events of pre-implantation development, and how these systems connect to open possibilities for targeted manipulation of reproductive technologies and animal production systems.
CRISPR/Cas9-mediated correction of mutated copper transporter ATP7B

Wilson's disease (WD) is a monogenetic liver disease that is based on a mutation of the ATP7B gene and leads to a functional deterioration in copper (Cu) excretion in the liver. The excess Cu accumulates in various organs such as the liver and brain. WD patients show clinical heterogeneity, which can range from acute or chronic liver failure to neurological symptoms. The course of the disease can be improved by a life-long treatment with zinc or chelators such as D-penicillamine in a majority of patients, but serious side effects have been observed in a significant portion of patients, e.g. neurological deterioration and nephrotoxicity, so that a liver transplant would be inevitable. An alternative therapy option would be the genetic correction of the ATP7B gene. The novel gene therapy method CRISPR/Cas9, which has recently been used in the clinic, may represent a suitable therapeutic opportunity. In this study, we first initiated an artificial ATP7B point mutation in a human cell line using CRISPR/Cas9 gene editing, and corrected this mutation by the additional use of single-stranded oligo DNA nucleotides (ssODNs), simulating a gene correction of a WD point mutation in vitro. By the addition of 0.5 mM of Cu three days after lipofection, a high yield of CRISPR/Cas9-mediated ATP7B repaired cell clones was achieved (60%). Moreover, the repair efficiency was enhanced using ssODNs that incorporated three blocking mutations. The repaired cell clones showed a high resistance to Cu after exposure to increasing Cu concentrations. Our findings indicate that CRISPR/Cas9-mediated correction of ATP7B point mutations is feasible and may have the potential to be transferred to the clinic.
Sealing Ability of AH Plus and GuttaFlow Bioseal

The objective of root canal obturation is to achieve a fluid-tight seal. Recently, GuttaFlow bioseal (GB), a root canal sealer composed of polydimethylsiloxane, gutta-percha particles, and bioactive glass ceramics, has been developed, to enhance the sealing ability of root canal filling material. The objective of this study was to assess the sealing ability of GB using a subnanoliter-scaled fluid-flow measuring device and to compare with that of AH Plus (AH). The fluid flow in root canal-filled teeth using either gutta-percha cone (GP) with AH (GAR; n = 10) or GP with GB (GBR; n = 10) and in GP inserted in AH blocks (GA; n = 10) or GP inserted in GB blocks (GB; n = 10) was measured. In addition, fluid flow in sealer blocks of AH (A; n = 10) and GB (B; n = 10), which served as negative controls, was measured. Root canal-filled teeth using GP without any sealer (GR) acted as positive controls (n = 10). The leakage was obtained by calculating the volume of moved water by time (s), after stabilization of the fluid flow was achieved. Statistical analysis was performed using the Kruskal–Wallis test and Mann–Whitney U-test with Bonferroni correction. A p value less than 0.00238 (0.05/21) was considered significantly different. The mean leakages (nL/s) in the groups are as follows: GAR, 0.0958 ± 0.0543; GBR, 0.0223 ± 0.0246; GA, 0.0644 ± 0.0803; GB, 0.0267 ± 0.0182; A, 0.0055 ± 0.0057; B, 0.0052 ± 0.005; and GR, 0.2892 ± 0.3018. The mean leakage in the GBR group was lower than that in the GAR group (p = 0.001), while the mean leakages in the GA and GB groups were not significantly different. GuttaFlow bioseal can be useful in single-cone obturation technique.
Eukoenenia florenciae (Arachnida: Palpigradi) from the Munich Botanical Garden – first record of microwhip scorpions in Germany

Abstract. Seven female specimens of Eukoenenia florenciae (Rucker, 1903) were collected in greenhouses of the Munich Botanical Garden (Munich, Germany). Morphological determination is supported by sequencing and comparison of the 18S and 28S genes in BLAST. This is the first record of the arachnid order Palpigradi in Germany.
No evidence of male-biased sexual selection in a snake with conventional Darwinian sex roles

Decades of research on sexual selection have demonstrated that ‘conventional’ Darwinian sex roles are common in species with anisogamous gametes, with those species often exhibiting male-biased sexual selection. Yet, mating system characteristics such as long-term sperm storage and polyandry have the capacity to disrupt this pattern. Here, these ideas were explored by quantifying sexual selection metrics for the western diamond-backed rattlesnake (Crotalus atrox). A significant standardized sexual selection gradient was not found for males (βSS = 0.588, p = 0.199) or females (βSS = 0.151, p = 0.664), and opportunities for sexual selection (Is) and selection (I) did not differ between males (Is = 0.069, I = 0.360) and females (Is = 0.284, I = 0.424; both p > 0.05). Furthermore, the sexes did not differ in the maximum intensity of precopulatory sexual selection (males: s′max = 0.155, females: s′max = 0.080; p > 0.05). Finally, there was no evidence that male snout–vent length, a trait associated with mating advantage, is a target of sexual selection (p > 0.05). These results suggest a lack of male-biased sexual selection in this population. Mating system characteristics that could erode male-biased sexual selection, despite the presence of conventional Darwinian sex roles, are discussed.
Alkaloids of Abuta panurensis Eichler: In silico and in vitro study of acetylcholinesterase inhibition, cytotoxic and immunomodulatory activities

Natural products obtained from species of the genus Abuta (Menispermaceae) are known as ethnobotanicals that are attracting increasing attention due to a wide range of their pharmacological properties. In this study, the alkaloids stepharine and 5-N-methylmaytenine were first isolated from branches of Abuta panurensis Eichler, an endemic species from the Amazonian rainforest. Structure of the compounds was elucidated by a combination of 1D and 2D NMR spectroscopic and MS and HRMS spectrometric techniques. Interaction of the above-mentioned alkaloids with acetylcholinesterase enzyme and interleukins IL-6 and IL-8 was investigated in silico by molecular docking. The molecules under investigation were able to bind effectively with the active sites of the AChE enzyme, IL-6, and IL-8 showing affinity towards the proteins. Along with the theoretical study, acetylcholinesterase enzyme inhibition, cytotoxic, and immunomodulatory activity of the compounds were assessed by in vitro assays. The data obtained in silico corroborate the results of AChE enzyme inhibition, the IC50 values of 61. 24μM for stepharine and 19. 55μM for 5-N-methylmaytenine were found. The compounds showed cytotoxic activity against two tumor cell lines (K562 and U937) with IC50 values ranging from 11.77 μM to 28.48 μM. The in vitro assays revealed that both alkaloids were non-toxic to Vero and human PBMC cells. As for the immunomodulatory activity, both compounds inhibited the production of IL-6 at similar levels. Stepharine inhibited considerably the production of IL-8 in comparison to 5-N-methylmaytenine, which showed a dose dependent action (inhibitory at the IC50 dose, and stimulatory at the twofold IC50 one). Such a behavior may possibly be explained by different binding modes of the alkaloids to the interleukin structural fragments. Occurrence of the polyamine alkaloid 5-N-methylmaytenine was reported for the first time for the Menispermaceae family, as well as the presence of stepharine in A. panurensis.
AHEAD: Ad Hoc Electronic Auction Design

We introduce a new matching design for financial transactions in an electronic market. In this mechanism, called ad-hoc electronic auction design (AHEAD), market participants can trade between themselves at a fixed price and trigger an auction when they are no longer satisfied with this fixed price. In this context, we prove that a Nash equilibrium is obtained between market participants. Furthermore, we are able to assess quantitatively the relevance of ad-hoc auctions and to compare them with periodic auctions and continuous limit order books. We show that from the investors' viewpoint, the microstructure of the asset is usually significantly improved when using AHEAD.
Personality composition determines social learning pathways within shoaling fish

In shaping how individuals explore their environment and interact with others, personality may mediate both individual and social learning. Yet increasing evidence indicates that personality expression is contingent on social context, suggesting that group personality composition may be key in determining how individuals learn about their environment. Here, we used recovery latency following simulated predator attacks to identify Trinidadian guppies (Poecilia reticulata) that acted in a consistently bold or shy manner. We then employed network-based diffusion analysis to track the spread of a novel foraging behaviour through groups containing different proportions of bold and shy fish. Informed associates promoted learning to a greater extent in bold individuals, but only within groups composed predominately of bold fish. As the proportion of shy fish within groups increased, bold individuals instead emerged as especially effective demonstrators that facilitated learning in others. Individuals were also more likely to learn overall within shy-dominated groups than in bold-dominated ones. We demonstrate that whether and how individuals learn is conditional on group personality composition, indicating that selection may favour traits enabling individuals to better match their behavioural phenotype to their social environment.
Childhood maltreatment is associated with changes in mitochondrial bioenergetics in maternal, but not in neonatal immune cells

Significance Mitochondrial physiology affected by childhood maltreatment (CM) might be a biological link for the intergenerational transmission of CM-related consequences. As mitochondria are intergenerationally transmitted from mother to child, alterations in mitochondrial bioenergetics might influence how maternal CM affects physical and mental development as well as functioning in their children. Our study reports data on mitochondrial bioenergetics in peripheral mononuclear immune cells of mother-newborn dyads, which were positively correlated. Higher maternal maltreatment load was associated with higher mitochondrial respiration and density in mothers, but not in their newborns. Thus, we found no evidence for an intergenerational effect of maternal CM on mitochondrial bioenergetics in immune cells of their newborns. Childhood maltreatment (CM) comprises experiences of abuse and neglect during childhood. CM causes psychological as well as biological alterations in affected individuals. In humans, it is hardly explored whether these CM consequences can be transmitted directly on a biological level to the next generation. Here, we investigated the associations between maternal CM and mitochondrial bioenergetics (mitochondrial respiration and intracellular mitochondrial density) in immune cells of mothers and compared them with those of their newborns. In n = 102 healthy mother-newborn dyads, maternal peripheral blood mononuclear cells and neonatal umbilical cord blood mononuclear cells were collected and cryopreserved shortly after parturition to measure mitochondrial respiration and intracellular mitochondrial density with high-resolution respirometry and spectrophotometric analyses, respectively. Maternal CM was assessed with the Childhood Trauma Questionnaire. Maternal and neonatal mitochondrial bioenergetics were quantitatively comparable and positively correlated. Female newborns showed higher mitochondrial respiration compared to male newborns. Maternal CM load was significantly and positively associated with mitochondrial respiration and density in mothers, but not with mitochondrial respiration in newborns. Although maternal and neonatal mitochondrial bioenergetics were positively correlated, maternal CM only had a small effect on mitochondrial density in newborns, which was not significant in this study after adjustment for multiple comparisons. The biological relevance of our finding and its consequences for child development need further investigation in future larger studies. This study reports data on mitochondrial bioenergetics of healthy mother-newborn dyads with varying degrees of CM.
A New Antifungal Agent (4-phenyl-1, 3-thiazol-2-yl) Hydrazine Induces Oxidative Damage in Candida albicans

A gradual rise in immunocompromised patients over past years has led to the increasing incidence of invasive fungal infections. Development of effective fungicides can not only provide new means for clinical treatment, but also reduce the occurrence of fungal resistance. We identified a new antifungal agent (4-phenyl-1, 3-thiazol-2-yl), hydrazine (numbered as 31C) which showed high-efficiency, broad-spectrum and specific activities. The minimum inhibitory concentration of 31C against pathogenic fungi was between 0.0625-4 μg/ml in vitro, while 31C had no obvious cytotoxicity to human umbilical vein endothelial cells with the concentration of 4 μg/ml. In addition, 31C of 0.5 μg/ml could exhibit significant fungicidal activity and inhibit the biofilm formation of C. albicans. In vivo fungal infection model showed that 31C of 10 mg/kg significantly increased the survival rate of Galleria mellonella. Further study revealed that 31C-treatment increased the reactive oxygen species (ROS) in C. albicans and elevated the expression of some genes related to anti-oxidative stress response, including CAP1, CTA1, TRR1, and SODs. Consistently, 31C-induced high levels of intracellular ROS resulted in considerable DNA damage, which played a critical role in antifungal-induced cellular death. The addition of ROS scavengers, such as glutathione (GSH), N-Acetyl-L-cysteine (NAC) or oligomeric proanthocyanidins (OPC), dramatically reduced the antifungal activities of 31C and rescued the 31C-induced filamentation defect. Collectively, these results showed that 31C exhibited strong antifungal activity and induced obvious oxidative damage, which indicated that compounds with a structure similar to 31C may provide new sight for antifungal drug development.
A Comment on Surgical Eigenstructure Assignment via State Feedback

Assignability of all eigenvalues and a subset of key eigenvectors/generalized eigenvectors of a linear time-invariant system via state feedback is considered. We clarify that, if the key eigenvectors/generalized eigenvectors and their associated eigenvalues satisfy the classical conditions for full eigenstructure assignment, the remaining eigenvalues can be assigned at will.
Global soil moisture from in-situ measurements using machine learning - SoMo.ml

While soil moisture information is essential for a wide range of hydrologic and climate applications, spatially-continuous soil moisture data is only available from satellite observations or model simulations. Here we present a global, long-term dataset of soil moisture generated from in-situ measurements using machine learning, this http URL. We train a Long Short-Term Memory (LSTM) model to extrapolate daily soil moisture dynamics in space and in time, based on in-situ data collected from more than 1,000 stations across the globe. this http URL provides multi-layer soil moisture data (0-10 cm, 10-30 cm, and 30-50 cm) at 0.25° spatial and daily temporal resolution over the period 2000-2019. The performance of the resulting dataset is evaluated through cross validation and inter-comparison with existing soil moisture datasets. this http URL performs especially well in terms of temporal dynamics, making it particularly useful for applications requiring time-varying soil moisture, such as anomaly detection and memory analyses. this http URL complements the existing suite of modelled and satellite-based datasets given its independent and novel derivation, to support large-scale hydrological, meteorological, and ecological analyses.
Policy learning in SE(3) action spaces

In the spatial action representation, the action space spans the space of target poses for robot motion commands, i.e. SE(2) or SE(3). This approach has been used to solve challenging robotic manipulation problems and shows promise. However, the method is often limited to a three dimensional action space and short horizon tasks. This paper proposes ASRSE3, a new method for handling higher dimensional spatial action spaces that transforms an original MDP with high dimensional action space into a new MDP with reduced action space and augmented state space. We also propose SDQfD, a variation of DQfD designed for large action spaces. ASRSE3 and SDQfD are evaluated in the context of a set of challenging block construction tasks. We show that both methods outperform standard baselines and can be used in practice on real robotics systems.
Friendship is All we Need: A Multi-graph Embedding Approach for Modeling Customer Behavior

Understanding customer behavior is fundamental for many use-cases in industry, especially in accelerated growth areas such as fin-tech and e-commerce. Structured data are often expensive, time-consuming and inadequate to analyze and study complex customer behaviors. In this paper, we propose a multi-graph embedding approach for creating a non-linear representation of customers in order to have a better knowledge of their characteristics without having any prior information about their financial status or their interests. By applying the current method we are able to predict users' future behavior with a reasonably high accuracy only by having the information of their friendship network. Potential applications include recommendation systems and credit risk forecasting.
Acrostic Poem Generation

We propose a new task in the area of computational creativity: acrostic poem generation in English. Acrostic poems are poems that contain a hidden message; typically, the first letter of each line spells out a word or short phrase. We define the task as a generation task with multiple constraints: given an input word, 1) the initial letters of each line should spell out the provided word, 2) the poem's semantics should also relate to it, and 3) the poem should conform to a rhyming scheme. We further provide a baseline model for the task, which consists of a conditional neural language model in combination with a neural rhyming model. Since no dedicated datasets for acrostic poem generation exist, we create training data for our task by first training a separate topic prediction model on a small set of topic-annotated poems and then predicting topics for additional poems. Our experiments show that the acrostic poems generated by our baseline are received well by humans and do not lose much quality due to the additional constraints. Last, we confirm that poems generated by our model are indeed closely related to the provided prompts, and that pretraining on Wikipedia can boost performance.
Reflectionless excitation of arbitrary photonic structures: a general theory

Abstract We outline and interpret a recently developed theory of impedance matching or reflectionless excitation of arbitrary finite photonic structures in any dimension. The theory includes both the case of guided wave and free-space excitation. It describes the necessary and sufficient conditions for perfectly reflectionless excitation to be possible and specifies how many physical parameters must be tuned to achieve this. In the absence of geometric symmetries, such as parity and time-reversal, the product of parity and time-reversal, or rotational symmetry, the tuning of at least one structural parameter will be necessary to achieve reflectionless excitation. The theory employs a recently identified set of complex frequency solutions of the Maxwell equations as a starting point, which are defined by having zero reflection into a chosen set of input channels, and which are referred to as R-zeros. Tuning is generically necessary in order to move an R-zero to the real frequency axis, where it becomes a physical steady-state impedance-matched solution, which we refer to as a reflectionless scattering mode (RSM). In addition, except in single-channel systems, the RSM corresponds to a particular input wavefront, and any other wavefront will generally not be reflectionless. It is useful to consider the theory as representing a generalization of the concept of critical coupling of a resonator, but it holds in arbitrary dimension, for arbitrary number of channels, and even when resonances are not spectrally isolated. In a structure with parity and time-reversal symmetry (a real dielectric function) or with parity–time symmetry, generically a subset of the R-zeros has real frequencies, and reflectionless states exist at discrete frequencies without tuning. However, they do not exist within every spectral range, as they do in the special case of the Fabry–Pérot or two-mirror resonator, due to a spontaneous symmetry-breaking phenomenon when two RSMs meet. Such symmetry-breaking transitions correspond to a new kind of exceptional point, only recently identified, at which the shape of the reflection and transmission resonance lineshape is flattened. Numerical examples of RSMs are given for one-dimensional multimirror cavities, a two-dimensional multiwaveguide junction, and a multimode waveguide functioning as a perfect mode converter. Two solution methods to find R-zeros and RSMs are discussed. The first one is a straightforward generalization of the complex scaling or perfectly matched layer method and is applicable in a number of important cases; the second one involves a mode-specific boundary matching method that has only recently been demonstrated and can be applied to all geometries for which the theory is valid, including free space and multimode waveguide problems of the type solved here.