Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of dental topography of marmosets and tamarins (Callitrichidae) to other platyrrhine primates using a novel freeware pipeline

Dental topographic metrics (DTMs), which quantify different aspects of the shape of teeth, are powerful tools for studying dietary adaptation and evolution in mammals. However, comparative samples of scanned mammal teeth suitable for analysis with DTMs remain limited in size and scope, with little or no representation of some major lineages, even within well-studied clades such as primates. In addition, current DTM protocols usually rely on proprietary software, which may be unavailable to many researchers for reasons of cost. We address these issues in the context of a DTM analysis of the primate clade Platyrrhini (“New World monkeys”) by: 1) presenting a large comparative sample of scanned second lower molars (m2s) of callitrichids (marmosets and tamarins), which were previously underrepresented in publicly available platyrrhine datasets; and 2) giving full details of an entirely freeware pipeline for DTM analysis. We also present an updated discrete dietary classification scheme for extant platyrrhines, based on cluster analysis of dietary data extracted from 98 primary studies. Our freeware pipeline performs equally well in dietary classification accuracy of an existing sample of platyrrhine m2s (excluding callitrichids) as a published protocol that uses proprietary software, at least when multiple DTMs are combined. Individual DTMs however, sometimes showed very different results in classification accuracies between that of our freeware pipeline and that of the proprietary protocol, most likely due to the differences in the smoothing functions used. The addition of callitrichids still resulted in high classification accuracy in predicting diet with combined DTMs, although accuracy was considerably higher when molar size was included (90%) than excluded (73%). We conclude that our new freeware DTM pipeline is capable of accurately predicting diet in platyrrhines based on tooth shape and size, and so is suitable for inferring probable diet of taxa for which direct dietary information is unavailable, such as fossil species.
Navigating Pubertal Goldilocks: The Optimal Pace for Hierarchical Brain Organization

Adolescence is a timed process with an onset, tempo, and duration. Nevertheless, the temporal dimension, especially the pace of maturation, remains an insufficiently studied aspect of developmental progression. This study focuses on the modifications due to the different timings of developmental shifts during adolescence and addresses the impact of adolescent maturation on brain development. To reveal potential relationships between pubertal pace and the advancement of brain organisation, we analyse the connection between skeletal age-based maturation stages and hierarchical organisation in the temporal dynamics of resting-state EEG recordings (alpha frequency range). By adopting skeletal maturity as a proxy for pubertal progress and employing entropy production to measure hierarchical brain organisation, our findings indicate that an average maturational trajectory optimally aligns with cerebral hierarchical order. Adaptive developmental plasticity may not fully compensate for accelerated or decelerated timelines, potentially increasing the risk of behavioural problems and psychiatric disorders consequent to such alterations.
Differential reaction norms to ocean acidification in two oyster species from contrasting habitats

Ocean acidification (OA), a consequence of the increase in anthropogenic emissions of carbon dioxide, causes major changes in the chemistry of carbonates in the ocean with deleterious effects on calcifying organisms. The pH/pCO2 range to which species are exposed in nature is important to consider when interpreting the response of coastal organisms to OA. In this context, emerging approaches, which assess the reaction norms of organisms to a wide pH gradient, are improving our understanding of tolerance thresholds and acclimation potential to OA. In this study, we decipher the reaction norms of two oyster species living in contrasting habitats: the intertidal oyster Crassostrea gigas and the subtidal flat oyster Ostrea edulis, which are two economically and ecologically valuable species in temperate ecosystems. Six-month-old oysters of each species were exposed in common garden for 48 days to a pH gradient ranging from 7.7 to 6.4 (total scale). Both species are tolerant down to a pH of 6.6 with high plasticity in fitness-related traits such as survival and growth. However, oysters undergo remodelling of membrane fatty acids to cope with decreasing pH along with shell bleaching impairing shell integrity and consequently animal fitness. Finally, our work reveals species-specific physiological responses and highlights that intertidal C. gigas seems to have a better acclimation potential to rapid and extreme OA changes than O. edulis. Overall, our study provides important data about the phenotypic plasticity and its limits in two oyster species, which is essential for assessing the challenges posed to marine organisms by OA.
Consideration of a Liquid mutation-accumulation Experiment to Measure Mutation Rates by Successive Serial Dilution

The mutation-accumulation (MA) experiment is a fixture of evolutionary biology, though it is laborious to perform. MA experiments typically take between months and years to acquire sufficient mutations to measure DNA mutation rates and mutation spectra. MA experiments for many organisms rely on colony formation on agar plates and repetitive streaking, an environment which at first glance appears somewhat contrived, a poor imitation of real environmental living conditions. We propose that a fully liquid-phase mutation-accumulation experiment may at times more accurately reflect the environment of an organism. We note also that whereas automation of streaking plates is a daunting prospect, automation of liquid handling and serial dilution is already commonplace. In principle, this type of MA experiment can be automated so as to reduce the human capital requirements of measuring mutation rates. We demonstrate that a liquid MA recapitulates the mutation rate estimated for MMR- E. coli in liquid LB culture vs. plate LB culture. We detect a modified mutation spectrum with a transition skew of 4:1 of A:T→G:C vs G:C→A:T mutations, highlighting the potential role of tautomerization as a DNA mutation mechanism. We also find that using a plate reader to measure OD600 as a proxy for cell growth to be incapable of measuring carrying capacity for MA lines burdened with many mutations.
Whole-genome sequence and annotation of Penstemon davidsonii

Penstemon is the most speciose flowering plant genus endemic to North America. Penstemon species’ diverse morphology and adaptation to various environments have made them a valuable model system for studying evolution, but the absence of publicly available reference genomes limits possible research directions. Here we report the first reference genome assembly and annotation for Penstemon davidsonii. Using PacBio long-read sequencing and Hi-C scaffolding technology, we constructed a de novo reference genome of 437,568,744 bases, with a contig N50 of 40 Mb and L50 of 5. The annotation includes 18,199 gene models, and both the genome and transcriptome assembly contain over 95% complete eudicot BUSCOs. This genome assembly will serve as a valuable reference for studying the evolutionary history and genetic diversity of the Penstemon genus.
The exponential behavior and stabilizability of the stochastic 3D Navier–Stokes equations with damping

The stochastic 3D Navier–Stokes equation with damping driven by a multiplicative noise is considered in this paper. The stability of weak solutions to the stochastic 3D Navier–Stokes equations with damping is proved for any [Formula: see text] with any [Formula: see text] and [Formula: see text] as [Formula: see text]. The weak solutions converge exponentially in the mean square and almost surely exponentially to the stationary solutions are proved for any [Formula: see text] with any [Formula: see text] and [Formula: see text] as [Formula: see text]. The stabilization of these equations is obtained for any [Formula: see text] with any [Formula: see text] and [Formula: see text] as [Formula: see text].
Software Engineering for Self-Adaptive Systems: A Second Research Roadmap (Draft Version of May 20, 2011)

The goal of this roadmap paper is to summarize the stateof-the-art and identify research challenges when developing, deploying and managing self-adaptive software systems. Instead of dealing with a wide range of topics associated with the eld, we focus on four essential topics of self-adaptation: design space for adaptive solutions, processes, from centralized to decentralized control, and practical run-time verication and validation. For each topic, we present an overview, suggest future directions, and focus on selected challenges. This paper complements and extends a previous roadmap on software engineering for self-adaptive systems published in 2009 covering a dierent
Variational Temporal Deconfounder for Individualized Treatment Effect Estimation with Longitudinal Observational Data

Purpose This paper proposes a new approach, Variational Temporal Deconfounder (VTD), for estimating individualized treatment effects (ITE) from longitudinal observational data, where we address the hidden confounding issues by using proxies (i.e., surrogate variables that serve for unobservable variables). Methods We build VTD by incorporating a variational recurrent autoencoder that learns the latent encodings of hidden confounders from observed proxies and an ITE estimation network that takes the learned hidden encodings to predict the probability of receiving treatments and potential outcomes. Results We test VTD on both synthetic and real-world clinical data, and the results from synthetic data experiments demonstrate VTD’s effectiveness in deconfounding by outperforming existing methods, while results from two real-world datasets (i.e., Medical Information Mart for Intensive Care version III [MIMIC-III] and the National Alzheimer’s Coordinating Center [NACC] database) suggest that the performance of the VTD model outperforms existing baseline models, however, varies depending on the assumptions of underlying causal structures and availability of proxies for hidden confounders. Conclusion The VTD offers a unique solution to address the confounding bias without the “unconfoundedness” assumption when estimating the ITE from longitudinal observational data. The elimination of the requirement for the “unconfoundedness” assumption makes the VTD more versatile and practical in real-world clinical applications of personalized medicine.
Synthetic Streamflow Generation Using Autoregressive Modeling in the Upper Nakdong River Basin

The analysis and synthesis of various types of hydrologic variables such as precipitation, surface runoff, and discharge are usually required in planning and management of water resources. These hydrologic variables are mostly represented using stochastic models. One of which is the autoregressive model, that gives promising results in time series modeling. This study is an application of this model, which aimed to determine the AR model that best represents the historical monthly streamflow of the two gauging stations, namely Andong Dam and Imha Dam, both located in the upper Nakdong River Basin. AR(3) model was found to be the best model for both gauging stations. Parameters of the determined order of AR model (, and ) were also estimated. Using several diagnostic tests, the efficiency of the determined AR(3) model was tested. These tests indicated the accuracy of the determined AR(3) model.
VoxMg: An Automatic Speech Recognition Dataset for Malagasy

African languages are not well-represented in Natural Language Processing (NLP). The main reason is a lack of resources for training models. Low-resource languages, such as Malagasy, cannot benefit from modern NLP methods if no datasets are available. This paper presents the curation and annotation of VoxMg, a speech dataset for Malagasy that consists of 3873 audio files totaling 10.80 hours. We also run a baseline, which is the first Automatic Speech Recognition (ASR) model ever built in this language and obtained a Word Error Rate (WER) of 33%. Automatic Speech Recognition, Data Collection, Low-Resource Languages, Malagasy
Unusual Changes in the U.S. Treasury Security Market During the Fourth Round of Quantitative Easing

Abstract The Covid-19 Pandemic and policy response rattled the US Treasury markets. Conventional US Treasuries, inflation adjusted US Treasuries, and the relationship between the two developed in ways such that ignoring changes in real interest rates yielded distorted inflation expectations estimates. Since the beginning of the pandemic, monetary policy kept nominal rates low and close to zero, but positive. Real rates, on the other hand, became increasingly negative. The relationship between the two market rates became negatively correlated, and distorted because of the fourth round of quantitative easing, along with the Fed preventing nominal yields from turning negative. Federal Reserve actions during the Covid-19 pandemic drove a larger wedge between nominal interest rates and real interest rates in the inflation adjusted market.
Portraying Trawl Fishery in Albanian Waters: Case Study from the Sarandë Area (Southern Albania)

Abstract The current study provides valuable insight into the trawl fishery operating in southern Albanian waters via an integrated approach based on high-frequency onboard monitoring trawl vessels and on-site interviews with local fishers. Multivariate analyses of the composition of species landings or economic revenue revealed groups that, depending on the group, were distinguished by improved fisheries landings and economic efficiency. The majority of the catch consisted of a variety of demersal and small- and medium-sized pelagic species, confirming the Adriatic Sea's multispecies nature. Target species identified in terms of catches and revenue imply a systematic tactic over a long period of time, and incidental catches are equally important in terms of overall group similarity. The identification of target species groups may be useful in assessing the current sampling stratification schemes.
M&A Prediction Model: Will Investors Benefit?

In this paper, we study the development of investment strategies by predicting M&A deals using a logistic model with the financial and non-financial indicators of public companies. A random sample of 1510 acquired and non-acquired companies in Germany, the United Kingdom, France, Sweden, and Russia over the period 2000-2021 was used to design an M&A logit prediction model with high predictive power. The use of interaction variables significantly improved the model’s predictive power and allowed it to obtain more than 70% of correct out-of-sample predictions. Then the model’s ability to generate abnormal returns was tested with the help of an event study using share price data over the period 2011-2021. We show that an M&A prediction model can also efficiently generate abnormal returns (up to 49% on average) for a portfolio of companies that are expected to be acquired. Moreover, we uncover evidence that reduction in false positive and negative predictions has a positive effect on abnormal returns due to the added model flexibility resulting from interaction terms. Our positive theoretical and empirical results can help both private and institutional investors to design investment strategies. In addition, there are indirect implications that support the practical importance of an efficient M&A prediction model.
Graph Minor Theory

A monumental project in graph theory was recently completed. The project, started by Robertson and Seymour, and later joined by Thomas, led to entirely new concepts and a new way of looking at graph theory. The motivating problem was Kuratowski’s characterization of planar graphs, and a far-reaching generalization of this, conjectured by Wagner: If a class of graphs is minor-closed (i.e., it is closed under deleting and contracting edges), then it can be characterized by a finite number of excluded minors. The proof of this conjecture is based on a very general theorem about the structure of large graphs: If a minor-closed class of graphs does not contain all graphs, then every graph in it is glued together in a tree-like fashion from graphs that can almost be embedded in a fixed surface. We describe the precise formulation of the main results and survey some of its applications to algorithmic and structural problems in graph theory.
Bring the Noise: Introducing Noise Robustness to Pretrained Automatic Speech Recognition

In recent research, in the domain of speech processing, large End-to-End (E2E) systems for Automatic Speech Recognition (ASR) have reported state-of-the-art performance on various benchmarks. These systems intrinsically learn how to handle and remove noise conditions from speech. Previous research has shown, that it is possible to extract the denoising capabilities of these models into a preprocessor network, which can be used as a frontend for downstream ASR models. However, the proposed methods were limited to specific fully convolutional architectures. In this work, we propose a novel method to extract the denoising capabilities, that can be applied to any encoder-decoder architecture. We propose the Cleancoder preprocessor architecture that extracts hidden activations from the Conformer ASR model and feeds them to a decoder to predict denoised spectrograms. We train our pre-processor on the Noisy Speech Database (NSD) to reconstruct denoised spectrograms from noisy inputs. Then, we evaluate our model as a frontend to a pretrained Conformer ASR model as well as a frontend to train smaller Conformer ASR models from scratch. We show that the Cleancoder is able to filter noise from speech and that it improves the total Word Error Rate (WER) of the downstream model in noisy conditions for both applications.
Learning disorders related to exposure to general anesthetic in children

Background: There are many animal studies demonstrating increased neuroapoptose in the first periods of development, especially in stronger neural development regions. In young cobais neuroapoptose also noted, however, more localized area as the dentate nucleus and the olfactory bulb of the brain regions that show sinaptogense even in adulthood and is responsible for learning. Objective: To describe the current studies about learning disabilities and cognitive impairment related to exposure to general anesthetics in children. Method: This is a systematic review, performed from the search in the PubMed database using the keywords "general anesthetics," "neurotoxicity", "children", "young child" and "pediatric" with the criterion inclusion, published in the last five years, in English and related exposure to anesthetics in human children . Were excluded from the articles concerning the studies in experimental animals or that they focus on side effects of other substances on the central nervous system, such as alcohol. Results: So were found 108 articles. All were analyzed by two researchers individually. Only 27 met the inclusion criteria. Discussion: In recent years, several studies have been conducted addressing neurotoxicity triggered by general anesthetics. The vast majority using experimental animals or stem cells. Suggest that both inhaled anesthetics such as venous are able to trigger the activation neuroapoptose with release of caspase 3:09, especially in phases of high growth and neural development. There is a strong association between duration of anesthesia and multiple exposures with learning disabilities and behavior. Conclusion: Currently, you can not say that the damage caused by agents in animals can be replicated humans. However, the severity of outcomes, the FDA recommends avoiding anesthesia and surgery in children under three years, at least those that do not have an emergency basis.
Olivine Exit Interviews—Piecing Together Magmatic Puzzles

When magmas erupt at the surface, they may have undergone many changes since their inception. While olivine drives some of these changes through crystallization and fractionation, it also records the magma evolution via mineral chemistry and by trapping mineral and melt inclusions. Olivine is an effective recorder of intensive parameters, such as temperature and melt composition, and provides an outstanding petrological tool for constraining dynamic processes, such as ascent, mixing, and cooling. Olivine sheds light on magmatic puzzles that involve both mafic and more evolved magmas, with protracted and complex magmatic histories that often obscure earlier and deeper processes. This contribution summarizes the current state of how olivine helps reconstruct source-to-surface magma assembly through its chemistry, inclusions, and textures.
LA ENTONACIÓN EN EL ESPAÑOL DOMINICANO DEL ESTE

espanolPor medio de un modelo metrico y autosegmental (AM) revisado, se estudian los acentos tonales prenucleares dentro del marco de la silaba acentuada y el contexto fonetico pretonico y postonico. Se analizan por medio de una interfaz entre el componente fonetico y fonologico teniendo en cuenta los umbrales perceptivos. Esta metodologia permite un taxonomia tonal sin la ambiguedad producida por los fenomenos de superficie en la alineacion del pico. Se estudian cinco discursos en espanol dominicano de la zona este del pais. Los resultados indican una frecuencia de aparicion relevante de acentos prenucleares (H*, L+H*, H*+L, y (L+H)*+L). Los resultados son similares a los obtenidos en Argentina, Cuba, en la Peninsula Iberica y en discursos de las Islas Canarias y opuesto a lo obtenido en habla de laboratorio y en habla semiespontanea en el espanol dominicano del norte. EnglishBy means of a revised AutosegmentalMetrical model, prenuclear accents within a sequence integrated by the pretonic, the accented and the posttonic syllable with an interface between the phonetic and phonological component ruled by perceptual thresholds are analyzed. This methodology allows a contrastive tonal taxonomy without autosegmental and metrical ambiguity produced by surface preshooting and overshoting on peak alignment. Five broadcasting discourses in East Dominican Spanish are acoustically studied. Results indicate a high frequency of appearance of prenuclear accents (H*, L+ H*, H*+L, and (L+H)*+L). Findings are similar to the obtained in Argentinian, Cuban, Peninsular, and Canary Islands discourses and opposed to the obtained elsewhere in North Dominican Spanish laboratory and spontaneous data