Miracle-dz/UniFAR-FTUs huggingface dataset:
Interspecific differences in the effects of masking and distraction on anti-predator behavior in suburban anthropogenic noise

Predation is a common threat to animal survival. The detection of predators or anti-predator communication signals can be disrupted by anthropogenic noise; however, the mechanism by which responses are affected is unclear. Masking and distraction are the two hypotheses that have emerged as likely explanations for changes in behavior in noise. Masking occurs when the signal and noise fall within the same sensory domain; noise overlapping the energy in the signal reduces signal detection. Distraction can occur when noise in any sensory domain contributes to a greater cognitive load, thereby reducing signal detection. Here, we used a repeated measures field experiment to determine the relative contributions of masking and distraction in mediating reduced anti-predator responses in noise. We recorded the approaches and vocalizations of black-capped chickadees (Poecile atricapillus), tufted titmice (Baeolophus bicolor), and white-breasted nuthatches (Sitta carolinensis) to both visual and acoustic cues of predator presence, either with or without simultaneous exposure to anthropogenic noise. Titmice increased their calling to both visual and acoustic cues of predator presence. However, there was no significant effect of noise on the calling responses of titmice regardless of stimulus modality. Noise appeared to produce a distraction effect in chickadees; however, this effect was small, suggesting that chickadees may be relatively unaffected by low levels of anthropogenic noise in suburban environments. White-breasted nuthatch calling behavior was affected by the interaction of the modality of the predator stimulus and the noise condition. Nuthatches had a delayed response to the predator presentations, with a greater calling rate following the presentation of the acoustic stimulus in quiet compared to the presentation of the acoustic stimulus in noise. However, there was no difference in calling rate between the quiet and noise conditions for the visual stimulus. Together this suggests that even moderate levels of noise have some masking effect for white-breasted nuthatches. We suggest that the mechanisms through which noise influences anti-predator behavior may depend on the social roles, foraging ecology and auditory capabilities of each species.
Organoid cell fate dynamics in space and time

Organoids are a major new tool to study tissue renewal. However, characterizing the underlying differentiation dynamics remains challenging. Here, we developed TypeTracker, which identifies cell fates by AI-enabled cell tracking and propagating end point fates back along the branched lineage trees. Cells that ultimately migrate to the villus commit to their new type early, when still deep inside the crypt, with important consequences: (i) Secretory cells commit before terminal division, with secretory fates emerging symmetrically in sister cells. (ii) Different secretory types descend from distinct stem cell lineages rather than an omnipotent secretory progenitor. (iii) The ratio between secretory and absorptive cells is strongly affected by proliferation after commitment. (iv) Spatial patterning occurs after commitment through type-dependent cell rearrangements. This “commit-then-sort” model contrasts with the conventional conveyor belt picture, where cells differentiate by moving up the crypt-villus axis and hence raises new questions about the underlying commitment and sorting mechanisms.
Optimal barbell force-velocity profiles can contribute to maximize weightlifting performance

Maximal barbell power output (Pmax) and vertical barbell threshold velocity (vthres) are major determinants of weightlifting performance. Moreover, an optimal force-velocity relationship (FvR) profile is an additional variable that has the potential to maximize sports performance. The aims of this study were (i) to present a biomechanical model to calculate an optimal FvR profile for weightlifting, and (ii) to determine how vthres, Pmax, and the optimal FvR profile influence theoretical snatch performance (snatchth). To address these aims, simulations were applied to quantify the respective influence on snatchth. The main findings confirmed that at constant vthres and Pmax, snatchth is maximized at an optimal FvR profile. With increasing Pmax and decreasing vthres, the optimal FvR profile becomes more force dominated and more effective to enhance snatchth. However, sensitivity analysis showed that vthres and Pmax have a larger effect on snatchth than the optimal FvR profile. It can be concluded that in weightlifting, training protocols should be designed with the goal to improve Pmax and to reduce vthres to ultimately enhance snatchth. Training programs designed to achieve the optimal FvR profile may constitute an additional training goal to further develop weightlifting performance in elite athletes that already present high Pmax levels.
Environmental Science and Technology

The Department of Environmental Science and Technology (ENST) is The Place for Ecological Discovery and Natural Solutions! Our primary mission is to educate students on the fundamentals of environmental science, while instilling a deep fascination and intellectual capacity to work in their chosen area of specialization, whether its Natural Resources Management, Ecological Design, Soil and Watershed Science or Environmental Health. When our students graduate, we want them to be top-notch environmental stewards with a broad framework from which they can advance professionally, personally and socially.
Lateralization of major white matter tracts during infancy is time-varying and tract-specific

Abstract Lateralization patterns are a major structural feature of brain white matter and have been investigated as a neural architecture that indicates and supports the specialization of cognitive processing and observed behaviors, e.g. language skills. Many neurodevelopmental disorders have been associated with atypical lateralization, reinforcing the need for careful measurement and study of this structural characteristic. Unfortunately, there is little consensus on the direction and magnitude of lateralization in major white matter tracts during the first months and years of life—the period of most rapid postnatal brain growth and cognitive maturation. In addition, no studies have examined white matter lateralization in a longitudinal pediatric sample—preventing confirmation of if and how white matter lateralization changes over time. Using a densely sampled longitudinal data set from neurotypical infants aged 0–6 months, we aim to (i) chart trajectories of white matter lateralization in 9 major tracts and (ii) link variable findings from cross-sectional studies of white matter lateralization in early infancy. We show that patterns of lateralization are time-varying and tract-specific and that differences in lateralization results during this period may reflect the dynamic nature of lateralization through development, which can be missed in cross-sectional studies.
MMT: Cross Domain Few-Shot Learning via Meta-Memory Transfer

Few-shot learning aims to recognize novel categories solely relying on a few labeled samples, with existing few-shot methods primarily focusing on the categories sampled from the same distribution. Nevertheless, this assumption cannot always be ensured, and the actual domain shift problem significantly reduces the performance of few-shot learning. To remedy this problem, we investigate an interesting and challenging cross-domain few-shot learning task, where the training and testing tasks employ different domains. Specifically, we propose a Meta-Memory scheme to bridge the domain gap between source and target domains, leveraging style-memory and content-memory components. The former stores intra-domain style information from source domain instances and provides a richer feature distribution. The latter stores semantic information through exploration of knowledge of different categories. Under the contrastive learning strategy, our model effectively alleviates the cross-domain problem in few-shot learning. Extensive experiments demonstrate that our proposed method achieves state-of-the-art performance on cross-domain few-shot semantic segmentation tasks on the COCO-20<inline-formula><tex-math notation="LaTeX">$^{i}$</tex-math><alternatives><mml:math><mml:msup><mml:mrow/><mml:mi>i</mml:mi></mml:msup></mml:math><inline-graphic xlink:href="wang-ieq1-3306352.gif"/></alternatives></inline-formula>, PASCAL-5<inline-formula><tex-math notation="LaTeX">$^{i}$</tex-math><alternatives><mml:math><mml:msup><mml:mrow/><mml:mi>i</mml:mi></mml:msup></mml:math><inline-graphic xlink:href="wang-ieq2-3306352.gif"/></alternatives></inline-formula>, FSS-1000, and SUIM datasets and positively affects few-shot classification tasks on Meta-Dataset.
Uniform Central Limit Theorems: The Two-Sample Case, the Bootstrap, and Confidence Sets

Preface 1. Introduction: Donsker's theorem, metric entropy and inequalities 2. Gaussian measures and processes sample continuity 3. Foundations of uniform central limit theorems: Donsker classes 4. Vapnik-Cervonenkis combinatorics 5. Measurability 6. Limit theorems for Vapnik-Cervonenkis and related classes 7. Metric entropy, with inclusion and bracketing 8. Approximation of functions and sets 9. Sums in general Banach spaces and invariance principles 10. Universal and uniform central limit theorems 11. The two-sample case, the bootstrap, and confidence sets 12. Classes of sets or functions too large for central limit theorems Appendices Subject index Author index Index of notation.
Bacterial assemblages structure in intensive cultivations of the microalga Tetradesmus obliquus

The present study shows the characterization of the bacterial communities associated with different systems during the cultivation of the microalga Tetradesmus obliquus. For that, sequential cultivation was performed in three different systems: (1) Photobioreactor bench‐scale; (2) flat‐panel photobioreactor; and (3) thin‐layer cascade. Cultures were monitored daily for growth parameters and biomass samples were collected for characterization of bacterial communities using metagenomic. A total of 195,177 reads were produced, resulting in the identification of 72 OTUs. In the grouping of bacterial communities, 3 phyla, 6 classes, 28 families, and 35 taxa were found. The bacteria Brevundimonas and Porphyrobacter had a higher relative abundance compared with other taxa found. These taxa were present in all cultivation systems forming a possible core community. Bacterial communities associated with different cultivation systems of the microalga T. obliquus showed an increase in taxa richness and diversity in the super‐intensive and intensive systems.
Empirical studies on human capital and natural resources

El primer capitulo de la tesis sobre Estudios Empiricos sobre Capital Humano e Instituciones presenta estimaciones de retornos a la educacion en Alemania y analiza los determinantes de las preferencias educativas. El segundo capitulo utiliza estimaciones de retornos a la experiencia en el pais de origen de inmigrantes en Estados Unidos para proporcionar evidencia empirica que el comercio aumenta la acumulacion de capital humano en el trabajo, incluso en los paises menos desarrollados, resolviendo la ambiguedad teorica si el comercio aumenta o disminuye learning-by-doing. La acumulacion de capital humano en el trabajo es tambien positivamente asociada con el PIB per capita, un alto nivel de educacion y una mayor calidad de politicas e instituciones. El ultimo capitulo analiza el efecto de recursos naturales y asistencia externa sobre la calidad de instituciones, proporcionando evidencia empirica que -contrario a la asistencia externa, la abundancia de mineral y combustible tiende a ser asociada negativamente con la calidad de instituciones si la fragmentacion etnica es grande.
Introduction to Numerical Geodynamic Modelling

Acknowledgements Introduction 1. The continuity equation 2. Density and gravity 3. Numerical solutions of partial differential equations 4. Stress and strain 5. The momentum equation 6. Viscous rheology of rocks 7. Numerical solutions of the momentum and continuity equations 8. The advection equation and marker-in-cell method 9. The heat conservation equation 10. Numerical solution of the heat conservation equation 11. 2-D thermomechanical code structure 12. Elasticity and plasticity 13. 2-D implementation of visco-elastic-plastic rheology 14. The multi-grid method 15. Programming of 3-D problems 16. Numerical benchmarks 17. Design of 2-D numerical geodynamic models Epilogue: outlook Appendix: MATLAB program examples References Index.
Targeting endothelial vascular cell adhesion molecule-1 in atherosclerosis: drug discovery and development of vascular cell adhesion molecule-1–directed novel therapeutics

Abstract Vascular cell adhesion molecule-1 (VCAM-1) has been well established as a critical contributor to atherosclerosis and consequently as an attractive therapeutic target for anti-atherosclerotic drug candidates. Many publications have demonstrated that disrupting the VCAM-1 function blocks monocyte infiltration into the sub-endothelial space, which effectively prevents macrophage maturation and foam cell transformation necessary for atherosclerotic lesion formation. Currently, most VCAM-1-inhibiting drug candidates in pre-clinical and clinical testing do not directly target VCAM-1 itself but rather down-regulate its expression by inhibiting upstream cytokines and transcriptional regulators. However, the pleiotropic nature of these regulators within innate immunity means that optimizing dosage to a level that suppresses pathological activity while preserving normal physiological function is extremely challenging and oftentimes infeasible. In recent years, highly specific pharmacological strategies that selectively inhibit VCAM-1 function have emerged, particularly peptide- and antibody-based novel therapeutics. Studies in such VCAM-1–directed therapies so far remain scarce and are limited by the constraints of current experimental atherosclerosis models in accurately representing the complex pathophysiology of the disease. This has prompted the need for a comprehensive review that recounts the evolution of VCAM-1–directed pharmaceuticals and addresses the current challenges in novel anti-atherosclerotic drug development.
Ploidetect enables pan-cancer analysis of the causes and impacts of chromosomal instability

Cancers routinely exhibit chromosomal instability, resulting in the accumulation of changes in the abundance of genomic material, known as copy number variants (CNVs). Unfortunately, the detection of these variants in cancer genomes is difficult. We developed Ploidetect, a software package that effectively identifies CNVs within whole-genome sequenced tumors. Ploidetect was more sensitive to CNVs in cancer related genes within advanced, pre-treated metastatic cancers than other tools, while also segmenting the most contiguously. Chromosomal instability, as measured by segment contiguity, was associated with several biological and clinical variables, including tumor mutation burden, tumor type, duration of therapy and immune microenvironment, highlighting the relevance of measuring CNV across the cancer genome. Investigation of gene mutations in samples revealed and the mutation status of several genes including ROCK2 and AC074391.1. Leveraging our heightened ability to detect CNVs, we identified 282 genes which were recurrently homozygously deleted in metastatic tumors. Further analysis of one recurrently deleted gene, MACROD2, identified a putative fragile tumor suppressor locus associated with response to chromosomal instability and chemotherapeutic agents. Our results outline the multifaceted impacts of CNVs in cancer by providing evidence of their involvement in tumorigenic behaviors and their utility as biomarkers for biological processes. We propose that increasingly accurate determination of CNVs is critical for their productive study in cancer, and our work demonstrates advances made possible by progress in this regard.
Theoretical Investigation of Optoelectronics Properties of Titanium Dichalcogenides Materials TiX2 (X=S, Se, Te) Using Quantum Espresso

In this work, we present the results of the calculation of the electronic and optical properties of titanium dichalcogenide materials TiX2 (X=S, Se, Te). These calculations were performed using the QUANTUM-ESPRESSO package, based on the density functional theory and the pseudopotential technique. The results obtained showed that TiS2 is a semi-metallic compound, this character is due to a very small overlap between the density of states p-orbitals of S and d-orbitals of the Ti atom in the vicinity of the Fermi level. While TiSe2 and TiTe2 indicate the metallic characters. At the Fermi level, the total density of states is 0.77 states/eV and 1.13 states/eV for both compounds respectively. On the other hand, the optical properties of these materials such as the real and imaginary parts of dielectric function ε1 and ε2, respectively, the refractive index, the absorption, the reflectivity, and the loss function were investigated based on Kramers-Kroning relations in the energy range of 0 to 20 eV. In the infrared region, the reflectivity spectrum R(ω) is close to 100% for TiX2 (X= S, Se, Te), suggesting their potential application as a good coating material.
Real-time Quantification of in vivo cerebrospinal fluid velocity using fMRI inflow effect

In vivo estimation of cerebrospinal fluid (CSF) velocity is crucial for understanding the glymphatic system and its potential role in neurodegenerative disorders such as Alzheimer’s disease and Parkinson’s disease. Current cardiac or respiratory gated approaches, such as 4D flow MRI, cannot capture CSF movement in real time due to limited temporal resolution and in addition deteriorate in accuracy at low fluid velocities. Other techniques like real-time PC-MRI or time-spatial labeling inversion pulse are not limited by temporal averaging but have limited availability even in research settings. This study aims to quantify the inflow effect of dynamic CSF motion on functional magnetic resonance imaging (fMRI) for in vivo, real-time measurement of CSF flow velocity. We considered linear and nonlinear models of velocity waveforms and empirically fit them to fMRI data from a controlled flow experiment. To assess the utility of this methodology in human data, CSF flow velocities were computed from fMRI data acquired in eight healthy volunteers. Breath holding regimens were used to amplify CSF flow oscillations. Our experimental flow study revealed that CSF velocity is nonlinearly related to inflow effect-mediated signal increase and well estimated using an extension of a previous nonlinear framework. Using this relationship, we recovered velocity from in vivo fMRI signal, demonstrating the potential of our approach for estimating CSF flow velocity in the human brain. This novel method could serve as an alternative approach to quantifying slow flow velocities in real time, such as CSF flow in the ventricular system, thereby providing valuable insights into the glymphatic system’s function and its implications for neurological disorders.
TgF344-AD Rat Model of Alzheimer’s Disease: Spatial Disorientation and Asymmetry in Hemispheric Neurodegeneration

BACKGROUND The TgF344-AD ratline represents a transgenic animal model of Alzheimer’s disease (AD). We previously reported spatial memory impairment in TgF344-AD rats, yet the underlying mechanism remained unknown. We, therefore, set out to determine if spatial memory impairment in TgF344-AD rats is attributed to spatial disorientation. Also, we aimed to investigate whether TgF344-AD rats exhibit signs of asymmetry in hemispheric neurodegeneration, similar to what is reported in spatially disoriented AD patients. Finally, we sought to examine how spatial disorientation correlates with working memory performance. METHODS TgF344-AD rats were divided into two groups balanced by sex and genotype. The first group underwent the delayed match-to-sample (DMS) task for the assessment of spatial orientation and working memory, while the second group underwent positron emission tomography (PET) for the assessment of glucose metabolism and microglial activity as in-vivo markers of neurodegeneration. Rats were 13 months old during DMS training and 14-16 months old during DMS testing and PET. RESULTS In the DMS task, TgF344-AD rats were more likely than their wild-type littermates to display strong preference for one of the two levers, preventing working memory testing. Rats without lever-preference showed similar working memory, regardless of their genotype. PET revealed hemispherically asymmetric clusters of increased microglial activity and altered glucose metabolism in TgF344-AD rats. CONCLUSIONS TgF344-AD rats display spatial disorientation and hemispherically asymmetrical neurodegeneration, suggesting a potential causal relationship consistent with clinical observations. In rats without spatial disorientation, working memory remains intact.
The evolution of sexual dimorphism in gene expression in response to a manipulation of mate competition

Many genes are differentially expressed between males and females and patterns of sex-biased gene expression (SBGE) vary among species. Some of this variation is thought to have evolved in response to differences in mate competition among species that causes varying patterns of sex-specific selection. We used experimental evolution to test this by quantifying SBGE and sex-specific splicing in 15 Drosophila melanogaster populations that evolved for 104 generations in mating treatments that removed mate competition via enforced monogamy, or allowed mate competition in either small, simple or larger, structurally more complex mating environments. Consistent with sex-specific selection affecting SBGE, initially sex-biased genes diverged in expression more among treatments than unbiased genes, and there was greater expression divergence for male-than female-biased genes. It has been suggested the transcriptome should be ‘feminized’ under monogamy because of the removal of sexual selection on males; we did not observe this, likely because selection differs in additional ways between monogamy vs. polygamy. Significant divergence in average expression dimorphism between treatments was observed and, in some treatment comparisons, the direction of the divergence differed across different sex-bias categories. There was not a generalized reduction in expression dimorphism under enforced monogamy.