Miracle-dz/UniFAR-FTUs huggingface dataset:
Potentially limited detectability of short-term changes in boreal fire regimes: a simulation study

Climate change is expected to increase area burned in the boreal plains ecozone of Canada in the early 21st century (2001–50). I examined the influence of inter-annual variability in area burned and short observed time series on the probability of detecting if an increase has occurred, using a null model of present and future fire regimes. A wide range of fire cycles are consistent with annual area burned in the late 20th century (1959–99). Fire cycles estimated from the reciprocal of the average annual burn fraction over a 50-year period are not very precise, and overestimate the fire cycle if years with large annual area burned have not recently occurred. Under the default assumptions, the probability of detecting a doubling of annual area burned during 2001–50 is 73% if it occurred instantaneously, but only 31% if it occurred gradually. Imprecise estimates and uncertainty in the ability to detect changes in fire cycles poses challenges for implementing aspects of sustainable forest management. Alternate empirical or model-based statistics, such as return periods for annual areas burned of a given magnitude, may be useful for inferring frequencies and magnitudes of large fire years that have not yet been observed.
Phosphoproteomics identifies targets of Mos-MAPK regulating translation and spindle organization in oocyte meiosis

The Mos kinase is a constitutive activator of the ERK/MAPK pathway exclusively expressed during oocyte meiosis, mediating key meiotic functions across animal species. While a few of its downstream effectors have been studied in some detail, molecular targets under the control of Mos-MAPK have not yet been identified systematically. Here, we combined live-cell microscopy of starfish oocytes to characterize the cellular phenotypes caused by Mos-MAPK inhibition with phosphoproteomic analysis of synchronous oocyte populations at key transitions. This revealed a large set of proteins involved in regulation of translation through the CPE-element binding protein CPEB to be controlled by Mos-MAPK. Our data indicate that cyclin B is the main target of this regulation to drive the second meiotic division. A second large group of phospho-proteins we found to be controlled by Mos-MAPK are regulators of the actin and microtubule cytoskeleton, in particular regulators of centrosomal microtubule nucleation. Indeed, we show that Mos-MAPK inhibition increases the size of microtubule asters and promotes separation of spindle poles in meiotic anaphase, i.e turning meiotic spindles mitotic-like. Together, here we identified core molecular modules controlled by Mos-MAPK driving key meiotic functions, haploidization and the asymmetric polar body divisions. These molecular modules are highly conserved and are thus likely to be involved in reproductive processes across species including humans. In addition, our work may help understand disease mechanisms when Mos is expressed erroneously, acting as an oncogene.
Graded changes in local functional connectivity of the cerebral cortex in young people with depression

Major depressive disorder (MDD) is marked by significant changes to the coupling of spontaneous neural activity within various brain regions. However, many methods for assessing this local connectivity use fixed or arbitrary neighborhood sizes, resulting in a decreased capacity to capture smooth changes to the spatial gradient of local correlations. A newly developed method sensitive to classical anatomo-functional boundaries, Iso-Distant Average Correlation (IDAC), was therefore used to examine depression associated alterations to the local functional connectivity of the brain. One-hundred and forty-five adolescents and young adults with MDD and 95 healthy controls underwent a resting-state fMRI scan. Whole-brain functional connectivity maps of intracortical neural activity within iso-distant local areas (5-10mm, 15-20mm, and 25-30mm) were generated to characterize local fMRI signal similarities. Across all spatial distances, MDD participants demonstrated greater local functional connectivity of the bilateral posterior hippocampus, retrosplenial cortex, dorsal insula, fusiform gyrus, and supplementary motor area. Additionally, in the short and medium range connections there were depression associated alterations in the midcingulate (15-20mm and 25-30mm) and subgenual anterior cingulate (15-20mm). Our study identified increased synchrony of the neural activity in several regions commonly implicated in the neurobiology of depression; however, a subset of identified effects was dependent on the spatial distance under consideration. Longitudinal examination of these effects will clarify whether these differences are also found in other age groups and if this synchrony is additionally altered by continued disease progression.
Drivers of population dynamics of at-risk populations change with pathogen arrival

Successful wildlife conservation in an era of rapid global change requires understanding determinants of species population abundance and growth. However, when populations are faced with novel stressors, factors associated with healthy and growing populations can change, necessitating a shift in conservation strategies. For example, emerging infectious diseases can cause conditions previously beneficial or neutral to host populations to increase disease impacts. Here, we paired a population dataset of 265 colonies of the federally endangered Indiana bat (Myotis sodalis) with 50.7 logger-years of environmental data to explore factors that affected colony response to white-nose syndrome (WNS), an emerging fungal disease. We found wide variation in colony responses to WNS, ranging from extirpation to stabilization and persistence. Simulating future population dynamics suggests that most extirpations have already occurred, as the pathogen has been present for several years in most colonies, and that small colonies were more susceptible to extirpation than large ones. Further, while temperature and humidity conditions of hibernacula appeared unassociated with Indiana bat colony growth prior to WNS, extirpation risk following pathogen arrival was elevated in colonies that used colder and wetter hibernacula. Additionally, rates of decline were greater in colder hibernacula, opposite the association for a sympatric bat species. Overall, this study illustrates that emerging infectious diseases can change the factors associated with host population abundance and optimal growth, including through novel environmental associations, which can vary across host species. Consideration of these shifting associations and intrinsic differences between impacted host species will be essential to successful species conservation.
Social or Individual Disagreement? Perspectivism in the Annotation of Sexist Jokes

The purpose of this paper is to show that the disagreement expressed in the data does not come from individual differences but from diverse and sometimes conflicting, social positions. Using a medium size dataset, 210 sexist jokes and 76 annotators, we test the hypothesis that, from a certain point (size of 12 in our data), adding more subjects to the annotation process does not increase the disagreement. We also measure the attitudes of subjects in sexism, introducing a new scale of Hostile Neosexism , and the consistent or inconsistent behaviour of annotators regarding their attitudes. We propose that perspectives are a combination of attitudes and behaviours, and we explore how they affect inter-rater agreement and which will be the number of annotators that we need to include all the perspectives in an annotation strategy.
When Attention Turn To Be Explanation. A Case Study in Recommender Systems

Recent studies in deep learning aim to understand how intermediate representations learned from attention mechanisms motivates the decisions of a predictive model and, consequently, provides information on the model’s decision-making process. In fact, while the effectiveness of attention is a well-established topic, the power of attention coefficients to express explanations remains a somewhat controversial issue in the literature. In this work, we empirically evaluate the possibility of using attention coefficients to obtain faithful explanations for recommender systems. In particular, after showing how to use attention for explaining recommendations, we examine the robustness of our proposal.
Dissolution in a porous rock: effect on the concentration–discharge relationships

: Various empirical or physically-based theory have been proposed to understand how the solute concentration of a stream varies with the discharge. We focus here on the influence of the dynamics of the groundwater flow on the chemical erosion rate. To do so, we couple a one-dimensional aquifer model to a first order dissolution equation. If the aquifer extends far below the stream level, the theoretical discharge–concentration equation corresponds to the empirical “working model” proposed by Johnson in 1969, thus providing a physical interpretation of its parameters. Conversely, if the aquifer lays mainly above the stream level, a significantly different relationship is found. These theoretical findings are then compared to two field-data sets. From this comparison, we conclude that the dynamics of the groundwater flow could play a significant role in moderating the impact of dilution on the stream concentration at large discharges.
Timing of cattle grazing alters impacts on stream banks in an Oregon mountain watershed

Timing of grazing by cattle may be a critical consideration to minimize impacts on stream banks. Damage to stream banks may be less when cattle preferentially graze uplands. We tested the hypothesis that early summer grazing (28 days; mid-June to mid-July) would have less impact on stream bank cover and stability compared to late summer grazing (28 days; mid-August to mid-September). The two-year study was conducted at the Eastern Oregon Agriculture Research Center in northeastern Oregon. Three replications each of three grazing treatments were examined: (1) nongrazed, (2) early summer grazing, and (3) late summer grazing. Each grazed pasture (approximately 11.5 ha [28.4 ac]) was stocked with cow-calf pairs for a mean stocking rate of 0.7 ha per animal unit month (AUM−1) (1.7 ac AUM−1) (range 0.5 to 9.0 ha AUM−1 [1.2 to 22.2 ac AUM−1]) to achieve moderate grazing intensity of 35% to 50% utilization. Estimates of stream bank cover (“covered” or “uncovered”) and stability (“stable” or “unstable”) were taken before and after each grazing period by examining plots approximately 0.5 × 0.3 m (19.7 × 11.8 in) placed on the greenline (the first vegetation at water's edge). Additionally, frequency of cattle hoof prints (plots with hoof prints ÷ total number of plots within the treatment pasture) was measured as an indicator of cattle presence. Treatments were compared using multifactor analysis of variance (ANOVA). Stream bank effects were consistent with observations of cattle distribution, with 53% (standard error [SE] ± 11%) of the greenline in early summer pastures showing cattle presence (hoof prints), versus 90% (SE ± 1%) for late summer pastures. In early summer, cattle spent more time in the uplands, resulting in the development of just 3% (SE ± 2%) uncovered stream banks, compared to 8% (SE ± 2%) late season. Similarly, early summer grazing resulted in 13% (SE ± 2%) unstable stream banks compared to 31% (SE ± 2%) in late summer. The primary cause of instability was sloughing of the bank into the stream channel. An “erosion index” indicated potential erosion was 1.62 times greater during late summer compared to early summer grazing. Our study suggests that grazing riparian areas when adjacent uplands are attractive to cattle may help reduce deleterious impacts on stream banks. Land managers should consider impacts of timing of grazing on individual streams when developing best management practices to meet grazing objectives in riparian areas.
Optimizing Deep Q-Learning Experience Replay with SHAP Explanations: Exploring Minimum Experience Replay Buffer Sizes in Reinforcement Learning

Explainable Reinforcement Learning (xRL) faces challenges in debugging and interpreting Deep Rein-forcement Learning (DRL) models. A lack of understanding for internal components like Experience Replay, which samples and stores data from the environment, risks burdening resources. This paper presents an xRL-based Deep Q-Learning (DQL) system using SHAP (SHapley Additive exPlanations) to explain input feature contributions. Data is sampled from Experience Replay, creating SHAP Heatmaps to understand how it influences the neural network Q-value approximator’s actions. The xRL-based system aids in determining the smallest Experience Replay size for 23 simulations of varying complexities. It contributes an xRL optimization method, alongside traditional approaches, for tuning the Experience Replay size hyperparameter. This visual and creative approach achieves over 40% reduction in Experience Replay size for 18 of the 23 tested simulations, smaller than the commonly used sizes of 1 million transitions or 90% of total environment transitions.
Geometric TSP on Sets

In One-of-a-Set TSP , also known as the Generalised TSP , the input is a collection P := { P 1 , . , P r } of sets in a metric space and the goal is to compute a minimum-length tour that visits one element from each set. In the Euclidean variant of this problem, each P i is a set of points in R d that is contained in a given hypercube H i . We investigate how the complexity of Euclidean One-of-a-Set TSP depends on λ , the ply of the set H := { H 1 , . , H r } of hypercubes (The ply is the smallest λ such that every point in R d is in at most λ of the hypercubes). Furthermore, we show that the problem can be solved in 2 O ( λ 1 /d n 1 − 1 /d ) time, where n := P r i =1 | P i | is the total number of points. Finally, we show that the problem cannot be solved in 2 o ( n ) time when λ = Θ( n ), unless the Exponential Time Hypothesis (ETH) fails. In Rectilinear One-of-a-Cube TSP , the input is a set H of hypercubes in R d and the goal is to compute a minimum-length rectilinear tour that visits every hypercube. We show that the problem can be solved in 2 O ( λ 1 /d n 1 − 1 /d log n ) time, where n is the number of hypercubes.
Diet Induced Obesity Alters Muscle Spindle Afferent Function in Adult Mice

DIET INDUCED OBESITY ALTERS MUSCLE SPINDLE AFFERENT FUNCTION IN ADULT MICE by Lubayna Elahi Individuals with obesity are more likely to fall and exhibit balance instability. The reason for this is likely multifactorial, but there is some evidence that sensory function is impaired during obesity. We tested the hypothesis that muscle proprioceptor function is compromised in a mouse model of diet induced obesity. We used an in vitro musclenerve preparation to record muscle spindle afferent responses to physiological stretch and sinusoidal vibration. We compared the responses of mice on a control diet (10% kcal fat) with those eating a high fat diet (60% kcal fat) alone or in combination with either aspirin (120mg/kg/day in drinking water) or rosiglitazone (0.01% in chow) for 10 weeks. Following high fat diet feeding, adult mice exhibited decreased muscle spindle afferent responses to stretch and lower dynamic sensitivity. Treatment with aspirin or rosiglitazone did not completely rescue muscle spindle afferent responsiveness. Due to the importance of muscle spindle afferents to proprioception and motor control, decreased muscle spindle afferent responsiveness may contribute to balance instability during obesity. Future studies should test this hypothesis in the human population.
Ostrácodos (Crustacea, Ostracoda) y carófitos (Chlorophyta, Charales) de la Formación Desencuentro (Mioceno superior), provincia de La Rioja, Argentina

Resumen. Se describen e ilustran los ostracodos y carofitos de la Formacion Desencuentro, provincia de La Rioja, Argentina. La asociacion muestra baja diversidad con seis taxones de ostracodos: Eucypris sp. , Darwinula sp. , Cyamocytheridea sp. , Cyprideissalebrosahartmanni Ramirez, Limnocythere aff. L. reticulata Sharpe, Limnocythere sp. , y dos especies de carofitos: Charazeylanica s. l. Klein exWilldenow y Charamusacchioi Garcia sp. nov. El hallazgo de veinte girogonites bien preservados de Charamusacchioi permitio evaluar su variabilidad morfologica, establecer su relacion con la especie actual CharahornemanniiWallman, y arribar a la conclusion de que se trata de una nueva especie. Estos taxones indican un ambiente acuatico de aguas tranquilas oligohalinas a mesohalinas, con posible aporte de agua dulce, en un area tropical a subtropical, con temperatura media de alrededor de 15-20oC. Abstract. OSTRACODS (CRUSTACEA, OSTRACODA) AND CHAROPHYTES (CHLOROPHYTA, CHARALES) FROM THE DESENCUENTRO FORMATION (UPPER MIOCENE), LA RIOJA PROVINCE, ARGENTINA. Ostracods and charophytes from the Desencuentro Formation (La Rioja Province, Argentina) are described and illustrated. The association has low diversity with six ostracod taxa: Eucypris sp. , Darwinula sp. , Cyamocytheridea sp. , Cyprideis salebrosahartmanni Ramirez, Limnocythere aff. L. reticulata Sharpe, Limnocythere sp. and two charophytes: Charazeylanica s. l. Klein exWilldenow and Charamusacchioi Garcia sp. nov. The availability of twenty well preserved gyrogonites of Charamusacchioi sp. nov. allowed to observe the intra-populational morphological variability, to relate the new species with the extant Charahornemannii Wallman, and to conclude that it is a new species. The assemblage indicates a calm aquatic environment with oligohaline to mesohaline water, with a possible input of fresher water, in a tropical to subtropical area, with mean temperature of about 15-20oC.
Machine Learning Algorithms for Identification of Cohesive Zone Parameters for Mixed-Mode Fracture in Composite Sandwich Structure

We investigate three machine-learning algorithms to identify the cohesive zone parameters used in the fracture analysis of a honeycomb/carbon-epoxy sandwich structure. Determining the cohesive parameters from experimental results can be complicated because multiple parameters can fit the experimental results equally well, resulting in non-unique solutions that do not capture the correct values. Numerically, determining the cohesive zone parameters can be time-consuming due to modeling challenges, such as fine meshes needed near the crack tip. In this study, we apply three machine learning algorithms, namely, Support Vector Regression (SVR), Random Forest (RF), and Artificial Neural Network (ANN), to identify the interfacial cohesive parameters between the honeycomb core and carbon-epoxy facesheets. Our study represents the interfacial fracture using a cohesive zone model in a finite element (FE) simulation of the Asymmetric Double Cantilever Beam (ADCB) specimen configuration. The input variables include four cohesive zone parameters: the maximum normal contact stress, critical fracture energy for normal separation, maximum equivalent tangential contact stress, and critical fracture energy for tangential slip. FE simulations with ranges of cohesive model parameters produce a database of load-displacement responses that serve as training data for the machine learning algorithms. The results show that the suggested methods demonstrate remarkable accuracy for situations where the interfacial characteristics lie within the training dataset or beyond and reveal the importance of specific
Measuring Fragmentation in Dissociative Identity Disorder: The Measuring Fragmentation in Dissociative Identity Disorder: The Integration Measure and Relationship to Switching and Time in Integration Measure and Relationship to Switching and Time in Therapy Therapy

Background : Some people with dissociative identity disorder (DID) have very little communication or awareness among the parts of their identity, while others experience a great deal of cooperation among alternate identities. Previous research on this topic has been sparse. Currently, there is no empirical measure of integration versus fragmentation in a person with DID. In this study, we report the development of such a measure. Objecti v e : The goal of this study was to pilot the integration measure (IM) and to address its psychometric properties and relationships to other measures. The IM is the first standardized measure of integration in DID. Method : Eleven women with DID participated in an experiment that included a variety of tasks. They filled out questionnaires about trauma and dissociation as well as the IM. They also provided verbal results about switching among alternate identities during the study sessions. Results : Participants switched among identities an average of 5.8 times during the first session, and switching was highly correlated with trauma. Integration was related to switching, though this relationship may be non-linear. Integration was not related to time in psychotherapy. Conclusions : The IM provides a useful beginning to quantify and study integration and fragmentation in DID. Directions for future research are also discussed, including expanding the IM from this pilot. The IM may be useful in treatment settings to assess progress or change over time.
Quantitative Proteomics Analysis Reveals the Effect of a MarR Family Transcriptional Regulator AHA_2124 on Aeromonas hydrophila

Simple Summary Aeromonas hydrophila is a major pathogen with human–animal–fish comorbidity that causes many diseases. To better investigate the roles of different genes in Aeromonas hydrophila, our aim is to knock out a gene in A. hydrophila and study whether the gene affects the physiological phenotypes or not. We found that AHA_2124, encoding a multiple antibiotic resistance regulator (MarR) family regulator, affected the extracellular protease activity, hemolytic activity, and motility of the phytopathogenic bacterium Aeromonas hydrophila. The MarR family of the transcriptional regulators of bacteria are mainly involved in the regulation of various cellular processes. In this work, we call for further research on the bioinformatics analysis based on the comparison of the ΔAHA_2124 strain and wild type. Abstract The transcriptional regulators of the MarR family play an important role in diverse bacterial physiologic functions, whereas their effect and intrinsic regulatory mechanism on the aquatic pathogenic bacterium Aeromonas hydrophila are, clearly, still unknown. In this study, we firstly constructed a deletion strain of AHA_2124 (ΔAHA_2124) of a MarR family transcriptional regulator in Aeromonas hydrophila ATCC 7966 (wild type), and found that the deletion of AHA_2124 caused significantly enhanced hemolytic activity, extracellular protease activity, and motility when compared with the wild type. The differentially abundant proteins (DAPs) were compared by using data-independent acquisition (DIA), based on a quantitative proteomics technology, between the ΔAHA_2124 strain and wild type, and there were 178 DAPs including 80 proteins up-regulated and 98 proteins down-regulated. The bioinformatics analysis showed that the deletion of gene AHA_2124 led to some changes in the abundance of proteins related to multiple biological processes, such as translation, peptide transport, and oxidation and reduction. These results provided a theoretical basis for better exploring the regulatory mechanism of the MarR family transcriptional regulators of Aeromonas hydrophila on bacterial physiological functions.