Miracle-dz/UniFAR-FTUs huggingface dataset:
Prognostic Significance of Pregnancy Zone Protein and Its Correlation with Immune Infiltrates in Hepatocellular Carcinoma

Aim Human pregnancy zone protein (PZP) is a pregnancy-related protein which is increased dramatically during pregnancy. However, the expression of PZP and its prognostic value, association with tumor-infiltrating immune cells (TIICs) in microenvironment and potential biological process in HCC were unclear. Methods The PZP expression, clinicopathology analysis and its influence on survival were analyzed by GEPIA and HPA. Fifty-nine HCC samples and 30 corresponding noncancerous tissues were collected and retrospectively analyzed to verify the results of bioinformatics analysis. Further, TIMER and CIBERSORT were performed to identify the significantly alerted biological process and affections of PZP expression on the immune system in patients with HCC. Finally, IHC assay of CD4+ T cells and Treg cells was performed to confirm the results of immune infiltrates analysis by TIMER and CIBERSORT. Results PZP expression was downregulated in HCC tissues and its low level was substantially correlated with poor prognosis in patients with HCC. TIMER analysis showed that PZP expression had a positive correlation with the levels of macrophage and neutrophil. Furthermore, CIBERSORT analysis showed that resting memory CD4 T cells were increased in high PZP expression group, while the results of Tregs were the opposite. Finally, the IHC results of CD4+ T cells and Treg cells showed that only Tregs were negatively associated with PZP expression. Conclusion PZP was identified as a novel prognosis biomarker of HCC and might play a vital role in the regulation and recruitment of TIICs in HCC immune microenvironment.
DP-MERF: Differentially Private Mean Embeddings with RandomFeatures for Practical Privacy-preserving Data Generation

We propose a differentially private data generation paradigm using random feature representations of kernel mean embeddings when comparing the distribution of true data with that of synthetic data. We exploit the random feature representations for two important benefits. First, we require a minimal privacy cost for training deep generative models. This is because unlike kernel-based distance metrics that require computing the kernel matrix on all pairs of true and synthetic data points, we can detach the data-dependent term from the term solely dependent on synthetic data. Hence, we need to perturb the data-dependent term once and for all and then use it repeatedly during the generator training. Second, we can obtain an analytic sensitivity of the kernel mean embedding as the random features are norm bounded by construction. This removes the necessity of hyper-parameter search for a clipping norm to handle the unknown sensitivity of a generator network. We provide several variants of our algorithm, differentially private mean embeddings with random features (DP-MERF) to jointly generate labels and input features for datasets such as heterogeneous tabular data and image data. Our algorithm achieves drastically better privacy-utility trade-offs than existing methods when tested on several datasets.
Relative Flatness and Generalization in the Interpolation Regime.

Traditional generalization bounds are based on analyzing the limits of the model capacity. Therefore, they become vacuous in the \emph{interpolation} (over-parameterized) regime of modern machine learning models where training data can be fitted perfectly. This paper proposes a new approach to meaningful generalization bounds in the interpolation regime by decomposing the generalization gap into a notion of \emph{representativeness} and \emph{feature robustness}. Representativeness captures properties of the data distribution and mitigates the dependence on the data dimension by exploiting the low-dimensional feature representation used implicitly by the model, and feature robustness captures the expected change in loss resulting from perturbations of these implicit features. We show that feature robustness can be bounded by a relative flatness measure of the empirical loss surface for models that locally minimize the training loss. This yields an algorithm-agnostic bound potentially explaining the abundance of empirical observations that flatness of the loss surface is correlated with generalization.
The effect of different levels of Ferulago angulata sub. carduchorum on total serum antioxidant activity and some of the humoral immune responses in broiler chicks

Background & Aim: Ferulago angulata sub. carduchorum (ref. to locally Chavir or Chavil) is an important medicinal plant in Iran. The powder of aerial parts of this plant contains variety of components with different therapeutical effects such as antioxidant activities (AOA). This study was conducted to investigate the effect of dietary supplementation powder of aerial parts of this plant on total activities of serum antioxidant and some of the humoral immune responses in broiler chicks. Experimental: Three hundred of sixty day-old Commercial Chicks (Ross 308) was randomly allocated to six treatments with five replicates. The dietary treatments consisted of the basal diet as control (A), 100 ppm (150 IU) of vitamin E (B), 70 g / 100 kg Flavofosfolipol (C), %0.3 (D), %0.6 (E) and %1 (F) of the powder of aerial parts of this plant added to the basal diet. At 25 days, from each treatment of experiment two chicks were randomly selected and sheep red blood cell (SRBC) was injected through their wings veins. At 30 days blood simples (ten simple of per treatment) for the test of antibody measurement produced against SRBC, the influenza virus and Newcastle were prepared. Moreover, with the blood extension and numbering of Hetrophil and Lymphocyte calculated and hetrophil to lymphocyte ratio were estimated. At 42 days Blood Samples (ten samples per treatment) were taken for measuring total activities of serum antioxidant. Results & Discussion: Results indicated that supplementing of %0.6 of F. angulata significantly increased total activities of serum antioxidant compared to control birds (p ≤ 0.05). There is no significant difference among the treatments of experiment in the number of Hetrophil, Lymphocyte their ratio and the antibody against the virus of Newcastle and SRBC. However this antibody against the influenza virus at the treatment of 3 g/kg F. angulata in comparison to control treatment was more.
Motor constraints influence cultural evolution of rhythm

While widely acknowledged in the cultural evolution literature, ecological factors—aspects of the physical environment that affect the way in which cultural productions evolve—have not been investigated experimentally. Here, we present an experimental investigation of this type of factor by using a transmission chain (iterated learning) experiment. We predicted that differences in the distance between identical tools (drums) and in the order in which they are to be used would cause the evolution of different rhythms. The evidence confirms our predictions and thus provides a proof of concept that ecological factors—here a motor constraint—can influence cultural productions and that their effects can be experimentally isolated and measured. One noteworthy finding is that ecological factors can on their own lead to more complex rhythms.
Microplastic exposure interacts with habitat degradation to affect behaviour and survival of juvenile fish in the field

Coral reefs are degrading globally due to increased environmental stressors including warming and elevated levels of pollutants. These stressors affect not only habitat-forming organisms, such as corals, but they may also directly affect the organisms that inhabit these ecosystems. Here, we explore how the dual threat of habitat degradation and microplastic exposure may affect the behaviour and survival of coral reef fish in the field. Fish were caught prior to settlement and pulse-fed polystyrene microplastics six times over 4 days, then placed in the field on live or dead-degraded coral patches. Exposure to microplastics or dead coral led fish to be bolder, more active and stray further from shelter compared to control fish. Effect sizes indicated that plastic exposure had a greater effect on behaviour than degraded habitat, and we found no evidence of synergistic effects. This pattern was also displayed in their survival in the field. Our results highlight that attaining low concentrations of microplastic in the environment will be a useful management strategy, since minimizing microplastic intake by fishes may work concurrently with reef restoration strategies to enhance the resilience of coral reef populations.
A general mathematical method for predicting spatio-temporal correlations emerging from agent-based models

Agent-based models are used to study complex phenomena in many fields of science. While simulating agent-based models is often straightforward, predicting their behaviour mathematically has remained a key challenge. Recently developed mathematical methods allow the prediction of the emerging spatial patterns for a general class of agent-based models, whereas the prediction of spatio-temporal pattern has been thus far achieved only for special cases. We present a general and mathematically rigorous methodology that allows deriving the spatio-temporal correlation structure for a general class of individual-based models. To do so, we define an auxiliary model, in which each agent type of the primary model expands to three types, called the original, the past and the new agents. In this way, the auxiliary model keeps track of both the initial and current state of the primary model, and hence the spatio-temporal correlations of the primary model can be derived from the spatial correlations of the auxiliary model. We illustrate the agreement between analytical predictions and agent-based simulations using two example models from theoretical ecology. In particular, we show that the methodology is able to correctly predict the dynamical behaviour of a host–parasite model that shows spatially localized oscillations.
Continuous population declines for specialist farmland birds 1987-2014 in Denmark indicates no halt in biodiversity loss in agricultural habitats

Summary The 2020 EU biodiversity strategy aims to halt the loss of biodiversity and ecosystem services, but this requires effective monitoring to determine whether these aims are achieved. Common bird monitoring continuously assesses changes in the avian community, providing a powerful tool for monitoring temporal changes in the abundance and distribution of these upper trophic level consumers. Two-thirds of Denmark’s land area is intensively farmed, so agricultural habitats make a major contribution to Danish biodiversity. We looked for changes in abundance amongst farmland birds in Denmark during 1987–2014 to test for reductions in declines and to predict whether the 2020-target can be expected to be achieved. Sixteen specialist farmland species were those showing the most rapid declines amongst 102 common breeding species in Denmark. Of these, those species nesting on the ground showed significant long-term declines, which was not the case for those that nest elsewhere, i.e. in hedgerows, trees and buildings. There was no evidence to suggest that these trends were attributable to widespread declines in long-distance migrant species (as reported elsewhere), which may be affected by conditions at other times in the annual cycle. We therefore conclude that continued declines in specialist farmland breeding bird species are due to contemporary agricultural changes within Denmark and urge habitat- and species-specific analysis to identify the core causes of these changes and halt the declines.
Do social environments affect the use of exaggerated traits in the dobsonfly Corydalus bidenticulatus?

Male–male competition is strongly affected by female presence. In insects with primitive features such as megalopterans, however, it is not known how aggressiveness is expressed in the context of female presence. Here we examined the effect of social environments on the use of secondary sexual traits in the sexual behavior of the Mexican dobsonfly Corydalus bidenticulatus (Megaloptera: Corydalidae). Males of this species have exaggerated traits such as disproportionally elongated mandibles with no dentition, which is a secondary sexual trait used in competition over female access as well as males of other Corydalus species. We investigated how male–male interactions are carried out, and the scaling relationships of sexual and non‐sexual traits. Our results show that males of C. bidenticulatus are not indiscriminately aggressive. The decision whether to fight or not is affected by their social environments: males are aggressive against other males only when the presence of a female is detected. Results also suggest that mandibles and antennae are sexually dimorphic, being exaggerated and showing positive allometry only in males. In contrast, male genitalia, a sex‐specific trait, show negative allometry.
Future changes of global potential evapotranspiration simulated from CMIP5 to CMIP6 models

ABSTRACT This research evaluated the ability of different coupled climate models to simulate the historical variability of potential evapotranspiration (PET) for the time period 1979–2017 in phases 5 and 6 of the Coupled Model Intercomparison Project (CMIP5 and CMIP6, respectively). Their projected future changes of PET under two emission scenarios for the 21st century were also compared. Results show that PET has an increasing trend of 0.2–0.6 mm d−1/50 yr over most land surfaces and that there are clear regional differences. The future value of PET is higher in the CMIP6 multi-model simulations than in the CMIP5 ones under the same emissions scenario, possibly because CMIP6 models simulate stronger warming for a given forcing or scenario. The contributions of each individual climate driver to future changes in PET were examined and revealed that the surface vapor pressure deficit makes a major contribution to changes in PET. Shortwave radiation increases PET in most terrestrial regions, except for northern Africa, East Asia, South Asia, and Australia; the effect of longwave radiation is the opposite to that of shortwave radiation. The contribution of surface wind speed to PET is small, but results in a slight reduction.
The teacher career cycle and initial motivation: the case of Slovenian secondary school teachers

ABSTRACT This article focuses on the career cycle and initial motivation of secondary school teachers in Slovenia and is based on the Teacher Career Cycle Model. The aim of the study was to determine whether there are differences in the career stages and motivation in terms of teachers’ gender, mode of formal education and length of work experience in teaching and whether there are any correlations between the stages and motivation. The study included 94 secondary school teachers who completed the Slovenian version of the Career Choice Scale and Career Development Scale. The results show that female teachers are more intrinsically motivated in choosing the profession, while male teachers are more insecure in the profession. Teachers who completed concurrent programmes show a higher level of intrinsic motivation for the teaching profession and a major wind-down was apparent for teachers with 21 years or more of work experience in teaching.
Deep Reinforcement Learning-Based Vehicle Driving Strategy to Reduce Crash Risks in Traffic Oscillations

The primary objective of this study is to propose a deep reinforcement learning-based driving strategy for individual vehicles to mitigate oscillations and optimize traffic safety in stop-and-go waves. A deep deterministic policy gradient (DDPG)-based driving strategy, which requires information that is directly obtained by in-vehicle sensors, is proposed for system performance optimization. Two typical scenarios were simulated based on simulation software (SUMO): (i) the leading vehicle slowed down according to real trajectory data to produce one oscillation; (ii) the leading vehicle conducted several abrupt decelerations with various degrees of disturbance to produce multiple oscillations. The DDPG agents interacted with the SUMO platform to determine the optimal acceleration of vehicles that can reduce crash risks in various stop-and-go waves. The results showed that the proposed DDPG-based driving strategy successfully reduced the crash risk by 68.9%–78.4%. Scenarios with different penetration rates of DDPG agents and in various flow rates were compared to test the effect of the proposed strategy. The DDPG-based driving strategy reduced crash risk more with the increase of penetration rate and this strategy performed better when applied in the scenario with a high traffic flow rate. The proposed strategy is compared with the adaptive cruise control and jam-absorbing driving strategies. Results showed the proposed strategy outperformed other oscillation mitigating strategies in reducing crash risks.
Understanding the Effectiveness of Bus Rapid Transit Systems in Small and Medium-Sized Cities in North America

In response to a lack of existing academic literature in relation to bus rapid transit (BRT) system success in small and medium-sized cities, this research examines the operational, demographic, and socioeconomic aspects of BRT at the route and system level in 16 small and medium-sized cities across North America. The results are compared with BRTs of large North American metropolitan areas to establish how the determinants of and requirements for BRT success differ. A wide array of factors collected from transit agencies, the Canadian and American 2016 censuses, and General Transit Feed Specification (GTFS) data are analyzed alongside ridership, which represents the primary determinant of BRT system success. The findings suggest that BRT routes of larger cities generally enjoy higher ridership levels compared with smaller and medium-sized cities in North America. Operational variables including service frequency were considerably higher in larger cities, with shorter route lengths, compared to small and medium cities. Higher population density, local accessibility, and percentage of rented households can also be observed in larger cities’ BRT system catchment areas in comparison with smaller cities. However, some BRT routes of smaller and medium-sized cities in North America exhibit comparable ridership levels with those in large cities. These routes have similar levels in relation to rentership, route length, and headway, with good local accessibility, while falling behind in population density. This paper expands on previous research on BRT systems, helping transit planners and policymakers to better understand the relationship between the city size and BRT ridership levels.
Effects of increasing protein level on the performance, enzyme activity and body composition of the Brazilian sardine, Sardinella brasiliensis (Steindachner, 1879)

A six-week growth trial was performed to estimate the dietary protein requirements for maximum growth of juvenile Brazilian sardine (Sardinella brasiliensis) based on growth performance, feed utilization, body composition and digestive enzyme activity. Six isoenergetic diets were formulated to contain protein levels that increased from 250 to 500 g/kg. Each diet was randomly assigned to triplicate groups of 160 fish with mean initial body weight of 0.93 ± 0.13 g, which were fed four times a day to apparent satiation. Growth tended to increase with the increase in the dietary protein level up to 400 g/kg. Total protein intake was indirectly correlated to apparent protein utilization. No significant differences in whole-body composition were found between fish fed the different protein levels. Acid protease and neutral lipase activities did not show significant differences among the different protein dietary groups. Alkaline protease activity increased in fish fed up to 350 g/kg of protein and amylase activity in fish fed up to 400 g/kg. Using polynomial regression, 367 g/kg was estimated to be the optimum dietary protein requirement for maximum weight gain of juvenile Brazilian sardines.
The Role of Phosphorus Limitation in Shaping Soil Bacterial Communities and Their Metabolic Capabilities

Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands. ABSTRACT Phosphorus (P) is an essential nutrient that is often in limited supply, with P availability constraining biomass production in many terrestrial ecosystems. Despite decades of work on plant responses to P deficiency and the importance of soil microbes to terrestrial ecosystem processes, how soil microbes respond to, and cope with, P deficiencies remains poorly understood. We studied 583 soils from two independent sample sets that each span broad natural gradients in extractable soil P and collectively represent diverse biomes, including tropical forests, temperate grasslands, and arid shrublands. We paired marker gene and shotgun metagenomic analyses to determine how soil bacterial and archaeal communities respond to differences in soil P availability and to detect corresponding shifts in functional attributes. We identified microbial taxa that are consistently responsive to extractable soil P, with those taxa found in low P soils being more likely to have traits typical of oligotrophic life history strategies. Using environmental niche modeling of genes and gene pathways, we found an enriched abundance of key genes in low P soils linked to the carbon-phosphorus (C-P) lyase and phosphonotase degradation pathways, along with key components of the high-affinity phosphate-specific transporter (Pst) and phosphate regulon (Pho) systems. Taken together, these analyses suggest that catabolism of phosphonates is an important strategy used by bacteria to scavenge phosphate in P-limited soils. Surprisingly, these same pathways are important for bacterial growth in P-limited marine waters, highlighting the shared metabolic strategies used by both terrestrial and marine microbes to cope with P limitation.
Tell Me Where You’ve Been and I’ll Tell You How You’ll Evolve

The reproducibility of adaptive evolution is a long-standing debate in evolutionary biology. Kempher et al. (M. L. Kempher, X. Tao, R. Song, B. Wu, et al., mBio 11:e00569-20, 2020, https://doi.org/10.1128/mBio.00569-20) used experimental evolution to investigate the effect of previous evolutionary trajectories on the ability of microbial populations to adapt to high temperatures. Despite the divergence caused by adaptation to previous environments, all populations reproducibly converged on similar final levels of fitness. ABSTRACT The reproducibility of adaptive evolution is a long-standing debate in evolutionary biology. Kempher et al. (M. L. Kempher, X. Tao, R. Song, B. Wu, et al., mBio 11:e00569-20, 2020, https://doi.org/10.1128/mBio.00569-20) used experimental evolution to investigate the effect of previous evolutionary trajectories on the ability of microbial populations to adapt to high temperatures. Despite the divergence caused by adaptation to previous environments, all populations reproducibly converged on similar final levels of fitness. Nevertheless, the genetic basis of adaptation depended on past selection experiments, reinforcing the idea that previous adaptation can dictate the trajectories of later evolutionary processes.