Miracle-dz/UniFAR-FTUs huggingface dataset:
Phylogenetic Relationships and Potential Functional Attributes of the Genus Parapedobacter: A Member of Family Sphingobacteriaceae

The genus Parapedobacter was established to describe a novel genus within the family Sphingobacteriaceae and derives its name from Pedobacter, with which it is shown to be evolutionarily related. Despite this, Parapedobacter and Pedobacter do not share very high 16S rRNA gene sequence similarities. Therefore, we hypothesized whether these substantial differences at the 16S rRNA gene level depict the true phylogeny or that these genomes have actually diverged. Thus, we performed genomic analysis of the four available genomes of Parapedobacter to better understand their phylogenomic position within family Sphingobacteriaceae. Our results demonstrated that Parapedobacter is more closely related to species of Olivibacter, as opposed to the genus Pedobacter. Further, we identified a significant class of enzymes called pectinases with potential industrial applications within the genomes of Parapedobacter luteus DSM 22899T and Parapedobacter composti DSM 22900T. These enzymes, specifically pectinesterases and pectate lyases, are presumed to have largely different catalytic activities based on very low sequence similarities to already known enzymes and thus may be exploited for industrial applications. We also determined the complete Bacteroides aerotolerance (Bat) operon (batA, batB, batC, batD, batE, hypothetical protein, moxR, and pa3071) within the genome of Parapedobacter indicus RK1T. This expands the definition of genus Parapedobacter to containing members that are able to tolerate oxygen stress using encoded oxidative stress responsive systems. By conducting a signal propagation network analysis, we determined that BatD, BatE, and hypothetical proteins are the major controlling hubs that drive the expression of Bat operon. As a key metabolic difference, we also annotated the complete iol operon within the P. indicus RK1T genome for utilization of all three stereoisomers of inositol, namely myo-inositol, scyllo-inositol, and 1D-chiro-inositol, which are abundant sources of organic phosphate found in soils. The results suggest that the genus Parapedobacter holds promising applications owing to its environmentally relevant genomic adaptations, which may be exploited in the future.
Of Women Tech Pioneers and Tiny Experts of Ingenuity

This paper presents findings from a collective case study focusing on the efforts of a grassroots team of seven pioneering women: teachers, IT consultants, and tech enthusiasts. The team was formed to introduce, encourage, and establish makerspaces in the Icelandic compulsory school system by educating and supporting teachers and young students (6–15 years) as makers and advocates of maker culture. All seven team members have developed or supported different models of makerspaces in their area of work and offered guidance to other educators. Our research examines learning on a personal, relational, and institutional level, reviewing values and practices of participants and what characterizes their social interactions, agency and empowerment in relation to making. It introduces new models of pedagogy, often supported by school leadership and social media action facilitating the development of making and maker culture. It attempts to map how makerspaces can be integrated into school practice in alignment with curricular objectives to support diverse engagements, digital literacies and creative design skills. Our findings further reveal how an all-women team has taken agency and through collaborative actions, collective creativity and self-empowerment managed to overcome challenges and provide leadership in this emergent field in Icelandic school practice.
Decline Variability of Cortical and Subcortical Regions in Aging: A Longitudinal Study

Describing the trajectories of age-related change for different brain structures has been of interest in many recent studies. However, our knowledge regarding these trajectories and their associations is still limited due to small sample sizes and low numbers of repeated measures. For the present study, we used a large longitudinal dataset (four measurements over 4 years) comprising anatomical data from a sample of healthy older adults (N = 231 at baseline). This dataset enables us to gain new insights about volumetric cortical and subcortical changes and their associations in the context of healthy aging. Brain structure volumes were derived from T1-weighted MRI scans using FreeSurfer segmentation tools. Brain structure trajectories were fitted using mixed models and latent growth curve models to gain information about the mean extent and variability of decline trajectories for different brain structures as well as the associations between individual trajectories. On the group level, our analyses indicate similar linear changes for frontal and parietal brain regions, while medial temporal regions showed an accelerated decline with advancing age. Regarding subcortical regions, some structures showed strong declines (e.g., hippocampus), others showed little decline (e.g., pallidum). Our data provide little evidence for sex differences regarding the aforementioned trajectories. Between-person variability of the person-specific slopes (random slopes) was largest in subcortical and medial temporal brain structures. When looking at the associations between the random slopes from each brain structure, we found that the decline is largely homogenous across the majority of cortical brain structures. In subcortical and medial temporal brain structures, however, more heterogeneity of the decline was observed, meaning that the extent of the decline in one structure is less predictive of the decline in another structure. Taken together, our study contributes to enhancing our understanding of structural brain aging by demonstrating (1) that average volumetric change differs across the brain and (2) that there are regional differences with respect to between-person variability in the slopes. Moreover, our data suggest (3) that random slopes are highly correlated across large parts of the cerebral cortex but (4) that some brain regions (i.e., medial temporal regions) deviate from this homogeneity.
Prosodic addressee-detection: ensuring privacy in always-on spoken dialog systems

We analyze the addressee detection task for complexity-identical dialog for both human conversation and device-directed speech. Our recurrent neural model performs at least as good as humans, who have problems with this task, even native speakers, who profit from the relevant linguistic skills. We perform ablation experiments on the features used by our model and show that fundamental frequency variation is the single most relevant feature class. Therefore, we conclude that future systems can detect whether they are addressed based only on speech prosody which does not (or only to a very limited extent) reveal the content of conversations not intended for the system.
Cost Modeling and Analysis of TSV and Contactless 3D-ICs

Contactless three-dimensional (3-D) interconnects have been proposed as an alternative to through-silicon via (TSV) due to its manufacturing compatibility with two-dimensional (2-D) processes. Typically, contactless 3-D circuits are thought to require considerable silicon resources compared to TSV. However, recent manufacturing options, such as extreme wafer thinning, provide new opportunities for this approach. This paper, therefore, explores these opportunities for producing 3-D systems of lower cost. The presented cost analysis and models usefully combine fabrication cost with performance requirements for inter-tier communication as a critical component of 3-D systems. Thus, benchmark circuits are simulated for a two-tier system using a commercial 65 nm technology and communicating at a data rate of 1 Gbps per link, although the model is directly applicable to any technology or design specifications. Interestingly, inductive links can be a useful alternative to TSV for specific and expected manufacturing capabilities. Furthermore, the effectiveness of different multiplexing schemes and their effect on system cost is also evaluated.
Sanitizing Synthetic Training Data Generation for Question Answering over Knowledge Graphs

Synthetic data generation is important to training and evaluating neural models for question answering over knowledge graphs. The quality of the data and the partitioning of the datasets into training, validation and test splits impact the performance of the models trained on this data. If the synthetic data generation depends on templates, as is the predominant approach for this task, there may be a leakage of information via a shared basis of templates across data splits if the partitioning is not performed hygienically. This paper investigates the extent of such information leakage across data splits, and the ability of trained models to generalize to test data when the leakage is controlled. We find that information leakage indeed occurs and that it affects performance. At the same time, the trained models do generalize to test data under the sanitized partitioning presented here. Importantly, these findings extend beyond the particular flavor of question answering task we studied and raise a series of difficult questions around template-based synthetic data generation that will necessitate additional research.
Effects of Selenium-Enriched Yeast on Performance, Egg Quality, Antioxidant Balance, and Egg Selenium Content in Laying Ducks

This study investigated the effects of dietary selenium-enriched yeast (Se yeast) supplementation on the laying performance, egg quality, plasma antioxidant balance, and egg selenium (Se) content in laying Longyan ducks. A total of 480 32-week-old ducks were randomly divided into four dietary treatments, each consisting of six replicates of 20 ducks. The dietary treatments were a control basal diet and basal diets with supplementation of 0.05, 0.15, and 0.25 mg Se/kg via Se yeast. The analyzed Se contents of the four diets were 0.15, 0.21, 0.36, and 0.43 mg Se/kg, respectively. Dietary Se yeast supplementation had no apparent effects on laying performance and egg quality (p > 0.05), but it improved the antioxidant balance of ducks, as inferred by greater glutathione peroxidase and catalase activities, and decreased the malondialdehyde content in plasma of ducks (p < 0.05). It was suggested that the Se content in the basal diet containing 0.15 mg/kg of Se requirement is adequate for productive performance, but not for the antioxidant balance of laying ducks. Besides that, the Se contents in the yolk, albumen, and whole egg increased linearly as the Se supplementation levels increased. With more feeding days, the Se contents in the yolk and whole egg from non-Se-yeast-supplemented ducks increased linearly (p < 0.05), while those from Se-yeast-supplemented ducks showed a quadratic relationship (p < 0.05). In conclusion, the Se content of the basal diet at 0.15 mg/kg was adequate for laying performance and egg quality traits in laying ducks. Dietary Se yeast supplementation is beneficial to improve the antioxidant balance of laying ducks and increase the Se deposition in eggs for producing Se-enriched eggs. Based on the quadratic model or the quadratic broken-line model analyses, supplemental 0.19 mg Se/kg via Se yeast, with a total equivalent of 0.34 mg Se/kg in the diet, could provide the optimum antioxidant balance in laying ducks. Dietary supplementation of 0.25 mg Se/kg via Se yeast, with a total equivalent of 0.40 mg Se/kg in the diet, could lead to achieving the desired Se content in the whole egg.
Robust Unsupervised Factory Activity Recognition with Body-worn Accelerometer Using Temporal Structure of Multiple Sensor Data Motifs

This paper presents a robust unsupervised method for recognizing factory work using sensor data from body-worn acceleration sensors. In line-production systems, each factory worker repetitively performs a predefined work process with each process consisting of a sequence of operations. Because of the difficulty in collecting labeled sensor data from each factory worker, unsupervised factory activity recognition has been attracting attention in the ubicomp community. However, prior unsupervised factory activity recognition methods can be adversely affected by any outlier activities performed by the workers. In this study, we propose a robust factory activity recognition method that tracks frequent sensor data motifs, which can correspond to particular actions performed by the workers, that appear in each iteration of the work processes. Specifically, this study proposes tracking two types of motifs: period motifs and action motifs, during the unsupervised recognition process. A period motif is a unique data segment that occurs only once in each work period (one iteration of an overall work process). An action motif is a data segment that occurs several times in each work period, corresponding to an action that is performed several times in each period. Tracking multiple period motifs enables us to roughly capture the temporal structure and duration of the work period even when outlier activities occur. Action motifs, which are spread throughout the work period, permit us to precisely detect the start time of each operation. We evaluated the proposed method using sensor data collected from workers in actual factories and achieved state-of-the-art performance.
Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs

Though it is well-acknowledged that next generation sequencing (NGS) technologies can provide further insights into plant conservation management than traditional molecular markers, studies employing NGS to address conservation genomics and subsequent conservation strategies for threatened plants are still rare. Rhododendron is the largest genus of woody plants in China, and many species are threatened, however, to date there has been no conservation genetic research using NGS in this genus. In the present study, we investigated the conservation genetics of R. cyanocarpum, a threatened species endemic to the Cangshan Mountains in Yunnan, China, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. Due to the availability of sufficient SNPs, we were able to distinguish between neutral and putatively selected SNPs and were able to further investigate the genetic diversity, population structure, and differentiation in R. cyanocarpum, as well as make an estimation of its demographic history. A total of 6,584 SNPs were obtained, of which 5,729 were neutral (detected using Tajima’s D). In terms of the 5,729 neutral SNPs, R. cyanocarpum had a higher genetic diversity (π = 0.0702 ± 0.0017, He = 0.0675 ± 0.0016) than other plant species assessed using Rad-seq methods, while population differentiation (Fst from 0.0314 to 0.0452) was weak. Interestingly, contrasting patterns of population structure were revealed from all neutral and selected SNPs, with distinct genetic clusters forming for all SNPs and neutral SNPs, but no distinct subgroups for selected ones. Moreover, we were able to detect changes in effective population size (Ne) of R. cyanocarpum from 150,000 years ago, including a bottleneck event ca. 60,000 years ago, followed by recovery of Ne over a short period, and a subsequent gradual decline in Ne to date. Implications for conserving R. cyanocarpum based on these main results are then discussed.
Population Dynamics, Life History, and Production of Cyathura Carinata (Krøyer) (Isopoda: Anthuridae) in the Mondego Estuary, Portugal

ABSTRACT Previous studies of the benthic community in the Mondego estuary revealed that Cyathura carinata has spatially and temporally stable populations, has significant biomass throughout the year, and is one of the most abundant species in the estuary. The present work was carried out to study its population dynamics and life cycle in relation to physicochemical factors, and to estimate its productivity within intertidal mud flats. Cyathura carinata was sampled every two weeks from November 1990 to December 1991. It exhibited a contagious spatial distribution within the eulittoral zone, and its abundance changed seasonally, decreasing gradually from midfall to late spring, and increasing again from early summer to the following fall. Abundance appeared to be inversely related to emersion periods, and positively correlated with salinity and nitrate concentrations, while higher temperature and sediment organic enrichment appeared to have a negative effect on the abundance of organisms. Nevertheless, the correlations between abundance and environmental factors could not be considered as defining cause-andeffect, since environmental factors were also intercorrelated. Protogynous hermaphroditism was hypothesized, with males being present from March to September. Sexual activity began in early spring and recruitment took place through the summer. Two cohorts were produced, one in June and a second in August. Fecundity was significantly correlated with female size. In addition, higher salinities and pH favored higher fecundity. Although seasonal variations in growth rates were observed, growth was continuous through the life of the animal. Growth rates practically ceased during the winter, increased gradually from late winter to a maximum between early summer and midfall, and decreased again until the following winter. Life span was roughly estimated at 18-22 months. Sexual differentiation was estimated to occur within a period of 49-54 days from birth, for females, and 146-208 days for males. Sexual maturation in females was estimated to occur in 240-357 days (8-12 months). Cyathura carinata is a semiannual species in the Mondego estuary, with iteroparous females and an univoltine life cycle. Growth production (P) and elimination production (E) were estimated as, respectively, 5.6-9.9 and 11.8-22.3 g·m―2· year―1 ash-free dry weight. P/B and E/B ratios were estimated, respectively, as 1.65-2.03 and 3.74-4.37. Despite several differences with regard to the reproductive period, all populations of C. carinata studied along the European coasts show univoltine life cycles. Due to stable populations and life cycle characteristics, this species appears ideal for comparative ecophysiological and ecotoxicological studies in European estuaries.
Genetic Relationships of Three Species of Bathygobius from the Atlantic and Pacific Sides of Panama

Electrophoretic study of 26 gene loci was carried out on Bathygobius soporator from the Atlantic side of Panama, and B. ramosus and B. andrei from the Pacific side of Panama. The most closely related pair is B. soporator and B. andrei. The predicted divergence time is about 2.5 million years, which is in accord with geological evidence on the rise of the Panama land bridge. B. ramosus is the distant member of the trio, about equidistant from the other pair.
The suitability of leaf-off airborne laser scanning data in an area-based forest inventory of coniferous and deciduous trees

This study examined the suitability of airborne laser scanner (ALS) data collected under leaf-off conditions in a forest inventory, in which deciduous and coniferous trees need to be separated. All analyses were carried out with leaf-on and leaf-off ALS data collected from the same study area. Additionally, aerial photographs were utilized in the Nearest Neighbor (NN) imputations. An area-based approach was used in this study. Regression estimates of plot volume were more accurate in the case of leaf-off than leaf-on data. In addition, regression models were more accurate in coniferous plots than in deciduous plots. The results of applying leaf-on models with leaf-off data, and vice versa, indicate that leaf-on and leaf-off data should not be combined since this causes serious bias. The total volume and volume by coniferous and deciduous trees was estimated by the NN imputation. In terms of total volume, leaf-off data provided more accurate estimates than leaf-on data. In addition, leaf-off data discriminated between coniferous and deciduous trees, even without the use of aerial photographs. Accurate results were also obtained when leaf-off ALS data were used to classify sample plots into deciduous and coniferous dominated plots. The results indicate that the area-based method and ALS data collected under leaf-off conditions are suitable for forest inventory in which deciduous and coniferous trees need to be distinguished.
Sexual segregation in black-tailed deer : effects of scale

We studied sexual segregation in a migratory population of Columbian black-tailed deer (Odocoileus hemionus columbianus) on Big Flat in the Trinity Alps of northern California. During 20 June-20 August 1992, we examined the effects of spatial and temporal scales on measurements of sexual segregation by dividing our study area into 56 16-ha quadrats, the smallest area in which we could map locations of deer accurately. We observed and recorded locations of deer by driving a 9-km fixed transect each morning and evening. We analyzed observations made near parturition (29 Jun-31 Jul) to determine spatial separation of the sexes, and to avoid a bias from deer migrating to and from Big Flat. We combined adjacent quadrats to obtain sampling units of 32, 48, 64, 80, 96, 112, 128, 160, 176, and 192 ha. We arbitrarily required a quadrat to contain observations with ≥90% of a single sex to be considered segregated. We hypothesized that the scale of our analyses would influence measures of sexual segregation. We analyzed the degree of sexual segregation on a spatial (all observations of a quadrat combined for the entire 5 weeks) and a temporal-spatial scale (samples of a quadrat analyzed by week) to test the null hypothesis that quadrat size was unrelated to the degree of sexual segregation. For all quadrat sizes, the degree of segregation was greater (10-25%) for temporal-spatial than spatial analysis, but the pattern in declining degree of segregation with increasing quadrat size was similar for both methods. We assessed whether male:female ratios departed significantly from the 0.27:1.00 ratio for our 5-week sample of the study area to determine if the ratio of deer available to sample biased our measure of sexual segregation. Male: female ratios differed significantly from 0.27:1.00 for all quadrats, but the degree of difference declined with increasing quadrat size. We used a one-tailed runs test to determine whether the sexes were distributed contagiously (i.e., segregated) across our study for all sizes of quadrats. This analysis suggested that quadrats of 80 ha should be used to sample the degree of sexual segregation in our study area. The size of the sampling unit had considerable effect on degree of sexual segregation we measured; failure to consider scale in such samples holds the potential to misinterpret data. We suggest that natural variation in patches of vegetation may provide more reliable sampling units for measuring sexual segregation than arbitrarily chosen sizes of quadrats, or that the effects of scale need to be evaluated.