Miracle-dz/UniFAR-FTUs huggingface dataset:
Biosystematic studies on the genus Polygonatum (Convallariaceae) IV. Molecular phylogenetic analysis based on restriction site mapping of the chloroplast gene trnK

SUmmary Phylogenetic relationships of 14 species and one variety ofthe gents Polygonaturu as well as three species ofthe genus Disporopsis and Heteropolygonatum roseolumwere analyzed based on mapped restriction site variation in a PCR-amplified chloroplast genome region, trnK.In agreement with earlier taxonomic treatments it was found that Disporopsis and Heteropolygonatum should be distinguished from Polygonatum at generic level, and that P sect. Polygonatum canbe recognized as a monophyletic group. Earlier series concepts in P sect. Polygonatum based on chromosome number and characteristics of staminal filaments are not supported by the molecular data. The molecular data suggest that satellite chromosome morphology might prove valuable as a diagnostic character in Poly gonatum sect. P oly gonatum.
Winter temperature and forest cover have shaped red deer distribution in Europe and the Ural Mountains since the Late Pleistocene

The Expansion‐Contraction model has been used to explain the responses of species to climatic changes. During periods of unfavourable climatic conditions, species retreat to refugia from where they may later expand. This paper focuses on the palaeoecology of red deer over the past 54 ka across Europe and the Urals, to reveal patterns of change in their range and explore the role of environmental conditions in determining their distribution.
Towards Hallucinating Machines - Designing with Computational Vision

There are particular similarities in how machines learn about the nature of their environment, and how humans learn to process visual stimuli. Machine Learning (ML), more specifically Deep Neural network algorithms rely on expansive image databases and various training methods (supervised, unsupervised) to “make sense” out of the content of an image. Take for example how students of architecture learn to differentiate various architectural styles. Whether this be to differentiate between Gothic, Baroque or Modern Architecture, students are exposed to hundreds, or even thousands of images of the respective styles, while being trained by faculty to be able to differentiate between those styles. A reversal of the process, striving to produce imagery, instead of reading it and understanding its content, allows machine vision techniques to be utilized as a design methodology that profoundly interrogates aspects of agency and authorship in the presence of Artificial Intelligence in architecture design. This notion forms part of a larger conversation on the nature of human ingenuity operating within a posthuman design ecology. The inherent ability of Neural Networks to process large databases opens up the opportunity to sift through the enormous repositories of imagery generated by the architecture discipline through the ages in order to find novel and bespoke solutions to architectural problems. This article strives to demystify the romantic idea of individual artistic design choices in architecture by providing a glimpse under the hood of the inner workings of Neural Network processes, and thus the extent of their ability to inform architectural design. The approach takes cues from the language and methods employed by experts in Deep Learning such as Hallucinations, Dreaming, Style Transfer and Vision. The presented approach is the base for an in-depth exploration of its meaning as a cultural technique within the discipline. Culture in the extent of this article pertains to ideas such as the differentiation between symbolic and material cultures, in which symbols are defined as the common denominator of a specific group of people.1 The understanding and exchange of symbolic values is inherently connected to language and code, which ultimately form the ingrained texture of any form of coded environment, including the coded structure of Neural Networks. A first proof of concept project was devised by the authors in the form of the Robot Garden. What makes the Robot Garden a distinctively novel project is the motion from a purely two dimensional approach to designing with the aid of Neural Networks, to the exploration of 2D to 3D Neural Style Transfer methods in the design process.
Poor Self-Reported Sleep is Related to Regional Cortical Thinning in Aging but not Memory Decline—Results From the Lifebrain Consortium

Abstract We examined whether sleep quality and quantity are associated with cortical and memory changes in cognitively healthy participants across the adult lifespan. Associations between self-reported sleep parameters (Pittsburgh Sleep Quality Index, PSQI) and longitudinal cortical change were tested using five samples from the Lifebrain consortium (n = 2205, 4363 MRIs, 18–92 years). In additional analyses, we tested coherence with cell-specific gene expression maps from the Allen Human Brain Atlas, and relations to changes in memory performance. “PSQI # 1 Subjective sleep quality” and “PSQI #5 Sleep disturbances” were related to thinning of the right lateral temporal cortex, with lower quality and more disturbances being associated with faster thinning. The association with “PSQI #5 Sleep disturbances” emerged after 60 years, especially in regions with high expression of genes related to oligodendrocytes and S1 pyramidal neurons. None of the sleep scales were related to a longitudinal change in episodic memory function, suggesting that sleep-related cortical changes were independent of cognitive decline. The relationship to cortical brain change suggests that self-reported sleep parameters are relevant in lifespan studies, but small effect sizes indicate that self-reported sleep is not a good biomarker of general cortical degeneration in healthy older adults.
Understanding uncertainty in the Impact Classification for Alien Taxa (ICAT) assessments

The Environmental Impact Classification for Alien Taxa (EICAT) and the Socio-Economic Impact Classification of Alien Taxa (SEICAT) have been proposed to provide unified methods for classifying alien species according to their magnitude of impacts. EICAT and SEICAT (herein “ICAT” when refered together) were designed to facilitate the comparison between taxa and invasion contexts by using a standardised, semi-quantitative scoring scheme. The ICAT scores are assigned after conducting a literature review to evaluate all impact observations against the protocols’ criteria. EICAT classifies impacts on the native biota of the recipient environments, whereas SEICAT classifies impacts on human activities. A key component of the process is to assign a level of confidence (high, medium or low) to account for uncertainty. Assessors assign confidence scores to each impact record depending on how confident they are that the assigned impact magnitude reflects the true situation. All possible sources of epistemic uncertainty are expected to be captured by one overall confidence score, neglecting linguistic uncertainties that assessors should be aware of. The current way of handling uncertainty is prone to subjectivity and therefore might lead to inconsistencies amongst assessors. This paper identifies the major sources of uncertainty for impacts classified under the ICAT frameworks, where they emerge in the assessment process and how they are likely to be contributing to biases and inconsistency in assessments. In addition, as the current procedures only capture uncertainty at the individual impact report, interspecific comparisons may be limited by various factors, including data availability. Therefore, ranking species, based on impact magnitude under the present systems, does not account for such uncertainty. We identify three types of biases occurring beyond the individual impact report level (and not captured by the confidence score): biases in the existing data, data collection and data assessment. These biases should be recognised when comparing alien species based on their impacts. Clarifying uncertainty concepts relevant to the ICAT frameworks will lead to more consistent impact assessments and more robust intra- and inter-specific comparisons of impact magnitudes.
Detailed analysis of the flow within the boundary layer and wake of a full-scale ship

This article presents a detailed numerical flow assessment of the boundary layer and wake of a full-scale cargo ship. The assessment was conducted using a sophisticated numerical approach that is able to resolve large turbulent scale vortices contained in the flow. The physical flow features of the boundary layer and wake investigated include mean-velocity, near-wall shear stress and vorticity fields. Also, the evolution of the wake from the thick boundary layer over the stern is displayed and analysed in the highest possible detail. Additionally, the detailed information extracted from the boundary layer and wake was the primary input to assess the overall hydrodynamic efficiency of the full-scale general cargo ship.The analysis method followed during this work has been a determinant factor for fast and efficient design of energy saving devices, propellers or rudders that work within the limits of the boundary layer of a ship. In particular, this thorough analysis avoided the necessity to use the commonly used practice of trial and error that is typically followed in the maritime industry.
Evaluation of Diagnostic Hysteroscopy as a Tool for Diagnosis of Tubal Factor of Infertility in Comparison to Diagnostic Laparoscopy

Background: Fallopian tube obstruction is believed to play a role in 12-33% of subfertile couples. Therefore, the patency evaluation of fallopian tubes is a significant part of subfertile couple’s work. Objective: To compare the sensitivity and specificity of the hysteroscopic assessment of tubal patency by the bubble test to diagnostic laparoscopy and hysterosalpingogram in infertile patients. Subjects and Methods: A total of 100 women were recruited to the study during the period between January 2020 and June 2020. 100 patients underwent a diagnostic hysteroscopy followed by laparoscopy. Each Fallopian tube has been considered to be an individual case. Patency was evaluated in 200 Fallopian tubes. Results: A polyp was detected at three tubal orifice. Hyperemia was detected around two tubal orifice. Adhesions were detected at one tubal orifice. The tubes were patent in 113 cases with both methods. In 70 cases both laparoscopy and hysteroscopy found occluded tubes. The tubes were patent by laparoscopic dye in 10 cases, but could not be detected by hysteroscopy as such. Occlusion was observed by laparoscopy in 7 cases but patency was detected during hysteroscopy. Of the non-patent cases, 70 out of 77 laparoscopic findings were consistent with the hysteroscopic result, yielding a specificity estimate of 90.9% (95% CI 84.5% to 96.4%). Conclusion: Based on statistical analysis (sensitivity and specificity) of our data, diagnostic hysteroscopic bubble test is accurate and reliable compared to the laparoscopic test, which is considered a global standard criterion.
Estimation of direct and maternal genetic parameters for individual birth weight and probe weight using cross-fostering information

Abstract: A total of 246 357 measurements of birth (BW) and probe (PW) weights of purebred Yorkshire and Landrace pigs were used to compare the fitting of two alternate models including either common-litter effect or cross-fostering group effect to account for common environmental variation. PW, is a live ultrasonic weight measurement taken when the pigs are 100 ± 30 kg, following national standards. The common-litter effect was defined as piglets born into the same litter, and the group effect was used to account for cross-fostering, and defined as the effect common to piglets raised by the same nurse-sow, regardless of whether that piglet was born into that litter or not. It was found that the cross-fostering group explained 5% more environmental variation in BW when compared with the common-litter effect, indication that BW is a criterion in cross-fostering. Cross-fostering also explained 1% more environmental variation in PW in both the Yorkshire and Landrace. When the cross-fostering group effect was included in place of the common-litter effect, the direct and maternal genetic heritability estimates were similar, but residual variances were reduced. This study advanced the understanding of the effects of cross-fostering on PW, its association with BW and its implications in modern pig breeding programs.
Repli-seq: genome-wide analysis of replication timing by next-generation sequencing

Cycling cells duplicate their DNA content during S phase, following a defined program called replication timing (RT). Early and late replicating regions differ in terms of mutation rates, transcriptional activity, chromatin marks and sub-nuclear position. Moreover, RT is regulated during development and is altered in disease. Exploring mechanisms linking RT to other cellular processes in normal and diseased cells will be facilitated by rapid and robust methods with which to measure RT genome wide. Here, we describe a protocol to analyse genome-wide RT by next-generation sequencing (NGS). This protocol yields highly reproducible results across laboratories and platforms. We also provide the computational pipelines for analysis, parsing phased genomes using single nucleotide polymorphisms (SNP) for analyzing imprinted RT, and for direct comparison to Repli-chip data obtained by analyzing nascent DNA by microarrays.
The effect of clover silages on long chain fatty acid rumen transformations and digestion in beef steers

Lee, M. R. F. , Harris, L. J., Dewhurst, R. J., Merry, R. , Scollan, N. D. (2003). The effect of clover silages on long chain fatty acid rumen transformations and digestion in beef steers. Animal Science, 76, (3), 491-501.
Neural crest contribution to the avian shoulder girdle and implications to girdle evolution in vertebrates

This work was supported by equipment donations from the Russian Foundation for Basic Research (grant 10-04-05084-b) and Alexander von Humboldt Foundation (grant 3.4-8151/07074). A research visit of YM to University of Reading was supported by the Russian Foundation for Basic Research (grant 10-04-01202-а), while the final analysis and publication were supported by Saint Petersburg State University (grant 0.38.292.2015).
“We Are All Alive . . . But Dead”: Cultural Meanings of War Trauma in the Tamil Diaspora and Implications for Service Delivery

Providing culturally appropriate mental health services to war-affected refugees residing in the West continues to pose many challenges. Gaining firsthand knowledge from the refugee communities themselves is crucial to improving our knowledge and guiding our interventions. The purpose of this study is to understand perceptions of war trauma in the Tamil diaspora. Fifty-one Sri Lankan Tamils living in the Greater Toronto Area, Canada, were interviewed. Transcripts were thematically analyzed using content analysis. Findings indicate that war trauma is not viewed by the diaspora as a pathological notion. Positioned within a moral context, and independent from isolated events of war, manifestations of war trauma were discussed at an interpersonal and collective level. Diagnostic categories, including post-traumatic stress disorder (PTSD), do not seem to fully capture the breadth of war trauma in this diaspora community. Implications for service delivery, and for incorporating the unique aspects of suffering resulting from a fragmented community, are discussed.
Using Manual Ungual Morphology to Predict Substrate Use in the Drepanosauromorpha and the Description of a New Species

ABSTRACT Fossils of drepanosauromorphs, a clade of non-saurian diapsids, were once considered relatively rare in the Chinle Formation of the southwestern United States as well as in Upper Triassic rocks globally. Recent discoveries have shown that there are at least four drepanosauromorph taxa present in the Chinle Formation including Dolabrosaurus aquatilis, Drepanosaurus sp. , Ancistronychus paradoxus, and a new genus and species described here, Skybalonyx skapter. This new taxon is represented by disarticulated manual unguals and is preserved in a microvertebrate bearing bone-bed in the Blue Mesa Member (∼223–220 Ma) of the Chinle Formation at Petrified Forest National Park, which was deposited in a fluvio-lacustrine setting in equatorial Pangaea during the mid-Norian. Different types of substrate use have been hypothesized for the Drepanosauromorpha. By performing discriminant function analyses using the manual unguals of 173 mammal and 13 reptile species with known substrate use, we hope to infer the ecomorphology of drepanosauromorphs. We found that the enlarged second manual unguals of Drepanosaurus sp. are similar to hook-and-pull digging taxa (e.g., Tamandua mexicana and Cyclopes didactylus) although the smaller manual unguals referred to this taxon (likely pertaining to digits other than digit II) are similar to modern arboreal taxa. Our results support the inference of arboreality in some drepanosauromorph species. However, we found that the manual unguals of Ancistronychus paradoxus and Skybalonyx skapter fit within the range of variation of modern fossorial and subterranean taxa, which expands the functional diversity of the Drepanosauromorpha within the Chinle Formation.
Tendencia del NDVI en el período 2000-2014 como indicador de la degradación de tierras en Argentina: ventajas y limitaciones

Land degradation is one of the main environmental concerns in Argentina. Monitoring systems to detect trend and provide early warnings are required to deal with this issue. Recently, there have been developed monitoring methodologies based on indices derived from satellite images, among them the most widely used is the NDVI (Normalized Difference Vegetation Index). The trend of NDVI (from MODIS sensor) was analyzed, between 2000-2014, as a possible indicator of land degradation in Argentina. For each year (from 01-July until 30-June of the following year) the annual integral of NDVI and its trend was calculated using simple linear regression for each pixel. According to the sign and statistical significance of the regression slope were mapped areas with negative trends (TN, 37.9% of the country), positive (TP, 5.0%) and no trend (57.1%). The TN was concentrated in North Patagonia (associated with the deposition of volcanic ash and a dry cycle) and the Chaco Seco (associated with forest clearing for agriculture and a dry cycle). The TP was concentrated in the northwest of the country (possibly associated with the occurrence of a wet cycle). This methodology, along with other indicators based on field information and climate data, may be useful for developing a monitoring system of land degradation at a national scale.
An Efficient Bi-Gaussian Ensemble Kalman Filter for Satellite Infrared Radiance Data Assimilation

The introduction of infrared water vapor channel radiance ensemble data assimilation (DA) has improved numerical weather forecasting at operational centers. Further improvements might be possible through extending ensemble data assimilation methods to better assimilate infrared satellite radiances. Here, we will illustrate that ensemble statistics under clear-sky conditions are different from cloudy conditions. This difference suggests that extending the ensemble Kalman filter (EnKF) to handle bi-Gaussian prior distributions may yield better results than the standard EnKF. In this study, we propose a computationally efficient bi-Gaussian ensemble Kalman filter (BGEnKF) to handle bi-Gaussian prior distributions. As a proof-of-concept, we used the 40-variable Lorenz 1996 model as a proxy to examine the impacts of assimilating infrared radiances with the BGEnKF and EnKF. A nonlinear observation operator that constructs radiance-like bimodal ensemble statistics was used to generate and assimilate pseudoradiances. Inflation was required for both methods to effectively assimilate pseudoradiances. In both 800- and 20-member experiments, the BGEnKF generally outperformed the EnKF. The relative performance of the BGEnKF with respect to the EnKF improved when the observation spacing and time between DA cycles (cycling interval) are increased from small values. The relative performance then degraded when observation spacing and cycling interval become sufficiently large. The BGEnKF generated less noise than the EnKF, suggesting that the BGEnKF produces more balanced analysis states than the EnKF. This proof-of-concept study motivates future investigation into using the BGEnKF to assimilate infrared observations into high-order numerical weather models.
A safe human–robot interactive control structure with human arm movement detection for an upper-limb wearable robot used during lifting tasks

Manual lifting tasks involve repetitive raising, holding and stacking movements with heavy objects. These arm movements are notable risk factors for muscle pain, fatigue, and musculoskeletal disorders in workers. An upper-limb wearable robot, as a 6-DOF dual-arm exoskeleton, which was designed to augment workers’ strength and minimize muscular activation in the arm during repetitive lifting tasks. To adjust the robot joint trajectory, the user needs to apply an interactive torque to operate the robot during lifting tasks when a standard virtual mechanical impedance control structure is used. To reduce overshooting of the interactive torque on the user’s joint, a three-tier hierarchical control structure was developed for the robot in this study. At the highest level, a human arm movement detection module is used to detect the user’s arm motion according to the surface electromyography signals. Then, a Hammerstein adaptive virtual mechanical impedance controller is used at the middle level to reduce overshooting and yield an acceptable value of torque for the user’s elbow joint in actual lifting tasks. At the lowest level, the actuator controller on each joint of the robot controls the robot to complete lifting tasks. Several experiments were conducted, and the results showed that the interactive torque on the user’s elbow was limited and the muscular activations of erector spinae and biceps brachii muscles were effectively decreased. The proposed scheme prevents potential harm to the user due to excessive interactive torque on the human elbow joint, such as related muscle fatigue and joint injuries.