Miracle-dz/UniFAR-FTUs huggingface dataset:
Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen

The unclassified Succinivibrionaceae lineages are abundant in high yielding multiparous cows, and their presence is positively correlated with milk yield and fat percentage and reduces methane emissions. However, it is still unclear which species are associated with the most efficient feed nutrient utilization and productivity. Here, we used integrated whole genome sequencing and matrix-assisted laser desorption/ionization mass spectrometry, coupled with phenotypic and chemotaxonomic analysis, to characterize S. dextrinosolvens Z6, a species in Succinivibrionaceae isolated from the rumen. To assess the role of S. dextrinosolvens Z6 in nitrogen metabolism, cells grown in different nitrogen sources were analyzed by RNA sequencing. The whole genome sequence result revealed a genome size of 3.47 Mbp with 38.9% of G + C content. A total of 2993 encoding sequences account for 98%. The genes for regulating carbohydrate (10.6%) and amino acid (9%) transport and metabolism were the most abundant. ANI (Average nucleotide identity) showed that SD-Z6 was most closely related to SD-22B (99.96%). The whole genome alignment of SD-Z6 with SD-22B showed a more than 0.34 Mb nucleotide difference. Growth of SD-Z6 occurred at a temperature 36–42°C with an optimum at 39.7°C, pH 6–8; the optimum pH was 6.9 and with 0–1% (w/v) NaCl. The maximum growth (OD600 0.825 ± 0.12) and microbial crude protein (MCP) (178.2 μg/ml) were observed in cells grown in amino acid. The maximum concentration of ammonia (3.96 ± 1.2) was observed in urea containing media and 1.06 mM (26.7% of the produced) remained after 24 h incubation. Activities of urease and glutamine synthase (P < 0.01) and glutamate dehydrogenase (P < 0.05) were significantly different in nitrogen and growth phase. Glutamate synthetase (P < 0.01) was significantly different only at different growth phases. In total, 1246 differentially expressed genes (DEGs) were identified in all nitrogen. Among DEGs, 33 were related to nitrogen metabolism. Their expression correlated with nitrogen sources and the intensity of enzyme activity. This result enhances our understanding of the roles of Succinivibrionaceae in the efficient nitrogen utilization and on environmental protection.
Deep Convolutional Networks for Construction Object Detection Under Different Visual Conditions

Sensing and reality capture devices are widely used in construction sites. Among different technologies, vision-based sensors are by far the most common and ubiquitous. A large volume of images and videos is collected from construction projects every day to track work progress, measure productivity, litigate claims, and monitor safety compliance. Manual interpretation of such colossal amounts of data, however, is non-trivial, error-prone, and resource-intensive. This has motivated new research on soft computing methods that utilize high-power data processing, computer vision, and deep learning (DL) in the form of convolutional neural networks (CNNs). A fundamental step toward machine-driven interpretation of construction site scenery is to accurately identify objects of interest for a particular problem. The accuracy requirement, however, may offset the computational speed of the candidate method. While lightweight DL algorithms (e.g., Mask R-CNN) can perform visual recognition with relatively high accuracy, they suffer from low processing efficacy, which hinders their use in real-time decision-making. One of the most promising DL algorithms that balance speed and accuracy is YOLO (you-only-look-once). This paper investigates YOLO-based CNN models in fast detection of construction objects. First, a large-scale image dataset, named Pictor-v2, is created, which contains about 3,500 images and approximately 11,500 instances of common construction site objects (e.g., building, equipment, worker). To assess the agility of object detection, transfer learning is used to train two variations of this model, namely, YOLO-v2 and YOLO-v3, and test them on different data combinations (crowdsourced, web-mined, or both). Results indicate that performance is higher if the model is trained on both crowdsourced and web-mined images. Additionally, YOLO-v3 outperforms YOLO-v2 by focusing on smaller, harder-to-detect objects. The best-performing YOLO-v3 model has a 78.2% mAP when tested on crowdsourced data. Sensitivity analysis of the output shows that the model's strong suit is in detecting larger objects in less crowded and well-lit spaces. The proposed methodology can also be extended to predict the relative distance of the detected objects with reliable accuracy. Findings of this work lay the foundation for further research on technology-assistive systems to augment human capacities in quickly and reliably interpreting visual data in complex environments.
Development of Print-Speech Integration in the Brain of Beginning Readers With Varying Reading Skills

Learning print-speech sound correspondences is a crucial step at the beginning of reading acquisition and often impaired in children with developmental dyslexia. Despite increasing insight into audiovisual language processing, it remains largely unclear how integration of print and speech develops at the neural level during initial learning in the first years of schooling. To investigate this development, 32 healthy, German-speaking children at varying risk for developmental dyslexia (17 typical readers and 15 poor readers) participated in a longitudinal study including behavioral and fMRI measurements in first (T1) and second (T2) grade. We used an implicit audiovisual (AV) non-word target detection task aimed at characterizing differential activation to congruent (AVc) and incongruent (AVi) audiovisual non-word pairs. While children’s brain activation did not differ between AVc and AVi pairs in first grade, an incongruency effect (AVi > AVc) emerged in bilateral inferior temporal and superior frontal gyri in second grade. Of note, pseudoword reading performance improvements with time were associated with the development of the congruency effect (AVc > AVi) in the left posterior superior temporal gyrus (STG) from first to second grade. Finally, functional connectivity analyses indicated divergent development and reading expertise dependent coupling from the left occipito-temporal and superior temporal cortex to regions of the default mode (precuneus) and fronto-temporal language networks. Our results suggest that audiovisual integration areas as well as their functional coupling to other language areas and areas of the default mode network show a different development in poor vs. typical readers at varying familial risk for dyslexia.
Isozymes in North American Malus (Rosaceae): Hybridization and Species Differentiation

Isozyme phenotypes of Malus fusca, a native of western North America, differ strik- ingly from those of eastern North American sect. Chloromeles. Isozyme phenotypes vary little between the three taxa recognized within sect. Chloromeles: M. angustifolia, M. coronaria, and M. ioensis. Phe- notypes of seedlings from native taxa did not share diagnostic allozymes with the cultivated apple, M. x domestica, indicating little gene flow from the latter into native Malus. Isozyme patterns do, however, support earlier conclusions based on morphology that M. platycarpa and the flowering cultivar 'Kola' are hybrids of sect. Chloromeles and the domesticated apple, and that M. dawsoniana is a hybrid of the domesticated apple and M. fusca.
Stomatal Sensitivity to Vapor Pressure Deficit and the Loss of Hydraulic Conductivity Are Coordinated in Populus euphratica, a Desert Phreatophyte Species

There are considerable variations in the percentage loss of hydraulic conductivity (PLC) at mid-day minimum water potential among and within species, but the underpinning mechanism(s) are poorly understood. This study tested the hypothesis that plants can regulate leaf specific hydraulic conductance (Kl) via precise control over PLC under variable ΔΨ (water potential differential between soil and leaf) conditions to maintain the −m/b constant (−m: the sensitivity of stomatal conductance to VPD; b: reference stomatal conductance at 1.0 kPa VPD), where VPD is vapor pressure deficit. We used Populus euphratica, a phreatophyte species distributed in the desert of Northwestern China, to test the hypothesis. Field measurements of VPD, stomatal conductance (gs), gs responses to VPD, mid-day minimum leaf water potential (Ψlmin), and branch hydraulic architecture were taken in late June at four sites along the downstream of Tarim River at the north edge of the Taklamakan desert. We have found that: 1) the −m/b ratio was almost constant (=0.6) across all the sites; 2) the average Ψ50 (the xylem water potential with 50% loss of hydraulic conductivity) was −1.63 MPa, and mid-day PLC ranged from 62 to 83%; 3) there were tight correlations between Ψ50 and wood density/leaf specific hydraulic conductivity (kl) and between specific hydraulic conductance sensitivity to water potential [d(ks)/dln(−Ψ)] and specific hydraulic conductivity (ks). A modified hydraulic model was applied to investigate the relationship between gs and VPD under variable ΔΨ and Kl conditions. It was concluded that P. euphratica was able to control PLC in order to maintain a relatively constant −m/b under different site conditions. This study demonstrated that branchlet hydraulic architecture and stomatal response to VPD were well coordinated in order to maintain relatively water homeostasis of P. euphratica in the desert. Model simulations could explain the wide variations of PLC across and within woody species that are often observed in the field.
Trade Disruption, Industrialisation, and the Setting Sun of British Colonial Rule in India

Colonial trade prompted the colonies to specialise in primary products. Did this eliminate industrialisation opportunities in the colonies, and did it make them more politically dependent on the coloniser? To answer these questions, we examine the impact of the World War I trade shock on industrial growth and support for the anti-colonial movement in India. We find that districts more exposed to a drop in imports experienced faster industrial growth in 1911-21, thereafter remaining on a higher level of industrial employment. All evidence points to an increase in Indian productivities as the reason for this, suggesting that liberal trade policies may not have been optimal for colonial India. We also find that districts which industrialised faster thanks to WWI were more likely to support the Indian National Congress. This is consistent with the view that specialisation in primary products made the colonies more politically dependent on the coloniser
Disrupted Regional Homogeneity in Drug-Naive Patients With Bipolar Disorder

Objective Studies on alterations in the regional neural activity in the brain of patients with bipolar disorder (BD) have provided conflicting results because of different medications used and study designs. A low bone mineral density (BMD) is also observed in patients with BD. This study aimed to further explore regional neural activities in unmedicated patients with BD and their association with BMD. Methods In this study, 40 patients with BD and 42 healthy controls were scanned through resting-state functional magnetic resonance imaging (fMRI). Imaging data were analyzed with regional homogeneity (ReHo) and pattern classification. Pearson’s correlation analyses were performed to explore the correlations between abnormal ReHo and BMD. Results A significant increase in ReHo values in the left inferior frontal gyrus (IFG)/temporal pole, left cerebellum vermis I/vermis II/parahippocampal gyrus/brainstem, and right superior temporal gyrus (STG) and a decrease in ReHo in the occipital gyrus (OG; left middle OG/superior OG/bilateral cuneus) were found in the patients with BD (p < 0.05) compared with those in the healthy controls. No significant correlation was observed between the abnormal ReHo values in any of the brain regions of the patients with BMD.Support vector machine (SVM) analyses revealed that the ReHo values in the right STG for distinguishing patients from healthy controls showed an accuracy of 91.89%, a sensitivity of 75.68%, and a specificity of 83.78%. The ReHo values in the left cerebellum vermis I/vermis II/parahippocampal gyrus/brainstem indicated an accuracy of 78.38%, a sensitivity of 75.68%, and a specificity of 81.08%. Conclusion This study further confirms the abnormal brain activities in extensive regions, and these brain regions are primarily located in the fronto–temporal–occipital circuit and the cerebellum vermis of patients with BD. The regional neural activity in the right STG and the left cerebellum vermis I/vermis II/parahippocampal gyrus/brainstem may serve as potential imaging markers to distinguish patients with BD from healthy controls.
The Resource Limitation of Trophic Levels in Tropical Grassland Ecosystems

One feature of terrestrial ecosystems that is becoming widely recognized is the small proportion of primary production, measured on an annual basis, that is consumed by herbivores.t In grassland systems Wiegert & Evans (1967) found that consumption rarely exceeded 10% of the primary production and the only exceptions appeared to be in the East African tropical grasslands supporting large ungulate populations, where it was roughly estimated that between 30 and 60% of the primary production was consumed. But with further information Phillipson (1973) put forward a tentative model for the Serengeti ecosystem in Tanzania, and in this model only 18% of the net primary production was utilized by the herbivores. In woodland systems similar results have emerged: herbivores consumed less than 70 of the tree production in a deciduous woodland (Varley 1970), and Reichle et al. (1973) found that insects consumed only 2-6% of the primary production in a forest canopy. The more restricted studies of the energy flow in small mammal communities have all found that less than 20% and sometimes only 2% of the primary production is utilized (Grodzinski 1963, 1971; Grodzinski et al. 1970; Ryszkowski 1970). Slobodkin, Smith & Hairston (1967) have summarized other similar results all of which show that less than 10% of the primary production is consumed.
The Description of Taxonomic Relationships by Factor Analysis

THE PURPOSE of the study reported in this paper is to investigate whether multiple factor analysis could be used to describe and evaluate taxonomic relationships among organisms. Recent efforts to quantify taxonomic procedure have been termed "numerical taxonomy" by Sokal and Sneath (Sokal, 1960). Numerical methods are being developed for (1) estimating the relative degrees of similarity or affinity among organisms, based on many equally weighted characters, and (2) arranging organisms into taxa in which there is a greater degree of similarity between any two organisms within a taxon than there is between two organisms in different taxa at the same hierarchic level. There are several ways in which each of these two problems may be attacked. Sokal and Michener (1958) have used correlation coefficients as an index of similarity and the weighted variable-group method for constructing a tree-like diagram of relationships (dendrogram). Sneath (1957a, 1957b) has used a coefficient of association as an index of similarity and also a computer program which sorts the matrix of similarity coefficients into a form such that the relationships become immediately evident. Rogers and Tanimoto (1960) have developed a coefficient of association and yet another method of finding clumps or clusters from their similarity ratios. Sokal (1961) has proposed using geometric distance as a
Bedside Catheter Hematoma Evacuation in Vitamin K Antagonist-Related Intracerebral Hemorrhage: A Safe and Feasible Approach

Background and Purpose: Although outcome in intracerebral hemorrhage (ICH) patients is generally not improved by surgical intervention, the use of minimally invasive surgery (MIS) has shown promising results. However, vitamin K antagonist (VKA)-related ICH patients are underrepresented in surgical treatment trials. We therefore assessed the safety and efficacy of a bedside MIS approach including local application of urokinase in VKA-related ICH. Methods: Patients with a VKA-related ICH > 20 ml who received bedside hematoma evacuation treatment (n = 21) at the University Medical Center Freiburg were retrospectively included for analysis and compared to a historical control group (n = 35) selected from an institutional database (University Medical Center Erlangen) according to identical inclusion criteria. Propensity score matching was performed to obtain comparable cohorts. The evolution of hematoma and peri-hemorrhagic edema (PHE) volumes, midline shift, and the occurrence of adverse events were analyzed. Furthermore, we assessed the modified Rankin Scale and NIHSS scores recorded at discharge. Results: Propensity score matching resulted in 16 patients per group with well-balanced characteristics. Median ICH volume at admission was 45.7 (IQR: 24.2–56.7) ml in the control group and 48.4 (IQR: 28.7–59.6) ml in the treatment group (p = 0.327). ICH volume at day 7 was less pronounced in the treatment group [MIS: 23.2 ml (IQR: 15.8–32.3) vs. control: 43.2 ml (IQR: 27.5–52.4); p = 0.013], as was the increase in midline shift up to day 7 [MIS: −3.75 mM (IQR: −4.25 to −2) vs. control: 1 mM (IQR: 0–2); p < 0.001]. No group differences were observed in PHE volume on day 7 [MIS: 42.4 ml (IQR: 25.0–72.3) vs. control: 31.0 ml (IQR: 18.8–53.8); p = 0.274] or mRS at discharge [MIS: 5 (IQR: 4–5) and 5 (IQR: 4–5); p = 0.949]. No hematoma expansion was observed. The catheter had to be replaced in 1 patient (6%). Conclusions: Bedside catheter-based hematoma evacuation followed by local thrombolysis with urokinase appears to be feasible and safe in cases of large VKA-related ICH. Further studies that assess the functional outcome associated with this technique are warranted. Clinical Trial Registration: DRKS00007908 (German Clinical Trial Register; www.drks.de)
The effect of housing and food restriction during winter on growth of male red deer calves

Low winter growth is a characteristic of male red deer and is caused, in part by a combination of reduced appetite and higher energy expenditure due to cold weather. This study aimed to determine whether housing during winter would reduce energy expenditure and increase the growth rate of male red deer calves. An additional aim was to investigate whether food restriction in winter would be compensated for by increased spring growth. In each of two consecutive years, 80 calves were randomly allocated to eight groups (no. = 10) comprising two replicates of four treatments during winter. Groups were housed inside (I) or outside (O) and given food either ad libitum (AL) or restricted (R) to maintain live weight. Winter treatments (southern hemisphere) ran from 22 May to 25 August (year 1) and from 5 June to 5 September (year 2). During these periods, animals were weighed weekly and group food intake recorded daily. At the end of winter animals were moved outside onto pasture and weighed monthly until the end of spring (27 November, year 1 and 7 December, year 2). In year 2 weighing continued during summer, until 4 April. The animals were slaughtered on 28 November and 18 January (year 1) and 5 April (year 2). The effect of housing on live-weight gain (LWG) and dry-matter intake (DM1) in AL groups was not significant in either year. However in R groups, O had a higher DMI than I in both years (P In conclusion, housing calves given food ad libitum during winter did not reduce DMI or increase growth rate. When normal growth rates were prevented by restricting food intake, housing lowered DMI requirement, although such a situation is unlikely to be a useful farm management practice as recovery from the growth check was slow. Annual variations in climate may determine both the food savings made by housing and the extent of compensatory growth of food-restricted animals in spring.
The Impact of Covariates in Voxel-Wise Lesion-Symptom Mapping

Background: Voxel-wise lesion-symptom mapping (VLSM) is a statistical technique to infer the structure-function relationship in patients with cerebral strokes. Previous VLSM research suggests that it is important to adjust for various confounders such as lesion size to minimize the inflation of true effects. The aim of this work is to investigate the regional impact of covariates on true effects in VLSM. Methods: A total of 222 follow-up datasets of acute ischemic stroke patients with known NIH Stroke Scale (NIHSS) score at 48-h post-stroke were available for this study. Patient age, lesion volume, and follow-up imaging time were tested for multicollinearity using variance inflation factor analysis and used as covariates in VLSM analyses. Covariate importance maps were computed from the VLSM results by standardizing the beta coefficients of general linear models. Results: Covariates were found to have distinct regional importance with respect to lesion eloquence in the brain. Age has a relatively higher importance in the superior temporal gyrus, inferior parietal lobule, and in the pre- and post-central gyri. Volume explains more variability in the opercular area of the insula, inferior frontal gyrus, and caudate. Follow-up imaging time accounts for most of the variance in the globus pallidus, ventromedial- and dorsolateral putamen, dorsal caudate, pre-motor thalamus, and the dorsal insula. Conclusions: This is the first study investigating and revealing distinctive regional patterns of importance for covariates typically used in VLSM. These covariate importance maps can improve our understanding of the lesion-deficit relationships in patients and could prove valuable for patient-specific treatment and rehabilitation planning.
Perceptions of Cultured Meat Among Youth and Messaging Strategies

Cultured or “clean” meat (CM) is arguably a more ethical and environmentally sustainable alternative to farmed meat, but several potential psychological barriers exist to its acceptance in the marketplace. The perceptions of youth, as a specific consumer cohort, have not been reported to date despite young adults having more flexible dietary habits and being more likely to avoid red meat because of animal welfare and environmental concerns. Thus, youth represent a demographic that may be more accepting of CM and for whom the pro-environmental consequences of early adoption may be realized across an entire lifespan. In this study of college-aged Canadians (mean = 20 years), we examined perceptions of CM (mixed methods) and assessed the effects of educational messaging about its benefits and then naturalness framing on intention to consume it (within subjects quantitative experimental design). Results show that youth believe CM to be unnatural, ethical, and environmentally friendly, and that taste is an important element of acceptance. Linear regression showed that food disgust was a significant predictor for both intent to incorporate CM into regular diet and completely replace meat/meat substitutes with CM. In both instances, increasing food disgust was associated with lower behavioral intent. Environmental values were also a predictor for completely replacing meat/meat substitutes with CM, where it positively affected intent and showed a similar effect size to food disgust. Both messaging on the benefits of CM and naturalness framing increased intent to consume it across all three measures and by a similar magnitude [p (F) < 0.05]. These findings provide timely and actionable information for both CM producers and marketers and contribute to scholarship on the role of values and psychological traits in sustainable food choices.