Miracle-dz/UniFAR-FTUs huggingface dataset:
AnatomyNet: Deep 3D Squeeze-and-excitation U-Nets for fast and fully automated whole-volume anatomical segmentation

Purpose Radiation therapy (RT) is a common treatment for head and neck (HaN) cancer where therapists are often required to manually delineate boundaries of the organs-at-risks (OARs). The radiation therapy planning is time-consuming as each computed tomography (CT) volumetric data set typically consists of hundreds to thousands of slices and needs to be individually inspected. Automated head and neck anatomical segmentation provides a way to speed up and improve the reproducibility of radiation therapy planning. Previous work on anatomical segmentation is primarily based on atlas registrations, which takes up to hours for one patient and requires sophisticated atlas creation. In this work, we propose the AnatomyNet, an end-to-end and atlas-free three dimensional squeeze-and-excitation U-Net (3D SE U-Net), for fast and fully automated whole-volume HaN anatomical segmentation. Methods There are two main challenges for fully automated HaN OARs segmentation: 1) challenge in segmenting small anatomies (i.e., optic chiasm and optic nerves) occupying only a few slices, and 2) training model with inconsistent data annotations with missing ground truth for some anatomical structures because of different RT planning. We propose the AnatomyNet that has one down-sampling layer with the trade-off between GPU memory and feature representation capacity, and 3D SE residual blocks for effective feature learning to alleviate these challenges. Moreover, we design a hybrid loss function with the Dice loss and the focal loss. The Dice loss is a class level distribution loss that depends less on the number of voxels in the anatomy, and the focal loss is designed to deal with highly unbalanced segmentation. For missing annotations, we propose masked loss and weighted loss for accurate and balanced weights updating in the learning of the AnatomyNet. Results We collect 261 HaN CT images to train the AnatomyNet, and use MICCAI Head and Neck Auto Segmentation Challenge 2015 as the benchmark dataset to evaluate the performance of the AnatomyNet. The objective is to segment nine anatomies: brain stem, chiasm, mandible, optic nerve left, optic nerve right, parotid gland left, parotid gland right, submandibular gland left, and submandibular gland right. Compared to previous state-of-the-art methods for each anatomy from the MICCAI 2015 competition, the AnatomyNet increases Dice similarity coefficient (DSC) by 3.3% on average. The proposed AnatomyNet takes only 0.12 seconds on average to segment a whole-volume HaN CT image of an average dimension of 178 × 302 × 225. All the data and code will be availablea. Conclusion1 We propose an end-to-end, fast and fully automated deep convolutional network, AnatomyNet, for accurate and whole-volume HaN anatomical segmentation. The proposed Anato-myNet outperforms previous state-of-the-art methods on the benchmark dataset. Extensive experiments demonstrate the effectiveness and good generalization ability of the components in the AnatomyNet.
The Derwent River seastar: re-evaluation of a critically endangered marine invertebrate

The Derwent River seastar, ‘Marginaster’ littoralis (Echinodermata: Asteroidea), has been assessed as critically endangered owing to its highly restricted range within one estuary in Tasmania, Australia. However, there have been concerns about the validity and status of the species. Here, we use non-invasive X-ray computed tomography to review the morphology of the holotype. This reveals the presence of internal ossicles to strengthen the disc margin, a character that requires the taxonomic transfer of this species to the family Asterinidae, genus Patiriella. The presence of relatively long marginal spinelets (0.7–0.9 mm) reliably distinguishes this species from the invasive congeneric Patiriella regularis (0.2–0.35 mm). These findings remove doubt about the validity of the species; the recorded habitat and restricted range of Patiriella littoralis are not exceptional for an asterinid seastar. The weight of evidence suggests that it is an endemic species, rather than a transient exotic introduced to Tasmania via shipping or food importation. Its known habitat has been severely impacted by urbanization, poor water quality and invasive species. Targeted surveys in 1993 and 2010 failed to find this species, and it is highly probable that the Derwent River seastar is now extinct; one of the few documented recent marine invertebrate extinctions.
The travel attitudes and behaviours of South Asian international students: a study from Monash University

In recent years, the Australian transport system is struggling to cope with increased demand driven by population growth, which in turn is driven by immigration and much of this immigration occurs through international students who settle in Australia. Yet there isn’t much research on the travel behaviour of immigrants in Australia, let alone international university students. One of the fastest-growing immigrant groups in Australia is from South Asia, where the travel circumstances are distinctly different to the Australian context. This study is an attempt to explore the past and present travel habits, attitudes and related variables that may influence the travel behaviour of South Asian international students in Australia. We found an increased importance and significance of owning and using a car among international students from South Asia when compared to native-born Australians. They have lower car access yet a higher rate of licence holding than Australian students; more importantly, car use increases and catches up with native-born Australians within three years, which has important implications for transport policy. This is one of the first studies that looks at immigrants’ travel habits in Australia, and it is clear that more work needs to be done to build upon this under-researched topic in Australia.
Grain yield, adaptability and stability of soybean genotypes in different Cerrado environments of Piauí, Brazil

The objective of the present study was to evaluate the grain yield and the phenotypic adaptability and stability of soybean genotypes in different Cerrado environments of Piauí, Brazil, to provide indications for cultivation in the region. Therefore, we evaluated 23 soybean genotypes and three checks in three different site (Bom Jesus-PI, Monte Alegre-PI and Currais-PI) and environments (crop year 2010/11, 2011/12 and 2012/13). Experiments were carried out in a randomized complete block design with four replications. The behavior for the average grain yield of genotypes within and among environments was verified using the Scott Knott’s method of clustering of means (P <0.05). For the study of adaptability and stability, the methods of analysis of Eberhart and Russell and AMMI were used. Genotypes had the best performance of genetic potential in 2010/11 crop year. The best group in Bom Jesus-PI consisted of 16 genotypes and had an average grain yield higher than 3181.61 kg ha-1, what is well above the global average grain yield (2108.26 kg ha-1). G5 and G9 genotypes were the ones with greater adaptability and stability in the three environments with high average grain yield (2362.5 kg ha-1). Therefore, the identification of genotypes presenting such behavior is important for recommending cultivation in the studied environments or in similar areas. It was possible to identify genotypes that have high grain yield and that are stable and adapted for cultivation in the Cerrado at Piauí state.
Non-wetting drops: from impacts to self-propulsion

We investigate through several experiments the special dynamics generated by non-wetting objects.On a substrate textured with grooves forming a herringbone pattern, a Leidenfrost levitating liquid is propelled: the textures channel the vapor flow in a well-defined direction so that the slider above is driven by vapor viscosity. These deformable objects undergo very little friction on flat surfaces. However, on crenelated substrates, impacts on the texture sides greatly enhance dissipation. We extend this entrainment scenario to other situations where the liquid (and its deformable nature) is not involved anymore. A solid plate can levitate over a porous substrate through which air is blown. Again, escaping flow can be rectified by the textures and entrain the plate, leading to translation movement or even to rotation. If we create deeper channels (hence losing flow confinement), we observe motion in the opposite direction due to “rocket effect” (conservation of momentum). We are also interested in an extreme non-wetting situation: the falling drop. Indeed, all along the fall, the drop only experiences air drag friction, easily reaching high speeds. We tackle the problem of the dramatic issue of this fall: the impact. We first study the impact of a drop on a sieve. In this situation intermediate between a solid wall and no obstacle at all, mass either passes through the holes or gets stopped by the closings. We then focus on the impact force experienced by the substrates and characterize the force as a function of the drop and impact properties, but also of the nature of the solid on which impact takes place.
Citizen Science in the Class-Room: The Consistency of Student Collected Data and Its Value in Ecological Hypothesis Testing

Abstract Birds have long been considered indicator species of biodiversity and so ecologists use them as indices of abundance and diversity in order to assess environmental health. These indices are based on surveys which assess the number of species and number of individuals counted in an area over a set time. We can modify citizen science approaches as a way to increase the involvement of undergraduate students in research. However, undergraduate students may have little experience in ecological surveying. Therefore, we tested whether bird counts collected by inexperienced undergraduates were consistent and repeatable among observers. We also examined bird communities at three sites of different size in and around Kyoto University in Kyoto Prefecture. First, we found that there was a high level of consistency among inexperienced observers. We also found a positive relationship between urban park size and avian abundance and diversity. Finally, we found that the bird communities at the two larger sites were most similar to one another whilst the community at the smallest site was quite distinct from the two larger sites. Therefore, this study shows that using citizen science methods may be an effective tool for gathering meaningful scientific data with inexperienced undergraduate observers.
The complete mitochondrial DNA sequence of the Chinese red pika (Ochotona erythrotis)

Abstract In this study, we undertook the first complete Ochotona erythrotis mitochondrial genome. The genome sequence was 16,663 bp in length, including the typical structure of 22 transfer RNA genes, 13 protein-coding genes, 2 ribosomal RNA genes, and the non-coding control region. The overall base composition of O. erythrotis mitogenome is 31.8% A, 26.0% T, 28.6% G, and 13.6% C, with a high A + T content of 57.8%.
Nucleosome positioning stability is a significant modulator of germline mutation rate variation across the human genome

Nucleosome organization is suggested to affect local mutation rates in a genome. However, the lack of de novo mutation and high-resolution nucleosome data have limited investigation. Further, analyses using indirect mutation rate measurements have yielded contradictory and potentially confounded results. Combining >300,000 human de novo mutations with high-resolution nucleosome maps, we reveal substantially elevated mutation rates around translationally stable (‘strong’) nucleosomes. Translational stability is an under-appreciated nucleosomal property, with greater impact than better-known factors like occupancy and histone modifications. We show that the mutational mechanisms affected by strong nucleosomes are low-fidelity replication, insufficient mismatch repair and increased double-strand breaks. Strong nucleosomes preferentially locate within young SINE/LINE transposons; subject to increased mutation rates, transposons are then more rapidly inactivated. Depletion of strong nucleosomes in older transposons suggests frequent re-positioning during evolution, thus resolving a debate about selective pressure on nucleosome-positioning. The findings have important implications for human genetics and genome evolution.
Excessive deliberation in social anxiety

A goal of computational psychiatry is to ground symptoms in more fundamental computational mechanisms. Theory suggests that rumination and other symptoms in mood disorders reflect dysregulated mental simulation, a process that normally serves to evaluate candidate actions. If so, these covert symptoms should have observable consequences: excessively deliberative choices, specifically about options related to the content of rumination. In two large general population samples, we examined how symptoms of social anxiety disorder (SAD) predict choices in a socially framed reinforcement learning task, the Patent Race game. Using a computational learning model to assess learning strategy, we found that self-reported social anxiety was indeed associated with an increase in deliberative evaluation. The effect was specific to learning from a particular (“upward counterfactual”) subset of feedback, broadly matching the biased content of rumination in SAD. It was also robust to controlling for other psychiatric symptoms. These results ground the symptoms of SAD, such as overthinking and paralysis in social interactions, in well characterized neuro-computational mechanisms and offer a rare example of enhanced function in disease
Enzymatic extract from flowers of Algerian spontaneousCynara cardunculus: Milk-clotting properties and use in the manufacture of a Camembert-type cheese

The aim of this study was to assess the coagulant properties of crude extract from cardoon flowers (CECF) as a replacement for the imported coagulants used in the local Algerian cheese factories. Optimal coagulation activity of the extract was observed at pH 5 and 60 °C with a CaCl₂ concentration of 0.02 M. The electrophoretic pattern revealed that the crude extract contains mainly cardosins A and B. The study of interactions involved in the formation of milk gel coagulated by CECF showed that hydrogen forces, hydrophobic interactions and calcium bridges contributed highly to the formation of milk gel. Camembert‐type cheese obtained by CECF was judged by trained panellists and was found to be in agreement with standard specifications. The present study highlights the possibility of using Algerian CECF as a promising plant coagulant in cheesemaking for the dairy industry.
Supramolecular complex sacubitril/valsartan - the first representative of a new class of drugs for the treatment of chronic heart failure

The average prevalence of сhronic heart failure in the adult population, according to the statistics of different countries, ranges from 1.5 % to 5.5 % and therefore the study of this problem and of finding new approaches to the treatment of сhronic heart failure is also still relevant at present. Objective is to show an innovative strategy in the treatment of сhronic heart failure, to show the benefits of using the combined drug sacubitril/valsartan (LCZ696) in comparison with the group of the mentioned above drugs for treating patients with сhronic heart failure and a reduced left ventricular ejection fraction, according to the results of a large randomized clinical research, based on its biochemical properties. Conclusions. The main positive effects of sacubitril and valsartan in patients with сhronic heart failure are associated with an increase in the amount of the natriuretic peptide and the simultaneous suppression by valsartan of the negative effects of angiotensin II. The indication for the use of the sakubitril / valsartan complex is сhronic heart failure (II – IV FC according to the NYHA classification) in patients with systolic dysfunction in order to reduce the risk of cardiovascular mortality and hospitalization for heart failure.
Herbarium specimens reveal increasing herbivory over the past century

Predicting how ecological interactions will respond to global change is a major challenge. Plants and their associated insect herbivores compose much of macroscopic diversity, yet how their interactions have been altered by recent environmental change remains underexplored. To address this gap, we quantified herbivory on herbarium specimens of four plant species with records extending back 112 years. Our study focused on the northeastern US, where temperatures have increased rapidly over the last few decades. This region also represents a range of urban development, a form of global change that has shown variable effects on herbivores in the past studies. Herbarium specimens collected in the early 2000s were 23% more likely to be damaged by herbivores than those collected in the early 1900s. Herbivory was greater following warmer winters and at low latitudes, suggesting that climate warming may drive increasing insect damage over time. In contrast, human population densities were negatively associated with herbivore damage. To explore whether changes in insect occurrence or abundance might explain shifts in herbivory, we used insect observational records to build climate occupancy models for lepidopteran herbivores (butterflies and moths) of our focal plant species. These models show that higher winter temperatures were associated with higher probability of insect herbivore presence, while urbanization was associated with reduced probability of herbivore presence, supporting a link between insect herbivore occurrence and herbivory mediated through environment. Synthesis. Using a temporal record of plant herbivory that spans over a century, we show that both temperature and urbanization influence insect damage to plants, but in very different ways. Our results indicate that damage to plants by insect herbivores will likely continue to increase through time in the northeastern US as global temperatures rise, but that urbanization may disrupt local effects of winter warming on herbivory by excluding certain herbivores. These changes may scale to shape ecosystem processes that are driven by herbivory, including plant productivity.
Impact of Knowledge Sharing on Organizational Performance: The Moderating Role of Organizational Culture Proxies

The paper aims to test an explanation of how organizational culture affects the relationship between knowledge sharing and organizational performance. It was expected that organizational culture proxies significantly mediate the relationship between knowledge sharing and performance. The study used a quantitative survey method for the collection of data. A sample of 200 respondents was drawn from the higher education institutes (HEIs) situated in Lahore. The findings revealed that a positive relationship exists; except for when the components were tested individually for their role in moderating it, then learning environment became insignificant. The strong impact of interpersonal communication and trust highlights its significance in boosting knowledge sharing in an organization that results in improved performance. This finding helped the authors to draw on future research implications regarding the components of organizational culture.
Food waste drivers in Croatian households

A survey was conducted with the aim of analysing the knowledge and act of the Croatian population regarding food waste. Nearly half (48%) of the respondents reported that the main culprit in household food wastage was preparation of excessive amounts of food for meals, while, for one third of the respondents, in second place as a reason for occurrence of food waste was the purchasing of an excessive amount of food (28.5%). Respondents were also asked to assess what activities they conduct to reduce food waste in their households. Most respondents (34.8%) stated that they feed the dog or cat, while 27.6% store leftovers in the freezer. Almost a third of the respondents (27.6%) discard leftovers from the meal in the bin without any further use. Most respondents regard the discarding of food to be a financial loss to the household (68.1%) and to affect the environment negatively (63.1%), and most of them discard food when they suspect it is unsafe (54.3%). Answers to the question of differentiating date tags on foods showed that 36.8% of respondents do not understand the labels on food packaging. Only 13.8% of respondents reported having organized collection of bio-waste at their place of residence.
Optimization of culture conditions for high frequency in vitro shoot multiplication in sugarcane (Saccharum officinarum L.)

Present study deals with the optimization of various culture conditions for initiating high frequency in vitro shoot multiplication in two early maturing high yielding sugarcane genotypes namely Co98014 & Co89003. On the behalf of the findings of this study, it was concluded that the temperature, photoperiod and culture media pH affected the frequency of in vitro shoot multiplication in both sugarcane genotypes at a significant level. In both genotypes high frequency shoot multiplication was recorded at growth room temperature 25ÂoC, 16h/8h light/dark photoperiod and culture media pH 6.0. Genotype Co89003 exhibited highest shoot regeneration and multiplication under various culture conditions. The present study suggests the necessity of investigation of these culture conditions separately upon individual sugarcane genotypes prior to develop efficient in vitro plant regeneration protocol for commercial purposes.
Identification of Kinase Inhibitors that Regulate Nuclear Receptor Nurr1 (NR4A2) Cellular Activity

The ability to regulate the activity NR4A subfamily of nuclear receptors would be potentially useful in the treatment of multiple diseases, but to date, few regulators have been reported. This is likely due to the fact that the NR4A subfamily does not have a typical unoccupied nuclear receptor ligand binding pocket, but rather a pocket that is occupied with hydrophobic side chains of adjacent amino acids. It follows that traditional nuclear receptor assays that seek to identify ligands that bind within the ligand binding pocket would not be successful. We have thus focused on an alternate assay to identify NR4A regulators based on the fact that regulation of NR4A, at least partially, results from phosphorylation/dephosphorylation of the amino terminal region of the protein. We developed a medium throughput cellular assay using a fusion of the amino terminus of Nurr1 (NR4A2) with luciferase reporter and used the assay to screen a large and diverse protein kinase inhibitor set (PKIS). We identified multiple kinase inhibitor compounds from PKIS that significantly increased or decreased the cellular activity of Nurr1. These molecules serve as starting points to discover selective tools for regulation of Nurr1/Nurr1pathway. This work was supported by Shaw University Institutional funds and the experiments were performed in a laboratory containing equipment supplied from a previously funded NIH RIMI grant (Research Instrumentation for Minority Institutions).