bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying unusual neurological movement phenotypes in collective movement phenotypes
Authors: Owoeye Kehinde , Musolesi Mirco , Hailes Stephen 
Published: July 2021

AbstractBuilding models of anomalous behaviour in animals is important for monitoring animal welfare as well as assessing the efficacy of therapeutic interventions in preclinical trials. In this paper, we describe methods that allow for the automatic discrimination of sheep with a genetic mutation that causes Batten disease from an age-matched control group, using GPS movement traces as input. Batten disease is an autosomal recessive lysosomal storage abnormality with symptoms that are likely to affect the way that those with it move and socialise, including loss of vision and dementia. The sheep in this study displayed a full range of symptoms and during the experiment, the sheep were mixed with a large group of younger animals. We used data obtained from bespoke raw data GPS sensors carried by all animals, with a sampling rate of 1 sample/second and a positional accuracy of around 30cm. The distance covered in each ten minute period and, more specifically, outliers in each period, were used as the basis for estimating the abnormal behaviour. Our results show that, despite the variability in the sample, the bulk of the outliers during the period of observation across six days came from the sheep with Batten disease. Our results point towards the potential of using relatively simple movement metrics in identifying the onset of a phenotype in symptomatically similar conditions.
Accurate Automatic Glioma Segmentation in Brain MRI images Based on CapsNet
Authors: Aziz M. Jalili , Zade A. Amiri Tehrani , Farnia P. , Alimohamadi M. , Makkiabadi B. , Ahmadian A. , Alirezaie J. 
Published: July 2021

AbstractGlioma is a highly invasive type of brain tumor with an irregular morphology and blurred infiltrative borders that may affect different parts of the brain. Therefore, it is a challenging task to identify the exact boundaries of the tumor in an MR image. In recent years, deep learning-based Convolutional Neural Networks (CNNs) have gained popularity in the field of image processing and have been utilized for accurate image segmentation in medical applications. However, due to the inherent constraints of CNNs, tens of thousands of images are required for training, and collecting and annotating such a large number of images poses a serious challenge for their practical implementation. Here, for the first time, we have optimized a network based on the capsule neural network called SegCaps, to achieve accurate glioma segmentation on MR images. We have compared our results with a similar experiment conducted using the commonly utilized U-Net. Both experiments were performed on the BraTS2020 challenging dataset. For U-Net, network training was performed on the entire dataset, whereas a subset containing only 20% of the whole dataset was used for the SegCaps. To evaluate the results of our proposed method, the Dice Similarity Coefficient (DSC) was used. SegCaps and U-Net reached DSC of 87.96% and 85.56% on glioma tumor core segmentation, respectively. The SegCaps uses convolutional layers as the basic components and has the intrinsic capability to generalize novel viewpoints. The network learns the spatial relationship between features using dynamic routing of capsules. These capabilities of the capsule neural network have led to a 3% improvement in results of glioma segmentation with fewer data while it contains 95.4% fewer parameters than U-Net.
Invasive grass causes biotic homogenization in wetland birds
Authors: Robichaud C.D. , Rooney R.C. 
Published: July 2021

AbstractPlant invasions often lead to homogenization of the plant community, but the potential for plant invasions to cause homogenization of other trophic levels is under-studied in many systems. We tested whether the bird community in Phragmites australis-invaded marsh would exhibit spatial and temporal taxonomic homogenization compared to remnant cattail and meadow marsh. We compared the bird community using marsh invaded by P. australis and remnant, uninvaded marsh vegetation in a year with average water depths and a year with above-average water depths in the coastal marshes of a World Biosphere Reserve. Our results demonstrate strong evidence for spatial and temporal homogenization of the wetland bird community following P. australis invasion. The birds present in P. australis-invaded marsh were a nested subset of those present in remnant marsh, and total beta diversity decreased when water depths were above average. In contrast, total beta diversity was high in remnant marsh vegetation and stable between the two years. The distinctively structured vegetation zones in remnant (uninvaded) marsh yields structural complexity and habitat heterogeneity that supports greater taxonomic turnover in the bird community. Our study provides evidence that invasion by a plant has resulted in biological homogenization of the wetland bird community.
Open-source personal pipetting robots with live-cell incubation and microscopy compatibility
Authors: Dettinger Philip , Kull Tobias , Arekatla Geethika , Ahmed Nouraiz , Zhang Yang , Schneiter Florin , Wehling Arne , Schirmacher Daniel , Kawamura Shunsuke , Loeffler Dirk , Schroeder Timm 
Published: July 2021

AbstractLiquid handling robots have the potential to automate many procedures in life sciences. However, they are not in widespread use in academic settings, where funding, space and maintenance specialists are usually limiting. In addition, current robots require lengthy programming by specialists and are incompatible with most academic laboratories with constantly changing small-scale projects. Here, we present the Pipetting Helper Imaging Lid (PHIL), an inexpensive, small, open-source personal liquid handling robot. It is designed for inexperienced users, with self-production from cheap commercial and 3D-printable components and custom control software. PHIL successfully automated pipetting for e.g. tissue immunostainings and stimulations of live stem and progenitor cells during time-lapse microscopy. PHIL is cheap enough for any laboratory member to have their own personal pipetting robot(s), and enables users without programming skills to easily automate a large range of experiments.
Functional characterisation of the Nep1-like protein effectors of the necrotrophic pathogen - Alternaria brassicae
Authors: Duhan Deepak , Gajbhiye Shivani , Jaswal Rajdeep , Singh Ravindra Pal , Sharma Tilak Raj , Rajarammohan Sivasubramanian 
Published: July 2021

AbstractAlternaria brassicae is an important necrotrophic pathogen that infects the Brassicaceae family. Alternaria brassicae, like other necrotrophs, also secretes various proteinaceous effectors and metabolites that cause cell death to establish itself in the host. However, there has been no systematic study of A. brassicae effectors and their roles in pathogenesis. The availability of the genome sequence of A. brassicae in public domain has enabled the search for effectors and their functional characterisation. Nep1-like proteins are a superfamily of proteins that induce necrosis and ethylene biosynthesis. They have been reported from a variety of microbes including bacteria, fungi, and oomycetes. In this study, we identified two NLPs from A. brassicae viz. AbrNLP1 and AbrNLP2 and functionally characterised them. Although both AbrNLPs were found to be secretory in nature, they localised differentially inside the plant. AbrNLP2 was found to induce necrosis in both host and nonhost species, while AbrNLP1 could not induce necrosis in both species. Additionally, AbrNLP2 was shown to induce pathogen-associated molecular pattern (PAMP)-triggered immunity in both host and nonhost species. Overall, our study indicates that AbrNLPs are functionally and spatially (subcellular location) distinct and may play different but important roles during the pathogenesis of A. brassicae.
Which Index Should I Use? A Comparison of Indices for Enclosure Use Studies
Authors: Brereton James E. , Fernandez Eduardo J. 
Published: July 2021

AbstractEnclosure use assessments have gained popularity as one of the tools for animal welfare assessments and Post Occupancy Evaluations. There are now a plethora of studies and enclosure use indices available in published literature, and identification of the most appropriate index for each research question is often challenging. The benefits and limitations of four different enclosure use indices; Original and Modified Spread of Participation Index, Entropy, and Electivity Index were compared. Three artificial data sets were developed to represent the challenges commonly found in animal exhibits, and these indices were applied to these contrived enclosure settings. Three of the indices (Original SPI, Modified SPI, and Entropy) were used to assess a single measure of enclosure use variability. When zones within an exhibit were comparable in size, all three indices performed similarly. However, with less equal zone sizes, Modified SPI outperformed Original SPI and Entropy, suggesting that the Modified formula was more useful for assessing overall enclosure use variability under such conditions. Electivity Index assessed the use of individual zones, rather than the variability of use across the entire exhibit, and therefore could not be compared directly to the other three indices. This index is therefore most valuable for assessing individual resources, especially after exhibit modifications.
Naturalistic Audiovisual Stimulation Reveals the Topographic Organization of Human Auditory Cortex
Authors: Hedger Nicholas , Knapen Tomas 
Published: July 2021

AbstractDespite the importance of audition in spatial, semantic, and social function, there is no consensus regarding the detailed organisation of human auditory cortex. Using a novel computational model to analyse a high-powered naturalistic audiovisual movie-watching dataset, we simultaneously estimate spectral tuning properties and category selectivity to reveal the modes of organisation and computational motifs that characterise human auditory cortex. We find that regions more remote from the auditory core exhibit more compressive, non-linear response properties and finely-tuned, speech-selective receptive fields in low frequency portions of the tonotopic map. These patterns of organisation mirror aspects of the visual cortical hierarchy, wherein tuning properties progress from a stimulus category-agnostic ‘front end’ towards more advanced regions increasingly optimised for behaviorally relevant stimulus categories.
Flexibility of Short-chain dehydrogenase is interconnected to its promiscuity for the reduction of multiple ketone intermediates
Authors: Shanbhag Anirudh P , Rajagopal Sreenath , Ghatak Arindam , Katagihallimath Nainesh , S. Ramswamy , Datta Santanu 
Published: July 2021

AbstractShort-chain dehydrogenases/reductases (SDRs) are a convenient class of enzymes used to synthesize enantiopure alcohols. Several studies describe native or engineered SDRs for converting substrates of interest using cost and time-intensive high-throughput approaches. The classification of SDRs is based on chain length and cofactor binding site. Of these, the shorter ‘Classical’ and the longer ‘Extended’ enzymes participate in ketoreduction. However, comparative analysis of various modelled SDRs reveals a length independent conserved N-terminal Rossmann fold and a variable C-terminus region for both types. The general hypothesis is that the latter domain influences the enzyme’s flexibility that may affect the observed promiscuity of the enzyme. We have used a machine learning algorithm on this flexible domain to build a rationale to screen promiscuous candidates. We have built a data set consisting of physicochemical properties derived from the amino-acid composition of enzymes to select closely associated promiscuous mesophilic enzymes. The resulting in vitro studies on pro-pharmaceutical substrates illustrate a direct correlation between the C-terminal lid-loop structure, enzyme melting temperature and the turnover number. We present a walkthrough for exploring promiscuous SDRs for catalyzing enantiopure alcohols of industrial importance.
A chromatin phase transition protects mitotic chromosomes against microtubule perforation
Authors: Schneider Maximilian W. G. , Gibson Bryan A. , Otsuka Shotaro , Spicer Maximilian F.D. , Petrovic Mina , Blaukopf Claudia , Langer Christoph C. H. , Doolittle Lynda K. , Rosen Michael K. , Gerlich Daniel W. 
Published: July 2021

AbstractDividing eukaryotic cells package extremely long chromosomal DNA molecules into discrete bodies to enable microtubule-mediated transport of one genome copy to each of the newly forming daughter cells1–3. Assembly of mitotic chromosomes involves DNA looping by condensin4–8and chromatin compaction by global histone deacetylation9–13. While condensin confers mechanical resistance towards spindle pulling forces14–16, it is not known how histone deacetylation affects material properties and segregation mechanics of mitotic chromosomes. Here, we show how global histone deacetylation at the onset of mitosis induces a chromatin-intrinsic phase transition that endows chromosomes with specific characteristics necessary for their precise movement during cellular division. Deacetylation-mediated compaction of chromatin forms a structure dense in negative charge and allows mitotic chromosomes to resist perforation by microtubules as they are pushed to the metaphase plate. Hyperacetylated mitotic chromosomes lack a defined surface boundary, are frequently perforated by microtubules, and are prone to missegregation. Our study highlights the different contributions of DNA loop formation and chromatin-intrinsic phase separation to genome segregation in dividing cells.
Reversal of the renal hyperglycemic memory by targeting sustained tubular p21 expression
Authors: Al-Dabet Moh’d Mohanad , Shahzad Khurrum , Elwakiel Ahmed , Sulaj Alba , Kopf Stefan , Bock Fabian , Gadi Ihsan , Zimmermann Silke , Rana Rajiv , Krishnan Shruthi , Gupta Dheerendra , Nazir Sumra , Baber Ronny , Scholz Markus , Geffers Robert , Mertens Peter Rene , Nawroth Peter P. , Griffin John , Dockendorff Chris , Kohli Shrey , Isermann Berend 
Published: July 2021

AbstractA major therapeutic obstacle in diabetes mellitus is the metabolic or hyperglycemic memory: the persistence of impaired organ function despite improvement of blood glucose. Therapies reversing the hyperglycemic memory and thus improving already established organ-dysfunction are lacking, but urgently needed considering the increasing prevalence of diabetes mellitus worldwide. Here we show that glucose-mediated changes in gene expression largely persist in diabetic kidney disease (DKD) despite reversing hyperglycemia. The senescence-associated cyclin-dependent kinase inhibitor p21 (Cdkn1a) was the top hit among genes persistently induced by hyperglycemia and was associated with sustained induction of the p53-p21 pathway. Persistent p21 induction was confirmed in various animal models, in several independent human samples and in in vitro models. Tubular p21 expression and urinary p21-levels were associated with DKD severity and remained elevated despite improved blood glucose levels in humans, suggesting that p21 may be a biomarker indicating persistent (“memorized”) kidney damage. Glucose-mediated p21 induction and tubular senescence were enhanced in mice with reduced levels of the disease resolving protease activated protein C (aPC). Mechanistically, glucose-induced and sustained tubular p21 expression is linked with demethylation of its promoter and reduced DNMT1 expression. aPC reverses already established p21 expression independent of its anticoagulant function through receptor signaling. Accordingly, new pharmacological approaches specifically mimicking aPC signaling (3K3A-aPC, parmodulin-2) enabled the reversal of glucose-mediated sustained tubular p21 expression, tubular senescence, and DKD. Thus, p21-dependent tubular senescence contributes to the hyperglycemic memory but can be therapeutically targeted.Single sentence summaryaPC signaling targets persistent p21 expression and tubular senescence and reverses the hyperglycemic memory in diabetic kidney disease.
The E3 Ubiquitin Ligase Mindbomb1 controls zebrafish Planar Cell Polarity
Authors: Saraswathy Vishnu Muraleedharan , Sharma Priyanka , Kurup Akshai Janardhana , Polès Sophie , Poulain Morgane , Fürthauer Maximilian 
Published: July 2021

ABSTRACTVertebrate Delta/Notch signaling involves multiple ligands, receptors and transcription factors. Delta endocytosis – a critical event for Notch activation – is however essentially controlled by the E3 Ubiquitin ligase Mindbomb1 (Mib1). Due to its position at a molecular bottleneck of the pathway, Mib1 inactivation is often used to inhibit Notch signaling. However, recent findings indicate that the importance of Mib1 extends beyond the Notch pathway. We report an essential role of Mib1 in Planar Cell Polarity (PCP).mib1 null mutants or morphants display impaired gastrulation stage Convergence Extension (CE) movements. Comparison of different mib1 mutants and functional rescue experiments indicate that Mib1 controls CE independently of Notch. In contrast, Mib1-dependent CE defects can be rescued using the PCP downstream mediator RhoA. Mib1 regulates CE through the RING Finger domains that have been implicated in substrate ubiquitination, suggesting that Mib1 may control PCP protein trafficking. Accordingly, we show that Mib1 controls the endocytosis of the PCP component Ryk and that Ryk internalization is required for CE.Numerous morphogenetic processes involve both Notch and PCP signaling. We show that Mib1, a known Notch signaling regulator, is also an essential PCP pathway component. Care should therefore be taken when interpreting Mib1 loss of function phenotypes.
Periosteum-derived podoplanin-expressing stromal cells regulate nascent vascularization during epiphyseal marrow development
Authors: Tamura Shogo , Mukaide Masato , Katsuragi Yumi , Fujii Wataru , Odaira Koya , Suzuki Nobuaki , Okamoto Shuichi , Suzuki Atsuo , Kanematsu Takeshi , Katsumi Akira , Takagi Akira , Suzuki-Inoue Katsue , Matsushita Tadashi , Kojima Tetsuhito , Hayakawa Fumihiko 
Published: July 2021

AbstractBone marrow development and endochondral bone formation occur simultaneously. During endochondral ossification, periosteal vasculatures and stromal progenitors invade the primary avascular cartilaginous anlage; this induces primitive marrow development. We previously determined that bone marrow podoplanin (PDPN)-expressing stromal cells exist in a perivascular microenvironment, and promote megakaryopoiesis and erythropoiesis. In this study, we aimed to examine the involvement of PDPN-expressing stromal cells in the postnatal bone marrow generation. We found that periosteum-derived PDPN-expressing stromal cells regulate vascularization during postnatal epiphyseal marrow development. Our findings suggest that these cells act as pericytes on the primitive vasculature of the nascent marrow. They invade the cartilaginous epiphysis and regulate marrow development and homeostasis by maintaining vascular integrity. To the best of our knowledge, this is the first study to comprehensively examine how PDPN-expressing stromal cells contribute to marrow development and homeostasis.
Transcriptomic response of Cinachyrella cf. cavernosa sponges to spatial competition
Authors: Deshpande Aabha , Rivera-Vicéns Ramón E. , Thakur Narsinh L. , Wörheide Gert 
Published: July 2021

AbstractSpatial competition in the intertidal zones drives the community structure in marine benthic habitats. Organisms inhabiting these areas not only need to withstand fluctuations of temperature, water level, pH, and salinity, but also need to compete for the best available space. Sponges are key members of the intertidal zones, and their life history processes (e.g. growth, reproduction, and regeneration) are affected by competition. Here we used transcriptomics to investigate the effects of interspecific competition between the tetillid sponge Cinachyrella cf. cavernosa, the zoantharid Zoanthus sansibaricus, and the macroalgae Dictyota ciliolata. The analysis of differentially expressed genes showed that Z. sansibaricus was the most stressful competitor to C. cf. cavernosa, which showed an increased rate of cellular respiration under stress of competition. Similarly, an up-regulation of energy metabolism, lipid metabolism, and the heat-shock protein (HSP) 70 was also observed along with an indication of a viral infection and decreased ability to synthesise protein. A down-regulation of purine and pyrimidine metabolism indicated reduction in physiological activities of the competing sponges. Moreover, a putative case of possible kleptocnidism, not previously reported in Cinachyrella cf. cavernosa was also observed. This study opens the door for more detailed investigations of marine organisms competing for spatial resources using transcriptome data.
Meta-analysis of tree diversity effects on the abundance, diversity and activity of herbivores’ enemies
Authors: Stemmelen A. , Jactel H. , Brockerhoff E.G. , Castagneyrol B. 
Published: July 2021

AbstractThe natural enemies hypothesis predicts that the abundance and diversity of antagonists such as predators and parasitoids of herbivores increases with the diversity of plants, which can lead to more effective top-down control of insect herbivores. However, although the hypothesis has received large support in agricultural systems, fewer studies have been conducted in forest ecosystems and a comprehensive synthesis of previous research is still lacking.We conducted a meta-analysis of 65 publications comparing the diversity, abundance or activity of various groups of natural enemies (including birds, bats, spiders and insect parasitoids) in pure vs. mixed forest stands. We tested the effects of forest biome, natural enemy taxon and type of study (managed vs experimental forest).We found a significant positive effect of forest tree diversity on natural enemy abundance and diversity but not on their activity. The effect of tree diversity on natural enemies was stronger towards lower latitudes but was not contingent on the natural enemy taxon level.Overall, our study contributes toward a better understanding of the “natural enemies hypothesis” in forest systems and provides new insights about the mechanisms involved. Furthermore, we outline potential avenues for strengthening forest resistance to the growing threat of herbivorous insects.