Miracle-dz/UniFAR-FTUs huggingface dataset:
Digging up the dirt: Quantifying the effects on soil of a translocated ecosystem engineer

Digging mammals are often considered ecosystem engineers, as they affect important properties of soils and in turn nutrient exchange, vegetation dynamics and habitat quality. Returning such species, and their functions, to areas from where they have been extirpated could help restore degraded landscapes and is increasingly being trialled as a conservation tool. Studies examining the effects of digging mammals have largely been from arid and semi‐arid environments, with little known about their impacts and importance in mesic systems. To address this knowledge gap, we investigated the ecological role of a recently introduced population of eastern barred bandicoots (Perameles gunnii) on Churchill Island, Victoria, south‐eastern Australia, from which all digging mammals have been lost. We quantified the annual rate of soil turnover by estimating the number of foraging pits bandicoots created in 100‐m² plots over a 24‐h period. Foraging pit counts could not be completed in each season, and the overall turnover estimate assumes that autumn/winter months represent turnover rates for the entire year; however, this is likely to fluctuate between seasons. Ten fresh and ten old pits were compared to paired undug control sites to quantify the effect soil disturbance had on soil hydrophobicity, moisture content and soil strength. Plots contained between zero and 64 new foraging pits each day. We estimated that an individual eastern barred bandicoot digs ~487 (95% CI = 416–526) small foraging pits per night, displacing ~13.15 kg (95% CI = 11.2–14.2 kg) of soil, equating to ~400 kg (95% CI = 341–431 kg) of soil in a winter month. Foraging pits were associated with decreased soil compaction and increased soil moisture along the foraging pit profile. Eastern barred bandicoots likely play an important role in ecosystems through their effects on soil, which adds to an increasing body of knowledge suggesting restoration of ecosystems, via the return of ecosystem engineers and their functions, holds much promise for conserving biodiversity and ecological function.
Carcass additions increase juvenile salmonid growth, condition, and size in an interior Columbia River Basin tributary

Numbers of anadromous fish returning to freshwater ecosystems have declined precipitously across much of western North America, reducing a potentially important resource subsidy for juvenile salmonids. We added carcasses to three sections of a Snake River tributary and assessed juvenile Chinook salmon (Oncorhynchus tshawytcha) and steelhead trout (Oncorhynchus mykiss) growth, body condition, size, and diet responses in summer and early fall. Juvenile salmonids consumed an abundance of eggs and carcass tissue, which increased energy rations. Within 3 weeks of carcass additions, juvenile Chinook and steelhead growth rates were 1.1–5 and 6–23 times greater in treatment reaches relative to control reaches, respectively. We used long-term tagging and detection data from this system to assess the relationship between juvenile Chinook size and emigration survival for two different juvenile life histories. The increased growth rates and body size in response to carcass additions, coupled with a positive relationship between body size and survival, suggest that juvenile salmonid rearing productivity and emigration survival may be limited by depressed returns of anadromous fishes in this system and potentially other tributaries of the Columbia Basin.
The complete chloroplast genome sequences of Zanthoxylum nitidum var. nitidum and Z. nitidum var. tomentosum

Abstract Zanthoxylum nitidum (Rutaceae Juss.) is a traditional Chinese medicine with four morphological types. We assembled their complete chloroplast genome sequences. The assembled genomes are 156,999–157,349 bp in length, including a large single copy (LSC) region of 84,064–84,455 bp, a small single copy (SSC) region of 17,582–17,651 bp and a pair of inverted repeats (IRs) of 27,631–27,659 bp. All genomes contained 133 genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. The GC content is 38.5%. The further phylogenetic analysis showed that Z. nitidum clade was a monophyletic group separated from other Zanthoxylum species.
Detecting complex genetic mutations in large human genome data

All cellular forms of life contain Deoxyribonucleic acid (DNA). DNA is a molecule that carries all the information necessary to perform both, basic and complex cellular functions. DNA is replicated to form new tissue/organs, and to pass genetic information to future generations. DNA replication ideally yield an exact copy of the original DNA. While replication generally occurs without error, it may leave DNA vulnerable to accidental changes via mistakes made during the replication process. Those changes are called mutations. Mutations range in magnitude. Yet, mutations of any magnitude range in consequences, from no effect on the organism, to disease initiation (e.g. cancer), or even death. In this thesis, we limit our focus to mutations in human DNA, and in particular, MMBIR mutations. Recent literature in human genomics has found Microhomology-mediated break-induced replication (MMBIR) to be a common mechanism producing complex mutations in DNA. MMBIRFinder is a tool to detect MMBIR regions in Yeast DNA. Although MMBIRFinder is successful on Yeast DNA, MMBIRFinder is not capable of detecting MMBIR mutations in human DNA. Among several reasons, one major reason for its deficiency with human DNA is the amount of computations required to process human large data. Our contribution in this regard is two fold: 1) We utilize parallel computations to significantly reduce the processing time consumed by the original MMBIFinder, and address several performance degrading issues inherent in the original design;
Oligomerization of the NLR immune receptor RPP7 triggered by the atypical resistance protein RPW8/HR. Li et al

In certain plant hybrids, autoimmunity is triggered by immune components that interact in the absence of a pathogen trigger. Often, NLR immune receptors are involved, with a particularly interesting case in Arabidopsis thaliana involving variants of the NLR RPP7 as well as variants of RPW8/HR proteins, which are homologs of animal MLKL and fungal HELL domain proteins. We demonstrate that HR4Fei-0 but not the closely related HR4Col-0 protein directly disrupts intramolecular association of RPP7bLerik1-3, which in turn initiates P-loop dependent NLR signaling. In agreement, RPP7bLerik1-3 forms a higher-order complex only in the presence of HR4Fei-0 but not HR4Col-0. In addition, we find that HR4Fei-0 on its own can form detergent-resistant oligomers suggestive of amyloid-like aggregates, which in turn can directly kill cells in an RPP7bLerik1-3-independent manner. Our work provides in vivo biochemical evidence for a plant resistosome complex and the mechanisms by which RPW8/HR proteins trigger cell death.
Population genetic models of GERP scores suggest pervasive turnover of constrained sites across mammalian evolution

Comparative genomic approaches have been used to identify sites where mutations are under purifying selection and of functional consequence by searching for sequences that are conserved across distantly related species. However, the performance of these approaches has not been rigorously evaluated under population genetic models. Further, short-lived functional elements may not leave a footprint of sequence conservation across many species. Here, we use simulations to study how one measure of conservation, the GERP score, relates to the strength of selection (Nes). We show that the GERP score is related to the strength of purifying selection. However, changes in selection coefficients or functional elements over time (i.e. functional turnover) can strongly affect the GERP distribution, leading to unexpected relationships between GERP and Nes. Further, we show that for functional elements that have a high turnover rate, the optimal tree size is not necessarily the largest possible tree, and more turnover reduces the optimal tree size. Finally, we use the distribution of GERP scores across the human genome to compare models with and without turnover of sites where mutations under purifying selection. We show that mutations in 4.51% of the noncoding human genome are under purifying selection and that most of this sequence has likely experienced changes in selection coefficients throughout mammalian evolution.
Comparison of products of whey proteins concentrate proteolysis, obtained by different proteolytic preparations

An important source of bioactive peptides is hydrolyzed products based on milk whey: hypoallergenic products, hydrolyzates for baby food, and products for athletes. However, in their production, proteolytic preparations of different origin are used. This may affect the degree of proteolysis of the biologically active peptides (BAP) proteins-precursors, the proteolysis products molecular weight distribution and, accordingly, the probability of BAP formation. A comparison of the degree of whey protein concentrate (WPC) proteins proteolysis and the molecular weight distribution of proteolysis products obtained by the action of proteolytic preparations of animal, plant and microbiological origin has been carried out. The following enzyme preparations were used for proteolysis: papain, neutral protease, trypsin, chymotrypsin and pancreatin. WPC was used as the substrate. The proteins fractional composition and the molecular weight distribution of proteins and peptides were characterized in it before the proteolysis. Proteolysis of 15 % WPC solution was carried out at a temperature of 37°C, pH 7.9 and enzyme: substrate ratio 1:20. During proteolysis, samples were periodically taken off for spectrophotometric determination of proteolysis products soluble in 5 % trichloroacetic acid (TCA). Molecular weight distribution of the resulting polypeptides and peptides was established by gel filtration of the reaction mixture after deposition of the unsplit proteins in 5 % TCA. As a result of the research, it was found that the majority of proteolysis products were formed during the first 30–60 minutes. Proteolysis was mostly completed by 120 minutes. Gel filtration on Sephadex G-50 showed that hydrolysates differ by molecular weight distribution. The highest amount of low molecular weight peptides (M<1,500 Da) was obtained by the action of neutral protease (29 %) and pancreatin (25 %). The main precursor of BAP – β-lactoglobulin, according to the results of electrophoresis, showed the highest sensitivity to the action of neutral protease (79 %), pancreatin (81 %) and trypsin (71 %)
Compared the mini-midvastus with mini-paramedian approach for the total knee arthroplasty

Objective To compare the short-term results of the mini-midvastus(MMV) approach with the mini-paramedian (MPM) approach for total knee arthroplasty. Methods Methods From January 2006 to March 2007, fifty-one patients were prospectively randomized to either MMV group (26 knees) or MPM group (25 knees), matched by gender, age, body mass index (BMI), etiology of arthritis, preoperative range of motion and functional scores. Genesis Ⅱ (Smith and Nephew,Memphis,TN) posterior-stabilized cemented knee components and minimally invasive instruments were used in all patients. Postoperative periarticular injection with multimodal drugs was used according to Busch′s prescription. The mean length of follow-up was 15 months (range 10 to 23 months). Results There were no infection, neurovascular injury, wound necrosis or other complications. Between both groups, there were no difference in length of incision, blood loss from drainage, HB reduction, VAS scores,an additional use of narcotic and NSAIDs analgesics, postoperative range of motion, Knee Society score and radiographic alignment. But the rate of lateral release in MMV group was significantly lower than MPM group, the time of straight-leg raise and beginning to weight bearing walk in MMV group was significantly earlier than that of MPM group. Operation time in MPM group was significantly shorter than MMV group. Conclusion MMV approach had faster quadriceps functional recovery and better improvement of patellar tracking than MPM approach, but MPM approach had better exposure than MMV approach. Other aspects included pain, blood loss, knee motion, Knee Society scores and components alignment were similar in two groups.
A framework for closed-loop neurofeedback for real-time EEG decoding

Neurofeedback based on real-time brain imaging allows for targeted training of brain activity with demonstrated clinical applications. A rapid technical development of electroen-cephalography (EEG)-based systems and an increasing interest in cognitive training has lead to a call for accessible and adaptable software frameworks. Here, we present and outline the core components of a novel open-source neurofeedback framework based on scalp EEG signals for real-time neuroimaging, state classification and closed-loop feedback. The software framework includes real-time signal preprocessing, adaptive artifact rejection, and cognitive state classification from scalp EEG. The framework is implemented using exclusively Python source code to allow for diverse functionality, high modularity, and easy extendibility of software development depending on the experimenter’s needs. As a proof of concept, we demonstrate the functionality of our new software framework by implementing an attention training paradigm using a consumer-grade, dry-electrode EEG system. Twenty-two participants were trained on a single neurofeedback session with behavioral pre- and post-training sessions within three consecutive days. We demonstrate a mean decoding error rate of 34.3% (chance=50%) of subjective attentional states. Hence, cognitive states were decoded in real-time by continuously updating classification models on recently recorded EEG data without the need for any EEG recordings prior to the neurofeedback session. The proposed software framework allows a wide range of users to actively engage in the development of novel neurofeedback tools to accelerate improvements in neurofeedback as a translational and therapeutic tool.
Diffusion Histology Imaging Detects and Classifies Glioblastoma Pathology Missed by Conventional Magnetic Resonance Imaging

Background Glioblastoma (GBM) is one of the deadliest cancers with no cure. While conventional MRI has been widely adopted for examining GBM clinically, accurate neuroimaging assessment of tumor histopathology for improved diagnosis, surgical planning, and treatment evaluation, remains an unmet need in the clinical management of GBMs. Methods We employ a novel Diffusion Histology Imaging (DHI) approach, combining diffusion basis spectrum imaging (DBSI) and machine learning, to detect, differentiate, and quantify areas of high cellularity, tumor necrosis, and tumor infiltration in GBM. Results Gd-enhanced T1W or hyper-intense FLAIR failed to reflect the morphological complexity underlying tumor in GBM patients. Contrary to the conventional wisdom that apparent diffusion coefficient (ADC) negatively correlates with increased tumor cellularity, we demonstrate disagreement between ADC and histologically confirmed tumor cellularity in glioblastoma specimens, whereas DBSI-derived restricted isotropic diffusion fraction positively correlated with tumor cellularity in the same specimens. By incorporating DBSI metrics as classifiers for a supervised machine learning algorithm, we accurately predicted high tumor cellularity, tumor necrosis, and tumor infiltration with 87.5%, 89.0% and 93.4% accuracy, respectively. Conclusion Our results suggest that DHI might serve as a favorable alternative to current neuroimaging techniques for guiding biopsy or surgery as well as monitoring therapeutic response in the treatment of glioblastoma. Key Points Clinical MRI lacks specificity and sensitivity in detecting morphological features in GBM. DBSI-derived morphological metrics reflect tumor cellularity, necrosis, and white matter tracts. DHI predicts and classifies key histopathological features of GBM. Importance of the Study Current clinical diagnosis, surgical resection planning, and assessment of treatment response for GBM patients relies heavily on gadolinium enhanced T1-weighted MRI, despite the enhancement is non-specific to tumor growth merely reflecting a disrupted blood-brain barrier. The complex tumor microenvironment and spatial heterogeneity make GBM very difficult to characterize using current clinical imaging modalities. In this study, we developed a novel imaging technique to characterize key histological features of GBM to accurately predict high tumor cellularity, tumor necrosis, and tumor infiltration. Current proof-of-concept approach if validated in a larger cohort of GBM patients could provide a solution resolve issues such as pseudoprogression and radiation necrosis currently plague neuroimaging modalities to assess GBM in living patients.
Recent Developments in Genomic Selection for Minor Gene Quantitative Disease Resistance Plant Breeding

To speed up the development of improved crop varieties, genomics assisted plant breeding is becoming an important tool. With traditional breeding and marker assisted selection, there have been several achievements in breeding for diseases resistance. Most research for disease resistance has been focused on major disease resistance genes which are highly effective although very vulnerable to breakdown with rapid changes in pathogenic races. In contrast, breeding for minor gene quantitative resistance can produce more durable plant varieties although it is very slow and challenging breeding. As the genetic architecture of the plant disease resistance shifts from single major R genes to many minor quantitative genes, the most appropriate approach for molecular plant breeding is genomic selection (GS) than marker assisted selection or conventional breeding. With the advent of new genomic tools, GS has emerged as one of the most important approaches for predicting genotype performance to improve genetically complex quantitative traits. Consequently, GS helps to accelerate the rate of genetic gain in breeding by using whole genome sequence data to predict the breeding value of offspring. GS breeding for quantitative resistance will therefore necessitate whole genome prediction models and selection methodology as implemented for classical complex traits. With the implementation of GS for yield and other economically important traits, whole genome marker profiles are available for the entire set of breeding lines, enabling genomic selection for disease resistance with no additional direct cost. Therefore, recent developments in GS including a two stream GS + de novo GWAS models (GS+) and GS for combined highest level of quantitative resistance with R genes (QR +R gene) individuals are expected to further advance disease resistance plant breeding and briefly discussed.
Effects of curcumine on expressions of toll-like receptor 2 and 6 in rat peritoneum during acute peritonitis

Objective:Curcumine has a long history of use in Chinese medicine as a treatment for inflammatory conditions. The purpose of this study was to investigate the preventive effects of curcumin against acute peritonitis induced by Staphylococcus epidermidis in rat and to elucidate possible mechanism of Curcumin action. Methodology:Curcumin [50 mg/(kg·d)] was intraperitoneally injected to rat for 24h,followed by injection of Staphylococcus epidermidis to induce acute peritonitis. After a survival time of 3,6,12,24 and 48 h,TLR2,TLR6 RT-PCR was performed. The expression of NF-κB was analyzed by Western blot and immunohistochemistry,TNF-α level in rat peritoneal fluid was detected by ELISA. Results:The histological examination with HE staining showed that the submesothelial zone became thickened with the edematous changes and obvious WBC infiltration in both parietal and viscera peritoneum. Curcumin treatment inhibited the elevation of expression of TLR2 and TLR6 in peritoneum of acute peritonitis rats. Both TLR2-and TLR6-RT-PCR were revealed identical patterns in peritoneum of acute peritonitis rats. The expressions both TLR2 and TLR6 were progressively enhanced in 3h,6h,12,24 hours after infection. In Curcumin treatment group,there had a similar tendency for the expression of TLR2 and TLR6 in peritoneum of acute peritonitis rats,whereas the expressions were weakened in 6,12,48 after infection compared with model group. The expression of NF-κB at 24 hours after infection and a statistically was significant reduction in rat peritoneum as compared to that in model group. Staphylococcus epidermidis could significantly induce the expression of TNF-α in rat peritoneal fluid,which could be partially reversed by Curcumin. Conclusion:Our results suggest that Curcumin could attenuate peritoneum tissue injury by inhibiting the expression both TLR2 and TLR6 and the release of inflammatory cytokine TNF-α. These effects may involve downregulation of NF-κB.
Defining the Layers of a Sensory Cilium with STORM and Cryo-Electron Nanoscopies

Primary cilia are cylindrical organelles extending from the surface of most animal cells that have been implicated in a host of signaling and sensory functions. Genetic defects in their component molecules, known as “ciliopathies” give rise to devastating symptoms, ranging from defective development, to kidney disease, to progressive blindness. The detailed structures of these organelles and the true functions of proteins encoded by ciliopathy genes are poorly understood because of the small size of cilia and the limitations of conventional microscopic techniques. We describe the combination of cryo-electron tomography, enhanced by sub-tomogram averaging, with super-resolution stochastic reconstruction microscopy (STORM) to define substructures and subdomains within the light-sensing rod sensory cilium of the mammalian retina. Longitudinal and radial domains are demarcated by structural features such as the axoneme and its connections to the ciliary membrane, and are correlated with molecular markers of these compartments, including Ca2+-binding protein centrin-2 in the lumen of the axoneme, acetylated tubulin forming the axoneme, the glycocalyx extending outward from the surface of the plasma membrane, and molecular residents of the space between axoneme and ciliary membrane, including Arl13B, intraflagellar transport proteins, BBS5, and syntaxin-3. Within this framework we document that deficiencies in the ciliopathy proteins BBS2, BBS7 and BBS9 lead to inappropriate accumulation of proteins in rod outer segments while largely preserving their sub-domain localization within the connecting cilium region, but alter the distribution of syntaxin-3 clusters.