Miracle-dz/UniFAR-FTUs huggingface dataset:
MRI-based Parcellation and Morphometry of the Individual Rhesus Monkey Brain: a translational system referencing a standardized ontology

The rhesus macaque is the closest animal model to the human, and investigations into the brain of the rhesus monkey has shed light on the function and organization of the primate brain at a scale and resolution not yet possible in studies of the human brain A cornerstone of the linkage between non-human primate and human studies of the brain is magnetic resonance imaging, which allows for an association to be made between the detailed structural and physiological analysis of the non-human primate and that of the human brain. To further this end, we present a novel parcellation system for the rhesus monkey brain, referred to as the monkey Harvard Oxford Atlas (mHOA) which is based on the human Harvard-Oxford Atlas (HOA) and grounded in an ontological and taxonomic framework. Consistent anatomical features were used to delimit and parcellate brain regions in the macaque, which were then categorized according to functional systems. This system of parcellation will be expanded with advances in technology and like the HOA, will provide a framework upon which the results from other experimental studies (e.g., functional magnetic resonance imaging (fMRI), physiology, connection, graph theory) can be interpreted.
Positive relationship between soil fertility, plant diversity, and gall richness

The complexity of nutrient distribution patterns in soils is a determinant environmental component of the structure of plant communities. Numerous insect species that interact with plants are associated with these communities, and some of these interactions result in the formation of unusual structures called galls. In this study, we investigated the relationship of galls, soil fertility and plant communities in three vegetation types, herbaceous restinga (HR), shrub restinga (SR) and shrub-tree restinga (STR), in an area of restinga in southern Brazil. We identified 217 species belonging to 159 genera and 82 families. The plant diversity recorded in the STR was 42.8% higher than the diversity in the other vegetation types. Gall richness increased significantly with increased plant richness. The edaphic gradient was correlated with the floristic diversity in the vegetation types. Our data suggest that an increment in soil fertility (organic matter and litter thickness), associated with climatic conditions, should increase the number of plants that can potentially host galls and, consequently, the richness of galling insects. Gall richness may also be influenced by a higher occurrence of woody plants, due to an increase in leaf surface area available in the tree canopy, especially in STR.
Laboratory evaluations of woods from Pakistan and their extractives against Postia placenta and Trametes versicolor

Natural durable wood species are those which exhibit innate tolerance to wood decay organisms such as fungi and termites. The goal of this study was to evaluate 4 wood species ( Dalbergia sissoo, Cedrus deodara, Morus alba and Pinus roxburghii ) from Pakistan in order to determine their resistance to both a model brown ( Postia placenta ) and white ( Trametes versicolor ) rot fungus compared to a durable reference species ( Tectonis grandis ). In a 12 week soil bottle test, C. deodara and M. alba were found to be resistant to decay, D. sissoo was moderately resistant and P. roxbughii was non-resistant. This resistance was greatly reduced when blocks were leached with a series of solvents. When a non-durable species was treated with extractives from these species, decay resistance did not improve against either brown or white rot test fungi.
Role of Synaptic Inhibition in the Coupling of the Respiratory Rhythms that Underlie Eupnea and Sigh Behaviors

Abstract The preBötzinger complex (preBötC) gives rise to two types of breathing behavior under normal physiological conditions: eupnea and sighing. Here, we examine the neural mechanisms that couple their underlying rhythms. We measured breathing in awake intact adult mice and recorded inspiratory rhythms from the preBötC in neonatal mouse brainstem slice preparations. We show previously undocumented variability in the temporal relationship between sigh breaths or bursts and their preceding eupneic breaths or inspiratory bursts. Investigating the synaptic mechanisms for this variability in vitro, we further show that pharmacological blockade of chloride-mediated synaptic inhibition strengthens inspiratory-to-sigh temporal coupling. These findings contrast with previous literature, which suggested glycinergic inhibition linked sigh bursts to their preceding inspiratory bursts with minimal time intervals. Furthermore, we verify that pharmacological disinhibition did not alter the duration of the prolonged interval that follows a sigh burst before resumption of the inspiratory rhythm. These results demonstrate that synaptic inhibition does not enhance coupling between sighs and preceding inspiratory events or contribute to post-sigh apneas. Instead, we conclude that excitatory synaptic mechanisms coordinate inspiratory (eupnea) and sigh rhythms.
Recent insights into the genotype–phenotype relationship from massively parallel genetic assays

With the molecular revolution in Biology, a mechanistic understanding of the genotype–phenotype relationship became possible. Recently, advances in DNA synthesis and sequencing have enabled the development of deep mutational scanning assays, capable of scoring comprehensive libraries of genotypes for fitness and a variety of phenotypes in massively parallel fashion. The resulting empirical genotype–fitness maps pave the way to predictive models, potentially accelerating our ability to anticipate the behaviour of pathogen and cancerous cell populations from sequencing data. Besides from cellular fitness, phenotypes of direct application in industry (e.g. enzyme activity) and medicine (e.g. antibody binding) can be quantified and even selected directly by these assays. This review discusses the technological basis of and recent developments in massively parallel genetics, along with the trends it is uncovering in the genotype–phenotype relationship (distribution of mutation effects, epistasis), their possible mechanistic bases and future directions for advancing towards the goal of predictive genetics.
Lake resilience: concept, observation and management

Worldwide, lake ecosystems face threats arising from multiple pressures, related to nutrient runoff (Abell et al. 2011), biological invasions (MacIsaac et al. 2004), hydrological modifications (Zohary and Ostrovsky 2011), exploitation of edible aquatic life (Youn et al. 2014) and climate change (Adrian et al. 2009). New Zealand boasts a great diversity of lakes, which are of cultural importance and environmental, social and economic significance. Their ecosystem services include the provision of water for various purposes, including power generation, transportation, fisheries, tourism, and recreational enjoyment (Schallenberg et al. 2013). Many lakes in New Zealand have been under increasing anthropogenic pressures such as the intensification of land use, urbanisation and the introduction of invasive species. Declining water quality, biodiversity loss, and cyanobacteria blooms are now observed frequently (Ministry for the Environment and StatsNZ 2017; David et al. 2018). In this special issue, attention is directed towards the implications of those pressures for lake ecosystem dynamics, under the unifying theme of ‘Lake Resilience’. This issue presents a series of forum and research papers promoting a better understanding of resilience mechanisms through the integration of applied research in a multidisciplinary framework. Resilience is defined as the ability of a system to maintain its state by absorbing both internal and external change and disturbances to its state variables, driving variables, and parameters (Holling 1973; Cumming et al. 2005). Resilience can be described mathematically as a property of nonlinear systems in which perturbations may move the system away from a point of equilibrium, but after the perturbation, balance is restored and the system returns to this steady state. Lake ecosystems, like most natural systems, have the capacity to maintain their natural ecological state when exposed to some level of pressure. For example, a moderately small gradual development in a lake’s catchment can increase nutrient inputs without causing concomitant deterioration of water quality. A lake with the ability to maintain its state in the face of both internal change and external shocks and disturbances is said to be resilient (Carpenter and Cottingham 1997). All possible ecosystem states may be thought of as a multidimensional surface where troughs and peaks represent stable and unstable steady states. This can be visualised by a marble moving around a three-dimensional surface (see cover image to this special issue for an abstract representation of this concept) or, simpler, as a marble on a two-dimensional track (Figure 1). A marble, representing current ecosystem state, would be drawn to troughs in which case resilience would be analogous to the depth of a depression that keeps an
An analysis of respiratory function and mitochondrial morphology in Candida albicans

Respiratory function and mitochondrial dynamics have been well characterised in a number of cell types, including the model yeast Saccharomyces cerevisiae, but remain under-researched in fungal pathogens such as Candida albicans. An understanding of mitochondrial activity and morphology is important if we are to understand the role that this organelle plays in adaption and response to stress. Here we examine the respiratory profiles of several prominent pathogenic Candida species and present a useful GFP probe for the study of mitochondrial morphology. We examine mitochondrial morphology under a variety of conditions that Candida species may encounter within the host, such as acidic pH, respiratory and oxidative stress. The GFP probe also allowed for the visualisation of mitochondria during hyphal development, during growth following macrophage engulfment and distribution within biofilms. These data demonstrate that the mitochondrial network of C. albicans is highly responsive to both environmental conditions and developmental cues, suggesting important roles for this organelle in environmental adaption.
A Responsible De-Identification Of The Real Data Corpus: Building A Framework For PII Management

Abstract : De-identification methods have helped government organizations provide the public with useful informationpromoting transparency and accountability while also protecting the individual privacy of the data subjects. However, due to the recent massive increase in data collection and improved methods of analysis, de-identification has become a more difficult task. This work outlines challenges and discusses procedures for making a potentially sensitive data set available to extramural researchers and institutions without significant risk to human subject privacy. We provide a detailed explanation of personally identifiable information to help us understand what forms of personally identifiable information can cause the most harm. Furthermore, we discuss the legality and ethics behind working with personally identifiable information to illustrate the importance of protecting privacy. We then offer a taxonomy of threats, vulnerabilities, and impacts and describe how these determine risk. Based on this taxonomy, we develop a framework to assess risk on the Real Data Corpus, a collection of forensic disk images containing personally identifiable information. In addition, we analyzed-identification methods such as pseudonymization and anonymization, and consider re-identification risks. Finally, we apply our framework and methodology to a real-world scenario to determine the risk of data disclosure to an extramural researcher.
Supply chain management scholar's research impact: moderated mediation analysis

Purpose The purpose of this paper is to draw on social capital theory to develop a model to explain the determinants of a supply chain management scholar’s academic research impact. Design/methodology/approach Drawing from a database of 450 supply chain management scholars in different countries collected from ResearchGate and the World Bank, the bootstrapping method was applied on the moderated mediation analysis. Findings Analysis of the mediating role of a scholar’s social capital suggests that social capital theory has a strong explanatory power on the relationship between a scholar’s research skill and academic impact. To account for the boundary effect at the country-level, the authors further examine if this mechanism differs by country in the supply chain management research context. Research limitations/implications The findings from this study are from a single research area, which limits the generalizability of the study. Although the data are collected from different sources, including ResearchGate and the World Bank, it is cross-sectional in nature. The variables in this model do not have strong causal relationships. Practical implications The results suggest that supply chain management scholars can reap the benefits of their social capital. Specifically, scholars can enhance their academic impact by increasing their social capital. Originality/value The results provide a reference for supply chain management scholars keen on enhancing their academic research impact. It also provides a reference to explain why country-level differences can influence these scholars.
Random noise attenuation using the novel Estimated Noise Pattern Denoising Algorithm

This paper introduces the estimated pattern denoising (EPD) wavelet transform for random noise attenuation in geophysical data. The proposed approach combines the capability of the Gaussian filter and dual-tree rational dilation wavelet transform (DT-RADWT) in random noise detection and suppression; we called this method Estimated Pattern Denoising (EPD). The EPD is an innovative approach in terms of estimation of the location and amplitude of the noise pattern, directly from the data. The employed approach produces a higher quality factor (Q-factor) than the conventional dyadic discrete wavelet transform (DWT) and separates the noise from the signal with higher accuracy. The EPD provides a data-driven scheme that resolves the complexity of the random noise model in noise suppression, using an auxiliary Gaussian filter. This approach does not require prior information about the noise source, statistical distribution, or frequency range. We show successful suppression of random noise using the proposed approach on synthetic and real field data.
Identifying branch-specific positive selection throughout the regulatory genome using an appropriate neutral proxy

Adaptive changes in cis-regulatory elements are an essential component of evolution by natural selection. Identifying adaptive and functional noncoding DNA elements throughout the genome is therefore crucial for understanding the relationship between phenotype and genotype. Here, we introduce a method we called adaptyPhy, which adds significant improvements to our earlier method that tests for branch-specific directional selection in noncoding sequences. The motivation for these improvements is to provide a more sensitive and better targeted characterization of directional selection and neutral evolution across the genome. We use ENCODE annotations to identify appropriate proxy neutral sequences and demonstrate that the conservativeness of the test can be modulated during the filtration of reference alignments. We apply the method to noncoding Human Accelerated Elements as well as open chromatin elements previously identified in 125 human tissues and cell lines to demonstrate its utility. We also simulate sequence alignments under different classes of evolution in order to validate the ability of adaptiPhy to distinguish positive selection from relaxation of constraint and neutral evolution. Finally, we evaluate the impact of query region length, proxy neutral sequence length, and branch count on test sensitivity.
UNC-10/SYD-2 complex is sufficient to link kinesin-3 UNC-104 to RAB-3 containing synaptic vesicles in the absence of the motor’s PH domain

KIF1A (UNC-104 in C. elegans) is the major fast axonal transporter of STVs (synaptic vesicle protein transport vesicles) containing synaptic precursors such as RAB-3 or synaptobrevin-1 (SNB-1). Heritable mutations in neuronal motor proteins (and their adaptors) lead to numerous neurodegenerative diseases. The C-terminal PH (pleckstrin homolog) domain of UNC-104 directly binds to phosphatidylinositol 4,5-bisphosphate that form the lipid bilayers of STVs. Based on literature evidences, we hypothesize that RAB-3-bound STVs may employ a dual linker UNC-10/SYD-2 to connect to UNC-104. This RAB-3/UNC-10/SYD-2 linker may act as an additional reinforcement for the (supposed) weak motor-lipid interaction. Results from RT-PCR and Western blot experiments favor a genetic relation between SYD-2, UNC-10 and RAB-3, as well as co-immunoprecipitation assays revealed changes in binding affinities between SYD-2 and UNC-104 depending on the presence or absence of UNC-10 or RAB-3. Such changes in binding properties between SYD-2 and UNC-104 (depending on unc-10 and rab-3) can be also seen in colocalization and BiFC (bimolecular fluorescence complementation) assays. In sublateral neuronal bundles, as well as in single ALM mechanosensory neurons, UNC-104 expression appears to be more diffused and is restricted to short travel distances (with visibly reduced speeds) in unc-10 and rab-3 mutants. Similar results were revealed when observing RAB-3-containing vesicles but not synaptobrevin-1 (SNB-1)-containing vesicles. Moreover, deletion of UNC-104’s PH domain did not affect UNC-104/RAB-3 colocalization while it did affect UNC-104/SNB-1 colocalization. These findings solidly support the model a dual UNC-10/SYD-2 linker acting as a sufficient buttress to connect the motor to RAB-3-containing vesicles.
Bootstrapped OCR error detection for a less-resourced language variant

This study focuses on isolated error detection in a retro-digitized newspaper corpus published from 1946 to 1990 in the former German Democratic Republic. As there are OCR errors throughout the corpus but no clean reference for this variant of German, automatic OCR correction implies to overcome data sparseness and non-standard spelling, including compounds and inflected forms. The contributions of this paper are (1) a method to bootstrap detection of potential misspellings, (2) an assessment of several types of training data, and (3) an evaluation of several off-the-shelf candidate selection techniques. The chosen solution based on statistical affix analysis reaches an accuracy 10 points higher than existing morphological analysis systems on error detection, while a combination of fuzzy and approximate string search performs best for error correction. The criteria are met since it is possible to correct erroneous tokens without introducing too much noise.
Morphological and Mechanical Properties of the Quadriceps Femoris Muscle-Tendon Unit From Adolescence to Adulthood: Effects of Age and Athletic Training

The combined effects of mechanical loading and maturation during adolescence are still not well understood. The purpose of the study was to investigate the development of the quadriceps femoris muscle-tendon unit from early adolescence (EA), late adolescence (LA) to young adulthood (YA), and examine how it is influenced by athletic training in a cross-sectional design. Forty-one male athletes and forty male non-athletes from three different age groups (EA: 12–14 years, n = 29; LA: 16–18 years, n = 27; and YA: 20–35 years, n = 25) participated in the present study. Maximum strength of the knee extensor muscles, architecture of the vastus lateralis (VL) muscle and patellar tendon stiffness were examined using dynamometry, motion capture, electromyography, and ultrasonography. Muscle strength and tendon stiffness significantly increased (p < 0.001) from EA to LA without any further alterations (p > 0.05) from LA to YA. Athletes compared to non-athletes showed significantly greater (p < 0.001) absolute muscle strength (EA: 3.52 ± 0.75 vs. 3.20 ± 0.42 Nm/kg; LA: 4.47 ± 0.61 vs. 3.83 ± 0.56 Nm/kg; and YA: 4.61 ± 0.55 vs. 3.60 ± 0.53), tendon stiffness (EA: 990 ± 317 vs. 814 ± 299 N/mm; LA: 1266 ± 275 vs. 1110 ± 255 N/mm; and YA: 1487 ± 354 vs. 1257 ± 328), and VL thickness (EA: 19.7 ± 3.2 vs. 16.2 ± 3.4 mm; LA: 23.0 ± 4.2 vs. 20.1 ± 3.3 mm; and YA: 25.5 ± 4.2 vs. 23.9 ± 3.9 mm). Athletes were more likely to reach strain magnitudes higher than 9% strain compared to non-athlete controls (EA: 28 vs. 15%; LA: 46 vs. 16%; and YA: 66 vs. 33%) indicating an increased mechanical demand for the tendon. Although the properties of the quadriceps femoris muscle-tendon unit are enhanced by athletic training, their development from early-adolescence to adulthood remain similar in athletes and non-athletes with the major alterations between early and LA. However, both age and athletic training was associated with a higher prevalence of imbalances within the muscle-tendon unit and a resultant increased mechanical demand for the patellar tendon.
The value of STEAP1, C-myc and P63 Immuno-expression in differentiation of prostatic carcinoma from its mimickers

Submit Date: 10-07-2019 Revise Date: 13-07-2019 Accept Date: 20-07-2019 ABSTRACT Background: Prostatic adenocarcinoma is the 2 nd most common cancer in males. It is important to differentiate between prostatic adenocarcinoma and its benign mimickers with novel and reliable immunohistochemical markers for early diagnosis of prostatic adenocarcinoma, (6-transmembrane epithelial antigen of prostate (STEAP1), C-myc and basal cell marker P63 can be helpful in distinguishing prostatic adenocarcinoma from benign lesions. The aim of this study is to diagnose prostatic adenocarcinoma and differentiate it from its benign mimickers using STEAP1, C-myc and P63 immunoexpression and toevaluate the role of STEAP1 overexpression in prostate cancer initiation and progression. Methods: Retrospective cross-sectional study was conducted on 20 cases of prostatic adenocarcinoma, 8 cases of high grade prostatic intraepithelial neoplasia (HGPIN) and 18 cases of benign prostatic mimickers. All lesions were submitted for STEAP1, C-myc and P63 immunohistochemistry and the results were correlated with clinicopathological and histopathological parameters. Results: P63, STEAP1 and C-myc showed highly significant difference in expression in prostatic adenocarcinoma in relation to its benign mimickers (p-value<0.001). STEAP1 immunoexpression was significantly associated with Gleason score, grade grouping and perineural invasion of prostatic adenocarcinoma (p-value <0.05). Positive STEAP1 and Cmyc expression along with negative P63 showed high sensitivity (80.0%, 85.0% and 95.0%) respectively and considerable specificity (86.9%, 73.1% and 96.2%) respectively for differentiating between prostatic adenocarcinoma and its benign mimickers. Conclusion: STEAP1, C-myc and P63 immunoexpression was helpful in differentiation between prostatic adenocarcinoma and benign mimickers. STEAP1 may have a valuable prognostic role in prostatic adenocarcinoma.