Miracle-dz/UniFAR-FTUs huggingface dataset:
Community structure and diversity of the microbiomes of two microhabitats at the root-soil interface: implications of meta-analysis of the root-zone soil and root endosphere microbial communities in Xiong'an New Area.

The diversity of the microbial compositions of the root-zone soil (the rhizosphere-surrounding soil) and root endosphere (all inner root tissues) of the two plant genera Pinus tabulaeformis Carr. and Ginkgo biloba L. were evaluated in Xiong'an New Area using high-throughput sequencing, as well as the influence of the soil edaphic parameters on microbial community compositions. Our results showed that both the taxonomic and phylogenetic diversity of the root endosphere were lower than those of the root-zone soil, but the variation in the endosphere microbial community structure was remarkably higher than that of the root-zone soil. Spearman correlation analysis showed that the soil organic matter (SOM), total nitrogen (TN), total phosphate (TP), total potassium (TK), ratio of carbon to nitrogen (C/N) and pH significantly explained the alpha diversity of the bacterial community and that TN differentially contributed to the alpha diversity of the fungal community. Variation partitioning analysis (VPA) showed that the effect of plant species on microbial composition variations was higher than the influence of any other soil properties, although soil chemical parameters explained more variation when integrated. Together, our results suggest that both plant species and soil chemical parameters played a critical role in shaping the microbial community composition.
To walk or to run – a question of movement attractor stability

ABSTRACT During locomotion, humans change gait mode between walking and running as locomotion speed is either increased or decreased. Dynamical systems theory predicts that the self-organization of coordinated motor behaviors dictates the transition from one distinct stable attractor behavior to another distinct attractor behavior (e.g. walk to run or vice versa) as the speed is changed. To evaluate this prediction, the present study investigated the attractor stability of walking and running across a range of speeds evoking both self-selected gait mode and non-self-selected gait mode. Eleven subjects completed treadmill walking for 3 min at 0.89, 1.12, 1.34, 1.56, 1.79, 2.01, 2.24 and 2.46 m s−1 and running for 3 min at 1.79, 2.01, 2.24, 2.46, 2.68, 2.91, 3.13 and 3.35 m s−1 in randomized order while lower limb joint angles and sacrum displacements was recorded. Attractor stability was quantified by continuous relative phase and deviation phase of lower limb segment angles, and the largest Lyapunov exponent, correlation dimension and movement variability of the sacrum marker displacement and the hip, knee and ankle joint angles. Lower limb attractor stability during walking was maximized at speeds close to the self-selected preferred walking speed and increased during running as speed was increased. Furthermore, lower limb attractor stability was highest at a particular gait mode closest to the corresponding preferred speed, in support of the prediction of dynamical systems theory. This was not the case for the sacrum displacement attractor, suggesting that lower limb attractor behavior provides a more appropriate order parameter compared with sacrum displacement. Summary: In accordance with the dynamical systems theory, lower limb attractor stability is highest at a particular gait mode closest to the corresponding preferred speed.
Keep calm and hang on: EMG activation in the forelimb musculature of three-toed sloths (Bradypus variegatus)

ABSTRACT Sloths exhibit below branch locomotion whereby their limbs are loaded in tension to support the body weight. Suspensory behaviors require both strength and fatigue resistance from the limb flexors; however, skeletal muscle mass of sloths is reduced compared with other arboreal mammals. Although suspensory locomotion demands that muscles are active to counteract the pull of gravity, it is possible that sloths minimize muscle activation and/or selectively recruit slow motor units to maintain support, thus indicating neuromuscular specializations to conserve energy. Electromyography (EMG) was evaluated in a sample of three-toed sloths (Bradypus variegatus; N=6) to test this hypothesis. EMG was recorded at 2000 Hz via fine-wire electrodes implanted into two suites of four muscles in the left forelimb while sloths performed suspensory hanging (SH), suspensory walking (SW) and vertical climbing (VC). All muscles were minimally active for SH. During SW and VC, sloths moved slowly (duty factor: 0.83) and activation patterns were consistent between behaviors; the flexors were activated early and for a large percentage of limb contact, whereas the extensors were activated for shorter burst durations on average and showed biphasic (contact and swing) activity. Muscle activities were maximal for the elbow flexors and lowest for the carpal/digital flexors, and overall activity was significantly greater for SW and VC compared with SH. Wavelet analysis indicated high mean EMG frequencies from the myoelectric intensity spectra coupled with low burst intensities for SH, although the opposite pattern occurred for SW and VC, with the shoulder flexors and elbow flexor, m. brachioradialis, having extremely low mean EMG frequencies that are consistent with recruitment of slow fibers. Collectively, these findings support the hypothesis and suggest that sloths may selectively recruit smaller, fast motor units for suspensory postures but have the ability to offset the cost of force production by recruitment of large, slow motor units during locomotion. Summary: Three-toed sloths minimize activation of their limb muscles while hanging and appear to offset the cost of force production when walking and climbing by preferentially recruiting large, slow-contracting muscle fibers.
Pain interference and catastrophizing are not associated with polysubstance use among treatment-seeking patients with substance use disorders and chronic pain

ABSTRACT Background: People with substance use disorders (SUD) and co-occurring chronic pain report the use of myriad substances, which is concerning due to the heightened risk of overdose associated with polysubstance use. Identifying malleable factors associated with polysubstance use in this population can inform interventions. In this study, we examined whether two pain processes – pain interference and pain catastrophizing – were associated with polysubstance use. Objectives: We examined the cross-sectional associations among self-reported pain interference and catastrophizing and polysubstance use. We also determined if sex and primary SUD moderated these associations. Methods: Participants were 236 (36% female) adults receiving inpatient treatment for SUD (58% alcohol use disorder, 42% opioid use disorder) who met criteria for chronic pain. We utilized negative binomial regression to examine associations between pain interference and catastrophizing (focal independent variables) and the number of substances used in the month before treatment (i.e., polysubstance use; outcome). Results: Participants used three substances, on average, in the month prior to treatment. Neither pain interference (IRR = 1.05, p = .06) nor pain catastrophizing (IRR = 1.00, p = .37) were associated with polysubstance use. The association between pain interference and polysubstance use was moderated by sex and primary SUD (ps<0.01), such that these variables were positively related in men and those with alcohol use disorder. Conclusion: Pain interference and catastrophizing were not uniformly associated with polysubstance use, underscoring the need to examine other factors associated with polysubstance use in this population. However, men and those with alcohol use disorder might benefit from interventions targeting pain interference to reduce polysubstance use.
Extinction Thresholds in Demographic Models of Territorial Populations

A basic demographic model is constructed for territorial species in a region where patches of habitat suitable for survival and reproduction are randomly (or evenly) interspersed with patches of unsuitable habitat. The model predicts the equilibrium occupancy of suitable habitat as a function of the proportion of the region composed of suitable habitat, h, and of the demographic potential of the population, k, which is determined by parameters of the life history and dispersal behavior of individuals. If 0 < k < 1, the demographic potential gives the equilibrium occupancy in a completely suitable region, and the population will become extinct in the region if h $\leq$ 1 - k. Difficulty in finding a mate, the finite extent of the region containing suitable habitat, and serially uncorrelated fluctuations in life history parameters all increase the minimum value of h necessary to sustain a population. Models of this type should be useful for predicting the effects of habitat destruction and fragmentation, or habitat improvement, on the population sizes of rare or endangered species with territorial behavior.
High strength polyvinyl alcohol/polyacrylic acid (PVA/PAA) hydrogel fabricated by Cold-Drawn method for cartilage tissue substitutes

Abstract Poly (vinyl alcohol) (PVA) hydrogel has been considered as promising cartilage replacement materials due to its excellent characteristics such as high water content, low frictional behavior and excellent biocompatibility. However, lack of sufficient mechanical properties and cytocompatibility are two key obstacles for PVA hydrogel to be applied as cartilage substitutes. Herein, Polyacrylic acid (PAA) has been introduced into PVA hydrogel to balance these problems. Compared with pure PVA hydrogel, PVA/PAA hydrogel has the equal excellent biocompatibility, and its cell adhesion is significantly improved. In order to further improve the mechanical properties of hydrogels, Cold-Drawn treatment of hydrogels is performed in this paper. Compared to pure 12% PVA hydrogel, 40.8‐fold, 50.8‐fold, and 46.8‐fold increase in tensile strength, tensile modulus, and toughness, respectively, which can be obtained from 12% PVA/PAA Cold-Drawn hydrogel. These biocompatible composite hydrogels have a great application potential as cartilage tissue substitutes.
The Reuniens and Rhomboid Nuclei Are Required for Acquisition of Pavlovian Trace Fear Conditioning in Rats

Abstract The reuniens (Re) and rhomboid (Rh) nuclei (ReRh) of the midline thalamus interconnects the hippocampus (HPC) and the medial prefrontal cortex (mPFC). Several studies have suggested that the ReRh participates in various cognitive tasks. However, little is known about the contribution of the ReRh in Pavlovian trace fear conditioning, a procedure with a temporal gap between the conditioned stimulus (CS) and the unconditioned stimulus (US), and therefore making it harder for the animals to acquire. Because the HPC and mPFC are involved in trace, but not delay, fear conditioning and given the role of the ReRh in mediating this neurocircuitry, we hypothesized that ReRh inactivation leads to a learning deficit only in trace conditioning. In a series of experiments, we first examined the c-Fos expression in male Long–Evans rats and established that the ReRh was recruited in the encoding, but not the retrieval phase, of fear memory. Next, we performed behavioral pharmacology experiments and found that ReRh inactivation impaired only the acquisition, but not the consolidation or retrieval, of trace fear. However, although the ReRh was recruited during the encoding of delay fear demonstrated by c-Fos results, ReRh inactivation in any phases did not interfere with delay conditioning. Finally, we found that trace fear acquired under ReRh inactivation reprised when the ReRh was brought off-line during retrieval. Together, our data revealed the essential role of the ReRh in a learning task with temporally discontinuous stimuli.
Growth rates in the articulated coralline Calliarthron (Rhodophyta)

Specimens of the articulated coralline alga Calliarthron tuberculosum growing on an underwater reef off the coast of central California were photographed over a period of 2 years, during which time the mean increase in branch length was 1.7 mm per month. A tier of medullary cells 50–75 μ high is formed about once a day and flexible genicula develop every 1.5–2.7 months. Mean growth rates are 1.3 mm per month in summer (April–Sept.) and 2.3 mm per month in winter (Oct–March). On glass and plexiglass settling surfaces placed among the algae, basal crusts under 1 mm in diameter were visible in less than 1 month, fronds were evident after 2 months, and the fronds bore conceptacles after 11 months. Measurements of photographed and collected specimens reveal that the plants mostly branch during two different times of the year, from March to June and again from September to December.
Deep Learning als Virtual-High-Throughput-Screening-Methode unter Verwendung von gerasterten Molekülstrukturen

Virtual high-throughput screening is the use of machine learning classification methods to estimate the probability of molecules to show a desired biological activity. The goal in most cases is to preselect the molecules that have the highest probability and thereby reduce the amount of molecules that have to be tested in the lab. In the past few years, deep learning has become one of the most successful methods to classify data in the area of image recognition. This is usually done with the use of convolutional neural networks that first generate abstract features based on the raw pixel input. These features are then used to classify the data. The goal of this thesis is to adapt these methods so that they can be used for virtual high-throughput screening. This is done by converting the structure of a molecule into a grid-based format that is similar to an image. The layout of the atoms in this grid is based on the 2D-rendering of the structure. The element symbol and the chemical properties of an atom are utilized as its features. The used network architecture consists of convolutional layers that generate abstract features and dense layers that use these features to classify the molecule. By splitting the network into these two tasks, it is also possible to only use the convolutional part of the network to generate features which are then used in combination with different methods. Another goal of this thesis is to interpret what the network actually learned from the data. For this saliency maps are used to compute which areas of the input data had the biggest influence on the resulting class. This computed influence can then be used to visualize the substructures that, according to the network, are responsible for the molecules activity. These substructures can then also automatically be extracted by using a threshold-based method. These can also be sorted by relevance, by assigning a score to each substructure. The software architecture that has been implemented in the course of this thesis is also introduced. It enables efficient use of parallel resources by preprocessing new data using all processor cores while the previous data is used for training in the graphics card. The architecture also saves intermediate results which make it easy to resume experiments that have been halted or did crash. The experimental part of the thesis searches for good hyperparameters for the presented method. It also compares the method with other virtual high-throughput screening methods. In this comparison the presented method ends up with results similar to those
PHASE EQUILIBRIA AND KINETICS OF ORTHOPHOSPHATE IN SOME IRAQI SOILS

We collected soil samples from four different agricultural projects. Potassium orthophosphate was added to the samples at rates of 0, 25, 100, 200, 400, 800, and 1600 ppm P. The samples were incubated for 0.5, 24, 168, 1000, and 3000 h at constant temperature and moisture. Ec, pH, and concentrations of water-soluble orthophosphate, calcium, and magnesium were determined in the soil water extracts after the incubation. The results showed that a sharp decrease occurred in the concentration of water-soluble P, within 0.5 h after P addition. Using calcium phosphate equilibria phases indicated that β-tricalcium phosphate was the dominant form after 3000 h of addition. Precipitated forms were dicalcium phosphate dihydrate, octacalcium phosphate and β-tricalcium phosphate. Using Mg-phosphate equilibria phases revealed that bobiernite was the dominant form after a short time and a high level of P addition. Calcium phosphate controlled the solubility of phosphate more than Mg-phosphate.
Trajectory Visibility

We study the problem of testing whether there exists a time at which two entities moving along diﬀerent piece-wise linear trajectories among polygonal obstacles are mutually visible. We study several variants, depending on whether or not the obstacles form a simple polygon, trajectories may intersect the polygon edges, and both or only one of the entities are moving. For constant complexity trajectories contained in a simple polygon with n vertices, we provide an O ( n ) time algorithm to test if there is a time at which the entities can see each other. If the polygon contains holes, we present an O ( n log n ) algorithm. We show that this is tight. We then consider storing the obstacles in a data structure, such that queries consisting of two line segments can be eﬃciently answered. We show that for all variants it is possible to answer queries in sublinear time using polynomial space and preprocessing time. As a critical intermediate step, we provide an eﬃcient solution to a problem of independent interest: preprocess a convex polygon such that we can eﬃciently test intersection with a quadratic curve segment. If the obstacles form a simple polygon, this allows us to answer visibility queries in O ( n 34 log 3 n ) time using O ( n log 5 n ) space. For more general obstacles the query time is O (log k n ), for a constant but large value k , using O ( n 3 k ) space. We provide more eﬃcient solutions when one of the entities remains stationary.
Avaliações químicas e bioquímicas dos grãos, extratos e tofus de soja comum e de soja livre de Lipoxigenase

Com este trabalho, objetivou-se avaliar a composicao quimica e aspectos bioquimicos de soja comum, comum branqueada e livre de lipoxigenases e o efeito do processamento dos seus respectivos extratos de soja e tofus. A composicao centesimal das cultivares de soja comum e livre de lipoxigenase nao se diferenciaram (p>0,05). Alteracoes na composicao centesimal e de minerais dos extratos de soja e dos tofus foram atribuidas ao tratamento termico (98 oC/5 minutos) a que foi submetido o grao de soja comum e a etapa de maceracao dos graos, ficando evidente que algumas substâncias hidrossoluveis, foram migradas para a agua de maceracao dos graos; o branqueamento na soja comum no inicio do processamento reduziu o teor de alguns minerais do extrato de soja (leite de soja), bem como no tofu. Ficou evidente as perdas de isoflavonas com o processamento na obtencao do tofu, na ordem de 38% no de SC, 31% no de SCB e 56% no de SLL. O processamento termico utilizado para obtencao dos tofus foi suficiente para eliminar a atividade dos inibidores de tripsina em 79% do tofu de soja comum, 81% no tofu de soja branqueada e 82% nos tofus de soja livre de lipoxigenase.
A colorimetric chemosensor for the sequential detection of copper ion and amino acids (cysteine and histidine) in aqueous solution

A simple and selective colorimetric chemosensor 1 was reported for the sequential detection of Cu2+, cysteine (Cys) and histidine (His) in aqueous solution. The presence of Cu2+ led to a distinct naked-eye color change from pale yellow to orange. Also, the receptor enabled analysis of Cu2+ ions with a sensitivity limit of 0.37 μM, which is far below the WHO acceptable limit (31.5 μM) in drinking water. 1 could be also used as a practical, visible colorimetric test strip for Cu2+ (down to 10 μM) in aqueous media. Moreover, the resulting 1–Cu2+ complex sensed cysteine and histidine with an absorption change via UV-visible or a naked-eye color change, although His and Cys were indistinguishable with the method proposed herein.
Resolving the adsorption of molecular O2 on the rutile TiO2(110) surface by noncontact atomic force microscopy

Significance Molecular O2 on semiconducting metal oxides, its adsorption, response to thermal treatment, UV irradiation, and electron/hole injection is at the heart of a wide range of technologies. These processes were studied molecule by molecule on the prototypical model oxide TiO2(110), using noncontact AFM. We show that the nonintrusive nature of the nc-AFM and its exceptional spatial resolution due to the functionalization of the tip with a terminal O atom allow identifying oxygen adsorption geometries which were not previously determined by other techniques. In combination with density functional theory calculations, we explain the charge states of the various adsorbed oxygen species, their dynamics upon annealing and UV irradiation, and the role of electron exchange with the TiO2 substrate. Interaction of molecular oxygen with semiconducting oxide surfaces plays a key role in many technologies. The topic is difficult to approach both by experiment and in theory, mainly due to multiple stable charge states, adsorption configurations, and reaction channels of adsorbed oxygen species. Here we use a combination of noncontact atomic force microscopy (AFM) and density functional theory (DFT) to resolve O2 adsorption on the rutile TiO2(110) surface, which presents a longstanding challenge in the surface chemistry of metal oxides. We show that chemically inert AFM tips terminated by an oxygen adatom provide excellent resolution of both the adsorbed species and the oxygen sublattice of the substrate. Adsorbed O2 molecules can accept either one or two electron polarons from the surface, forming superoxo or peroxo species. The peroxo state is energetically preferred under any conditions relevant for applications. The possibility of nonintrusive imaging allows us to explain behavior related to electron/hole injection from the tip, interaction with UV light, and the effect of thermal annealing.
Total phenolics, flavonoids, tannins and antioxidant activity of lima beans conserved in a Brazilian Genebank

The objective of this study was to characterize for the first time polyphenols and DPPH (2-diphenyl-1-picryhydrazyl radical) antioxidant activity in commonly cultivated accessions of Phaseolus lunatus from an ex situ germplasm collection maintained by Embrapa, in Brazil. Furthermore, the study aimed to detect changes in total polyphenols, total flavonoids and condensed tannin for the same accessions after regeneration in a greenhouse. The results showed the diversity of the lima bean collection for phenolic compounds, which were strongly correlated with antioxidant activity. Lima beans accessions with the highest polyphenols and antioxidant activity were those with colored seeds. Conservation through cold storage of P. lunatus seeds in a cold chamber in the germplasm collection did not necessarily affect phenolic compounds. Variations observed in values after regeneration seeds may be mainly results of biotic and abiotic factors, including not only cultivar, but also environmental conditions. This study suggests that polyphenols in the lima beans present antioxidant activity, with possible beneficial effects for human health. It was expected that the potential of this tasty legume can be also used as a functional food crop and/or as a new ingredient in gastronomy.