Miracle-dz/UniFAR-FTUs huggingface dataset:
The Passive Contact Stability of Blue Sheep Hoof Based on Structure, Mechanical Properties, and Surface Morphology

As the only component that contacts the ground and rock, the hooves of blue sheep may play a crucial role in their excellent climbing abilities. In this study, we used a combination of techniques, including scanning electron microscopy, infrared spectroscopy and nanoindentation, to characterize the surface morphology, structure, material composition, and mechanical properties of blue sheep hoof and investigate the potential contributions of these properties to the establishment of passive contact stability. Straight and curled microscopic lamellar morphology were found on the hoof surfaces. The cross section of the hoof revealed four layers, and each layer had a unique structure. Finite element analysis was employed to verify that the surface morphology and microstructure effectively contributed to the slip resistance and impact cushioning, respectively. Analyses of the energy and infrared spectra showed that the organic and inorganic substances in different regions of the hoof had similar components but different contents of those components. The hoof was mainly composed of keratin. From the outside to the inside, gradients in both the modulus and hardness were observed. These factors help the hoof alleviate high impact strengths and increase contact stability. These findings further our understanding of the unique mechanism of blue sheep hoof and may help in the development of novel biomimetic materials and mechanical components with enhanced friction and contact stability properties.
Elucidating the Regulon of a Fur-like Protein in Mycobacterium avium subsp. paratuberculosis (MAP)

Intracellular iron concentration is tightly regulated to maintain cell viability. Iron plays important roles in electron transport, nucleic acid synthesis, and oxidative stress. A Mycobacterium avium subsp. paratuberculosis (MAP)-specific genomic island carries a putative metal transport operon that includes MAP3773c, which encodes a Fur-like protein. Although well characterized as a global regulator of iron homeostasis in multiple bacteria, the function of Fur (ferric uptake regulator) in MAP is unknown as this organism also carries IdeR (iron dependent regulator), a native iron regulatory protein specific to mycobacteria. Computational analysis using PRODORIC identified 23 different pathways involved in respiration, metabolism, and virulence that were likely regulated by MAP3773c. Thus, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) was performed to confirm the putative regulon of MAP3773c (Fur-like protein) in MAP. ChIP-Seq revealed enriched binding to 58 regions by Fur under iron-replete and -deplete conditions, located mostly within open reading frames (ORFs). Three ChIP peaks were identified in genes that are directly related to iron regulation: MAP3638c (hemophore-like protein), MAP3736c (Fur box), and MAP3776c (ABC transporter). Fur box consensus sequence was identified, and binding specificity and dependence on Mn2+ availability was confirmed by a chemiluminescent electrophoresis mobility shift assay (EMSA). The results confirmed that MAP3773c is a Fur ortholog that recognizes a 19 bp DNA sequence motif (Fur box) and it is involved in metal homeostasis. This work provides a regulatory network of MAP Fur binding sites during iron-replete and -deplete conditions, highlighting unique properties of Fur regulon in MAP.
Clinical Significance of an m6A Reader Gene, IGF2BP2, in Head and Neck Squamous Cell Carcinoma

The importance of N6-methyladenosine (m6A) in tumor recurrence and prognosis has been recognized in recent years. The role of m6A readers, such as insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2), in regulating head and neck squamous cell carcinoma (HNSCC) remains unclear. We, therefore, assessed the prognostic role of IGF2BP2 in HNSCC using openly available data from The Cancer Genome Atlas (TCGA) in conjunction with HNSCC patient sample immunohistochemistry (n = 36). The correlation between IGF2BP2 expression and clinical characteristics was then examined. The role of IGF2BP2 in prognosis was assessed by Kaplan–Meier curves and Cox analysis. Finally, TCGA data was used to explore possible carcinogenic mechanisms with multi-GSEA (gene set enrichment analysis). Analysis of TCGA data and IHC results revealed that IGF2BP2 was upregulated in HNSCC tumor tissues, and the expression level was related to the T stage. Simultaneously, Kaplan–Meier curves and Cox analysis indicated that highly expressed IGF2BP2 correlated with poor prognosis and that IGF2BP2 was a potential prognostic factor for HNSCC. Gene set enrichment analysis revealed that scavenging and degradation, synthesis and metabolism, cell growth, death and motility, and cancer pathways were differentially enriched in patients with high IGF2BP2 expression. Our results demonstrate that IGF2BP2 plays an important role in tumor progression and may serve as an important biological prognostic factor for HNSCC.
CORES

The relatively high cost of record deserialization is increasingly becoming the bottleneck of column-based storage systems in tree-structured applications [58]. Due to record transformation in the storage layer, unnecessary processing costs derived from fields and rows irrelevant to queries may be very heavy in nested schemas, significantly wasting the computational resources in large-scale analytical workloads. This leads to the question of how to reduce both the deserialization and IO costs of queries with highly selective filters following arbitrary paths in a nested schema. We present CORES (Column-Oriented Regeneration Embedding Scheme) to push highly selective filters down into column-based storage engines, where each filter consists of several filtering conditions on a field. By applying highly selective filters in the storage layer, we demonstrate that both the deserialization and IO costs could be significantly reduced. We show how to introduce fine-grained composition on filtering results. We generalize this technique by two pair-wise operations, rollup and drilldown, such that a series of conjunctive filters can effectively deliver their payloads in nested schema. The proposed methods are implemented on an open-source platform. For practical purposes, we highlight how to build a column storage engine and how to drive a query efficiently based on a cost model. We apply this design to the nested relational model especially when hierarchical entities are frequently required by ad hoc queries. The experiments, including a real workload and the modified TPCH benchmark, demonstrate that CORES improves the performance by 0.7×--26.9× compared to state-of-the-art platforms in scan-intensive workloads.
Distribution and Suitable Habitat of the Cold-Water Corals Lophelia pertusa, Paragorgia arborea, and Primnoa resedaeformis on the Norwegian Continental Shelf

Cold-water corals are habitat-forming species that are also classified as indicators of vulnerable marine ecosystems (VMEs) due to the threat of various anthropogenic impacts, e.g., fisheries and oil/mineral exploration. To best protect VMEs, knowledge of their habitat requirements and distribution is essential. However, comprehensive sampling of the deep sea is difficult due to access and cost constraints, so species distribution modeling (SDM) is often used to predict overall distributions and ecological preferences of species based on limited data. We used Maximum Entropy (Maxent) modeling to predict the probability of presence of the reef-building scleractinian Lophelia pertusa and the octocorals Paragorgia arborea and Primnoa resedaeformis using a total of 2149 coral presence points and 15 environmental predictor variables. The environmental variables used in the analysis were processed to 176 m resolution and included bathymetry, depth, geomorphometric characteristics [slope, aspect, and bathymetric position index (BPI)], oceanography (temperature, salinity, current directions, and speed), surface chlorophyll a concentration, sediment type, and marine landscape type. Comparing presence points with environmental data showed that the temperature and depth range for Lophelia was narrower compared to the gorgonians, and it occurred in shallower, warmer water. Observations showed that Lophelia had a broad, bimodal response to Broad BPI, while the predicted model indicated a more narrow response. Paragorgia tolerated the greatest range of sloping according to the model. All three species were observed with a bimodal pattern along a wide range of mean current speed, while the models indicated a high response to faster current speed. Jackknife tests showed that sediment type was an important predictor for gorgonian corals, while BPI and minimum temperature were more important for Lophelia. The spatial precision of the models could be further increased by applying environmental layers with a higher and uniform spatial resolution. The predicted distribution of corals and their relation to environmental variables provides an important background for prioritizing areas for detailed mapping surveys and will aid in the conservation efforts for these VMEs in Norwegian waters and beyond.
Double-Step Paradigm in Microgravity: Preservation of Sensorimotor Flexibility in Altered Gravitational Force Field

The way we can correct our ongoing movements to sudden and unforeseen perturbations is key to our ability to rapidly adjust our behavior to novel environmental demands. Referred to as sensorimotor flexibility, this ability can be assessed by the double-step paradigm in which participants must correct their ongoing arm movements to reach targets that unexpectedly change location (i.e., target jump). While this type of corrections has been demonstrated in normogravity in the extent of reasonable spatiotemporal constraints underpinning the target jumps, less is known about sensorimotor flexibility in altered gravitational force fields. We thus aimed to assess sensorimotor flexibility by comparing online arm pointing corrections observed during microgravity episodes of parabolic flights with normogravity standards. Seven participants were asked to point as fast and as accurately as possible toward one of two visual targets with their right index finger. The targets were aligned vertically in the mid-sagittal plane and were separated by 10 cm. In 20% of the trials, the initially illuminated lower target was switched off at movement onset while the upper target was concomitantly switched on prompting participants to change the trajectory of their ongoing movements. Results showed that, both in normogravity and microgravity, participants successfully performed the pointing task including when the target jumped unexpectedly (i.e., comparable success rate). Most importantly, no significant difference was found in target jump trials regarding arm kinematics between both gravitational environments, neither in terms of peak velocity, relative deceleration duration, peak acceleration or time to peak acceleration. Using inverse dynamics based on experimental and anthropometrical data, we demonstrated that the shoulder torques for accelerating and decelerating the vertical arm movements substantially differed between microgravity and normogravity. Our data therefore highlight the capacity of the central nervous system to perform very fast neuromuscular adjustments that are adapted to the gravitational constraints. We discuss our findings by considering the contribution of feedforward and feedback mechanisms in the online control of arm pointing movements.
An Optimization-Based Locomotion Controller for Quadruped Robots Leveraging Cartesian Impedance Control

Quadruped robots require compliance to handle unexpected external forces, such as impulsive contact forces from rough terrain, or from physical human-robot interaction. This paper presents a locomotion controller using Cartesian impedance control to coordinate tracking performance and desired compliance, along with Quadratic Programming (QP) to satisfy friction cone constraints, unilateral constraints, and torque limits. First, we resort to projected inverse-dynamics to derive an analytical control law of Cartesian impedance control for constrained and underactuated systems (typically a quadruped robot). Second, we formulate a QP to compute the optimal torques that are as close as possible to the desired values resulting from Cartesian impedance control while satisfying all of the physical constraints. When the desired motion torques lead to violation of physical constraints, the QP will result in a trade-off solution that sacrifices motion performance to ensure physical constraints. The proposed algorithm gives us more insight into the system that benefits from an analytical derivation and more efficient computation compared to hierarchical QP (HQP) controllers that typically require a solution of three QPs or more. Experiments applied on the ANYmal robot with various challenging terrains show the efficiency and performance of our controller.
Effects of Surgery on Survival of Early-Stage Patients With SCLC: Propensity Score Analysis and Nomogram Construction in SEER Database

Purpose: We aimed to assess the survival benefit of surgery for patients with stage IA–IIB small cell lung cancer (SCLC) and construct a nomogram for predicting overall survival (OS). Methods: Patients who had been diagnosed with stage IA–IIB SCLC between 2004 and 2014 and who had received active treatment were selected from the Surveillance, Epidemiology, and End Results database. The primary endpoint was OS. Cox proportional hazards models and propensity score (PS) analyses were used to compare the associations between surgery and OS. The probability of 1- and 3-year OS was predicted using a nomogram. Results: We reviewed 2,246 patients. The median OS of the surgery and non-surgery groups was 35 months and 19 months, respectively. Multivariable Cox proportional hazards models showed a survival benefit in the surgery group (hazards ratio [HR], 0.642; 95% confidence interval [CI], 0.557–0.740; P < 0.001). To balance the between-group measurable confounders, the impact of surgery on OS was assessed using PS matching. After PS matching, OS analysis still favored surgical resection. The PS-stratification, PS-weighting, and PS-adjustment models showed similar results to demonstrate a statistically significant benefit for surgery. Further, the nomogram was well calibrated and had good discriminative ability (Harrell's C-index = 0.645). Conclusion: Our analysis suggests that surgery is a viable option for patients with early-stage SCLC. Our nomogram is a viable tool for quantifying treatment trade-off assumptions and may assist clinicians in decision-making. Future work is needed to validate our results and improve our tools.
Genetic and Comparative Transcriptome Analysis Revealed DEGs Involved in the Purple Leaf Formation in Brassica juncea

Brassica juncea is an important dietary vegetable cultivated and consumed in China for its edible stalks and leaves. The purple leaf mustard, which is rich in anthocyanins, is eye-catching and delivers valuable nutrition. However, the molecular mechanism involved in anthocyanin biosynthesis has not been well studied in B. juncea. Here, histological and transcriptome analyses were used to characterize the purple leaf color and gene expression profiles. Free-hand section analysis showed that the anthocyanin was mainly accumulated in the adaxial epidermal leaf cells. The anthocyanin content in the purple leaves was significantly higher than that in the green leaves. To investigate the critical genes and pathways involved in anthocyanin biosynthesis and accumulation, the transcriptome analysis was used to identify the differentially expressed genes (DEGs) between the purple and green leaves from the backcrossed BC3 segregation population in B. juncea. A total of 2,286 different expressed genes were identified between the purple and green leaves. Among them, 1,593 DEGs were up-regulated and 693 DEGs were down-regulated. There were 213 differently expressed transcription factors among them. The MYB and bHLH transcription factors, which may regulate anthocyanin biosynthesis, were up-regulated in the purple leaves. Interestingly, most of the genes involved in plant–pathogen interaction pathway were also up-regulated in the purple leaves. The late biosynthetic genes involved in anthocyanin biosynthesis were highly up-regulated in the purple leaves of B. juncea. The up regulation of BjTT8 and BjMYC2 and anthocyanin biosynthetic genes (BjC4H, BjDFR, and BjANS) may activate the purple leaf formation in B. juncea. This study may help to understand the transcriptional regulation of anthocyanin biosynthesis in B. juncea.
mRSC

When evaluating the impact of a policy (e.g., gun control) on a metric of interest (e.g., crime-rate), it may not be possible or feasible to conduct a randomized control trial. In such settings where only observational data is available, synthetic control (SC) methods [1-3] provide a popular data-driven approach to estimate a "synthetic" or "virtual" control by combining measurements of "similar" alternatives or units (called "donors"). Recently, robust synthetic control (RSC) [4] was proposed as a generalization of SC to overcome the challenges of missing data and high levels of noise, while removing the reliance on expert domain knowledge for selecting donors. However, both SC and RSC (and its variants) suffer from poor estimation when the pre-intervention period is too short.
Optimized Production of Xylanase by Penicillium purpurogenum and Ultrasound Impact on Enzyme Kinetics for the Production of Monomeric Sugars From Pretreated Corn Cobs

Corn cob is an abundant organic source with significant potential in sustainable energy development. For the effective conversion of the feedstocks to valued commodities, effective biocatalysts are highly desired. The present study aims at optimizing the critical parameters required for xylanase production by Penicillium purpurogenum isolated from rotten wood sample using the Taguchi orthogonal array layout of L25 (5∧6). The optimized conditions like temperature 40°C, pH 3, size of inoculum 1.2 × 108 spores/ml, moisture 70%, peptone 0.8%, and 5 days of incubation resulted in 1,097 ± 6.76 U/gram dry substrate (gds) xylanase which was 65.72% more when compared to un-optimized production of xylanase. The xylanase thus produced, effectively carried out pretreated corn cob saccharification and the reaction was further improved with ultrasound assistance which has increased the saccharification yield to 12.02% along with significant reduction in reaction time. The saccharification efficiency of pretreated corn cob was found to be 80.29% more compared to the raw corn cob, reflecting its recalcitrance to digestion. Indeed, xylan being the second most abundant polymer in lignocellulosic biomass, considerable attention is being paid for its effective conversion to valued products. Graphical Abstract An overview of xylanase production by P. purpurogenum and its application in corn cob saccharification.
Compositional and Quantitative Insights Into Bacterial and Archaeal Communities of South Pacific Deep-Sea Sponges (Demospongiae and Hexactinellida)

In the present study, we profiled bacterial and archaeal communities from 13 phylogenetically diverse deep-sea sponge species (Demospongiae and Hexactinellida) from the South Pacific by 16S rRNA-gene amplicon sequencing. Additionally, the associated bacteria and archaea were quantified by real-time qPCR. Our results show that bacterial communities from the deep-sea sponges are mostly host-species specific similar to what has been observed for shallow-water demosponges. The archaeal deep-sea sponge community structures are different from the bacterial community structures in that they are almost completely dominated by a single family, which are the ammonia-oxidizing genera within the Nitrosopumilaceae. Remarkably, the archaeal communities are mostly specific to individual sponges (rather than sponge-species), and this observation applies to both hexactinellids and demosponges. Finally, archaeal 16s gene numbers, as detected by quantitative real-time PCR, were up to three orders of magnitude higher than in shallow-water sponges, highlighting the importance of the archaea for deep-sea sponges in general.
The impact of psychological support on psychological outcomes and patients’ experiences of the bariatric service 1 and 2 years after bariatric surgery

Background: Although bariatric surgery is widely considered the most effective form of obesity management, some patients receiving surgery describe how their psychological issues remain neglected. This study evaluated the impact of additional psychological support (a Bariatric Rehabilitation Service (BRS)) on patients’ psychological outcomes at 12 months and their experiences of the bariatric service at 24 months. Methods: Patients were randomised to receive either usual care or the BRS and rated a range of psychological outcomes at 12 months. Completed psychological data was obtained from 70 patients (usual care: n=32; BRS: n=38). At 24 months post surgery patients (n=68) gave written feedback regarding the content and timing of their experiences and a sub group (n=16) took part in telephone interviews about their experiences of the bariatric service they had received. Results: By 12 months those who received the BRS reported greater improvement in their psychological outcomes compared to the usual care group in terms of vigour (p=0.02, eta2=0.08), approach coping (p=0.04, eta2=0.06), quality of life (p=0.04, eta2=0.06) and self-reported hunger (p=0.05, eta2=0.05). By 24 months a large majority of those who had received the BRS reported satisfaction with the service’s timing and content. However the majority of all patients, regardless of condition, reported wanting further psychological support up to 24 months post-operatively. A minority, however, stated that as their problems were not emotional the additional support was unnecessary. Conclusion: The BRS resulted in some small improvements in psychological outcomes. Psychological support before and after surgery could be delivered in relation to individual patient need rather than as a blanket provision. Further research is needed to determine both the timing of such support and to identify those who would show most benefit.
Why Does Therapy Work? An Idiographic Approach to Explore Mechanisms of Change Over the Course of Psychotherapy Using Digital Assessments

Background and Objective(s) While psychotherapy treatments are largely effective, the processes and mechanisms underlying such positive changes remain somewhat unknown. Focusing on a single participant from a treatment outcome study that used a modular-based cognitive behavior therapy protocol, this article aims to answer this question by identifying changes in specific symptomatology over the course of the treatment. Using quantitative data derived from digital health methodology, we analyzed whether a given therapeutic intervention was related to downstream effects in predicted symptom domains, to assess the accuracy of our interventions. Methods This case study employed an observational N-of-1 study design. The participant (n = 1) was a female in the age range of 25–35 years. Using digital health data from ambulatory assessment surveys completed prior to and during therapy, separate linear regression analyses were conducted to assess if hypothesized treatment targets reduced after a given module, or intervention. Results Support was found for some of the hypothesized quantitative changes (e.g., decreases in avoidance after exposures module), yet not for others (e.g., decreases in rumination following the mindfulness module). Conclusion We present data and results from our analyses to offer an example of a novel design that may allow for a greater understanding of the nature of symptom changes with increased granularity throughout the course of a psychological treatment from the use of digital health tools.