Miracle-dz/UniFAR-FTUs huggingface dataset:
Laccase Directed Lignification Is One of the Major Processes Associated With the Defense Response Against Pythium ultimum Infection in Apple Roots

Apple replant disease (ARD), incited by a pathogen complex including Pythium ultimum, causes stunted growth or death of newly planted trees at replant sites. Development and deployment of resistant or tolerant rootstocks offers a cost-effective, ecologically friendly, and durable approach for ARD management. Maximized exploitation of natural resistance requires integrated efforts to identify key regulatory mechanisms underlying resistance traits in apple. In this study, miRNA profiling and degradome sequencing identified major miRNA pathways and candidate genes using six apple rootstock genotypes with contrasting phenotypes to P. ultimum infection. The comprehensive RNA-seq dataset offered an expansive view of post-transcriptional regulation of apple root defense activation in response to infection from P. ultimum. Several pairs of miRNA families and their corresponding targets were identified for their roles in defense response in apple roots, including miR397-laccase, miR398-superoxide dismutase, miR10986-polyphenol oxidase, miR482-resistance genes, and miR160-auxin response factor. Of these families, the genotype-specific expression patterns of miR397 indicated its fundamental role in developing defense response patterns to P. ultimum infection. Combined with other identified copper proteins, the importance of cellular fortification, such as lignification of root tissues by the action of laccase, may critically contribute to genotype-specific resistance traits. Our findings suggest that quick and enhanced lignification of apple roots may significantly impede pathogen penetration and minimize the disruption of effective defense activation in roots of resistant genotypes. The identified target miRNA species and target genes consist of a valuable resource for subsequent functional analysis of their roles during interaction between apple roots and P. ultimum.
A Perturbed Postural Balance Test Using an Instrumented Treadmill – Precision and Accuracy of Belt Movement and Test-Retest Reliability of Balance Measures

A perturbed postural balance test can be used to investigate balance control under mechanical disturbances. The test is typically performed using purpose-built movable force plates. As instrumented treadmills become increasingly common in biomechanics laboratories and in clinical settings, these devices could be potentially used to assess and train balance control. The purpose of the study was to investigate how an instrumented treadmill applies to perturbed postural balance test. This was investigated by assessing the precision and reliability of the treadmill belt movement and the test-retest reliability of perturbed postural balance test over 5 days. Postural balance variables were calculated from the center of pressure trajectory and included peak displacement, time to peak displacement, and recovery displacement. Additionally, the study investigated short-term learning effects over the 5 days. Eight healthy participants (aged 24–43 years) were assessed for 5 consecutive days with four different perturbation protocols. Center of pressure (COP) data were collected using the force plates of the treadmill while participant and belt movements were measured with an optical motion capture system. The results show that the treadmill can reliably deliver the intended perturbations with <1% deviation in total displacement and with minimal variability between days and participants (typical errors 0.06–2.71%). However, the treadmill was not able to reach the programmed 4 m/s2 acceleration, reaching only about 75% of it. Test–retest reliability of the selected postural balance variables ranged from poor to good (ICC 0.156–0.752) with typical errors between 4.3 and 28.2%. Learning effects were detected based on linear or quadratic trends (p < 0.05) in peak displacement of the slow forward and fast backward protocols and in time to peak displacement in slow and fast backward protocols. The participants altered the initial location of the COP relative to the foot depending on the direction of the perturbation. In conclusion, the precision and accuracy of belt movement were found to be excellent. Test-retest reliability of the balance test utilizing an instrumented treadmill ranged from poor to good which is, in line with previous investigations using purpose-built devices for perturbed postural balance assessment.
YTHDF2 is a Potential Biomarker and Associated with Immune Infiltration in Kidney Renal Clear Cell Carcinoma

Clear cell renal cell carcinoma (ccRCC or KIRC) has a high mortality rate globally. It is necessary to identify biomarkers and investigate the mechanisms those biomarkers are associated with, to improve the prognosis of patients with KIRC. N6-Methyladenosine (m6A) affects the fate of modified RNA molecules and is involved in tumor progression. Different webservers were used in our research to investigate the mRNA transcription and clinical significance of YTHDF2 in KIRC. Survival analysis revealed that patients with elevated YTHDF2 transcription had a slightly longer OS and DFS than those with low YTHDF2 expression. YTHDF2 expression was shown to be significantly associated with the abundance of immune cells such as B cells, CD8+ T cells, CD4+ T cells, macrophages, neutrophils, and dendritic cells. For a series of enrichment studies, we combined information on YTHDF2-binding molecules and expression-linked genes and identified the possible influence of “mRNA surveillance pathway,” “RNA degradation,” and “RNA transport” in the biology or pathogeny of KIRC. In addition, we identified multiple miRNA, kinase, and transcription factor targets of YTHDF2 in KIRC and constructed target networks. Overall, our findings show that YTHDF2 is a possible indicator of immune infiltration in the KIRC.
Distribution of Aldh1L1-CreERT2 Recombination in Astrocytes Versus Neural Stem Cells in the Neurogenic Niches of the Adult Mouse Brain

In the adult central nervous system, neural stem cells (NSCs) reside in two discrete niches: the subependymal zone (SEZ) of the lateral ventricle and the subgranular zone (SGZ) of the dentate gyrus (DG). Here, NSCs represent a population of highly specialized astrocytes that are able to proliferate and give rise to neuronal and glial progeny. This process, termed adult neurogenesis, is extrinsically regulated by other niche cells such as non-stem cell astrocytes. Studying these non-stem cell niche astrocytes and their role during adult neuro- and gliogenesis has been hampered by the lack of genetic tools to discriminate between transcriptionally similar NSCs and niche astrocytes. Recently, Aldh1L1 has been shown to be a pan-astrocyte marker and that its promoter can be used to specifically target astrocytes using the Cre-loxP system. In this study we explored whether the recently described Aldh1L1-CreERT2 mouse line (Winchenbach et al., 2016) can serve to specifically target niche astrocytes without inducing recombination in NSCs in adult neurogenic niches. Using short- and long-term tamoxifen protocols we revealed high recombination efficiency and specificity in non-stem cell astrocytes and little to no recombination in NSCs of the adult DG. However, in the SEZ we observed recombination in ependymal cells, astrocytes, and NSCs, the latter giving rise to neuronal progeny of the rostral migratory stream and olfactory bulb. Thus, we recommend the here described Aldh1L1-CreERT2 mouse line for predominantly studying the functions of non-stem cell astrocytes in the DG under physiological and pathological conditions.
Power Minimization Using Rate Splitting With Statistical CSI in Cloud-Radio Access Networks

Minimizing the power consumption in mobile communication networks while ensuring a minimum quality of service (QoS) for applications is essential in light of the unprecedented expected increase in the number of connected devices and the associated data traffic beyond the fifth generation of wireless networks (B5G). This paper considers a cloud-radio access network (C-RAN) model where a central processor (CP) is connected to the base stations (BSs) via limited capacity fronthaul links. In the context of our C-RAN setting, we consider the practical case where the CP has only statistical knowledge of channel state information (CSI). While conventional wireless systems adopt the treating interference as noise (TIN) strategy to deal with the interference in the network, this paper instead considers that the CP applies the rate splitting (RS) strategy by dividing each user’s message into two parts: a private part to be decoded by the intended user only and a common part to be decoded by a subset of users, for the sole reason of interference mitigation in the network. To best account for the channel estimation errors, this paper addresses the problem of transmit power minimization under minimum QoS constraints on the achievable ergodic rate per user, so as to determine the beamforming vectors of the private and common messages as well as the rate allocated to all the users. The considered problem is of stochastic, complex, and non-convex nature. This paper addresses the problem intricacies through an iterative approach that leverages both the sample average approximation (SAA) technique and the weighted minimum mean squared error (WMMSE) algorithm to obtain a stationary point of the optimization problem in the asymptotic regime. The numerical results demonstrate the gain achieved with the RS strategy as compared to TIN, especially under high QoS requirements.
An Overview of Engineered Hydrogel-Based Biomaterials for Improved β-Cell Survival and Insulin Secretion

Islet transplantation provides a promising strategy in treating type 1 diabetes as an autoimmune disease, in which damaged β-cells are replaced with new islets in a minimally invasive procedure. Although islet transplantation avoids the complications associated with whole pancreas transplantations, its clinical applications maintain significant drawbacks, including long-term immunosuppression, a lack of compatible donors, and blood-mediated inflammatory responses. Biomaterial-assisted islet transplantation is an emerging technology that embeds desired cells into biomaterials, which are then directly transplanted into the patient, overcoming the aforementioned challenges. Among various biomaterials, hydrogels are the preferred biomaterial of choice in these transplants due to their ECM-like structure and tunable properties. This review aims to present a comprehensive overview of hydrogel-based biomaterials that are engineered for encapsulation of insulin-secreting cells, focusing on new hydrogel design and modification strategies to improve β-cell viability, decrease inflammatory responses, and enhance insulin secretion. We will discuss the current status of clinical studies using therapeutic bioengineering hydrogels in insulin release and prospective approaches.
Diagnostic Accuracy of Female Pelvic Ultrasonography in Differentiating Precocious Puberty From Premature Thelarche: A Systematic Review and Meta-analysis

Background The gonadotropin-releasing hormone (GnRH) stimulation test is the benchmark for diagnosing precocious puberty (PP). However, it is invasive, time-consuming, costly, and may create an unpleasant experience for participants. Moreover, some overlaps may occur between PP and premature thelarche (PT) in the early stage of PP. Female pelvic ultrasonography may provide additional information to help differentiate PP from PT and subsequently initiate early treatment. In this study, we aimed to first directly compare pelvic ultrasonography parameters between PP and PT groups and secondly, investigate their diagnostic accuracy compared with the GnRH stimulation test. Methods A systematic search of the PubMed/MEDLINE, EMBASE, Scopus, and Cochrane Library databases was performed up to March 31, 2021. All types of studies, except for case reports and review articles, were included. The GnRH stimulation test was used to confirm PP diagnosis. Those whose organic conditions might cause PP were excluded. The mean, standard deviation, sensitivity, and specificity of each parameter were documented. Forest plots were constructed to display the estimated standardized mean differences (SMDs) from each included study and the overall calculations. A bivariate model was used to calculate the pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR). Results A total of 13 studies were included for analysis. The SMDs (95% confidence interval – CI) in ovarian volume, fundal-cervical ratio, uterine length, uterine cross-sectional area, and uterine volume between PP and PT groups were 1.12 (0.78–1.45; p < 0.01), 0.90 (0.07–1.73; p = 0.03), 1.38 (0.99–1.78; p < 0.01), 1.06 (0.61–1.50; p < 0.01), and 1.21 (0.84–1.58; p <0.01), respectively. A uterine length of 3.20 cm yielded a pooled sensitivity of 81.8% (95% CI 78.3%–84.9%), specificity of 82.0% (95% CI 61.0%–93.0%), PLR of 4.56 (95% CI 2.15–9.69), NLR of 0.26 (95% CI 0.17–0.39), and DOR of 19.62 (95% CI 6.45–59.68). The area under the summary receiver operating characteristics curve was 0.82. Conclusion Female pelvic ultrasonography may serve as a complementary tool to the GnRH stimulation test in differentiating PP from PT. Systematic Review Registration https://www.crd. york.ac. uk/prospero/display_record. php? ID=CRD42021232427, ID: CRD42021232427.
Genetic Differentiation of Reintroduced Père David’s Deer (Elaphurus davidianus) Based on Population Genomics Analysis

The reintroduction is an important conservation tool to restore a species in its historically distribution area, but the rate of reintroduction success varies across species or regions due to different reasons. Genetic evaluation is important to the conservation management of reintroduced species. Conservation concerns relate to genetic threats for species with a small population size or severely historically bottle-necked species, such as negative consequences associated with loss of genetic diversity and inbreeding. The last 40years have seen a rapid increasing of population size for Père David’s deer (Elaphurus davidianus), which originated from a limited founder population. However, the genetic structure of reintroduced Père David’s deer has not been investigated in terms of population genomics, and it is still not clear about the evolutionary history of Père David’s deer and to what extent the inbreeding level is. Conservation genomics methods were used to reconstruct the demographic history of Père David’s deer, evaluate genetic diversity, and characterize genetic structure among 18 individuals from the captive, free-ranging and wild populations. The results showed that 1,456,457 single nucleotide polymorphisms (SNPs) were obtained for Père David’s deer, and low levels of genome-wide genetic diversity were observed in Père David’s deer compared with Red deer (Cervus elaphus) and Sika deer (Cervus nippon). A moderate population genetic differentiation was detected among three populations of Père David’s deer, especially between the captive population in Beijing Père David’s deer park and the free-ranging population in Jiangsu Dafeng National Nature Reserve. The effective population size of Père David’s deer started to decline ~25.8ka, and the similar levels of three populations’ LD reflected the genetic impacts of long-term population bottlenecks in the Père David’s deer. The findings of this study could highlight the necessity of individual exchange between different facilities, and genetic management should generally be integrated into conservation planning with other management considerations.
The Promise of Lung Organoids for Growth and Investigation of Pneumocystis Species

Pneumocystis species (spp.) are host-obligate fungal parasites that colonize and propagate almost exclusively in the alveolar lumen within the lungs of mammals where they can cause a lethal pneumonia. The emergence of this pneumonia in non-HIV infected persons caused by Pneumocystis jirovecii (PjP), illustrates the continued importance of and the need to understand its associated pathologies and to develop new therapies and preventative strategies. In the proposed life cycle, Pneumocystis spp. attach to alveolar type 1 epithelial cells (AEC1) and prevent gas exchange. This process among other mechanisms of Pneumocystis spp. pathogenesis is challenging to observe in real time due to the absence of a continuous ex vivo or in vitro culture system. The study presented here provides a proof-of-concept for the development of murine lung organoids that mimic the lung alveolar sacs expressing alveolar epithelial type 1 cells (AEC1) and alveolar type 2 epithelial cells (AEC2). Use of these 3-dimensional organoids should facilitate studies of a multitude of unanswered questions and serve as an improved means to screen new anti- PjP agents.
Dynamic Development of White Lupin Rootlets Along a Cluster Root

White lupin produces cluster roots in response to phosphorus deficiency. Along the cluster root, numerous short rootlets successively appear, creating a spatial and temporal gradient of developmental stages that constitutes a powerful biological model to study the dynamics of the structural and functional evolution of these organs. The present study proposes a fine histochemical, transcriptomic and functional analysis of the rootlet development from its emergence to its final length. Between these two stages, the tissue structures of the rootlets were observed, the course of transcript expressions for the genes differentially expressed was monitored and some physiological events linked to Pi nutrition were followed. A switch between (i) a growing phase, in which a normal apical meristem is present and (ii) a specialized phase for nutrition, in which the rootlet is completely differentiated, was highlighted. In the final stage of its determinate growth, the rootlet is an organ with a very active metabolism, especially for the solubilization and absorption of several nutrients. This work discusses how the transition between a growing to a determinate state in response to nutritional stresses is found in other species and underlines the fundamental dilemma of roots between soil exploration and soil exploitation.
Conditional Input Gated Low-Rank Perturbations for Continual Learning

We address the problem of learning convolution neural networks (CNN) in the continual setting when tasks arrive sequentially, and only the data of the current task is available. In this setting CNNs are prone to reduce their quality on all old task drastically. In this work, we extend the idea of the (Abati et al., 2020) of data-conditional expansion of the CNN architecture. We propose to use low-rank and hence more weak additive perturbations for CNN ﬁlters, which is enough due to the composition structure of the CNN layers. Such low-rank adaptation modules allow us to reduce computational costs and promote sparseness in the adaptation of CNN to new tasks. We validate our approach empirically on the split MNIST and CIFAR10 tasks.
Far-UVC light applications: sterilization of MRSA on a surface and inactivation of aerosolized influenza virus

Methicillin-resistant Staphylococcus aureus (MRSA) and influenza A virus are two of the major targets for new antimicrobial technologies. In contrast to conventional germicidal lamps emitting primarily at 254 nm, which are both carcinogenic and cataractogenic, recent work has shown the potential of far-UVC technology, mainly between 207 and 222 nm, to be an effective means of sterilization of pathogens without apparent harm to mammalian cells. This is because, due to its strong absorbance in biological materials, far-UVC light cannot penetrate even the outer (non living) layers of human skin or eye; however, because bacteria and viruses are of micrometer or smaller dimensions, far-UVC can penetrate and inactivate them. With this report, we present progress on in vitro tests to inactivate MRSA on a surface using far-UVC light from a laser delivered using an optical diffuser. Qualitative and quantitative results show that this means of far-UVC exposure is adequate to inactivate MRSA with a dose comparable to that which would be required using a conventional germicidal lamp. Also included is a report on progress on inactivation of aerosolized influenza A virus. A custom benchtop aerosol exposure chamber was constructed and used to determine the effectiveness of far- UVC. Results indicate that far-UVC efficiently inactivates airborne aerosolized viruses, with a very low dose of 2 mJ/cm2 of 222-nm light inactivating >95% of aerosolized H1N1 influenza virus. Together these studies help to further establish far-UVC technology as a promising, safe and inexpensive tool for sterilization in many environments.
Temperature Dependence of the Amplified Spontaneous Emission from CsPbBr3 Nanocrystal Thin Films

Cesius lead halide perovskite colloidal nanocrystals are among the most promising perovskite systems for light-emitting devices applications due to their high fluorescence quantum yield and high optical gain at room temperature. In this letter, we report on the first investigation of temperature dependence of amplified spontaneous emission (ASE) properties of thin films of CsPbBr3 nanocrystals. We demonstrate that ASE is strongly temperature-dependent, with a complex variation in temperature of the ASE intensity, threshold, and peak wavelength. The joint investigation of the photoluminescence (PL) spectra below and above the ASE threshold allows us to conclude that the temperature increase results in the formation of disordered subdomains emitting in the low-energy tail of the PL spectra, leading to the existence of three emission regimes with transitions at about 90 and 170 K, with individually different temperature dependences.
Psychometric and accuracy comparison of three commonly used questionnaires for the diagnosis of neuropathic pain

Objectives: Diagnosis of neuropathic pain is challenging. Recently, scientists developed multiple questionnaires to expedite this diagnosis including the Self-completed Leeds Assessment of Neuropathic Symptoms and Signs (S-LANSS), Douleur Neuropathique 4 questionnaire (DN4), and Neuropathic Pain Questionnaire–Short Form (NPQ-SF). Materials and Methods: We conducted a prospective cohort study to compare the psychometric characteristics and accuracy of the three questionnaires. We assessed reliability with the Cronbach's α reliability coefficient and inter-item correlations, and validity with receiver operating characteristic (ROC) and correlation analyses. We assessed agreement between the diagnosis of the questionnaires and the reference clinical diagnosis using Cohen's kappa coefficient. Results: 188 patients were analyzed: 141 (75%) had “definite neuropathic” and 47 (25%) had “nonneuropathic” pain. The NPQ-SF and S-LANSS questionnaires demonstrated acceptable reliability with Cronbach's α coefficient values of 0.54 (95% CI: 0.41–0.64) and 0.65, (95%CI: 0.57–0.72), respectively. The DN4 questionnaire demonstrated high reliability with Cronbach's α coefficient of 0.74 (95%CI: 0.68–0.79). The NPQ-SF, DN4, and S-LANSS questionnaires demonstrated “excellent” diagnostic ability with an area under the ROC curve of 0.82 (95% CI: 0.75–0.89), 0.89 (95% CI: 0.83–0.95), and 0.83 (95% CI: 0.75–0.90), respectively. Based on their optimal cutoff values, the DN4 had the highest sensitivity and lowest specificity in discriminating between neuropathic and nonneuropathic patients, while the S-LANSS had the lowest sensitivity and highest specificity. Conclusion: Both NPQ-SF and S-LANSS demonstrated acceptable reliability, while DN4 demonstrated high reliability. All three demonstrated excellent diagnostic validities; however, it is important to consider the sensitivity and specificity of each.