Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptomics and metabolomics reveal effect of arbuscular mycorrhizal fungi on growth and development of apple plants

Arbuscular mycorrhizal fungi (AMF) and plants form a symbiotic relationship that promotes plant growth and development. However, the regulatory mechanisms through which AMF promote plant growth and development are largely unexplored. In this study, the apple rootstock M26 was assessed physiologically, transcriptionally and metabolically when grown with and without AMF inoculation. AMF significantly promoted the number of lateral root (LR) increase and shoot elongation. Root transcriptomic and metabolic data showed that AMF promoted lateral root development mainly by affecting glucose metabolism, fatty acid metabolism, and hormone metabolism. Shoot transcriptomic and metabolic data showed that AMF promoted shoot elongation mainly by affecting hormone metabolism and the expression of genes associated with cell morphogenesis. To investigate whether shoot elongation is caused by root development, we analyzed the root/shoot dry weight ratio. There was a correlation between shoot growth and root development, but analysis of root and shoot metabolites showed that the regulation of AMF on plant shoot metabolites is independent of root growth. Our study bridged the gap in the field of growth and development related to AMF.
Neighborhood influences on the development of self-regulation among children of color living in historically disinvested neighborhoods: Moderators and mediating mechanisms

We present a conceptual model of the ways in which built and social environments shape the development of self-regulation in early childhood. Importantly, in centering children of color growing up in historically disinvested neighborhoods, we first describe how systemic structures of racism and social stratification have shaped neighborhood built and social environment features. We then present evidence linking these neighborhood features to children’s development of self-regulation. Furthermore, we take a multilevel approach to examining three potential pathways linking neighborhood contexts to self-regulation: school environment and resources, home environment and resources, and child health behaviors. Finally, we consider how racial-ethnic-cultural strengths and multilevel interventions have the potential to buffer children’s development of self-regulation in disinvested neighborhood contexts. Advancing multilevel approaches to understand the development of self-regulation among children of color living in historically disinvested neighborhoods is an important step in efforts to promote equity in health and education.
Phytoplankton photophysiology varies depending on nitrogen and light availability at the subsurface chlorophyll maximum in the northern Chukchi Sea

Vertical distributions of phytoplankton in the Arctic Ocean are characterized by a very narrow subsurface chlorophyll maximum (SCM) layer formed every summer after the sea ice retreats. Despite the prevalence of this narrow SCM layer, phytoplankton photosynthetic response to climate change remains to be elucidated. Here, we examined the photophysiological properties of phytoplankton in the SCM layer in the northern Chukchi Sea during the summers of 2015–2018. There was a significant difference in the SCM depth between the northwestern and northeastern Chukchi Sea determined by the distribution of Pacific Summer Water (PSW) around the SCM layer (34 ± 14 m vs. 49 ± 10 m, respectively). The maximum quantum yield of photochemistry in photosystem II (F v/F m) in the SCM phytoplankton was high (F v/F m ≥ 0.54) and similar in both regions until 2016; however, since then, F v/F m in the northeastern Chukchi Sea has decreased by approximately 10%. This decrease was accompanied by a marked decrease in the fraction of microplankton, which are known to be susceptible to nutrient limitation. This result suggests a reduction in nitrogen availability in the SCM layer in the northeastern Chukchi Sea. Meanwhile, the maximum electron transfer rate (ETRmax) did not have a significant relationship with the nitrogen availability and phytoplankton community size structure in the SCM layer; however the improved light conditions (with an approximately two-fold increase in the relative ratio of surface PAR reaching the SCM layer) increased ETRmax by up to 30% in the SCM phytoplankton in the northwestern Chukchi Sea. Therefore, these results provide a better understanding of how changes in nitrogen and light availability could affect phytoplankton photosynthesis and primary production in the Arctic Ocean.
Fundamentals of Laser Cooling of Rare-Earth-Ion Doped Solids and its Enhancement Using Nanopowders.

Fundamentals of Laser Cooling of Rare-earth-ion Doped Solids and its Enhancement Using Nanopowders by Xiulin Ruan Chair: Massoud Kaviany The Fermi golden rule is applied as the primary theory for laser cooling of solids, by recognizing that the absorption is a photon-induced, phonon-assisted, electronic transition. The limiting factors are identified as the coupling and population of the energy carriers (photon, electron, and phonon), which include the photon-electron coupling, electron-phonon coupling, ion-dopant concentration, phonon density of states, and the photon population. The photon-electron and electron-vibration coupling rates for ion-doped materials are calculated using ab initio methods for the first time. Using the calculated firstprinciple wavefunctions, the electric transition dipole moment between the ground and excited states is determined by its definition. The electron-phonon coupling is calculated by taking into account the modification of the electronic wavefunction in response to the nuclei motion, and the modifications of the vibrational modes before and after the transition. This ab initio approach does not require any fitting to experiment, providing a theoretical foundation for the optimal selection of laser cooling materials (both dopant and host). Nanostructure is proposed for the first time to enhance laser cooling performance, through the optimization of carrier populations using nanopowders. The concept of optimum dopant concentration is established and determined using the energy transfer theory, and is found to be larger than that currently used. The phonon density of states of nanopowders, calculated using molecular dynamics simulations, exhibits broadened modes, and extended tails at low and high frequencies. This is advantageous over the bulk material since more phonon modes are available in the desired range. The pumping field energy is calculated by solving the Maxwell equations in random nanopowder media. Photons are multiply scattered and do not propagate through the medium, and large field enhancement is observed. This leads to the trapping of more photons in nanopowder media, compared to the bulk material, implying more efficient absorption and cooling performance. Due to these enhancement effects, thermal predictions show that nanopowders can be cooled to the cryogenic temperature range, for the first time. FUNDAMENTALS OF LASER COOLING OF RARE-EARTH-ION DOPED SOLIDS AND ITS ENHANCEMENT USING NANOPOWDERS
Inconsistency between ship- and Argo float-based pCO2 at the intense upwelling region of the Drake Passage, Southern Ocean

The Southern Ocean absorbs a quarter of anthropogenic carbon dioxide (CO2) from the atmosphere to modulate the climate system. However, less attention has been paid to the CO2 outgassing phenomenon at the Antarctic Circumpolar Current (ACC) region of the Southern Ocean due to strong upwelling. Recent studies using autonomous biogeochemical-Argo float revealed a greater winter CO2 outgassing than previously estimated at ACC zone of the Southern Ocean, which, however, remains controversial and urgently needs to be validated. Here we take the Drake Passage as a case study to present new insights into the Southern Ocean carbon cycle and examine the validity of float-based CO2 outgassing. Upon integrating the ship-based data over the past two decades, we investigate the spatiotemporal variability of sea surface CO2 partial pressure (pCO2) in Drake Passage. We show that Drake Passage is acting as a year-round weak CO2 sink, although some CO2 uptake is counteracted by winter CO2 outgassing. The float-based pCO2 values are overall higher than ship-based values in winter, by 6 to 20 µatm (averaged 14 µatm) at the most intensive upwelling region. We then develop a surface carbon balance calculation (considering mixing between surface, subsurface, and upwelled waters) to estimate the potential of surface pCO2 increase due to upwelling, and we find that upwelling of CO2-rich subsurface waters in Drake Passage cannot support an excess ΔpCO2 of 14 µatm as suggested by float detections. We further compare our results to previous study and find that, although we used same datasets and obtained comparable results, the way to conclude the bias in float-based pCO2 would cause significant difference: an uncertainty of ±2.7% (i.e., ± 11 µatm) in float-based pCO2 estimated by other study seems acceptable, however, it is five times larger than the typical ship-based pCO2 uncertainty ( ± 2 µatm), and would cause ~180% bias in CO2 flux estimates. Going forward, there is special need for caution when interpreting the float-based CO2 flux; meanwhile, further comparisons and corrections between float- and ship-based pCO2 are clearly warranted.
Thin dielectric layers in active plasmonic devices

In this paper a design study on active plasmonic lasers is presented. In active plasmonic devices the semiconductor layer stack needs to be electrically isolated from the metal cladding that supports the plasmon modes. Secondly, surface states, created during processing of the devices, need to be passivated. Thin dielectric layers can fulfill both functions. These layers however have overlap with the optical field and therefore influence the optical mode structure of the device. The influences of the layer thickness and the refractive index are investigated.
EBV-associated diseases: Current therapeutics and emerging technologies

EBV is a prevalent virus, infecting >90% of the world’s population. This is an oncogenic virus that causes ~200,000 cancer-related deaths annually. It is, in addition, a significant contributor to the burden of autoimmune diseases. Thus, EBV represents a significant public health burden. Upon infection, EBV remains dormant in host cells for long periods of time. However, the presence or episodic reactivation of the virus increases the risk of transforming healthy cells to malignant cells that routinely escape host immune surveillance or of producing pathogenic autoantibodies. Cancers caused by EBV display distinct molecular behaviors compared to those of the same tissue type that are not caused by EBV, presenting opportunities for targeted treatments. Despite some encouraging results from exploration of vaccines, antiviral agents and immune- and cell-based treatments, the efficacy and safety of most therapeutics remain unclear. Here, we provide an up-to-date review focusing on underlying immune and environmental mechanisms, current therapeutics and vaccines, animal models and emerging technologies to study EBV-associated diseases that may help provide insights for the development of novel effective treatments.
Significantly different noun-verb distinguishing mechanisms in written Chinese and Chinese sign language: An event-related potential study of bilingual native signers

Little is known about: (a) whether bilingual signers possess dissociated neural mechanisms for noun and verb processing in written language (just like native non-signers), or they utilize similar neural mechanisms for those processing (due to general lack of part-of-speech criterion in sign languages); and (b) whether learning a language from another modality (L2) influences corresponding neural mechanism of L1. In order to address these issues, we conducted an electroencephalogram (EEG) based reading comprehension study on bimodal bilinguals, namely Chinese native deaf signers, whose L1 is Chinese Sign Language and L2 is written Chinese. Analyses identified significantly dissociated neural mechanisms in the bilingual signers’ written noun and verb processing (which also became more explicit along with increase in their written Chinese understanding levels), but not in their understanding of verbal and nominal meanings in Chinese Sign Language. These findings reveal relevance between modality-based linguistic features and processing mechanisms, which suggests that: processing modality-based features of a language is unlikely affected by learning another language in a different modality; and cross-modal language transfer is subject to modal constraints rather than explicit linguistic features.
Aberrant frontolimbic circuit in female depressed adolescents with and without suicidal attempts: A resting-state functional magnetic resonance imaging study

Background The neurobiological basis of suicidal behaviors among female adolescents with major depressive disorder (MDD) remains largely unclear. Materials and methods Fifty-eight drug-naïve, first-episode female adolescent MDD [including 31 patients with suicidal attempt (SA group) and 27 patients without SA (non-SA group)], and 36 matched healthy controls (HCs) participated in the present study. Resting-state functional magnetic resonance imaging (MRI) was performed on each subject. The metrics of the amplitude of low-frequency fluctuation (ALFF), fractional ALFF (fALFF), and regional homogeneity (ReHo) were compared among the three groups. Then seed-based functional connectivity (FC) was conducted based on the ALFF/fALFF and ReHo results, which were then correlated to clinical variables. Results Compared with the non-SA group, the SA group exhibited increased fALFF in the bilateral insula and right precentral gyrus, and enhanced ReHo in the left superior temporal gyrus, left middle cingulate cortex, right insula, and right precentral gyrus. Relative to the HCs, the SA group demonstrated additionally reduced fALFF and ReHo in the left middle frontal gyrus. Moreover, the SA group showed increased FC between the right precentral gyrus and the left middle frontal gyrus and left insula, and between the right insula and anterior/middle cingulate cortex compared to the non-SA and HC groups. In addition, the fALFF in the left middle frontal gyrus was positively correlated with the 17-item Hamilton Depression Rating Scale scores, and the values in the fALFF/ReHo in the right insula were positively correlated with the duration of MDD within the patient group. Conclusion These findings highlight the multiple abnormalities of the frontolimbic circuit, which may enhance our understanding of the neurobiological basis underlying female MDD with SA during adolescence.
Mid-Infrared Variation in Young Stars

Since 2003, the Spitzer Space Telescope has provided groundbreaking views of Galactic star formation in bands from 3.6 past 24 microns. During the cryogenic mission (the first 5.5 years), variability of young stars at these bands was noted, although typically with just a few epochs of observation. The cryogen ran out in 2009, and we are now in the warm mission era where the shortest two bands (3.6 and 4.5 microns) continue to function essentially as before. The phenomenal sensitivity and stability of Spitzer at these bands has enabled several dedicated monitoring programs studying the variability of young stars at timescales from minutes to years. The largest of these programs is YSOVAR (Stauffer et al.), but there are several smaller programs as well. With at least as many as 2200 young star light curves likely to come out of this, these programs as a whole enable more detailed study of the young star-disk interaction in the infrared for a wider range of ages and masses than has ever been accomplished before. Early results suggest a wide variety of sources of variability, including dust clouds in the disk, disk warps, star spots, and accretion. This contribution will review some of the most recent results from these programs.
Characterization of KLH-driven immune responses in clinical studies: A systematic review

The pharmacological activity assessment of novel immunomodulatory drugs in early-stage drug development is challenging as healthy volunteers do not express relevant immune biomarkers. Alternatively, the immune system can be challenged with keyhole limpet hemocyanin (KLH), a suitable antigen for studying adaptive immune responses. This report systemically reviews the KLH challenge in clinical studies focusing on the characterization of the KLH-driven systemic and local immune responses, identification of the KLH-induced biomarkers, and the evaluation of the effect of pharmacological interventions and diseases on the KLH response. A systematic literature review was carried out in PubMed spanning from 1967 to 2022. The systemic humoral KLH responses could be characterized by ELISA after 3 weeks following immunization. For the systemic cellular and molecular immune responses multiple KLH immunizations and the use of novel techniques such as flow cytometry and ELISpot yield optimal results. The objective evaluation of dermal KLH rechallenge allows for more accurate and sensitive quantification of the local response compared to subjective scoring. For the local cellular and molecular assays after KLH dermal rechallenge we also advocate the use of multiple KLH immunizations. Furthermore, oral KLH feeding, age, physical activity, alcohol consumption, stress, as well as certain auto-immune diseases also play a role in the KLH-induced immune response. Importantly, based on the KLH challenges, the effect of (novel) immunomodulatory drugs could be demonstrated in healthy volunteers, providing valuable information for the clinical development of these compounds. This review underlines the value of KLH challenges in clinical studies, but also the need for standardized and well-controlled methodology to induce and evaluate KLH responses. Systematic Review Registration: https://www.crd. york.ac. uk/prospero/, identifier CRD42022335419
Carotenoid-derived bioactive metabolites shape plant root architecture to adapt to the rhizospheric environments

Roots are important plant organs for the uptake of water and nutrient elements. Plant root development is finely regulated by endogenous signals and environmental cues, which shapes the root system architecture to optimize the plant growth and adapt to the rhizospheric environments. Carotenoids are precursors of plant hormones strigolactones (SLs) and ABA, as well as multiple bioactive molecules. Numerous studies have demonstrated SLs and ABA as essential regulators of plant root growth and development. In addition, a lot carotenoid-derived bioactive metabolites are recently identified as plant root growth regulators, such as anchorene, β-cyclocitral, retinal and zaxinone. However, our knowledge on how these metabolites affect the root architecture to cope with various stressors and how they interact with each other during these processes is still quite limited. In the present review, we will briefly introduce the biosynthesis of carotenoid-derived root regulators and elaborate their biological functions on root development and architecture, focusing on their contribution to the rhizospheric environmental adaption of plants.
Development and validation of a scatter-corrected CBCT image-guided method for cervical cancer brachytherapy

Background and purpose Multiple patient transfers have a nonnegligible impact on the accuracy of dose delivery for cervical cancer brachytherapy. We consider using on-site cone-beam CT (CBCT) to resolve this problem. However, CBCT clinical applications are limited due to inadequate image quality. This paper implements a scatter correction method using planning CT (pCT) prior to obtaining high-quality CBCT images and evaluates the dose calculation accuracy of CBCT-guided brachytherapy for cervical cancer. Materials and methods The CBCT of a self-developed female pelvis phantom and five patients was first corrected using empirical uniform scatter correction in the projection domain and further corrected in the image domain. In both phantom and patient studies, the CBCT image quality before and after scatter correction was evaluated with registered pCT (rCT). Model-based dose calculation was performed using the commercial package Acuros®BV. The dose distributions of rCT-based plans and corrected CBCT-based plans in the phantom and patients were compared using 3D local gamma analysis. A statistical analysis of the differences in dosimetric parameters of five patients was also performed. Results In both phantom and patient studies, the HU error of selected ROIs was reduced to less than 15 HU. Using the dose distribution of the rCT-based plan as the baseline, the γ pass rate (2%, 2 mm) of the corrected CBCT-based plan in phantom and patients all exceeded 98% and 93%, respectively, with the threshold dose set to 3, 6, 9, and 12 Gy. The average percentage deviation (APD) of D90 of HRCTV and D2cc of OARs was less than 1% between rCT-based and corrected CBCT-based plans. Conclusion Scatter correction using a pCT prior can effectively improve the CBCT image quality and CBCT-based cervical brachytherapy dose calculation accuracy, indicating promising prospects in both simplified brachytherapy processes and accurate brachytherapy dose delivery.
rAAV immunogenicity, toxicity, and durability in 255 clinical trials: A meta-analysis

Recombinant Adeno-associated virus (rAAV) is one of the main delivery vectors for gene therapy. To assess immunogenicity, toxicity, and features of AAV gene therapy in clinical settings, a meta-analysis of 255 clinical trials was performed. A total of 7,289 patients are planned to be dosed. AAV2 was the most dominantly used serotype (29.8%, n=72), and 8.3% (n=20) of trials used engineered capsids. 38.7% (n=91) of trials employed neutralizing antibody assays for patient enrollment, while 15.3% (n=36) used ELISA-based total antibody assays. However, there was high variability in the eligibility criteria with cut-off tiers ranging from 1:1 to 1:1,600. To address potential immunogenicity, 46.3% (n=118) of trials applied immunosuppressants (prophylactic or reactive), while 32.7% (n=18) of CNS and 37.5% (n=24) of ocular-directed trials employed immunosuppressants, possibly due to the immune-privileged status of CNS and retina. There were a total of 11 patient deaths across 8 trials, and 18 out of 30 clinical holds were due to toxicity findings in clinical studies. 30.6% (n=78) of trials had treatment-emergent serious adverse events (TESAEs), with hepatotoxicity and thrombotic microangiopathy (systemic delivery) and neurotoxicity (CNS delivery) being the most prominent. Additionally, the durability of gene therapy may be impacted by two distinct decline mechanisms: 1) rapid decline presumably due to immune responses; or 2) gradual decline due to vector dilution. The durability varied significantly depending on disease indication, dose, serotypes, and patient individuals. Most CNS (90.0%) and muscle trials (73.3%) achieved durable transgene expression, while only 43.6% of ocular trials had sustained clinical outcomes. The rAAV production system can affect rAAV quality and thus immunogenicity and toxicity. Out of 186 trials that have disclosed production system information, 63.0% (n=126) of trials used the transient transfection of the HEK293/HEK293T system, while 18.0% (n=36) applied the baculovirus/Sf9 (rBac/Sf9) system. There were no significant differences in TESAEs and durability between AAV generated by rBac/Sf9 and HEK293/HEK293T systems. In summary, rAAV immunogenicity and toxicity poses significant challenges for clinical development of rAAV gene therapies, and it warrants collaborative efforts to standardize monitoring/measurement methods, design novel strategies to overcome immune responses, and openly share relevant information.