Miracle-dz/UniFAR-FTUs huggingface dataset:
Limited thermal acclimation of photosynthesis in tropical montane tree species

The temperature sensitivity of physiological processes and growth of tropical trees remains a key uncertainty in predicting how tropical forests will adjust to future climates. In particular, our knowledge regarding warming responses of photosynthesis, and its underlying biochemical mechanisms, is very limited. We grew seedlings of two tropical montane rainforest tree species, the early‐successional species Harungana montana and the late‐successional species Syzygium guineense, at three different sites along an elevation gradient, differing by 6.8℃ in daytime ambient air temperature. Their physiological and growth performance was investigated at each site. The optimum temperature of net photosynthesis (ToptA) did not significantly increase in warm‐grown trees in either species. Similarly, the thermal optima (ToptV and ToptJ) and activation energies (EaV and EaJ) of maximum Rubisco carboxylation capacity (Vcmax) and maximum electron transport rate (Jmax) were largely unaffected by warming. However, Vcmax, Jmax and foliar dark respiration (Rd) at 25℃ were significantly reduced by warming in both species, and this decline was partly associated with concomitant reduction in total leaf nitrogen content. The ratio of Jmax/Vcmax decreased with increasing leaf temperature for both species, but the ratio at 25℃ was constant across sites. Furthermore, in H. montana, stomatal conductance at 25℃ remained constant across the different temperature treatments, while in S. guineense it increased with warming. Total dry biomass increased with warming in H. montana but remained constant in S. guineense. The biomass allocated to roots, stem and leaves was not affected by warming in H. montana, whereas the biomass allocated to roots significantly increased in S. guineense. Overall, our findings show that in these two tropical montane rainforest tree species, the capacity to acclimate the thermal optimum of photosynthesis is limited while warming‐induced reductions in respiration and photosynthetic capacity rates are tightly coupled and linked to responses of leaf nitrogen.
Regional gray matter volume associated with exercise dependence: A voxel‐based morphometry study

Although regular physical exercise has multiple positive benefits for the general population, excessive exercise may lead to exercise dependence (EXD), which is harmful to one's physical and mental health. Increasing evidence suggests that stress is a potential risk factor for the onset and development of EXD. However, little is known about the neural substrates of EXD and the underlying neuropsychological mechanism by which stress affects EXD. Herein, we investigate these issues in 86 individuals who exercise regularly by estimating their cortical gray matter volume (GMV) utilizing a voxel‐based morphometry method based on structural magnetic resonance imaging. Whole‐brain correlation analyses and prediction analyses showed negative relationships between EXD and GMV of the right orbitofrontal cortex (OFC), left subgenual cingulate gyrus (sgCG), and left inferior parietal lobe (IPL). Furthermore, mediation analyses found that the GMV of the right OFC was an important mediator between stress and EXD. Importantly, these results remained significant even when adjusting for sex, age, body mass index, family socioeconomic status, general intelligence and total intracranial volume, as well as depression and anxiety. Collectively, the results of the present study provide crucial evidence of the neuroanatomical basis of EXD and reveal a potential neuropsychological pathway in predicting EXD in which GMV mediates the relationship between stress and EXD.
A Large-Scale Virtual Dataset and Egocentric Localization for Disaster Responses

With the increasing social demands of disaster response, methods of visual observation for rescue and safety have become increasingly important. However, because of the shortage of datasets for disaster scenarios, there has been little progress in computer vision and robotics in this field. With this in mind, we present the first large-scale synthetic dataset of egocentric viewpoints for disaster scenarios. We simulate pre- and post-disaster cases with drastic changes in appearance, such as buildings on fire and earthquakes. The dataset consists of more than 300K high-resolution stereo image pairs, all annotated with ground-truth data for the semantic label, depth in metric scale, optical flow with sub-pixel precision, and surface normal as well as their corresponding camera poses. To create realistic disaster scenes, we manually augment the effects with 3D models using physically-based graphics tools. We train various state-of-the-art methods to perform computer vision tasks using our dataset, evaluate how well these methods recognize the disaster situations, and produce reliable results of virtual scenes as well as real-world images. We also present a convolutional neural network-based egocentric localization method that is robust to drastic appearance changes, such as the texture changes in a fire, and layout changes from a collapse. To address these key challenges, we propose a new model that learns a shape-based representation by training on stylized images, and incorporate the dominant planes of query images as approximate scene coordinates. We evaluate the proposed method using various scenes including a simulated disaster dataset to demonstrate the effectiveness of our method when confronted with significant changes in scene layout. Experimental results show that our method provides reliable camera pose predictions despite vastly changed conditions.
Within‐Body Distributions and Feeding Effects of the Neonicotinoid Insecticide Clothianidin in Bumblebees (Bombus terrestris)

Bumblebees can be exposed to neonicotinoid pesticides through nectar and pollen collected from treated crops, which can cause lethal and sublethal effects in these nontarget pollinators. However, the body distribution of the compound after exposure to neonicotinoids in bumblebees is not well studied. Bumblebee colonies (Bombus terrestris, n = 20) were exposed to field‐realistic concentrations of clothianidin through artificial nectar (3.6–13 µg/L) for 9 d. Comparison of the nominal with the measured exposure in nectar indicated good compliance, confirming the applicability of the method. When quantified, clothianidin showed a concentration‐dependent occurrence in the head and body of workers (head: <0.2–2.17 µg/kg; body: <0.2–3.17 µg/kg), and in the body of queens (<0.2–2.49 µg/kg), although concentrations were below those measured in the nectar (bioaccumulation factor = 0.2). Exposure to clothianidin did not affect mortality nor brood production, nor did it have a statistically significant effect on nectar consumption and size of food storage. However, visual inspection suggests higher nectar consumption of nectar with low clothianidin content compared with nectar with no or high clothianidin content. Our results show that dietary clothianidin is taken up in bumblebees, but does not bioaccumulate to elevated levels compared with exposure. Still, clothianidin may elicit responses that affect feeding behavior of the pollinator B. terrestris, although our endpoints were not significantly affected. Environ Toxicol Chem 2021;40:2781–2790. © 2021 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.
Reduced thyroxine production in young household contacts of tuberculosis patients increases active tuberculosis disease risk

In the current study, we followed 839 household contacts (HHCs) of tuberculosis (TB) patients for 2 years and identified the factors that enhanced the development of TB. Fourteen of the 17 HHCs who progressed to TB were in the 15- to 30-year-old age group. At baseline (the “0“ time point, when all the individuals were healthy), the concentration of the thyroid hormone thyroxine (T4) was lower, and there were increased numbers of Tregs in PBMCs of TB progressors. At baseline, PBMCs from TB progressors stimulated with early secretory antigenic target 6 (ESAT-6) and 10 kDa culture filtrate antigen (CFP-10) produced less IL-1α. Thyroid hormones inhibited Mycobacterium tuberculosis (Mtb) growth in macrophages in an IL-1α–dependent manner. Mtb-infected Thra1PV/+ (mutant thyroid hormone receptor) mice had increased mortality and reduced IL-1α production. Our findings suggest that young HHCs who exhibit decreased production of thyroid hormones are at high risk of developing active TB disease.
A bioreactor for studying negative pressure wound therapy on skin grafts

Negative pressure wound therapy (NPWT) has become the prevailing standard of care for treating complex soft tissue wounds and is now being considered for use in alternative applications including improving skin graft take. While it is generally agreed that negative pressure leads to improved wound healing, universal consensus on its optimal application is not supported in the literature. We describe the design and validation of a bioreactor to determine the prospective benefits of NPWT on skin grafts and engineered skin substitutes (ESS). Clinically relevant pressures were applied, and the native human skin was able to withstand greater negative pressures than the engineered substitutes. Both skin types were cultured under static, flow‐only, and −75 mm Hg conditions for 3 days. While it remained intact, there was damage to the epidermal‐dermal junction in the ESS after application of negative pressure. The normal skin remained viable under all culture conditions. The engineered skin underwent apoptosis in the flow‐only group; however, the application of negative pressure reduced apoptosis. Vascular endothelial growth factor levels were significantly higher in the normal flow‐only group, 152.0 ± 75.1 pg/mg protein, than the other culture conditions, 81.6 ± 35.5 pg/mg for the static and 103.6 ± pg/mg for the negative pressure conditions. The engineered skin had a similar trend but the differences were not significant. This bioreactor design can be used to evaluate the impacts of NPWT on the anatomy and physiology of skin to improve outcomes in wounds after grafting with normal or engineered skin.
Thermodynamic study of Cd(II) sorption on soil.

Sorption is a major process responsible for the fate of heavy metals in soils, since the mobility of heavy metals is directly related to their partitioning between the soil solid phase and soil solution. Among the heavy metals cadmium is one of the most toxic with adverse health effects. The objective of this study is to analyze the sorption of Cd(II) from aqueous solution on soil from the industrial area of the city of Iasi (Romania) as a function of temperature at natural pH of the solution using a batch technique. A maximum uptake of about 9.7 mg of cadmium per g of soil and aprox. 95 % removal of metal was observed at 20 g/L soil amount, 200 mg/L cadmium solution and 41 °C, with an equilibrium time of 24 hours. Sorption isotherm of Cd(II) on soil were represented by Freundlich and Dubinin-Radushkevich models and the parameters indicated that the sorption of Cd(II) increased with increasing temperature of the system. Enthalpy (ΔH), entropy (ΔS) and Gibbs free energy (ΔG) were calculated from the temperature dependent sorption data, and the results indicated that the sorption of Cd(II) on soil is a spontaneous, feasible and endothermic process.
Functional diversity and identity of plant genotypes regulate rhizodeposition and soil microbial activity.

Our understanding of the linkages between plant diversity and soil carbon and nutrient cycling is primarily derived from studies at the species level, while the importance and mechanisms of diversity effects at the genotype level are poorly understood. Here we examined how genotypic diversity and identity, and associated variation in functional traits, within a common grass species Anthoxanthum odoratum modified rhizodeposition, soil microbial activity and litter decomposition. Root litter quality was not significantly affected by plant genotypic diversity but decomposition was enhanced in soils with the legacy of higher genotypic diversity. Plant genotypic diversity and identity modified rhizodeposition and associated microbial activity via two independent pathways. Plant genotypic diversity enhanced soil functioning via positive effects on variation in specific leaf area and total rhizodeposition. Genotype identity affected both rhizodeposit quantity and quality, and these effects were mediated by differences in mean specific leaf area, shoot mass and plant height. Rhizodeposition was more strongly predicted by aboveground than belowground traits, suggesting strong linkages between photosynthesis and root exudation. Our study demonstrates that functional diversity and identity of plant genotypes modulates belowground carbon supply and quality, representing an important but overlooked pathway by which biodiversity affects ecosystem functioning.
Computational analysis of MRIs predicts osteosarcoma chemoresponsiveness.

Aim: This study aimed to improve osteosarcoma chemoresponsiveness prediction by optimization of computational analysis of MRIs. Patients & methods: Our retrospective predictive model involved osteosarcoma patients with MRI scans performed before OsteoSa MAP neoadjuvant cytotoxic chemotherapy. Results: We found that several monofractal and multifractal algorithms were able to classify tumors according to their chemoresponsiveness. The predictive clues were defined as morphological complexity, homogeneity and fractality. The monofractal feature CV for Λ'(G) provided the best predictive association (area under the ROC curve = 0.88; p <0.001), followed by Y-axis intersection of the regression line for box fractal dimension, r² for FDM and tumor circularity. Conclusion: This is the first full-scale study to indicate that computational analysis of pretreatment MRIs could provide imaging biomarkers for the classification of osteosarcoma according to their chemoresponsiveness.
Passive and active immunity in infants born to mothers with SARS-CoV-2 infection during pregnancy: Prospective cohort study

Objective To investigate maternal immunoglobulins’ (IgM, IgG) response to SARS-CoV-2 infection during pregnancy and IgG transplacental transfer, to characterise neonatal antibody response to SARS-CoV-2 infection, and to longitudinally follow actively and passively acquired antibodies in infants. Design A prospective observational study. Setting Public healthcare system in Santa Clara County (California, USA). Participants Women with symptomatic or asymptomatic SARS-CoV-2 infection during pregnancy and their infants were enrolled between 15 April 2020 and 31 March 2021. Outcomes SARS-CoV-2 serology analyses in the cord and maternal blood at delivery and longitudinally in infant blood between birth and 28 weeks of life. Results Of 145 mothers who tested positive for SARS-CoV-2 during pregnancy, 86 had symptomatic infections: 78 with mild-moderate symptoms, and 8 with severe-critical symptoms. The seropositivity rates of the mothers at delivery was 65% (95% CI 0.56% to 0.73%) and the cord blood was 58% (95% CI 0.49% to 0.66%). IgG levels significantly correlated between the maternal and cord blood (Rs=0.93, p<0.0001). IgG transplacental transfer ratio was significantly higher when the first maternal positive PCR was 60–180 days before delivery compared with <60 days (1.2 vs 0.6, p<0.0001). Infant IgG seroreversion rates over follow-up periods of 1–4, 5–12, and 13–28 weeks were 8% (4 of 48), 12% (3 of 25), and 38% (5 of 13), respectively. The IgG seropositivity in the infants was positively related to IgG levels in the cord blood and persisted up to 6 months of age. Two newborns showed seroconversion at 2 weeks of age with high levels of IgM and IgG, including one premature infant with confirmed intrapartum infection. Conclusions Maternal SARS-CoV-2 IgG is efficiently transferred across the placenta when infections occur more than 2 months before delivery. Maternally derived passive immunity may persist in infants up to 6 months of life. Neonates are capable of mounting a strong antibody response to perinatal SARS-CoV-2 infection.
The prognosis of glioblastoma: a large, multifactorial study

Abstract Objective Glioblastoma is the most common and fatal primary brain tumor in adults. Even with maximal resection and a series of postoperative adjuvant treatments, the median overall survival (OS) of glioblastoma patients remains approximately 15 months. The Huashan Hospital glioma bank contains more than 2000 glioma tissue samples with long-term follow-up data; almost half of these samples are from glioblastoma patients. Several large glioma databases with long-term follow-up data have reported outcomes of glioblastoma patients from countries other than China. We investigated the prognosis of glioblastoma patients in China and compared the survival outcomes among patients from different databases. Methods The data for 967 glioblastoma patients who underwent surgery at Huashan Hospital and had long-term follow-up records were obtained from our glioma registry (diagnosed from 29 March 2010, through 7 June 2017). Patients were eligible for inclusion if they underwent surgical resection for newly diagnosed glioblastomas and had available data of survival and personal information. Data of 778 glioblastoma patients were collected from three separate online databases (448 patients from The Cancer Genome Atlas (TCGA, https://cancergenome.nih.gov), 191 from REpository for Molecular BRAin Neoplasia DaTa (REMBRANDT) database (GSE108476) and 132 from data set GSE16011(Hereafter called as the French database). We compared the prognosis of glioblastoma patients from records among the different databases and the changes in survival outcomes of glioblastoma patients from Huashan Hospital over an 8-year period. Results The median OS of glioblastoma patients was 16.3 (95% CI: 15.4–17.2) months for Huashan Hospital, 13.8 (95% CI: 12.9–14.9) months for TCGA, 19.3 (95% CI: 17.0–20.0) months for the REMBRANDT database, and 9.1 months for the French database. The median OS of glioblastoma patients from Huashan Hospital improved from 15.6 (2010–2013, 95% CI: 14.4–16.6) months to 18.2 (2014–2017, 95% CI: 15.8–20.6) months over the study period (2010–2017). In addition, the prognosis of glioblastoma patients with total resection was significantly better than that of glioblastoma patients with sub-total resection or biopsy. Conclusions Our study confirms that treatment centered around maximal surgical resection brought survival benefits to glioblastoma patients after adjusting to validated prognostic factors. In addition, an improvement in prognosis was observed among glioblastoma patients from Huashan Hospital over the course of our study. We attributed it to the adoption of a new standard of neurosurgical treatment on the basis of neurosurgical multimodal technologies. Even though the prognosis of glioblastoma patients remains poor, gradual progress is being made.
Practice Patterns and Outcomes of Novel Targeted Agents for the Treatment of ERBB2-Positive Metastatic Breast Cancer.

Importance Clinical trials have shown that the addition of pertuzumab to trastuzumab-based chemotherapy for first-line treatment of ERBB2-positive metastatic breast cancer is associated with considerable improvement in overall survival (OS). In the second-line setting, trastuzumab emtansine (T-DM1) improves OS compared with capecitabine/lapatinib in patients previously treated with trastuzumab-based chemotherapy. However, there are few data describing long-term real-world outcomes with these agents. Objective To describe practice patterns and outcomes associated with pertuzumab and T-DM1 in routine clinical practice. Design, Setting, and Participants This population-based retrospective cohort study used the Ontario Cancer Registry linked to electronic treatment databases to identify all patients treated with pertuzumab and T-DM1 following reimbursement approval in Ontario, Canada, which has a single-payer public health system. Participants included women with stage IV ERBB2-positive metastatic breast cancer receiving treatment with pertuzumab for first-line metastatic indication from December 2013 through December 2017, and those treated with T-DM1 from May 2014 through December 2017. Pertuzumab and T-DM1 cohorts were analyzed separately. Data were analyzed December 2019 to December 2020. Exposures Treatment with pertuzumab or T-DM1. Main Outcomes and Measures The primary outcome was OS, determined using the Kaplan-Meier method. Factors associated with OS were identified using a Cox proportional hazard model. Results The median (interquartile range [IQR]) age of the 795 women who received pertuzumab and 506 women who received T-DM1 was 57 (49-67) and 56 (48-66) years, respectively. Among the entire population, the median (IQR) OS and time on treatment was 43 (16.2-unavailable) and 14 (6.0-26.2) months, respectively. In the T-DM1 cohort, the proportion of pertuzumab-naive patients decreased over time from 68 of 91 [74.7%] in 2014 to 16 of 89 [18.0%] in 2017 (P < .001). The median (IQR) OS and time on treatment was 15 (6.7-27.7) and 4 (1.4-9.0) months, respectively. Median OS was shorter for patients with prior pertuzumab treatment than in the pertuzumab-naive subgroup (12 vs 19 months; adjusted hazard ratio, 0.70; 95% CI, 0.55-0.89; P = .004). Conclusions and Relevance In this population-based cohort study, the survival of patients treated with pertuzumab and T-DM1 in routine practice appeared inferior to results from pivotal clinical trials. Differences in outcome likely reflect differences in patient population and previous lines of therapy in routine practice. Further work is needed to understand the effectiveness of T-DM1 after pertuzumab exposure.
Translational Pharmacogenomics: Discovery, Evidence Synthesis and Delivery of Race‐Conscious Medicine

Response to medications, the principal treatment modality for acute and chronic diseases, is highly variable, with 40–70% of patients exhibiting lack of efficacy or adverse drug reactions. With ~ 15–30% of this variability explained by genetic variants, pharmacogenomics has become a valuable tool in our armamentarium for optimizing treatments and is poised to play an increasing role in clinical care. This review presents the progress made toward elucidating genetic underpinnings of drug response including discovery of race/ancestry‐specific pharmacogenetic variants and discusses the current evidence and evidence framework for actionability. The review is framed in the context of changing demographics and evolving views related to race and ancestry. Finally, it highlights the vital role played by cohort studies in elucidating genetic differences in drug response across race and ancestry and the informal collaborations that have enabled the field to bridge the “bench to bedside” translational gap.