Miracle-dz/UniFAR-FTUs huggingface dataset:
Topographic variation in heterotrophic and autotrophic soil respiration in a tropical seasonal forest in Thailand

Soil respiration is a carbon flux that is indispensable for determining carbon balance despite variations over time and space in forest ecosystems. In Kanchanaburi, western Thailand, we measured the soil respiration rates at different slope positions—ridge (plot R), upper slope (plot U), and lower slope (plot L)—on a hill in a seasonal tropical forest [mixed deciduous forest (MDF)] to determine the seasonal and spatial variations in soil respiration on the slope. The heterotrophic (organic layer and soil) and autotrophic (root) respiration was differentiated by trenching. Soil respiration rates showed clear seasonal patterns: high and low rates in rainy and dry seasons respectively, at all plots, and tended to decrease up the slope. Soil respiration rates responded significantly to soil water content in the 0–30 cm layer, but the response patterns differed between the lower slope (plot L) and the upper slope (plots R and U): a linear model could be applied to the lower slope but exponential quadratic models to the upper slope. The annual carbon dioxide (CO2) efflux from the forest floor was also associated with the slope position and ranged from 1908 gC m−2 year−1 in plot L to 1199 gC m−2 year−1 in plot R. With ascending position from plot L to R, the contribution of autotrophic respiration increased from 19.4 to 36.6% of total soil respiration, while that of the organic layer decreased from 26.2 to 9.4%. Mineral soil contributed to 46.3 to 54.4% of the total soil respiration. Soil water content was the key factor in controlling the soil respiration rate and the contribution of the respiration sources. However, the variable responses of soil respiration to soil water content create a complex distribution of soil respiration at the watershed scale.
Risk and Predictors of Depression Following Acute Ischemic Stroke in the Elderly

Objective We sought to comprehensively evaluate predictors of poststroke depression (PSD) in the United States and to compare PSD to post–myocardial infarction (MI) depression to determine whether ischemic stroke uniquely elevates risk of depression. Methods This is a retrospective cohort study of 100% deidentified inpatient, outpatient, and subacute nursing Medicare data from 2016 to 2017 for US patients ≥65 years of age from July 1, 2016, to December 31, 2017. We calculated Kaplan-Meier unadjusted cumulative risk of depression up to 1.5 years after the index admission. We performed Cox regression to report the hazard ratio for diagnosis of depression up to 1.5 years after stroke vs MI and independent predictors of PSD, and we controlled for patient demographics, comorbid conditions, length of stay, and acute stroke interventions. Results In fully adjusted models, patients with stroke (n = 174,901) were ≈50% more likely than patients with MI (n = 193,418) to develop depression during the 1.5-year follow-up period (Kaplan-Meier cumulative risk 0.1596 ± 0.001 in patients with stroke vs 0.0973 ± 0.000778 in patients with MI, log-rank p < 0.0001). History of anxiety was the strongest predictor of PSD, while discharge home was most protective. Female patients, White patients, and patients <75 years of age were more likely to be diagnosed with depression after stroke. Conclusions Despite the similarities between MI and stroke, patients with stroke were significantly more likely to develop depression. There were several predictors of PSD, most significantly history of anxiety. Our findings lend credibility to a stroke-specific process causing depression and highlight the need for consistent depression screening in all patients with stroke.
Cardiotoxicities of novel cancer immunotherapies

Immunotherapy revolutionised oncology by harnessing the native immune system to effectively treat a wide variety of malignancies even at advanced stages. Off-target immune activation leads to immune-related adverse events affecting multiple organ systems, including the cardiovascular system. In this review, we discuss the current literature describing the epidemiology, mechanisms and proposed management of cardiotoxicities related to immune checkpoint inhibitors (ICIs), chimeric antigen receptor (CAR) T-cell therapies and bispecific T-cell engagers. ICIs are monoclonal antibody antagonists that block a co-inhibitory pathway used by tumour cells to evade a T cell-mediated immune response. ICI-associated cardiotoxicities include myocarditis, pericarditis, atherosclerosis, arrhythmias and vasculitis. ICI-associated myocarditis is the most recognised and potentially fatal cardiotoxicity with mortality approaching 50%. Recently, ICI-associated dysregulation of the atherosclerotic plaque immune response with prolonged use has been linked to early progression of atherosclerosis and myocardial infarction. Treatment strategies include immunosuppression with corticosteroids and supportive care. In CAR T-cell therapy, autologous T cells are genetically engineered to express receptors targeted to cancer cells. While stimulating an effective tumour response, they also elicit a profound immune reaction called cytokine release syndrome (CRS). High-grade CRS causes significant systemic abnormalities, including cardiovascular effects such as arrhythmias, haemodynamic compromise and cardiomyopathy. Treatment with interleukin-6 inhibitors and corticosteroids is associated with improved outcomes. The evidence shows that, although uncommon, immunotherapy-related cardiovascular toxicities confer significant risk of morbidity and mortality and benefit from rapid immunosuppressive treatment. As new immunotherapies are developed and adopted, it will be imperative to closely monitor for cardiotoxicity.
Effect of COVID-19-related lockdown on ophthalmic practice in Italy: A report from 39 institutional centers

Background/objectives: To compare the number of eye surgical procedures performed in Italy in the 2 months following the beginning of lockdown (study period) because of COVID-19 epidemic with those performed in the two earlier months of the same year (intra-year control) and in the period of 2019 corresponding to the lockdown (inter-year control). Methods: Retrospective analysis of surgical procedures carried out at 39 Academic hospitals. A distinction was made between elective and urgent procedures. Intravitreal injections were also considered. Percentages for all surgical procedures and incidence rate ratios (IRR) for rhegmatogenous retinal detachment (RRD) events were calculated. A p value <0.05 was considered significant. Results: A total of 20,886 versus 55,259 and 56,640 patients underwent surgery during the lockdown versus intra-and inter-year control periods, respectively. During the lockdown, only 70% of patients for whom an operation/intravitreal injection was recommended, finally underwent surgery; the remaining patients did not attend because afraid of getting infected at the hospital (23%), taking public transportation (6.5%), or unavailable swabs (0.5%). Elective surgeries were reduced by 96.2% and 96.4%, urgent surgeries by 49.7% and 50.2%, and intravitreal injections by 48.5% and 48.6% in the lockdown period in comparison to intra-year and inter-year control periods, respectively. IRRs for RRDs during lockdown dropped significantly in comparison with intra- and inter-year control periods (CI: 0.65–0.80 and 0.61–0.75, respectively, p < 0.001 for both). Conclusion: This study provides a quantitative analysis of the reduction of eye surgical procedures performed in Italy because of the COVID-19 epidemic.
A review on the protective effects of naringenin against natural and chemical toxic agents

Naringenin (NRG), as a flavanone from flavonoids family, is widely found in grapefruit, lemon tomato, and Citrus fruits. NRG has shown strong anti‐inflammatory and antioxidant activities in body organs via mechanisms such as enhancement of glutathione S‐transferase (GST), superoxide dismutase (SOD), glutathione peroxidase (GSH‐Px), and catalase (CAT) activity, but reduction of serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), lactate dehydrogenase (LDH), and malondialdehyde (MDA). Furthermore, NRG anti‐apoptotic potential was indicated to be mediated by regulating B‐cell lymphoma (Bcl‐2), Bcl‐2‐associated X protein (Bax) and caspase3/9. Overall, these properties make NRG a highly fascinating compound with beneficial pharmacological effects. Based on the literature, NRG‐induced protective effects against toxicities produced by natural toxins, pharmaceuticals, heavy metals, and environmental chemicals, were mainly mediated via suppression of lipid peroxidation, oxidative stress (through boosting the antioxidant arsenal), and inflammatory factors (e.g., TNF‐α, interleukin [IL]‐6, IL‐10, and IL‐12), and activation of PI3K/Akt and MAPK survival signaling pathways. Despite considerable body of evidence on protective properties of NRG against a variety of toxic compounds, more well‐designed experimental studies and particularly, clinical trials are required before reaching a concrete conclusion. The present review discusses how NRG protects against the above‐noted toxic compounds.
Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain

The Liverpool epidemic strain (LES) is an important transmissible clonal lineage of Pseudomonas aeruginosa that chronically infects the lungs of people with cystic fibrosis (CF). Previous studies have focused on the genomics of the LES in a limited number of isolates, mostly from one CF centre in the UK, and from studies highlighting identification of the LES in Canada. Here we significantly extend the current LES genome database by genome sequencing 91 isolates from multiple CF centres across the UK, and we describe the comparative genomics of this large collection of LES isolates from the UK and Canada. Phylogenetic analysis revealed that the 145 LES genomes analysed formed a distinct clonal lineage when compared with the wider P. aeruginosa population. Notably, the isolates formed two clades: one associated with isolates from Canada, and the other associated with UK isolates. Further analysis of the UK LES isolates revealed clustering by clinic geography. Where isolates clustered closely together, the association was often supported by clinical data linking isolates or patients. When compared with the earliest known isolate, LESB58 (from 1988), many UK LES isolates shared common loss-of-function mutations, such as in genes gltR and fleR. Other loss-of-function mutations identified in previous studies as common adaptations during CF chronic lung infections were also identified in multiple LES isolates. Analysis of the LES accessory genome (including genomic islands and prophages) revealed variations in the carriage of large genomic regions, with some evidence for shared genomic island/prophage complement according to clinic location. Our study reveals divergence and adaptation during the spread of the LES, within the UK and between continents.
The regulatory network for petal anthocyanin pigmentation is shaped by the MYB5a/NEGAN transcription factor in Mimulus

Abstract Much of the visual diversity of angiosperms is due to the frequent evolution of novel pigmentation patterns in flowers. The gene network responsible for anthocyanin pigmentation, in particular, has become a model for investigating how genetic changes give rise to phenotypic innovation. In the monkeyflower genus Mimulus, an evolutionarily recent gain of petal lobe anthocyanin pigmentation in M. luteus var. variegatus was previously mapped to genomic region pla2. Here, we use sequence and expression analysis, followed by transgenic manipulation of gene expression, to identify MYB5a—orthologous to the NEGAN transcriptional activator from M. lewisii—as the gene responsible for the transition to anthocyanin-pigmented petals in M. l. variegatus. In other monkeyflower taxa, MYB5a/NEGAN is part of a reaction-diffusion network that produces semi-repeating spotting patterns, such as the array of spots in the nectar guides of both M. lewisii and M. guttatus. Its co-option for the evolution of an apparently non-patterned trait—the solid petal lobe pigmentation of M. l. variegatus—illustrates how reaction-diffusion can contribute to evolutionary novelty in non-obvious ways. Transcriptome sequencing of a MYB5a RNAi line of M. l. variegatus reveals that this genetically simple change, which we hypothesize to be a regulatory mutation in cis to MYB5a, has cascading effects on gene expression, not only on the enzyme-encoding genes traditionally thought of as the targets of MYB5a but also on all of its known partners in the anthocyanin regulatory network.
Differential impact of antiretroviral therapy initiated before or during pregnancy on placenta pathology in HIV-positive women.

OBJECTIVE To examine the association between timing of antiretroviral treatment (ART) initiation in HIV-infected women and placental histopathology. DESIGN A nested substudy in a larger cohort of HIV-infected women which examined the association between ART status and birth outcomes. METHODS Placentas (n = 130) were examined for histopathology from two ART groups: stable (n = 53), who initiated ART before conception and initiating (n = 77), who started ART during pregnancy [median (interquartile range) 15 weeks gestation (11-18)]. Using binomial regression we quantified associations between ART initiation timing with placental histopathology and pregnancy outcomes. RESULTS One-third of all placentas were less than 10th percentile weight-for-gestation and there was no significant difference between ART groups. Placental diameter, thickness, cord insertion position and foetal-placental weight ratio were also similar by group. However, placentas from the stable group showed increased maternal vascular malperfusion (MVM) (39.6 vs. 19.4%), and decreased weight (392 vs. 422 g, P = 0.09). MVM risk was twice as high [risk ratios 2.03 (95% confidence interval: 1.16-3.57); P = 0.01] in the stable group; the increased risk remaining significant when adjusting for maternal age [risk ratios 2.04 (95% confidence interval: 1.12-3.72); P = 0.02]. Furthermore, MVM was significantly associated with preterm delivery and low birth weight (P = 0.002 and <0.0001, respectively). CONCLUSION Preconception initiation of ART was associated with an increased MVM risk, and may contribute to placental dysfunction. The association between MVM with preterm delivery and low birth weight suggests that a placenta-mediated mechanism likely links the putative association between long-term use of ART and adverse birth outcomes.
Inositol polyphosphate–protein interactions: Implications for microbial pathogenicity

Inositol polyphosphates (IPs) and inositol pyrophosphates (PP–IPs) regulate diverse cellular processes in eukaryotic cells. IPs and PP–IPs are highly negatively charged and exert their biological effects by interacting with specific protein targets. Studies performed predominantly in mammalian cells and model yeasts have shown that IPs and PP–IPs modulate target function through allosteric regulation, by promoting intra‐ and intermolecular stabilization and, in the case of PP–IPs, by donating a phosphate from their pyrophosphate (PP) group to the target protein. Technological advances in genetics have extended studies of IP function to microbial pathogens and demonstrated that disrupting PP–IP biosynthesis and PP–IP‐protein interaction has a profound impact on pathogenicity. This review summarises the complexity of IP‐mediated regulation in eukaryotes, including microbial pathogens. It also highlights examples of poor conservation of IP–protein interaction outcome despite the presence of conserved IP‐binding domains in eukaryotic proteomes.
Hyperoside attenuates neuroinflammation, cognitive impairment and oxidative stress via suppressing TNF-α/NF-κB/caspase-3 signaling in type 2 diabetes rats

ABSTRACT Objectives Literature findings have instituted the role of hyperglycemia-induced oxidative stress and inflammation in the pathogenesis of cognitive derangement in diabetes mellitus (DM). Hyperoside (HYP) is a flavanone glycoside reported to possess diverse pharmacological benefits such as antioxidant and anti-inflammatory properties. The study explored whether HYP could mitigate DM-induced cognitive dysfunction and further elucidate on potential molecular mechanism in rats. Methods Streptozotocin/high-fat diet-induced diabetic rats were treated orally with HYP (50, 200 and 400 mg/kg/day) for six consecutive weeks. The blood glucose and serum insulin levels, Morris water maze test, intraperitoneal glucose tolerance test, and brain acetylcholinesterase (AChE) activity were determined. The brain expression of inflammatory nuclear factor-kappa B (NF-κB), tumour necrosis factor-alpha (TNF-α), interleukin-1β (IL-1β) and interleukin-6 (IL-6), as well as superoxide dismutase (SOD), catalase (CAT), reduced glutathione (GSH), total antioxidant capacity (TAC), malondialdehyde (MDA), lipid profile and caspase-3 activity were estimated. Results DM evoked hyperlipidemia, hypoinsulinemia, cognitive dysfunction by markedly increased AChE and reduction in learning and memory capacity. Brain activities of SOD and CAT, and levels of TAC and GSH were considerably depressed, whereas levels of IL-1β, IL-6, TNF-α, NF-κB, caspase-3 and MDA were prominently increased. Interestingly, the HYP treatment dose-dependently abrogated the altered cognitive and biochemical parameters. Discussion The results suggested that hyperoside prevents DM-induced cognitive dysfunction, neuroinflammation and oxidative stress via antioxidant, anti-inflammatory and antiapoptotic mechanisms in rats.
Treatment approach, hospital practice patterns, and receipt of multimodality therapy as measures of quality for locally advanced gastric cancer

Adequate lymphadenectomy (AL) during surgical resection and delivery of multimodality therapy (MMT) are considered important for optimizing oncologic outcomes in patients with locally advanced gastric cancer. Both neoadjuvant and adjuvant approaches to MMT delivery are considered acceptable treatment strategies. Our goal was to evaluate the association between MMT treatment approach, hospital practice patterns, and survival and to explore whether AL and MMT might represent measures of quality for locally advanced gastric cancer.
Modular approach to the synthesis of unsaturated 1-monoacyl glycerols

A modular synthesis of unsaturated 1-monoacylglycerols (1) from cis-1-iodo-1-alkenes [cis-RCH=CHI] and unsaturated carboxylic acids [CH 2 =CH(CH 2 ) n CO 2 H] is described. The method revolves around a Suzuki coupling to establish olefin geometry.
Methodology of the fatigue after stroke educational recovery group randomized controlled trial

Rationale Post-stroke fatigue affects up to 92% of stroke survivors, causing significant burden. Educational cognitive behavioral therapy fatigue groups show positive results in other health conditions. Aims FASTER will determine if educational cognitive behavioral therapy fatigue management group reduces subjective fatigue in adults post-stroke. Design Prospective, multi-centre, two-arm, single-blind, phase III RCT (parallel, superiority design), with blinded assessments at baseline, six weeks, and three months post-program commencement. With n = 200 (100 per group, 20% drop-out), the trial will have 85% power (2-sided, p = 0.05) to detect minimally clinically important differences of 0.60 (SD = 1.27) in fatigue severity scale and 1.70 points (SD = 3.6) in multidimensional fatigue inventory-20 at three months. Outcomes Primary outcomes are self-reported fatigue severity and dimensionality (i.e. types of fatigue experienced – physical, psychological and/or cognitive) post-intervention (six weeks). Secondary outcomes include subjective fatigue at three months, and health-related quality of life, disability, sleep, pain, mood, service use/costs, and caregiver burden at each follow-up. Discussion FASTER will determine whether fatigue management group reduces fatigue post-stroke. Registered with the Australian New Zealand Clinical Trials Registry (ACTRN12619000626167).
Effect of education on cognitive performance in patients with mild cognitive impairment

Abstract This study aims to investigate if education (as a cognitive reserve proxy) modifies the profile of cognitive performance. We hypothesize that participants with higher education can remain functional (due to a better executive performance), despite a more severe memory impairment, compared with lower education individuals. One hundred and sixty-six mild cognitive impairment (MCI) individuals with at least one comprehensive neuropsychological evaluation were included in a retrospective, cross-sectional study and divided into two groups (Low Education—LE [1–4 years] and Medium-to-High Education—MHE [> 4 years]). A total of 22 neuropsychological measures were analyzed. Age-adjusted results were subject to simple regression analyses to determine the variance explained by education. Average scores and proportions of low performances were subject to group comparison. The results showed similar cognitive decline patterns between individuals with LE and MHE, with no significant difference in each cognitive domain. However, MHE revealed a steeper decline in certain cognitive domains, such as sustained attention and episodic memory, compared with the LE. Moreover, MHE showed a trend to higher proportion of tests affected when compared to LE. These suggest that individuals with higher education may remain in a MCI stage despite a more widespread cognitive impairment, reflecting a higher cognitive reserve.
Response of acid mobilization of iron-containing mineral dust to improvement of air quality projected in the future

Abstract. Acidification of dust aerosols may increase aerosol iron (Fe) solubility, which is linked to mineral properties. Combustion aerosols can also elevate aerosol iron solubility when aerosol loading is low. Here, we use an atmospheric chemical transport model to investigate the deposition of filterable iron and its response to changes in anthropogenic emissions of both combustion aerosols and precursor gases. By introducing three classes of iron-containing minerals into the detailed aerosol chemistry model, we provide a theoretical examination of the effects of different dissolution behaviors on the acid mobilization of iron. Comparisons of modeled Fe dissolution curves with the measured dissolution rates for African, east Asian, and Australian dust samples show overall good agreement under acidic conditions. The improved treatment of Fe in mineral dust and its dissolution scheme results in reasonable predictive capability for iron solubility over the oceans in the Northern Hemisphere. Our model results suggest that the improvement of air quality projected in the future will lead to a decrease of the filterable iron deposition from iron-containing mineral dust to the eastern North Pacific due to less acidification in Asian dust, which is mainly associated with the reduction of nitrogen oxides (NOx) emissions. These results could have important implications for iron fertilization of phytoplankton growth, and highlight the necessity of improving the process-based quantitative understanding of the response of the chemical modification in iron-containing minerals to environmental changes.
Novel compound heterozygous frameshift variants in WDR81 associated with congenital hydrocephalus 3 with brain anomalies: First Chinese prenatal case confirms WDR81 involvement

Congenital hydrocephalus‐3 with brain anomalies (HYC3, MIM 617967) is a rare form of congenital hydrocephalus characterized by severe hydrocephalus and cerebellar abnormalities, the onset of the disease occurs in utero even resulting in fetal death. A very limited spectrum of WDR81 pathogenic variants had been reported in three unrelated families with HYC3. This study aims at presenting novel compound heterozygous frameshift variants in WDR81 in a Chinese fetus.