Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomes of the willow-galling sawflies Euura lappo and Eupontania aestiva (Hymenoptera: Tenthredinidae): a resource for research on ecological speciation, adaptation, and gall induction

Abstract Hymenoptera is a hyperdiverse insect order represented by over 153,000 different species. As many hymenopteran species perform various crucial roles for our environments, such as pollination, herbivory, and parasitism, they are of high economic and ecological importance. There are 99 hymenopteran genomes in the NCBI database, yet only five are representative of the paraphyletic suborder Symphyta (sawflies, woodwasps, and horntails), while the rest represent the suborder Apocrita (bees, wasps, and ants). Here, using a combination of 10X Genomics linked-read sequencing, Oxford Nanopore long-read technology, and Illumina short-read data, we assembled the genomes of two willow-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae: Euurina): the bud-galling species Euura lappo and the leaf-galling species Eupontania aestiva. The final assembly for E. lappo is 259.85 Mbp in size, with a contig N50 of 209.0 kbp and a BUSCO score of 93.5%. The E. aestiva genome is 222.23 Mbp in size, with a contig N50 of 49.7 kbp and a 90.2% complete BUSCO score. De novo annotation of repetitive elements showed that 27.45% of the genome was composed of repetitive elements in E. lappo and 16.89% in E. aestiva, which is a marked increase compared to previously published hymenopteran genomes. The genomes presented here provide a resource for inferring phylogenetic relationships among basal hymenopterans, comparative studies on host-related genomic adaptation in plant-feeding insects, and research on the mechanisms of plant manipulation by gall-inducing insects.
Effects of Rearing on the Behaviour of Zoo-Housed Chimpanzees (Pan troglodytes)

Early-life experiences may considerably affect the behavioural patterns of adult primates. Particularly, atypical rearing practices might lead to abnormal behaviours and social-sexual deficiencies in captive, adult non-human primates. We conducted behavioural observations of mother-reared (n = 5) and hand-reared (n = 6) adult chimpanzees in a social group at Parco Natura Viva, Italy. We used continuous focal animal sampling to collect behavioural data focusing on individual and social behaviours. We found that all study subjects performed individual and social species-specific behaviours. However, mother-reared chimpanzees performed locomotion and affiliative behaviours significantly more than hand-reared subjects. In addition to these species-typical behaviours, hand-reared chimpanzees showed significantly more abnormal behaviours than mother-reared subjects. Therefore, these findings suggest that hand-rearing could have wide-reaching effects on the behavioural repertoire in adult zoo-housed chimpanzees. Hence, even if sometimes human intervention in rearing may be necessary to ensure the survival of captive infant chimpanzees, our results suggest that zoo-housed chimpanzees might benefit from minimised human-animal interactions and exposure to conspecifics throughout their development. These suggestions should be implemented in regular husbandry practices.
Trends in Blood Pressure and Hypertension Among US Children and Adolescents, 1999-2018

Key Points Question Have systolic blood pressure (SBP) and diastolic blood pressure (DBP) levels among US children changed during the past 20 years? Findings In this serial cross-sectional study of 19 273 children and adolescents included in the National Health and Nutrition Examination Survey (NHANES), age-adjusted mean SBP was lower in the 2015-2018 cycle compared with the 1999-2002 cycle among adolescents aged 13 to 17 years, and mean DBP was lower in the 2015-2018 cycle compared with the 1999-2002 cycle among children aged 8 to 12 and adolescents aged 13 to 17 years. Meaning These representative findings suggest that from 1999-2002 to 2015-2018, mean SBP decreased among adolescents aged 13 to 17 years and mean DBP decreased among children and adolescents aged 8 to 12 and 13 to 17 years, respectively, in the US.
Assessing Response to 177Lu-PSMA Radioligand Therapy Using Modified PSMA PET Progression Criteria

Visual Abstract PET/CT targeting the prostate-specific membrane antigen (PSMA) plays a key role in staging of patients with prostate cancer. Moreover, it is used not only for the assessment of adequate PSMA expression of prostate cancer cells before PSMA-targeting radioligand therapy (RLT) but also for restaging during the course of therapy to evaluate response to treatment. Whereas no established criteria exist for systematic response evaluation so far, recently proposed PSMA PET Progression (PPP) criteria might fill this gap. The aim of this study was to assess the feasibility of PPP criteria in patients undergoing PSMA RLT and their prognostic implications. Methods: In this retrospective analysis, PSMA PET/CT scans of 46 patients before and after completion of PSMA RLT were analyzed separately by 2 readers using modified PPP criteria. After interobserver agreement assessment, consensus results (progressive vs. nonprogressive disease) were compared in a multivariate Cox regression model (endpoint, overall survival [OS]). Results: Interobserver agreement using the modified PPP criteria was substantial (Cohen κ = 0.73), with a concordance in 87% of patients. The median OS of all patients after PSMA RLT (n = 46) was 9.0 mo (95% CI, 7.8–10.2 mo). Progression according to the modified PPP criteria was found in 32 patients and was a significant (P ≤ 0.001) prognostic marker for OS, with a hazard ratio of 15.5 (95% CI, 3.4–70.2). Conclusion: Response assessment in patients undergoing PSMA RLT using modified PPP criteria are reproducible and highly prognostic for OS. The modified PPP criteria should be validated in future prospective trials.
Cingulate networks associated with gray matter loss in Parkinson's disease show high expression of cholinergic genes in the healthy brain

Structural covariance networks are able to identify functionally organized brain regions by gray matter volume covariance across a population. We examined the transcriptomic signature of such anatomical networks in the healthy brain using postmortem microarray data from the Allen Human Brain Atlas. A previous study revealed that a posterior cingulate network and anterior cingulate network showed decreased gray matter in brains of Parkinson's disease patients. Therefore, we examined these two anatomical networks to understand the underlying molecular processes that may be involved in Parkinson's disease. Whole brain transcriptomics from the healthy brain revealed upregulation of genes associated with serotonin, GPCR, GABA, glutamate, and RAS‐signaling pathways. Our results also suggest involvement of the cholinergic circuit, in which genes NPPA, SOSTDC1, and TYRP1 may play a functional role. Finally, both networks were enriched for genes associated with neuropsychiatric disorders that overlap with Parkinson's disease symptoms. The identified genes and pathways contribute to healthy functions of the posterior and anterior cingulate networks and disruptions to these functions may in turn contribute to the pathological and clinical events observed in Parkinson's disease.
High frequency of concurrent anti-C1q and anti-dsDNA but not anti-C3b antibodies in patients with Lupus Nephritis

ABSTRACT Lupus Nephritis (LN) in patients with Systemic Lupus Erythematosus (SLE) is one of the most serious and prevalent manifestations. The procedure of renal biopsy is harmful and accompanied by potential hazards. Therefore, introducing reliable biomarkers to predict LN is exceedingly worthwhile. In the present study, we compared the diagnostic values of circulating autoantibodies against dsDNA, C1q, C3b, SSA, SSB, and Sm alone or in combination to predict LN. This study evaluated the abovementioned autoantibodies in 40 healthy controls (HCs) and 95 SLE patients with different kidney involvements, including absent (n = 40), inactive (n = 20), and active (n = 35) LN using EIA method. The frequency and odds ratio of anti-dsDNA (71.4%, OR = 4.2), anti-C1q (62.9%, OR = 5.1), and the simultaneous existence of anti-C1q and anti-dsDNA (51.4%, OR = 6) antibodies were significantly higher in the active LN group compared with both inactive and absent LN groups. Moreover, the levels of anti-C1q and anti-dsDNA antibodies positively correlated with disease activity in patients with SLE. The prevalence of these autoantibodies was associated with the severity of LN biopsies. These data suggest that anti-C1q and anti-dsDNA antibodies and also their simultaneous presence may be valuable diagnostic biomarkers for LN prediction in patients with SLE.
Retrospective analysis of predisposing factors for difficult lumbar punctures requiring image guidance in pediatric oncology patients

Abstract Success rates of lumbar punctures (LPs) in children are reportedly as low as 50%. In addition to procedural complications and failure, difficult LPs are a risk factor for traumatic LPs (TLPs), which can potentially affect diagnostic utility and alter treatment plans for pediatric oncology patients. To identify the intrinsic factors associated with technically difficult LPs in the pediatric oncology population, we performed a retrospective review of patients who required diagnostic imaging modalities for LP procedures at a single pediatric oncology institution between September 2008 and November 2018. We evaluated data from 64 LPs performed in 33 patients who were referred for image-guided LPs after undergoing technically difficult LPs that were unsuccessful using anatomic landmarks. In these cases, 96.9% of patients had at least one of the following intrinsic factors: body mass index (BMI) ≥ 25, anatomic spinal abnormalities, history of ≥ 5 previous LPs, age < 12 months, and history of back surgery. Elevated BMI was the most common factor associated with difficult LP (81.8%), followed by spinal abnormalities (51.5%), and history of ≥ 5 previous LPs (33.3%). Age < 12 months and history of back surgery were also associated with difficult LPs, but at a lower frequency. On the basis of these findings, we propose clinical recommendations for preprocedural identification of patients at risk of difficult LPs to reduce complications, including TLP, failure, and exposure to general anesthesia.
Containment of COVID-19: Simulating the impact of different policies and testing capacities for contact tracing, testing, and isolation

Efficient contact tracing and testing are fundamental tools to contain the transmission of SARS-CoV-2. We used multi-agent simulations to estimate the daily testing capacity required to find and isolate a number of infected agents sufficient to break the chain of transmission of SARS-CoV-2, so decreasing the risk of new waves of infections. Depending on the non-pharmaceutical mitigation policies in place, the size of secondary infection clusters allowed or the percentage of asymptomatic and paucisymptomatic (i.e., subclinical) infections, we estimated that the daily testing capacity required to contain the disease varies between 0.7 and 9.1 tests per thousand agents in the population. However, we also found that if contact tracing and testing efficacy dropped below 60% (e.g. due to false negatives or reduced tracing capability), the number of new daily infections did not always decrease and could even increase exponentially, irrespective of the testing capacity. Under these conditions, we show that population-level information about geographical distribution and travel behaviour could inform sampling policies to aid a successful containment, while avoiding concerns about government-controlled mass surveillance.
SARS-CoV-2 Serological testing in frontline health workers in Zimbabwe

Background In order to protect health workers from SARS-CoV-2, there is need to characterise the different types of patient facing health workers. Our first aim was to determine both the infection status and seroprevalence of SARS-CoV-2 in health workers. Our second aim was to evaluate the occupational and demographic predictors of seropositivity to inform the country’s infection prevention and control (IPC) strategy. Methods and principal findings We invited 713 staff members at 24 out of 35 health facilities in the City of Bulawayo in Zimbabwe. Compliance to testing was defined as the willingness to uptake COVID-19 testing by answering a questionnaire and providing samples for both antibody testing and PCR testing. SARS-COV-2 antibodies were detected using a rapid diagnostic test kit and SAR-COV-2 infection was determined by real-time (RT)-PCR. Of the 713 participants, 635(89%) consented to answering the questionnaire and providing blood sample for antibody testing while 560 (78.5%) agreed to provide nasopharyngeal swabs for the PCR SARS-CoV-2 testing. Of the 635 people (aged 18–73) providing a blood sample 39.1% reported a history of past COVID-19 symptoms while 14.2% reported having current symptoms of COVID-19. The most-prevalent co-morbidity among this group was hypertension (22.0%) followed by asthma (7.0%) and diabetes (6.0%). The SARS-CoV-2 sero-prevalence was 8.9%. Of the 560 participants tested for SARS-CoV-2 infection, 2 participants (0.36%) were positive for SAR-CoV-2 infection by PCR testing. None of the SARS-CoV-2 antibody positive people were positive for SAR-CoV-2 infection by PCR testing. Conclusion and interpretation In addition to clinical staff, several patient-facing health workers were characterised within Zimbabwe’s health system and the seroprevalence data indicated that previous exposure to SAR-CoV-2 had occurred across the full spectrum of patient-facing staff with nurses and nurse aides having the highest seroprevalence. Our results highlight the need for including the various health workers in IPC strategies in health centres to ensure effective biosecurity and biosafety.
Microbial Community Resilience across Ecosystems and Multiple Disturbances

The ability of ecosystems to withstand disturbances and maintain their functions is being increasingly tested as rates of change intensify due to climate change and other human activities. Microorganisms are crucial players underpinning ecosystem functions, and the recovery of microbial communities from disturbances is therefore a key part of the complex processes determining the fate of ecosystem functioning. SUMMARY The ability of ecosystems to withstand disturbances and maintain their functions is being increasingly tested as rates of change intensify due to climate change and other human activities. Microorganisms are crucial players underpinning ecosystem functions, and the recovery of microbial communities from disturbances is therefore a key part of the complex processes determining the fate of ecosystem functioning. However, despite global environmental change consisting of numerous pressures, it is unclear and controversial how multiple disturbances affect microbial community stability and what consequences this has for ecosystem functions. This is particularly the case for those multiple or compounded disturbances that occur more frequently than the normal recovery time. The aim of this review is to provide an overview of the mechanisms that can govern the responses of microbes to multiple disturbances across aquatic and terrestrial ecosystems. We first summarize and discuss properties and mechanisms that influence resilience in aquatic and soil biomes to determine whether there are generally applicable principles. Following, we focus on interactions resulting from inherent characteristics of compounded disturbances, such as the nature of the disturbance, timing, and chronology that can lead to complex and nonadditive effects that are modulating the response of microorganisms.
Exposure to formaldehyde and asthma outcomes: A systematic review, meta-analysis, and economic assessment

Background Every major federal regulation in the United States requires an economic analysis estimating its benefits and costs. Benefit-cost analyses related to regulations on formaldehyde exposure have not included asthma in part due to lack of clarity in the strength of the evidence. Objectives 1) To conduct a systematic review of evidence regarding human exposure to formaldehyde and diagnosis, signs, symptoms, exacerbations, or other measures of asthma in humans; and 2) quantify the annual economic benefit for decreases in formaldehyde exposure. Methods We developed and registered a protocol in PROSPERO (Record ID #38766, CRD 42016038766). We conducted a comprehensive search of articles published up to April 1, 2020. We evaluated potential risk of bias for included studies, identified a subset of studies to combine in a meta-analysis, and rated the overall quality and strength of the evidence. We quantified economics benefit to children from a decrease in formaldehyde exposure using assumptions consistent with EPA’s proposed formaldehyde rule. Results We screened 4,821 total references and identified 150 human studies that met inclusion criteria; of these, we focused on 90 studies reporting asthma status of all participants with quantified measures of formaldehyde directly relevant to our study question. Ten studies were combinable in a meta-analysis for childhood asthma diagnosis and five combinable for exacerbation of childhood asthma (wheezing and shortness of breath). Studies had low to probably-low risk of bias across most domains. A 10-μg/m3 increase in formaldehyde exposure was associated with increased childhood asthma diagnosis (OR = 1.20, 95% CI: [1.02, 1.41]). We also found a positive association with exacerbation of childhood asthma (OR = 1.08, 95% CI: [0.92, 1.28]). The overall quality and strength of the evidence was rated as “moderate” quality and “sufficient” for asthma diagnosis and asthma symptom exacerbation in both children and adults. We estimated that EPA’s proposed rule on pressed wood products would result in 2,805 fewer asthma cases and total economic benefit of $210 million annually. Conclusion We concluded there was “sufficient evidence of toxicity” for associations between exposure to formaldehyde and asthma diagnosis and asthma symptoms in both children and adults. Our research documented that when exposures are ubiquitous, excluding health outcomes from benefit-cost analysis can underestimate the true benefits to health from environmental regulations.
Increased Serum Alkaline Phosphatase and Functional Outcome in Patients with Acute Ischemic Stroke Presenting a Low Ankle–Brachial Index

Aims: Elevated serum alkaline phosphatase (ALP) levels are associated with an increased risk of cerebrocardiovascular diseases. However, the associations of ALP with peripheral arterial disease (PAD) and outcomes in patients with acute ischemic stroke (AIS) are not well-known. Methods: We examined the association between ALP levels and the ankle–brachial index (ABI) in 2111 consecutive patients with AIS. A poor functional outcome was defined as a modified Rankin Scale (mRS) score of 3–6 at 3 months after stroke. A low ABI was defined as a value of ≤ 0.9. Results: Of the total cohort, 482 patients (22.8%) had a low ABI. ALP levels were higher in patients with a low ABI than in those without (p＜0.001). The multivariable logistic analysis revealed that quartiles of ALP levels were significantly associated with a low ABI (odds ratio [OR]: 1.20, 95% confidence interval [CI]: 1.08–1.33). Of the 1322 patients with a premorbid mRS score of 0–2, 434 patients (32.8%) had a poor outcome. The multivariable analysis revealed that elevated serum ALP levels and a low ABI were independently associated with poor stroke outcomes after adjustment for baseline characteristics (OR: 1.21, 95% CI: 1.07–1.38, and OR: 2.00, 95% CI: 1.40–2.84, respectively). Conclusions: Increased serum ALP levels are significantly associated with a low ABI. These indicators are independent prognostic factors for poor stroke outcomes at 3 months.
Drought affects the rate and duration of organ growth but not inter organ growth coordination.

Drought at flowering and grain filling greatly reduces maize (Zea mays) yield. Climate change is causing earlier and longer lasting periods of drought, which affect the growth of multiple maize organs throughout development. To study how long periods of water deficit impact the dynamic nature of growth, and to determine how these relate to reproductive drought, we employed a high-throughput phenotyping platform featuring precise irrigation, imaging systems, and image-based biomass estimations. Prolonged drought resulted in a reduction of growth rate of individual organs-though an extension of growth duration partially compensated for this-culminating in lower biomass and delayed flowering. However, long periods of drought did not affect the highly organized succession of maximal growth rates of the distinct organs, i.e., leaves, stems, and ears. Two drought treatments negatively affected distinct seed yield components: prolonged drought mainly reduced the number of spikelets, and drought during the reproductive period increased the anthesis-silking interval. The identification of these divergent biomass and yield components, which were affected by the shift in duration and intensity of drought, will facilitate trait-specific breeding towards future climate-resilient crops.
Effects of nutrition education using a food-based approach, carbohydrate counting or routine care in type 1 diabetes: 12 months prospective randomized trial

Introduction Evidence on the effects of structured nutrition education is weak in adults with type 1 diabetes mellitus (T1D) with moderately impaired glycemic control. Objective was to compare the effects of different types of nutrition education programs on glycemic control, cardiovascular risk factors, quality of life, diet quality and food choices in T1D. Research design and methods A 12 months randomized controlled study conducted at nine diabetes specialist centers with three parallel arms: (i) a food-based approach (FBA) including foods with low glycemic index or (ii) carbohydrate counting (CC) according to today’s standard practice or (iii) individual sessions according to routine care (RC). The primary end point was difference in glycated hemoglobin A1c (HbA1c) between groups at 12 months. Results 159 patients were randomized (FBA: 51; CC: 52; RC: 55). Mean (SD) age 48.6 (12.0) years, 57.9% females and mean (SD) HbA1c level 63.9 (7.9) mmol/mol, 8% (0.7%). After 3 months, HbA1c improved in both FBA and CC compared with RC. However, there were no significant differences at 12 months in HbA1c; FBA versus RC (−0.4 mmol/mol (1.3), 0.04% (0.1%)), CC versus RC (−0.8 mmol/mol (1.2), 0.1% (0.1%)), FBA versus CC (0.4 mmol/mol (0.3), 0.04% (0.01%)). At 12 months, intake of legumes, nuts and vegetables was improved in FBA versus CC and RC. FBA also reported higher intake of monounsaturated and polyunsaturated fats compared with RC, and dietary fiber, monounsaturated and polyunsaturated fats compared with CC (all p values <0.05). There were no differences in blood pressure levels, lipids, body weight or quality of life. Conclusions Nutrition education using an FBA, CC or RC is equivalent in terms of HbA1c and cardiovascular risk factors in persons with T1D with moderately impaired glycemic control. An FBA had benefits regarding food choices compared with CC and RC.