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Overcoming difficulties in segmentation of hyperspectral plant images with small projection areas using machine learning
Abstract Segmentation of hyperspectral image data is a well-established technique in remote sensing. While it is commonly applied to individual field crops, its use for individual trees is less prevalent. Conifers are crucial in forestry, and assessing physiological status, or genetic diversity is required for effective early-age treatment in nurseries and hyperspectral imaging (HSI) combined with high-throughput phenotyping (HTP) offers faster and non-destructive evaluation. NDVI-based thresholding is sufficient for detection of leaves with large projection areas, but needles of conifers present challenges due to spatial resolution constraints and increased proportion of border pixels. This study monitored the offspring of three locally adapted Scots pine ( Pinus sylvestris L.) populations, representing distinct upland and lowland ecotypes. This study presents a hyperspectral image processing pipeline for segmenting and isolating individual Scots pine seedlings. Using a K-means algorithm, 23 hyperspectral centroids were successfully derived and subsequently classified into ten biologically distinct groups. Random forest classification model effectively differentiated Scots pine seedlings based on origin during water stress and recovery periods. This study highlights the potential of hyperspectral imaging and machine learning in evaluating the physiological state of conifer seedlings, demonstrating promising applications in forest tree physiology research and tree breeding.
Evaluating the effect of the SMART intervention in people with recently diagnosed breast cancer who are being treated at a public tertiary hospital in Australia: protocol and statistical analysis plan for a single-blinded, single centre randomised controlled trial
Introduction Adults undergoing treatment for breast cancer (BC) are advised to participate in regular exercise. However, many struggle to exercise consistently due to the side effects of systemic treatments including nausea, fatigue, and pain. In adults with newly diagnosed BC, this trial will evaluate the effectiveness of a new exercise intervention, compared with usual care, on outcomes including health-related quality of life (HRQoL). Materials This randomised controlled trial is underway at an Australian tertiary hospital. The protocol was prospectively registered (Australian New Zealand Clinical Trials RegistryACTRN12623001168640p). Consenting adults with BC diagnosed within the prior six months, with planned chemotherapy and/or endocrine treatment will be randomised to an intervention or control group. Both groups receive usual physiotherapy and medical care. Those allocated to the intervention group are offered participation in the ‘SMART’ intervention (Self-determined, Monitored, Adaptable, Rehabilitation with Telehealth support). This involves 16-weeks of tailored, one-on-one physiotherapy-led exercise sessions including behaviour change techniques and the weekly goal of completing 150 minutes of aerobic exercise and two resistance training sessions. The primary outcome is HRQoL and secondary outcomes include physical assessments (muscle strength, exercise tolerance, body composition), healthcare utilisation, workplace absenteeism, mood, psychological determinants of behaviour change, chemotherapy completion rates and endocrine therapy completion. All outcomes are measured prior to randomisation and 16 weeks following randomisation. Additional assessments of all outcomes (excluding the physical assessment) occur at 8 weeks and 52 weeks following randomisation. Ongoing recruitment for two years from June 2024 is expected to achieve a sample size of 260. No results have been analysed. Discussion If the SMART intervention produces favourable change, this will support its adoption in clinical practice. A greater understanding of factors including BC stage, treatment type or variables relating to the exercise program, that influence the magnitude of exercise-induced change on HRQoL will inform future exercise programs.
Covalent modification of a glutamic acid inspired by HaloTag technology
Abstract For targeted covalent protein modification at low-reactivity aspartates and glutamates, new methods are in high demand. We report a technique inspired by the HaloTag technology, which employs nucleophilic substitution at chloroalkane-functionalised ligands by a specific aspartate residue. Embedding of alkyl bromide warheads into non-covalent inhibitors enables covalent modification of a glutamate in the lipoprotein binding chaperone - phosphodiesterase of retinal rod subunit delta (PDEδ), which shuttles prenylated lipoproteins between cellular membranes and thereby mediates their activity. Its hydrophobic ligand-binding pocket contains p.E88 as the only accessible nucleophile for covalent targeting. We show that a covalent inhibitor, termed DeltaTag, overcomes limitations of non-covalent inhibitors. DeltaTag labels PDEδ at its p.E88 under biologically relevant conditions, modulates mammalian target of rapamycin (mTOR) signalling by disrupting the PDEδ-Rheb (Ras homologue enriched in brain)-mTORC1 (mTOR complex 1) axis and inhibits cancer cell proliferation. This proof-of-concept study demonstrates that the design strategy holds promise for the covalent modification of proteins with lipophilic binding sites that lack accessible reactive amino acids but contain specific carboxylates.
Tibetan herbal medicine improved the health status of calves by regulating the antioxidant ability, inflammatory reaction and microbiota of female Yaks
Correction: Absence of ultimate controller and investment efficiency: Evidence from China
Engineered internal architecture of core-shell lipid nanoparticles promotes efficient mRNA endosomal release
Research on surrounding rock control technology of roof cutting and pressure relieving for roadside filling in gob-side entry retaining of large mining height panel
Households’ poverty and inequality after the COVID-19: Insights from panel data of face-to-face surveys in Southeast Asia
The global COVID-19 pandemic has had catastrophic impacts on global economies and human health. The consequences of the COVID-19 pandemic include the fatalities of millions of people and increased poverty. Given the limited evidence at the micro level and on the heterogeneous impacts of the COVID-19, we use panel data of 2,517 households from Thailand and Vietnam to investigate the correlation and heterogeneous effects of the COVID-19 on household income and poverty and to examine the distributional effects on household income. The results show that the COVID-19 has a negative correlation with household income, while it has a positive correlation with the Gini coefficient of income inequality and poverty. Our results also show that there are unequal effects of the COVID-19 on household income, inequality, and poverty at the micro level. Further, the COVID-19 has the highest negative impact on daily per capita income of households in the 10th and 25th quantile groups. Policy implications are proposed to support households in disadvantageous groups.
Neglected tropical diseases: the need for an integrated approach to achieve the 2030 roadmap
Riprap mitigation of downstream scour at grade-control structures considering tailwater depth and layer thickness
Spinal cord perfusion pressure protocol for acute spinal cord injury: Pragmatic implementation and early results at two sites
Study design Retrospective chart review. Objective Describe safety/feasibility of implementing a novel clinical protocol for acute spinal cord injury (SCI) management. Summary of background data Spinal cord perfusion pressure (SCPP) has emerged as a promising target for the medical management of SCI patients. We report our early experience implementing a pragmatic SCPP-driven clinical protocol to supplant conventional mean arterial pressure (MAP) monitoring in the setting of acute SCI. Methods We retrospectively reviewed charts of all SCI patients managed by our SCPP protocol since its adoption at two clinical sites as of 2/1/2023. The SCPP protocol was applied for all adult SCI patients of any injury grade, at any injury level with cord tissue involvement. Intrathecal pressure (ITP) was transduced by lumbar drain (LD). MAP was determined from invasive blood pressure recordings. SCPP was calculated as the difference between MAP and ITP, with an SCPP goal of >65mmHg. Results Eighteen patients have been treated since our SCPP protocol was adopted. Patients were predominately male (77.8%); the average age was 52.0 ± 16.2 years. Most injuries involved the cervical segment (72.2%), all of which were manifest clinically as central cord syndrome. The most common presenting injury severity was ASIA Impairment Scale D (44.4%). All patients underwent surgical intervention. There were no complications related to surgery, LD placement, or LD maintenance/ITP transduction during hospitalization. The SCPP protocol was continued for an average 5.2 ± 1.8 days. Eight patients required vasopressor support (44.4%) during that period, for an average 3.1 ± 2.1 days. Five patients underwent therapeutic CSF drainage to augment SCPP (27.8%). All patients maintained an average SCPP above goal for the duration of monitoring. Conclusions This study further establishes the safety and feasibility of monitoring SCPP via LD measurement of ITP in acute SCI patients treated by clinical protocol at two clinical sites. There were no complications related to LD placement/maintenance or SCPP monitoring.
Briefing Chat: What Brazilian centenarians could reveal about the science of ageing
Association-induced folding governs surrogate light chain and pre-B cell receptor core assembly
Abstract Binding of the surrogate light chain (SLC) to the heavy chain (HC) of the pre-B cell receptor (preBCR) is an important quality control checkpoint during B cell development as roughly 50% of the rearranged HCs are defective. Unlike the regular light chain (LC), the SLC is a hetero-dimer of VpreB and λ5, both containing unstructured extensions, the unique regions. The molecular mechanisms that underlie the complex assembly processes which give rise to the final pre-BCR is not fully understood. Here we show, via reconstitution of the pre-BCR in vitro and in cells that λ5 plays a key role in the pre-BCR assembly. During SLC assembly, a β-strand, located between the λ5 domain and the unique region, induces structure in the largely unfolded VpreB, creating a high affinity complex. In addition, association of λ5 with the unstructured HC C H 1 domain is required for its folding. This is essential for pre-BCR assembly and its release from the endoplasmic reticulum (ER). Finally, the unique region of λ5 plays a pivotal role in the antigen interaction of the SLC-HC complex. Together, our results reveal a multi-step mechanism for SLC and pre-BCR assembly, governed by association-induced folding reactions required for structural integrity and function.
Computational strategies for unraveling insights from known inhibitors for further lead optimization: A case study on Celecoxib analogues
Transcriptome profiling indicates varied gene responses to Pasteurella multocida mutant infections in cattle
Pasteurella multocida is a pathogen that causes bovine respiratory disease, and the development of an effective vaccine is important for improving animal health. Live-attenuated vaccines induce a long-lasting immune response with minimal side effects. The objective of this study was to evaluate potential live vaccine candidates from three P. multocida mutants produced by separately disrupting the genes of filamentous hemagglutinin 2 ( fhaB2 ) , hydrogenase-1 operon ( hyaE ) , and n-acylneuraminate-9-phosphatase ( nanP ) of a serogroup 3 strain (P1062, WT) by clinical testing and transcriptome analysis. Challenge with WT and the three mutants conferred protection against P. multocida , with less lung lesions (4.7–6.2%) compared to 22.4% in the sham group. Transcriptome analysis identified 807 differentially expressed protein-coding transcripts (DETs) in the blood and 6473 DETs in the liver compared to the sham, WT, and each of the mutants. In total, 15 and 64 differentially expressed microRNAs (DEmiRNAs) and 12 and 74 differentially expressed long non-coding RNAs (DElncRNAs) were identified in blood and liver, respectively. The DEmiRNAs were not significantly associated with the DETs within each comparison. DElncRNAs were associated with 12 and 170 DETs in blood and liver respectively. The greatest number of unique DETs were found between hyaE and sham groups in the liver, which agreed with the low colonization rate in the nares and palatine tonsils. For the DETs between sham and WT the under-enriched gene ontology terms in blood were all included in the liver for the DETs identified by WT vs. sham, nanP vs. sham, and hyaE vs. sham, and were related to the signaling pathway, stimulus, and sensory perceptions in biological processes with the molecular function of olfactory receptor activity. The number of identified DETs, decreased percentage of lung lesions, and colonization rates indicate that fhaB2 could be a promising vaccine candidate.
Dynamic stretching beyond electron transfer in a homointerpenetrated metal‒organic framework for enhanced Fenton-like reactions
Synthesis and characterization of activated carbon from acrylic acid-modified black liquor of sugarcane bagasse for enhanced cadmium removal
Streptococcus pneumoniae upregulates Toll2, Toll9, and defensin genes in Bombyx larvae infection model
Pneumococcal diseases caused by the human pathogenic bacterium Streptococcus pneumoniae are a major public health concern worldwide. In this study, we examined the pathogenicity of a clinical isolate of S. pneumoniae in the silk moth, Bombyx mori , larvae infection model. The whole genome sequencing of a clinical isolate of S. pneumoniae , Spn1 identified the presence of genes responsible for its virulence and antibiotic resistance. Spn1 infection of Bombyx larvae resulted in death within 24 h concomitant with an increase of phenoloxidase activity in the hemolymph. The bacterial load increased in the hemolymph within 9 h post-infection (p.i.) Ampicillin, ceftriaxone, tetracycline, imipenem, and erythromycin showed therapeutic effect in infected larvae, although the bacterial strain was resistant to erythromycin in vitro . The Bombyx homologs of mammalian TLR2 and TLR4 , known as BmToll2 and BmToll9 ( BmToll9−1 and BmToll9−2 isoforms), were upregulated in both the fat body and trachea. The antimicrobial peptide (AMP) genes, BmdefensinA and BmdefensinB , known to be regulated by the Toll signaling pathway, were significantly upregulated in both fat body and trachea after S. pneumoniae infection through hemolymph. Our data indicate that the Bombyx larvae can be a suitable infection model to study the pathogenicity of S. pneumoniae .
Engineered alcohol oxidases catalyse transesterification in aqueous media without competing hydrolysis
Abstract Transesterification reactions are fundamental transformations in organic chemistry, yet performing them in aqueous media is challenging because of the competing hydrolysis reaction. In this study, we describe a mutant of alcohol oxidase from Phanerochaete chrysosporium ( Pc AOx-VPN) that also exhibits transesterification activity. Moreover, Pc AOx-VPN displays no detectable hydrolytic activity, owing to its hydrophobic active site, which effectively excludes water. These characteristics make Pc AOx-VPN a promising catalyst for transesterification reactions in aqueous media, a context that is typically compromised by competing hydrolysis.