RCPA: An Open-Source R Package for Data Processing, Differential Analysis, Consensus Pathway Analysis, and Visualization.

Identifying impacted pathways is important because it provides insights into the biology underlying conditions beyond the detection of differentially expressed genes. Because of the importance of such analysis, more than 100 pathway analysis methods have been developed thus far. Despite the availability of many methods, it is challenging for biomedical researchers to learn and properly perform pathway analysis. First, the sheer number of methods makes it challenging to learn and choose the correct method for a given experiment. Second, computational methods require users to be savvy with coding syntax, and comfortable with command-line environments, areas that are unfamiliar to most life scientists. Third, as learning tools and computational methods are typically implemented only for a few species (i.e., human and some model organisms), it is difficult to perform pathway analysis on other species that are not included in many of the current pathway analysis tools. Finally, existing pathway tools do not allow researchers to combine, compare, and contrast the results of different methods and experiments for both hypothesis testing and analysis purposes. To address these challenges, we developed an open-source R package for Consensus Pathway Analysis (RCPA) that allows researchers to conveniently: (1) download and process data from NCBI GEO; (2) perform differential analysis using established techniques developed for both microarray and sequencing data; (3) perform both gene set enrichment, as well as topology-based pathway analysis using different methods that seek to answer different research hypotheses; (4) combine methods and datasets to find consensus results; and (5) visualize analysis results and explore significantly impacted pathways across multiple analyses. This protocol provides many example code snippets with detailed explanations and supports the analysis of more than 1000 species, two pathway databases, three differential analysis techniques, eight pathway analysis tools, six meta-analysis methods, and two consensus analysis techniques. The package is freely available on the CRAN repository. © 2024 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Processing Affymetrix microarrays Basic Protocol 2: Processing Agilent microarrays Support Protocol: Processing RNA sequencing (RNA-Seq) data Basic Protocol 3: Differential analysis of microarray data (Affymetrix and Agilent) Basic Protocol 4: Differential analysis of RNA-Seq data Basic Protocol 5: Gene set enrichment analysis Basic Protocol 6: Topology-based (TB) pathway analysis Basic Protocol 7: Data integration and visualization.

Microencapsulation of noni fruit extract using gum arabic and maltodextrin - Optimization, stability and efficiency.

Noni fruit (Morinda citrifolia L.) has many health-supporting compounds, but its biological extracts need protection against environmental impacts for stability and efficiency. To address this, microencapsulation is an advanced technology in food applications that require optimization of coating component and temperature regime. Gum arabic (GA) and maltodextrin (MD) were suitably combined at 2:1 ratio, which showed good and stable structure as well as successful microencapsulation efficiency of the enzymatic-ultrasonic assisted noni extract. A coating density of 20 % for the GA:MD formula was with highest performance. The heat setting of spray drying was optimized at 175 and 82 °C for inlet and outlet, respectively using response surface methodology with experimental validation of maximized TFC and TSC at 88.3 and 90.3 %, respectively. Noni microencapsulated powder was assessed via a series of reliably advanced techniques such as microscopy, spectrophotometry, diffraction, and calorimetry for structural properties. Noni powder was additionally tested for storage stability, heat exposure stability, and release efficiency in pH condition and in vitro digestive tract. Promising results were obtained with at least one year storage stability, better microcapsule stability at 60 and 100 °C, quite good release at pH 7.4, and suitable release efficiency in digestive tract simulation. These properties of microencapsulated noni powder open further scalability potential and various industrial applications.

TSG-6-Mediated Extracellular Matrix Modifications Regulate Hypoxic-Ischemic Brain Injury.

Proteoglycans containing link domains modify the extracellular matrix (ECM) to regulate cellular homeostasis and can also sensitize tissues/organs to injury and stress. Hypoxic-ischemic (H-I) injury disrupts cellular homeostasis by activating inflammation and attenuating regeneration and repair pathways. In the brain, the main component of the ECM is the glycosaminoglycan hyaluronic acid (HA), but whether HA modifications of the ECM regulate cellular homeostasis and response to H-I injury is not known. In this report, employing both male and female mice, we demonstrate that link-domain-containing proteoglycan, TNFα-stimulated gene-6 (TSG-6), is active in the brain from birth onward and differentially modifies ECM HA during discrete neurodevelopmental windows. ECM HA modification by TSG-6 enables it to serve as a developmental switch to regulate the activity of the Hippo pathway effector protein, yes-associated protein 1 (YAP1), in the maturing brain and in response to H-I injury. Mice that lack TSG-6 expression display dysregulated expression of YAP1 targets, excitatory amino acid transporter 1 (EAAT1; glutamate-aspartate transporter) and 2 (EAAT2; glutamate transporter-1). Dysregulation of YAP1 activation in TSG-6-/- mice coincides with age- and sex-dependent sensitization of the brain to H-I injury such that 1-week-old neonates display an anti-inflammatory response in contrast to an enhanced proinflammatory injury reaction in 3-month-old adult males but not females. Our findings thus support that a key regulator of age- and sex-dependent H-I injury response in the mouse brain is modulation of the Hippo-YAP1 pathway by TSG-6-dependent ECM modifications.

Fourteen years of cellular deconvolution: methodology, applications, technical evaluation and outstanding challenges.

Single-cell RNA sequencing (scRNA-Seq) is a recent technology that allows for the measurement of the expression of all genes in each individual cell contained in a sample. Information at the single-cell level has been shown to be extremely useful in many areas. However, performing single-cell experiments is expensive. Although cellular deconvolution cannot provide the same comprehensive information as single-cell experiments, it can extract cell-type information from bulk RNA data, and therefore it allows researchers to conduct studies at cell-type resolution from existing bulk datasets. For these reasons, a great effort has been made to develop such methods for cellular deconvolution. The large number of methods available, the requirement of coding skills, inadequate documentation, and lack of performance assessment all make it extremely difficult for life scientists to choose a suitable method for their experiment. This paper aims to fill this gap by providing a comprehensive review of 53 deconvolution methods regarding their methodology, applications, performance, and outstanding challenges. More importantly, the article presents a benchmarking of all these 53 methods using 283 cell types from 30 tissues of 63 individuals. We also provide an R package named DeconBenchmark that allows readers to execute and benchmark the reviewed methods (https://github.com/tinnlab/DeconBenchmark).

Premise setting for sustainable developing adsorption in environmental remediation using graphitic carbon nitride@agar-derived porous carbon composite.

In the adsorption process for wastewater treatment, the adsorbent plays an important role. A composite adsorptive material composed of graphitic carbon nitride and agar-derived porous carbon (CNPC) was fabricated from simple precursors (melamine, thiourea, and agar) and through a facile procedure with different melamine and thiourea ratios. Characterization of CNPC proved a successful formation of a porous structure consisting of mesopores and macropores, wherein CNPC holds distinctive electrochemical (lowered resistance and higher specific capacity) and photochemical properties (lowered bandgap to 2.33 eV) thanks to the combination of graphitic carbon nitride (CN) and agar-derived porous carbon (PC). Inheriting the immanent nature, CNPC was subjected to the adsorption of methylene blue (MB) dye in an aqueous solution. The highest adsorption capacity was 133 mg/g for CNPC-4 which was prepared using a melamine to thiourea ratio of 4:4 - equivalent to the removal rate of 53.2 % and following the pseudo-I-order reaction rate. The effect of pH points out that pH 7 and 9 were susceptible to maximum removal and pretreatment is not required while the optimal ratio of 7.5 mg of MB and 30 mg of material was also determined to yield the highest performance. Furthermore, the reusability of the material for three consecutive cycles was evaluated based on two methods pyrolysis at 200 °C and photocatalytic degradation by irradiation under visible light. In general, the photocatalytic regeneration pathway is more ample and efficient than pyrolysis in terms of energy efficiency (saving energy over 10 times) and adsorption capacity stability. As a whole, the construction of accessible regenerative and stable adsorbent could be a venturing step into the sustainable development spearhead for industries.

Thermo-priming triggers species-specific physiological and transcriptome responses in Mediterranean seagrasses.

Heat-priming improves plants' tolerance to a recurring heat stress event. The underlying molecular mechanisms of heat-priming are largely unknown in seagrasses. Here, ad hoc mesocosm experiments were conducted with two Mediterranean seagrass species, Posidonia oceanica and Cymodocea nodosa. Plants were first exposed to heat-priming, followed by a heat-triggering event. A comprehensive assessment of plant stress response across different levels of biological organization was performed at the end of the triggering event. Morphological and physiological results showed an improved response of heat-primed P. oceanica plants while in C. nodosa both heat- and non-primed plants enhanced their growth rates at the end of the triggering event. As resulting from whole transcriptome sequencing, molecular functions related to several cellular compartments and processes were involved in the response to warming of non-primed plants, while the response of heat-primed plants involved a limited group of processes. Our results suggest that seagrasses acquire a primed state during the priming event, that eventually gives plants the ability to induce a more energy-effective response when the thermal stress event recurs. Different species may differ in their ability to perform an improved heat stress response after priming. This study provides pioneer molecular insights into the emerging topic of seagrass stress priming and may benefit future studies in the field.

Caspase-3-Responsive, Fluorogenic Bivalent Bottlebrush Polymers.

Controlling the access of proteases to cleavable peptides placed at specific locations within macromolecular architectures represents a powerful strategy for biologically responsive materials design. Here, we report the synthesis of peptide-containing bivalent bottlebrush (co)polymers (BBPs) featuring polyethylene glycol (PEG) and 7-amino-4-methylcoumarin (AMC) pendants on each backbone repeat unit. The AMCs are linked via caspase-3-cleavable peptides which, upon enzymatic cleavage, provide a "turn-on" fluorescence signal due to the release of free AMC. Time-dependent fluorscence measurements demonstrate that the caspase-3-induced peptide cleavage and AMC release from BBPs is strongly dependent on the BBP backbone length and the AMC-peptide linker location within the BBP architecture, revealing fundamental insights into the interactions of enzymes with BBPs.

Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences.

Repeat RNA sequences self-associate to form condensates. Simulations of a coarse-grained single-interaction site model for (CAG)n (n = 30 and 31) show that the salt-dependent free energy gap, ΔGS, between the ground (perfect hairpin) and the excited state (slipped hairpin (SH) with one CAG overhang) of the monomer for (n even) is the primary factor that determines the rates and yield of self-assembly. For odd n, the free energy (GS) of the ground state, which is an SH, is used to predict the self-association kinetics. As the monovalent salt concentration, CS, increases, ΔGS and GS increase, which decreases the rates of dimer formation. In contrast, ΔGS for shuffled sequences, with the same length and sequence composition as (CAG)31, is larger, which suppresses their propensities to aggregate. Although demonstrated explicitly for (CAG) polymers, the finding of inverse correlation between the free energy gap and RNA aggregation is general.

Palliative procedures for malignant gastric outlet obstruction: A network meta-analysis.

BACKGROUND: The optimal treatment for malignant gastric outlet obstruction (GOO) remains uncertain. The aim of this systematic review was to comprehensively investigate the efficacy and safety of four palliative treatments for malignant GOO: gastrojejunostomy (GJ), endoscopic ultrasound-guided gastroenterostomy (EGE), stomach-partitioning gastrojejunostomy (PGJ), and endoscopic stenting (ES). METHODS: We searched the PubMed, Embase, Cochrane Library, Scopus, and Web of Science databases; ClinicalTrials.gov; and the World Health Organization International Clinical Trials Registry Platform for randomized controlled trials (RCTs) and cohort studies comparing the aforementioned treatments for malignant GOO. We included studies that reported at least one of the following clinical outcomes: clinical success, 30-day mortality, reintervention rate, or length of hospital stay. Evidence from RCTs and non-RCTs was naïve combined to perform network meta-analysis through the frequentist approach using an inverse variance model. Treatments were ranked by P-score. RESULTS: This network meta-analysis included 3417 patients from 4 RCTs, 4 prospective cohort studies, and 32 retrospective cohort studies. PGJ was the optimal approach in terms of clinical success and reintervention (P-scores: 0.95 and 0.90, respectively). EGE had the highest probability of being the optimal treatment in terms of 30-day mortality and complications (P-scores: 0.82 and 0.99, respectively). Cluster ranking to combine the P-scores for 30-day mortality and reintervention indicated the benefits of PGJ and EGE (cophenetic correlation coefficient: 0.94; PGJ and EGE were in the same cluster). CONCLUSION: PGJ and EGE are recommended for malignant GOO. PGJ could be the alternative choice in centers with limited resources or cases unsuitable for EGE.

A single institution anesthetic experience with catheterization of pediatric pulmonary hypertension patients.

Cardiac catheterization remains the gold standard for the diagnosis and management of pediatric pulmonary hypertension (PH). There is lack of consensus regarding optimal anesthetic and airway regimen. This retrospective study describes the anesthetic/airway experience of our single center cohort of pediatric PH patients undergoing catheterization, in which obtaining hemodynamic data during spontaneous breathing is preferential. A total of 448 catheterizations were performed in 232 patients. Of the 379 cases that began with a natural airway, 274 (72%) completed the procedure without an invasive airway, 90 (24%) received a planned invasive airway, and 15 (4%) required an unplanned invasive airway. Median age was 3.4 years (interquartile range [IQR] 0.7-9.7); the majority were either Nice Classification Group 1 (48%) or Group 3 (42%). Vasoactive medications and cardiopulmonary resuscitation were required in 14 (3.7%) and eight (2.1%) cases, respectively; there was one death. Characteristics associated with use of an invasive airway included age <1 year, Group 3, congenital heart disease, trisomy 21, prematurity, bronchopulmonary dysplasia, WHO functional class III/IV, no PH therapy at time of case, preoperative respiratory support, and having had an intervention (p < 0.05). A composite predictor of age <1 year, Group 3, prematurity, and any preoperative respiratory support was significantly associated with unplanned airway escalation (26.7% vs. 6.9%, odds ratio: 4.9, confidence interval: 1.4-17.0). This approach appears safe, with serious adverse event rates similar to previous reports despite the predominant use of natural airways. However, research is needed to further investigate the optimal anesthetic regimen and respiratory support for pediatric PH patients undergoing cardiac catheterization.

Objective assessment of postural ergonomics in neurosurgery: integrating wearable technology in the operating room.

OBJECTIVE: Physical stress associated with the static posture of neurosurgeons over prolonged periods can result in fatigue and musculoskeletal disorders. Objective assessment of surgical ergonomics may contribute to postural awareness and prevent further complications. This pilot study examined the feasibility of using wearable technology as a biofeedback tool to address this gap. METHODS: Ten neurosurgeons, including 5 attendings (all faculty) and 5 trainees (1 fellow, 4 residents), were recruited and equipped with two wearable sensors attached to the back of their head and their upper back. The sensors collected the average time spent in extended (≤ -10°), neutral (> -10° and < 10°), and flexed (≥ 10°) static postures (undetected activity for more than 10 seconds) during spine and cranial procedures. Feasibility outcomes aimed for more than 70% of accurate data collection. Exploratory outcomes included the comparison of postural variability within and between participants adjusted to their demographics excluding nonrelated surgical activities, and postoperative self-assessment surveys. RESULTS: Sixteen (80%) of 20 possible recordings were successfully collected and analyzed from 11 procedures (8 spine, 3 cranial). Surgeons maintained a static posture during 52.7% of the active surgical time (mean 1.58 hrs). During spine procedures, all surgeons used an exoscope while standing, leading to a significantly longer time spent in a neutral static posture (p < 0.001, partial η2 = 0.14): attendings remained longer in a neutral static posture (36.4% ± 15.3%) than in the extended (9% ± 6.3%) and flexed (5.7% ± 3.4%) static postures; trainees also remained longer in a neutral static posture (30.2% ± 13.8%) than in the extended (11.1% ± 6.3%) and flexed (11.9% ± 6.6%) static postures. During cranial procedures, surgeons intermittently transitioned between standing/exoscope use and sitting/microscope use, with trainees spending a shorter time in a neutral static posture (16.3% vs 48.5%, p < 0.001) and a longer time in a flexed static posture (18.5% vs 2.7%, p < 0.001) compared with attendings. Additionally, longer cranial procedures correlated with surgeons spending a longer time (r = 0.94) in any static posture (extended, flexed, and neutral), with taller surgeons exhibiting longer periods in flexed and extended static postures (r = 0.86). Postoperative self-assessment revealed that attendings perceived spine procedures as more difficult than trainees (p = 0.029), while trainees found cranial procedures to be of greater difficulty than spine procedures (p = 0.012). Attendings felt more stressed (p = 0.048), less calmed (p = 0.024), less relaxed (p = 0.048), and experienced greater stiffness in their upper body (p = 0.048) and more shoulder pain (p = 0.024) during cranial versus spine procedures. CONCLUSIONS: Wearable technology is feasible to assess postural ergonomics and provide objective biofeedback to neurosurgeons during spine and cranial procedures. This study showed reproducibility for future comparative protocols focused on correcting posture and surgical ergonomic education.

Pituitary Suppression with Gonadotropin-Releasing Hormone Agonist Prior to Artificial Endometrial Preparation in Frozen-Thawed Embryo Transfer Cycles: A Systematic Review and Meta-Analysis of Different Protocols and Infertile Populations.

This study investigates the effect of GnRHa pretreatment on pregnancy outcomes in artificial endometrial preparation for frozen-thawed embryo transfer (AC-FET) cycles. A systematic review of English language studies published before 1 September 2022, was conducted, excluding conference papers and preprints. Forty-one studies involving 43,021 participants were analyzed using meta-analysis, with a sensitivity analysis ensuring result robustness. The study found that GnRHa pretreatment generally improved the clinical pregnancy rate (CPR), implantation rate (IR), and live birth rate (LBR). However, discrepancies existed between randomized controlled trials (RCTs) and observational studies; RCTs showed no significant differences in outcomes for GnRHa-treated cycles. Depot GnRHa protocols outperformed daily regimens in LBR. Extended GnRHa pretreatment (two to five cycles) significantly improved CPR and IR compared to shorter treatment. Women with polycystic ovary syndrome (PCOS) saw substantial benefits from GnRHa pretreatment, including improved CPR and LBR and reduced miscarriage rates. In contrast, no significant benefits were observed in women with regular menstruation. More rigorous research is needed to solidify these findings.

Effectiveness of Non-Pharmacological Interventions for Dementia among the Elderly: A Randomized Controlled Trial.

(1) Background: Up until now, there is still no medicine that can cure dementia, but there are some that can only help slow down the progression of the disease and reduce some symptoms. Pharmacological interventions for dementia have many side effects and are expensive, so non-pharmacological treatments for dementia become more urgent. This study aimed to evaluate the effectiveness of multifactorial non-pharmacological interventions in dementia patients; (2) Methods: This is a randomized controlled trial conducted in Hai Duong from July 2021 to December 2022. Selected subjects included 88 patients diagnosed with very mild, mild, and moderate dementia, of whom 44 patients were assigned to the intervention group and 44 patients to the control group; (3) Results: For the effectiveness of the non-pharmacological multifactorial intervention on depression severity: in the intervention group, the GDS 15 depression score decreased from 4.8 to 2.9, while, in the control group, the GDS 15 depression score increased by 1.3 points after six months of no intervention. For the effect of the non-pharmacological multifactorial intervention on the level of sleep disturbance, in the intervention group, the PSQI sleep disturbance score decreased by nearly half (from 10.2 to 5.6), while, in the control group, this trend was not clear. For the effect of the non-pharmacological multifactorial intervention on daily functioning: in the intervention group, the ADL and IADL scores improved (1.02 ± 1.32 and 1.23 ± 1.75), while, in the control group, the ADL and IADL scores decreased (0.93 ± 1.2 and 0.98 ± 2.19). For the effect of the non-pharmacological multifactorial intervention on quality of life: in the intervention group, the EQ-5D-5L scores improved (0.17 ± 0.19), while, in the control group, the EQ-5D-5L scores decreased (0.20 ± 0.30); (4) Conclusions: Non-pharmacological multifactorial interventions, including physical activity, cognitive training, listening to educational lectures, and organizing miniature social models, have been shown to improve mental health, self-control, and quality of life.

A Comprehensive Evaluation of Dioxins and Furans Occurrence in River Sediments from a Secondary Steel Recycling Craft Village in Northern Vietnam.

This first study investigated the presence of dioxins and furans in river sediments around a craft village in Vietnam, focusing on Secondary Steel Recycling. Sediment samples were collected from various locations along the riverbed near the Da Hoi Secondary Steel Recycling village in Bac Ninh province. The analysis was conducted using a HRGC/HRMS-DFS device, detecting a total of 17 dioxin/furan isomers in all samples, with an average total concentration of 288.86 ng/kg d.w. The concentrations of dioxin/furan congeners showed minimal variation among sediment samples, ranging from 253.9 to 344.2 ng/kg d.w. The predominant compounds in the dioxin group were OCDD, while in the furan group, they were 1,2,3,4,6,7,8-HpCDF and OCDF. The chlorine content in the molecule appeared to be closely related to the concentration of dioxins and their percentage distribution. However, the levels of furan isomers did not vary significantly. The distribution of these compounds was not dependent on the flow direction, as they were mainly found in solid waste and are not water-soluble. Although the hepta and octa congeners had high concentrations, when converted to TEQ values, the tetra and penta groups (for dioxins) and the penta and hexa groups (for furans) contributed more to toxicity. Furthermore, the source of dioxins in sediments at Da Hoi does not only originate from steel recycling production activities but also from other combustion sites. The average total toxicity was 10.92 ng TEQ/kg d.w, ranging from 4.99 to 17.88 ng TEQ/kg d.w, which did not exceed the threshold specified in QCVN 43:2017/BTNMT, the National Technical Regulation on Sediment Quality. Nonetheless, these levels are still concerning. The presence of these toxic substances not only impacts aquatic organisms in the sampled water environment but also poses potential health risks to residents living nearby.

Rifampicin resistant Mycobacterium tuberculosis in Vietnam, 2020-2022.

Objective: We conducted a descriptive analysis of multi-drug resistant tuberculosis (MDR-TB) in Vietnam's two largest cities, Hanoi and Ho Chi Minh city. Methods: All patients with rifampicin resistant tuberculosis were recruited from Hanoi and surrounding provinces between 2020 and 2022. Additional patients were recruited from Ho Chi Minh city over the same time period. Demographic data were recorded from all patients, and samples collected, cultured, whole genome sequenced and analysed for drug resistance mutations. Genomic susceptibility predictions were made on the basis of the World Health Organization's catalogue of mutations in Mycobacterium tuberculosis associated with drug resistance, version 2. Comparisons were made against phenotypic drug susceptibility test results where these were available. Multivariable logistic regression was used to assess risk factors for previous episodes of tuberculosis. Results: 233/265 sequenced isolates were of sufficient quality for analysis, 146 (63 %) from Ho Chi Minh City and 87 (37 %) from Hanoi. 198 (85 %) were lineage 2, 20 (9 %) were lineage 4, and 15 (6 %) were lineage 1. 17/211 (8 %) for whom HIV status was known were infected, and 109/214 (51 %) patients had had a previous episode of tuberculosis. The main risk factor for a previous episode was HIV infection (odds ratio 5.1 (95 % confidence interval 1.3-20.0); p = 0.021). Sensitivity for predicting first-line drug resistance from whole genome sequencing data was over 90 %, with the exception of pyrazinamide (85 %). For moxifloxacin and amikacin it was 50 % or less. Among rifampicin-resistant isolates, prevalence of resistance to each non-first-line drug was < 20 %. Conclusions: Drug resistance among most MDR-TB strains in Vietnam's two largest cities is confined largely to first-line drugs. Living with HIV is the main risk factor among patients with MDR-TB for having had a previous episode of tuberculosis.

Ophthalmate is a new regulator of motor functions via CaSR: Implications for movement disorders.

Dopamine's role as the principal neurotransmitter in motor functions has long been accepted. We broaden this conventional perspective by demonstrating the involvement of non-dopaminergic mechanisms. In mouse models of Parkinson's Disease (PD), we observed that L-DOPA elicited a substantial motor response even when its conversion to dopamine was blocked by inhibiting the enzyme aromatic amino acid decarboxylase (AADC). Remarkably, the motor activity response to L-DOPA in the presence of an AADC inhibitor (NSD1015) showed a delayed onset, yet greater intensity and longer duration, peaking at 7 hours, compared to when L-DOPA was administered alone. This suggests an alternative pathway or mechanism, independent of dopamine signaling, mediating the motor functions. We sought to determine the metabolites associated with the pronounced hyperactivity observed, using comprehensive metabolomics analysis. Our results revealed that the peak in motor activity induced by NSD1015/L-DOPA in PD mice is associated with a surge (20-fold) in brain levels of the tripeptide ophthalmic acid (OA, also known as ophthalmate in its anionic form). Interestingly, we found that administering ophthalmate directly to the brain rescued motor deficits in PD mice in a dose-dependent manner. We investigated the molecular mechanisms underlying ophthalmate's action and discovered, through radioligand binding and cAMP-luminescence assays, that ophthalmate binds to and activates the calcium-sensing receptor (CaSR). Additionally, our findings demonstrated that a CaSR antagonist inhibits the motor-enhancing effects of ophthalmate, further solidifying the evidence that ophthalmate modulates motor functions through the activation of the CaSR. The discovery of ophthalmate as a novel regulator of motor function presents significant potential to transform our understanding of brain mechanisms of movement control and the therapeutic management of related disorders.

An organometallic swap strategy for bottlebrush polymer-protein conjugate synthesis.

Polymer-protein bioconjugation offers a powerful strategy to alter the physical properties of proteins, and various synthetic polymer compositions and architectures have been investigated for this purpose. Nevertheless, conjugation of molecular bottlebrush polymers (BPs) to proteins remains an unsolved challenge due to the large size of BPs and a general lack of methods to transform the chain ends of BPs into functional groups suitable for bioconjugation. Here, we present a strategy to address this challenge in the context of BPs prepared by "graft-through" ring-opening metathesis polymerization (ROMP), one of the most powerful methods for BP synthesis. Quenching ROMP of PEGylated norbornene macromonomers with an activated enyne terminator facilitates the transformation of the BP Ru alkylidene chain ends into Pd oxidative addition complexes (OACs) for facile bioconjugation. This strategy is shown to be effective for the synthesis of two BP-protein conjugates (albumin and ERG), setting the stage for a new class of BP-protein conjugates for future therapeutic and imaging applications.

Natural variables separate the endemic areas of Clonorchis sinensis and Opisthorchis viverrini along a continuous, straight zone in Southeast Asia.

BACKGROUND: Clonorchiasis and opisthorchiasis, caused by the liver flukes Clonorchis sinensis and Opisthorchis viverrini respectively, represent significant neglected tropical diseases (NTDs) in Asia. The co-existence of these pathogens in overlapping regions complicates effective disease control strategies. This study aimed to clarify the distribution and interaction of these diseases within Southeast Asia. METHODS: We systematically collated occurrence records of human clonorchiasis (n = 1809) and opisthorchiasis (n = 731) across the Southeast Asia countries. Utilizing species distribution models incorporating environmental and climatic data, coupled machine learning algorithms with boosted regression trees, we predicted and distinguished endemic areas for each fluke species. Machine learning techniques, including geospatial analysis, were employed to delineate the boundaries between these flukes. RESULTS: Our analysis revealed that the endemic range of C. sinensis and O. viverrini in Southeast Asia primarily spans across part of China, Vietnam, Thailand, Laos, and Cambodia. During the period from 2000 to 2018, we identified C. sinensis infections in 84 distinct locations, predominantly in southern China (Guangxi Zhuang Autonomous Region) and northern Vietnam. In a stark contrast, O. viverrini was more widely distributed, with infections documented in 721 locations across Thailand, Laos, Cambodia, and Vietnam. Critical environmental determinants were quantitatively analyzed, revealing annual mean temperatures ranging between 14 and 20 °C in clonorchiasis-endemic areas and 24-30 °C in opisthorchiasis regions (P < 0.05). The machine learning model effectively mapped a distinct demarcation zone, demonstrating a clear separation between the endemic areas of these two liver flukes with AUC from 0.9 to1. The study in Vietnam delineates the coexistence and geographical boundaries of C. sinensis and O. viverrini, revealing distinct endemic zones and a transitional area where both liver fluke species overlap. CONCLUSIONS: Our findings highlight the critical role of specific climatic and environmental factors in influencing the geographical distribution of C. sinensis and O. viverrini. This spatial delineation offers valuable insights for integrated surveillance and control strategies, particularly in regions with sympatric transmission. The results underscore the need for tailored interventions, considering regional epidemiological variations. Future collaborations integrating eco-epidemiology, molecular epidemiology, and parasitology are essential to further elucidate the complex interplay of liver fluke distributions in Asia.

Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences.

Interplay between divalent cations (Mg2+ and Ca2+) and single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), as well as stacking interactions, is important in nucleosome stability and phase separation in nucleic acids. Quantitative techniques accounting for ion-DNA interactions are needed to obtain insights into these and related problems. Toward this end, we created a sequence-dependent computational TIS-ION model that explicitly accounts for monovalent and divalent ions. Simulations of the rigid 24 base-pair (bp) dsDNA and flexible ssDNA sequences, dT30 and dA30, with varying amounts of the divalent cations show that the calculated excess number of ions around the dsDNA and ssDNA agree quantitatively with ion-counting experiments. Using an ensemble of all-atom structures generated from coarse-grained simulations, we calculated the small-angle X-ray scattering profiles, which are in excellent agreement with experiments. Although ion-counting experiments mask the differences between Mg2+ and Ca2+, we find that Mg2+ binds to the minor grooves and phosphate groups, whereas Ca2+ binds specifically to the minor groove. Both Mg2+ and Ca2+ exhibit a tendency to bind to the minor groove of DNA as opposed to the major groove. The dA30 conformations are dominated by stacking interactions, resulting in structures with considerable helical order. The near cancellation of the favorable stacking and unfavorable electrostatic interactions leads to dT30 populating an ensemble of heterogeneous conformations. The successful applications of the TIS-ION model are poised to confront many problems in DNA biophysics.

Marine fish parasites in the Cat Ba Archipelago, Vietnam: the results of 2010-2023 field surveys.

Between 2010 and 2023, a longitudinal study was undertaken to uncover the diversity of the parasite fauna of marine fishes in the Cat Ba Archipelago, a world biosphere reserve, in Vietnam. A total of 1,042 specimens representing 80 different fish species were collected and examined. Of these, 68 fish species, represented by 994 specimens (95.39%), were infected with parasites. A total of 162 parasitic species were discovered, including 54 trematodes, 37 monogeneans, 27 crustaceans, 15 myxozoans, 10 acanthocephalans, 10 nematodes, 7 cestodes, and 2 hirudineans. Over the course of the survey, twenty new species were described, including 7 acanthocephalans and 13 trematodes. Additionally, twenty species were recorded for the first time from the Cat Ba Archipelago and twenty-two species had new host records reported. The prevalence and mean intensity of parasite infection were found to be unaffected by season. These data on the parasitic fauna of Cat Ba Archipelago not only expand our knowledge of the diversity of Vietnam, but also provide strong baseline data for measuring future change resulting from environmental perturbations.