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Journal of Equine Veterinary Science Jun 2024Mastication is the initial phase of digestion and is crucial to equine health due to its role in saliva production and food particle reduction. Hay nets have been...
Mastication is the initial phase of digestion and is crucial to equine health due to its role in saliva production and food particle reduction. Hay nets have been promoted to slow the rate of hay consumption, with many styles of slow feeders available. Limited research has shown that nets may slow consumption, but no research has examined their effect on the horse's chewing frequency and patterns. The objective of this study was to compare chew frequency (CF, total number of chews/kg consumed) and chew duration (CD, total minutes chewed/kg consumed), as well as distribution of chews over a feeding period, of horses eating bermudagrass hay in three styles of hay nets [large mesh (LM), small mesh (SM), bottom hole (BH)] as compared to a control of loose hay (CTL). Treatments were assigned in a replicated Latin square 4 × 4 using eight horses. Horses were given a 24-hr acclimation period prior to recording their chewing patterns over a 24-hr period using an automated halter fit with a pressure-sensor noseband. Results indicate that CF was not influenced by treatment. However, SM resulted in longer CD as compared to CTL (P=0.007). Additionally, BH resulted in a higher percentage of chews completed in the first 240 min compared to SM (P=0.039), indicating more rapid consumption. Results of this study indicate hay nets may not influence the number of chews a horse performs while masticating hay, but small mesh feeders may increase the CD and reduce early consumption rate.
PubMed: 38908808
DOI: 10.1016/j.jevs.2024.105133 -
Environmental Research Jun 2024To investigate the inhibitory effects of various transition metal ions on nitrogen removal and their underlying mechanisms, the single and combined effects of Cu Ni and...
To investigate the inhibitory effects of various transition metal ions on nitrogen removal and their underlying mechanisms, the single and combined effects of Cu Ni and Zn on Heterotrophic nitrification-aerobic denitrification (HN-AD) bacteria Acinetobacter sp. TAC-1 were studied in a batch experiment system. The results revealed that increasing concentrations of Cu and Ni had a detrimental effect on the removal of ammonium nitrogen (NH-N) and total nitrogen (TN). Specifically, Cu concentration of 10 mg/L, the TN degradation rate was 55.09%, compared to 77.60% in the control group. Cu exhibited a pronounced inhibitory effect. In contrast, Zn showed no apparent inhibitory effect on NH-N removal and even enhanced TN removal at lower concentrations. However, when the mixed ion concentration of Zn+Ni exceeded 5 mg/L, the removal rates of NH-N and TN were significantly reduced. Moreover, transition metal ions did not significantly impact the removal rates of chemical oxygen demand (COD). The inhibition model fitting results indicated that the inhibition sequence was Cu > Zn > Ni. Transcriptome analysis demonstrated that metal ions influence TAC-1 activity by modulating the expression of pivotal genes, including zinc ABC transporter substrate binding protein (znuA), ribosomal protein (rpsM), and chromosome replication initiation protein (dnaA) and DNA replication of TAC-1 under metal ion stress, leading to disruptions in transcription, translation, and cell membrane structure. Finally, a conceptual model was proposed by us to summarize the inhibition mechanism and possible response strategies of TAC-1 bacteria under metal ion stress, and to address the lack of understanding regarding the influence mechanism of TAC-1 on nitrogen removal in wastewater co-polluted by metal and ammonia nitrogen. The results provided practical guidance for the management of transition metal and ammonia nitrogen co-polluted water bodies, as well as the removal of high nitrogen.
PubMed: 38906451
DOI: 10.1016/j.envres.2024.119460 -
Journal of Chemical Theory and... Jun 2024One of the key challenges of -means clustering is the seed selection or the initial centroid estimation since the clustering result depends heavily on this choice....
One of the key challenges of -means clustering is the seed selection or the initial centroid estimation since the clustering result depends heavily on this choice. Alternatives such as -means++ have mitigated this limitation by estimating the centroids using an empirical probability distribution. However, with high-dimensional and complex data sets such as those obtained from molecular simulation, -means++ fails to partition the data in an optimal manner. Furthermore, stochastic elements in all flavors of -means++ will lead to a lack of reproducibility. -means -Ary Natural Initiation (NANI) is presented as an alternative to tackle this challenge by using efficient -ary comparisons to both identify high-density regions in the data and select a diverse set of initial conformations. Centroids generated from NANI are not only representative of the data and different from one another, helping -means to partition the data accurately, but also deterministic, providing consistent cluster populations across replicates. From peptide and protein folding molecular simulations, NANI was able to create compact and well-separated clusters as well as accurately find the metastable states that agree with the literature. NANI can cluster diverse data sets and be used as a standalone tool or as part of our MDANCE clustering package.
PubMed: 38905589
DOI: 10.1021/acs.jctc.4c00308 -
Frontiers in Genetics 2024The recognition of DNA Binding Proteins (DBPs) plays a crucial role in understanding biological functions such as replication, transcription, and repair. Although...
The recognition of DNA Binding Proteins (DBPs) plays a crucial role in understanding biological functions such as replication, transcription, and repair. Although current sequence-based methods have shown some effectiveness, they often fail to fully utilize the potential of deep learning in capturing complex patterns. This study introduces a novel model, LGC-DBP, which integrates Long Short-Term Memory (LSTM), Gated Inception Convolution, and Improved Channel Attention mechanisms to enhance the prediction of DBPs. Initially, the model transforms protein sequences into Position Specific Scoring Matrices (PSSM), then processed through our deep learning framework. Within this framework, Gated Inception Convolution merges the concepts of gating units with the advantages of Graph Convolutional Network (GCN) and Dilated Convolution, significantly surpassing traditional convolution methods. The Improved Channel Attention mechanism substantially enhances the model's responsiveness and accuracy by shifting from a single input to three inputs and integrating three sigmoid functions along with an additional layer output. These innovative combinations have significantly improved model performance, enabling LGC-DBP to recognize and interpret the complex relationships within DBP features more accurately. The evaluation results show that LGC-DBP achieves an accuracy of 88.26% and a Matthews correlation coefficient of 0.701, both surpassing existing methods. These achievements demonstrate the model's strong capability in integrating and analyzing multi-dimensional data and mark a significant advancement over traditional methods by capturing deeper, nonlinear interactions within the data.
PubMed: 38903752
DOI: 10.3389/fgene.2024.1411847 -
BioRxiv : the Preprint Server For... Jun 2024Evolutionary arms races can arise at the contact surfaces between host and viral proteins, producing dynamic spaces in which genetic variants are continually pursued....
Evolutionary arms races can arise at the contact surfaces between host and viral proteins, producing dynamic spaces in which genetic variants are continually pursued. However, the sampling of genetic variation must be balanced with the need to maintain protein function. A striking case is given by protein kinase R (PKR), a member of the mammalian innate immune system. PKR detects viral replication within the host cell and halts protein synthesis to prevent viral replication by phosphorylating eIF2α, a component of the translation initiation machinery. PKR is targeted by many viral antagonists, including poxvirus pseudosubstrate antagonists that inhibit PKR by interacting with the same binding surface as eIF2α. Remarkably, PKR has several rapidly evolving residues at this interface, suggesting it is engaging in an evolutionary arms race, despite the surface's critical role in phosphorylating eIF2α. To systematically explore the evolutionary opportunities available at this dynamic interface, we generated and characterized a library of 426 SNP-accessible nonsynonymous variants of human PKR for their ability to escape inhibition by the model pseudosubstrate inhibitor K3 from vaccinia virus. We identified key sites in the PKR kinase domain that harbor K3-resistant variants, as well as critical sites where variation leads to loss of function. We find K3-resistant variants are readily available throughout the interface and are enriched at sites under positive selection. Moreover, variants beneficial against K3 were also beneficial against an enhanced variant of K3, indicating resilience to viral adaptation. Overall, we find that the eIF2α-binding surface of PKR is highly malleable, potentiating its evolutionary ability to combat viral inhibition.
PubMed: 38903081
DOI: 10.1101/2024.05.29.596416 -
AIDS Research and Therapy Jun 2024The World Health Organisation has implemented multiple HIV prevention policies and strived to achieve the 90-90-90 goal by 2020, achieving the 95-95-95 goal by 2030,...
INTRODUCTION
The World Health Organisation has implemented multiple HIV prevention policies and strived to achieve the 90-90-90 goal by 2020, achieving the 95-95-95 goal by 2030, which refers to 95% of patients living with HIV knowing their HIV status, 95% of patients living with HIV receiving continual care and medication, and 95% of patients living with HIV exhibiting viral suppression. However, how to measure the status of viral suppression varies, and it is hard to indicate the quality of HIV care. The study aimed to examine the long-term viral load suppression in these cases and explore potential factors affecting the control of long-term viral load.
METHODS
This study analyzed viral load testing data from HIV patients who are still alive during the period from notification up to 2019-2020. Three indicators were calculated, including durable viral suppression, Viremia copy-years, and Viral load > 1,500 copies/ml, to assess the differences between them.
RESULTS
Among the 27,706 cases included in the study, the proportion of persistent viral load suppression was 87%, with 4% having viral loads exceeding 1,500 copies/ml. The average duration from notification to viral load suppression was 154 days, and the geometric mean of annual viral replication was 90 copies*years/ml. Regarding the last available viral load measurement, 96% of cases had an undetectable viral load. However, we observed that 9.3% of cases, while having an undetectable viral load for their last measurement, did not show consistent long-term viral load suppression. An analysis of factors associated with non-persistent viral load suppression revealed higher risk in younger age groups, individuals with an educational level of high school or below, injection drug users, cases from the eastern region, those seeking care at regional hospitals, cases with drug resistance data, individuals with lower healthcare continuity, and those with an initial CD4 count below 350 during the study period.
CONCLUSIONS
The recommendation is to combine it with the indicator of sustained viral load suppression for a more accurate assessment of the risk of HIV transmission within the infected community.
Topics: Humans; Viral Load; HIV Infections; Male; Female; Adult; Taiwan; Middle Aged; Anti-HIV Agents; Young Adult; Aged; Adolescent; HIV-1; Sustained Virologic Response
PubMed: 38902777
DOI: 10.1186/s12981-024-00626-3 -
BMC Genomics Jun 2024Autophagy is a conserved catabolic process in eukaryotes that contributes to cell survival in response to multiple stresses and is important for organism fitness....
BACKGROUND
Autophagy is a conserved catabolic process in eukaryotes that contributes to cell survival in response to multiple stresses and is important for organism fitness. Extensive research has shown that autophagy plays a pivotal role in both viral infection and replication processes. Despite the increasing research dedicated to autophagy, investigations into shrimp autophagy are relatively scarce.
RESULTS
Based on three different methods, a total of 20 members of the ATGs were identified from F. chinensis, all of which contained an autophagy domain. These genes were divided into 18 subfamilies based on their different C-terminal domains, and were found to be located on 16 chromosomes. Quantitative real-time PCR (qRT-PCR) results showed that ATG genes were extensively distributed in all the tested tissues, with the highest expression levels were detected in muscle and eyestalk. To clarify the comprehensive roles of ATG genes upon biotic and abiotic stresses, we examined their expression patterns. The expression levels of multiple ATGs showed an initial increase followed by a decrease, with the highest expression levels observed at 6 h and/or 24 h after WSSV injection. The expression levels of three genes (ATG1, ATG3, and ATG4B) gradually increased until 60 h after injection. Under low-salt conditions, 12 ATG genes were significantly induced, and their transcription abundance peaked at 96 h after treatment.
CONCLUSIONS
These results suggested that ATG genes may have significant roles in responding to various environmental stressors. Overall, this study provides a thorough characterization and expression analysis of ATG genes in F. chinensis, laying a strong foundation for further functional studies and promising potential in innate immunity.
Topics: Animals; Stress, Physiological; Penaeidae; Autophagy; Gene Expression Profiling; Phylogeny; Autophagy-Related Proteins; Transcriptome
PubMed: 38902611
DOI: 10.1186/s12864-024-10529-2 -
Psychology of Addictive Behaviors :... Jun 2024Alcohol use is an important, but understudied, risk factor for nonsuicidal self-injury (NSSI), defined as deliberate physical harm to oneself without intent to die....
Alcohol use prior to episodes of nonsuicidal self-injury in women with borderline personality disorder participating in a randomized clinical trial of dialectical behavior therapy.
OBJECTIVE
Alcohol use is an important, but understudied, risk factor for nonsuicidal self-injury (NSSI), defined as deliberate physical harm to oneself without intent to die. Alcohol use may facilitate engagement in NSSI by increasing impulsivity and physical pain tolerance. Limited data also suggest that people engage in more medically severe NSSI under the influence of alcohol.
METHOD
This secondary analysis study examined the use of alcohol prior to NSSI in a sample of 79 female patients with borderline personality disorder who were enrolled in a randomized clinical trial of dialectical behavior therapy. We used multilevel modeling (MLM) to examine preregistered hypotheses that alcohol use prior to NSSI would be related to the impulsivity of NSSI, physical pain experienced during NSSI, and the medical severity of injuries from NSSI.
RESULTS
Participants endorsed alcohol use prior to 21.96% (47/221) of NSSI episodes, and roughly one third of participants ( = 27) reported at least one episode of NSSI preceded by alcohol use. For NSSI episodes preceded by alcohol use, more than half (52.38%) of participants reported using alcohol up to the moment of initiating NSSI. Alcohol use was significantly associated with higher impulsivity of NSSI episodes ( = 1.16, = .041), but not physical pain from NSSI or medical severity of NSSI.
CONCLUSIONS
Findings need to be replicated but indicate that alcohol use occurs frequently prior to NSSI and could be a target for reducing impulsive episodes of NSSI. (PsycInfo Database Record (c) 2024 APA, all rights reserved).
PubMed: 38900501
DOI: 10.1037/adb0001016 -
Environmental Monitoring and Assessment Jun 2024The intensive global use of pesticides presents an escalating threat to human health, ecosystems, and water quality. To develop national and local environmental...
The intensive global use of pesticides presents an escalating threat to human health, ecosystems, and water quality. To develop national and local environmental management strategies for mitigating pollution caused by pesticides, it is essential to understand the quantities, timing, and location of their application. This study aims to estimate the spatial distribution of pesticide use in an agricultural region of La Plata River basin in Uruguay. Estimates of pesticide use were made by surveying doses applied to each crop. This information was spatialized through identifying agricultural rotations using remote sensing techniques. The study identified the 60 major agricultural rotations in the region and mapped the use and application amount of the nine most significant active ingredients (glyphosate, 2,4-dichlorophenoxyacetic acid, flumioxazin, S-metolachlor, clethodim, flumetsulam, triflumuron, chlorantraniliprole, and fipronil). The results reveal that glyphosate is the most extensively used pesticide (53.5% of the area) and highest amount of use (> 1.44 kg/ha). Moreover, in 19% of the area, at least seven active ingredients are applied in crop rotations. This study marks the initial step in identifying rotations and estimating pesticide applications with high spatial resolution at a regional scale in agricultural regions of La Plata River basin. The results improve the understanding of pesticide spatial distribution based on data obtained from agronomists, technicians, and producers and provide a replicable methodological approach for other geographic and productive contexts. Generating baseline information is key to environmental management and decision making, towards the design of more robust monitoring systems and human exposure assessment.
Topics: Environmental Monitoring; Uruguay; Pesticides; Rivers; Agriculture; Crops, Agricultural; Water Pollutants, Chemical
PubMed: 38900342
DOI: 10.1007/s10661-024-12759-z -
Environmental Science & Technology Jul 2024Organic molecules in the environment oxidatively degrade by a variety of free radical, microbial, and biogeochemical pathways. A significant pathway is heterogeneous...
Organic molecules in the environment oxidatively degrade by a variety of free radical, microbial, and biogeochemical pathways. A significant pathway is heterogeneous autoxidation, in which degradation occurs via a network of carbon and oxygen centered free radicals. Recently, we found evidence for a new heterogeneous autoxidation mechanism of squalene that is initiated by hydroxyl (OH) radical addition to a carbon-carbon double bond and apparently propagated through pathways involving Criegee Intermediates (CI) produced from β-hydroxy peroxy radicals (β-OH-RO•). It remains unclear, however, exactly how CI are formed from β-OH-RO•, which could occur by a unimolecular or bimolecular pathway. Combining kinetic models and multiphase OH oxidation measurements of squalene, we evaluate the kinetic viability of three mechanistic scenarios. Scenario 1 assumes that CI are formed by the unimolecular bond scission of β-OH-RO•, whereas Scenarios 2 and 3 test bimolecular pathways of β-OH-RO• to yield CI. Scenario 1 best replicates the entire experimental data set, which includes effective uptake coefficients vs [OH] as well as the formation kinetics of the major products (i.e., aldehydes and secondary ozonides). Although the unimolecular pathway appears to be kinetically viable, future high-level theory is needed to fully explain the mechanistic relationship between CI and β-OH-RO• in the condensed phase.
Topics: Squalene; Oxidation-Reduction; Kinetics; Hydroxyl Radical; Models, Chemical
PubMed: 38900151
DOI: 10.1021/acs.est.4c02590