Miracle-dz/UniFAR-FTUs huggingface dataset:
Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management

Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.
New Pathophysiological Insights from Serum Proteome Profiling in Equine Atypical Myopathy

Equine atypical myopathy (AM) is a severe environmental intoxication linked to the ingestion of protoxins contained in seeds and seedlings of the sycamore maple (Acer pseudoplatanus) in Europe. The toxic metabolites cause a frequently fatal rhabdomyolysis syndrome in grazing horses. Since these toxic metabolites can also be present in cograzing horses, it is still unclear as to why, in a similar environmental context, some horses show signs of AM, whereas others remain clinically healthy. Label-free proteomic analyses on the serum of 26 diseased AM, 23 cograzers, and 11 control horses were performed to provide insights into biological processes and pathways. A total of 43 and 44 differentially abundant proteins between “AM vs cograzing horses” and “AM vs control horses” were found. Disease-linked changes in the proteome of different groups were found to correlate with detected amounts of toxins, and principal component analyses were performed to identify the 29 proteins representing a robust AM signature. Among the pathway-specific changes, the glycolysis/gluconeogenesis pathway, the coagulation/complement cascade, and the biosynthesis of amino acids were affected. Sycamore maple poisoning results in a combination of inflammation, oxidative stress, and impaired lipid metabolism, which is trying to be counteracted by enhanced glycolysis.
Mapping and Monitoring Locust Habitats in the Aral Sea Region based on Satellite Earth Observation Data

Landuse classification • Classification of every single year (2006, 2007, 2008, 2009) • With multi-year RF model • In order to prevent large agricultural areas from devastation by locusts, it is important to make valid forecasts about locust development • The identified developments within the different land cover classes can be explained and confirmed with the Amudarya inflow data as measured at Nukus and can be confirmed with corresponding literature • The area of these risk zones was always less than the area surveyed against LMI in the observed years • Focus zones with a potential high risk for locust breeding areas where derived from the classification maps, and can help the survey teams to work more efficient on-site • Derive within-season information and get early information about the location of potential locust breading areas Conclusion / Outlook
Comparative study of illite clay and illite-based geopolymer products

Quaternary (Q-clay) clayey deposits are one of the dominating parts of mineral raw materials of the sedimentary cover at present area of Latvia. These clays can be characterised by illite content up to 75-80 %. Two ways for use of illite clays were studied: conventional and geopolymers method. Purpose of the second mentioned method was showing the influence of alkali (KOH) on the transformation of Q-clay/illite structure. Obtained products were investigated by IR–spectroscopy, DTA and XRD, pore size distribution was determined as well. Some ceramic properties and compressive strength were determined and compared. IR-spectrum showed the effect of alkali on the transformation of Q-clay/illite structure in three main absorption bands: 3620-3415 cm−1 which is related to the vibrational modes of adsorbed water between SiO4 and AlO6 layers; new stronger absorption bands at 1635 cm−1 and 1435 cm−1 indicate on the appearance of vibrations in Q-KOH and are related to the K-O-Si bonds; the most essential changes are vibrations at 850 cm−1 showing the changes in the coordination number of Al from 6 to 4 for Q-KOH. Investigations of the bulk density in dependence on temperature showed the small increase of bulk density for Q-clay while - the relatively remarkable decrease for Q-clay/KOH. Mentioned values correlate with the compressive strength of Q-clay and Q-KOH products.
Impacts of a Mesoscale Eddy Pair on Internal Solitary Waves in the Northern South China Sea revealed by Mooring Array Observations

AbstractBoth internal solitary waves (ISWs) and mesoscale eddies are ubiquitous in the northern South China Sea (SCS). In this study, the authors examine the impacts of mesoscale eddies on the ISWs transiting the northern SCS deep basin that evolve from the steepening internal tide generated in the Luzon Strait, using in situ data collected from a specifically designed mooring array. From November 2013 to January 2014, an energetic mesoscale eddy pair consisting of one anticyclonic eddy (AE) and one cyclonic eddy (CE) propagated across the mooring array. Observations revealed that the amplitude, propagation direction, and speed of the transbasin ISWs were significantly modulated by the eddy pair. When the moorings were covered by the southern portion of the AE, the ISW amplitudes decreased by as much as 67% because of the thermocline deepening along the wave direction and the energy divergence along the wave front. When the moorings were covered by the northern portions of both eddies, the amplitude of IS.
Decadal Change of East Asian Summer Monsoon: Contributions of Internal Variability and External Forcing

The East Asian Summer Monsoon (EASM) has exhibited robust inter-decadal changes. In this paper, the authors present a review on our current understanding of the observed changes. The weakening phase of the EASM in the 2 half of the 20 century is demonstrated to be primarily forced by the positive phase of IPO (Inter-decadal Pacific Oscillation) /PDO (Pacific Decadal Oscillation), and secondarily driven by the increased aerosol emission. The dominance of IPO/PDO to EASM is also evidenced by the recent recovery of EASM since the 1990s, associated with the transition of IPO/PDO from positive to negative phases. Both data diagnosis and numerical model experiments indicate that the decadal change of EASM is dominated by internal variability mode of IPO/PDO and also partly driven by anthropogenic external forcings. The IPO/PDO is traditionally regarded as internal climate variability mode at decadal time scale, but recent studies suggested that external forcings may also trigger the phase transition of IPO/PDO, this has posed a new issue calling for further study. In addition to long-term changes, the EASM also exhibits inter-decadal shift of interannual variability mode. The suggested mechanisms are reviewed, including changes in mean circulation, interannual variability and its ENSO relationship, and the climatological intraseasonal oscillation.
Relationship between Helicobacter pylori Infection and Gastroesophageal Reflux Disease (GERD)

Background: Helicobacter pylori infection is a gastrointestinal infection that affects about 50% of the world's population, however, its prevalence varies across geographic areas. The actual relationship of H. pylori with gastroesophageal reflux disease (GERD) is still unclear because some studies report a high prevalence of H. pylori in GERD patients, but some studies report the opposite. This study aims to determine the relationship between H. pylori infection and GERD and the prevalence of Helicobacter pylori infection in GERD patients at Eka Hospital Pekanbaru.Method: This study was a cross-sectional study of GERD patients who had undergone endoscopy at Eka Hospital Pekanbaru from January 2021 to December 2022. There were 219 patients. This research was then analyzed with the chi-square test using SPSS version 22.Results: A total of 219 GERD patients met the criteria for this study. 108 of them were positive for H. pylori from the results of endoscopic biopsies. The prevalence of GERD patients infected with H. pylori is 49.3%. 108 of them were positive patients, 14 (13%) GERD patients were ≥ 60 years old and 94 (87%) were 60 years old. Of the 108 positive patients, 53 (49.1%) were male, 55 (50.9%) were female. Where age and gender did not significantly increase the risk of H. pylori infection (p 0.05). The most common endoscopic biopsy finding is chronic erosive gastritis.Conclusion: Although the prevalence of GERD patients infected with H. pylori was quite large (49.3%), there was no significant association between GERD patients and the incidence of H. pylori infection.
High hymenopteran parasitoid infestation rates in Czech populations of the Euphydryas aurinia butterfly inferred using a new molecular marker

We apply a molecular approach to quantify the level of hymenopteran parasitoids infestation in the larvae of the marsh fritillary (Euphydryas aurinia), a declining butterfly species, in western Bohemia, Czech Republic, in two subsequent years. We used the novel primer HymR157 in combination with known universal 28SD1F to establish a PCR detection system which amplifies hymenopteran parasitoids, but not the lepidopteran host. In the 14 sampled E. aurinia colonies, the infestation rates per individuum were 33.3% and 40.2%; whereas per sampled larval colony, these were on average 38.5% (range 0–100) and 40.1% (0–78). The per-colony infestation rates correlated with the numbers of larval webs censused per colony the year prior to sampling the parasitoids, pointing to a time lag in parasitoid infestation rates. The levels of the hymenopteran parasitoid prevalence are thus relatively high, supporting the importance of parasitoids for the population dynamics of the threatened host. The detection primers we developed can detect a range of hymenopteran parasitoids on other butterfly hosts.
Multi-Scale Adaptive Graph Convolution Network for Skeleton-Based Action Recognition

The skeleton-based action recognition technology can effectively avoid the background interference and occlusion problems in the image. However, the recognition of similar actions is still a challenge. In this paper, a multi-scale dynamic topological modeling method (MDTM) is proposed to solve this problem. The topological modeling through the convolution kernel generated from the original data, increases the connection of the convolution process to the original data compared to the previous randomly generated ones, effectively distinguishing similar actions. In addition, MDTM uses a multi-scale temporal convolutional network to obtain a wider receptive field, which can effectively extract the temporal information in the action. At the same time, a dynamic topology learning method is utilized to design a spatiotemporal information extractor that can effectively extract the spatiotemporal information in the action to dynamically adjust the topology structure. Extensive experiments have performed on three large-scale datasets, NTU RGB + D 60, NTU RGB + D 120, and NW-UCLA to validate the effectiveness of MDTM. The results show that MART-GCN performs better than the others in terms of accuracy and number of parameters.
The Public Health Importance and Management of Infectious Poultry Diseases in Smallholder Systems in Africa

Poultry diseases pose major constraints on smallholder production in Africa, causing high flock mortality and economic hardship. Infectious diseases, especially viral diseases like Newcastle disease and highly pathogenic avian influenza (HPAI) and bacterial diseases, especially colibacillosis and salmonellosis, are responsible for most chicken losses, with downstream effects on human nutrition and health. Beyond production impacts, poultry diseases directly harm public health if zoonotic, can give rise to epidemics and pandemics, and facilitate antimicrobial resistance through treatment attempts. HPAI, campylobacteriosis, and salmonellosis are the priority zoonoses. Sustainable solutions for poultry health remain elusive despite recognition of the problem. This review summarises current knowledge on major poultry diseases in smallholder systems, their impacts, and options for prevention and control. We find biosecurity, vaccination, good husbandry, and disease-resistant breeds can reduce disease burden, but practical limitations exist in implementing these measures across smallholder systems. Treatment is often inefficient for viral diseases, and treatment for bacterial diseases risks antimicrobial resistance. Ethnoveterinary practices offer accessible alternatives but require more rigorous evaluation. Multisectoral collaboration and policies that reach smallholder poultry keepers are essential to alleviate disease constraints. Successful control will improve livelihoods, nutrition, and gender equity for millions of rural families. This review concludes that sustainable, scalable solutions for smallholder poultry disease control remain a critical unmet need in Africa.
ESCAPEMENT LEVELS AND PRODUCTIVITY OF THE NUSHAGAK SOCKEYE SALMON RUN FROM 1908 TO 1966

Since the inception of a commercial fishery for sockeye salmon in the Nushagak District, Bristol Bay, Alaska, the annual yields have followed a definite pattern. Catches increased during a relatively short development phase of the fishery, then stahilized for some years and then declined in two steps separated hy periods of relative stability. For years the cause of the decline had been thought to be overfishing, and various measures of cur­ tailment had been placed upon the fishing industry. Evidence is presented in this paper that the average escapement or the potential egg deposition re­ mained about the same during each of three periods (1908-1919, 1! )25-1945, and 1946-1966); hence the diminution in the runs was due not to lack of spawners but to a decline in the rate of return per spawner. So that the cause or causes of the present low reproductive potential can he ascertained, the effects of fishing on the stocks of salmon must be examined. Besides removing part of the run, the yearly commercial fishing operation may have altered either the age composition or the distribution of the escapement. Available historical records were examined for evidence of these types of changes hut largely with a negative result; therefore, the hypothesis was advanced that the observed declining rate of return per spawner is caused by a declining basic productivity of the nursery areas. The latter is then ascrib­ able to the cumulative effect of relatively little enrichment of hioenergetic elements from salmon carcas­ ses since the instigation of commercial fishing operations in comparison with the prefishing era when the entire virgin run escaped to the spawning grounds. Suggestions are made for future field testing of this hypothesis. In the development of the salmon fishery along the eastern perimeter of the Pacific Ocean, the most southern stocks were utilized first. As de­ mand increased and certain stocks declined, the fishery shifted northward until the runs of the entire southeastern Alaska and soon thereafter those of the western districts were exploited. The rapidity of growth of the salmon fishing in­ dustry in Alaska is astonishing. The firstcannery was built in southeastern Alaska at Klawak in 1878 (Rich and Ball, 1928), and only 6 years later exploratory fishing was conducted in Bristol Bay. The early Bristol Bay catch records show that, from 1884 to 1891, fishing was conducted only in Nushagak Bay (Figure 1). Four years later, salmon was harvested in the other watersheds of Bristol Bay, the Kvichak-Naknek, the Egegik,
Global cropland nitrous oxide emissions in fallow period are comparable to growing‐season emissions

Croplands account for ~ one‐third of global anthropogenic nitrous oxide (N2O) emissions. A number of recent field experiments found substantial fallow‐period N2O emissions, which have been neglected for decades. However, the global contribution of the fallow‐period emissions and the associated drivers remain unclear. Based on 360 observations across global agroecosystems, we simulated the ratio of the fallow to the whole‐year N2O emissions (Rfallow) by developing a mixed‐effect model and compiling cropping‐system‐specific input data. Our results revealed that the mean global gridded Rfallow was 44% (15%–75%, 95% confidence interval), with hotspots mainly in the northern high latitudes. For most cropping systems, soil pH was the dominant driver of global variation in Rfallow. Global cropland emission factors (i.e., the percentage of fertilizer N emitted as N2O, EFs) in EF‐based models doubled to 1.9% when the fallow‐period N2O emissions were included in our simulation, similar to EFs estimated by process‐based and atmospheric inversion models (1.8%–2.3%). Overall, our study highlights the importance of fallow‐period N2O emissions in annual totals, especially for single cropping systems and croplands in acidic areas. To accurately estimate N2O emissions for national greenhouse gas inventories, it is crucial to update current EFs with full consideration of the fallow‐period N2O emissions in the Intergovernmental Panel on Climate Change (IPCC) Tier 1 method.
Advancing Antibiotic Residue Analysis: LC-MS/MS Methodology for Ticarcillin Degradation Products in Tomato Leaves

The indiscriminate use of antibiotics in agriculture has raised concerns about antibiotic residues in food products, necessitating robust analytical methods for detection and quantification. In this study, our primary aim was to develop a robust and advanced liquid chromatography-tandem mass spectrometry (LC-MS/MS) methodology specifically designed for the accurate quantification of ticarcillin degradation products in tomato leaves. The choice of ticarcillin as the target analyte stems from its frequent use in agriculture and the potential formation of degradation products, which can pose a threat to food safety. The use of tomatoes as the target sample matrix in this study is justified by their significance in human diets, their widespread cultivation, and their suitability as a model for assessing antibiotic residue dynamics in diverse agricultural environments. By optimizing the MS/MS parameters, the study successfully demonstrates the practicality and reliability of the employed LC-MS/MS method in accurately assessing ticarcillin degradation product (Thiophene-2-Acetic acid and Thiophene-3-Acetic acid) levels. The chromatographic separation was achieved using a specialized column, ensuring high resolution and sensitivity in detecting analytes. Multiple reaction monitoring (MRM) data acquisition was employed to enhance the selectivity and accuracy of the analysis. The developed method exhibited excellent linearity and precision, meeting the stringent requirements for antibiotic residue analysis in complex matrices. Key outcomes of this study include the successful identification and quantification of ticarcillin and its degradation products in tomato leaves, providing crucial insights into the fate of this antibiotic in agricultural settings. The methodology’s applicability was further demonstrated by analyzing real-world samples, highlighting its potential for routine monitoring and ensuring food safety compliance. In summary, our study constitutes a noteworthy advancement in the domain of antibiotic residue analysis, offering a reliable method for quantifying ticarcillin degradation products in tomato leaves. The optimized parameters and MRM-based LC-MS/MS approach enhance the precision and sensitivity of the analysis, opening up opportunities for further studies in the assessment of antibiotic residues in agricultural ecosystems.
A Semantic, Syntactic, And Context-Aware Natural Language Adversarial Example Generator

Machine learning models are vulnerable to maliciously crafted Adversarial Examples (AEs). Training a machine learning model with AEs improves its robustness and stability against adversarial attacks. It is essential to develop models that produce high-quality AEs. Developing such models has been much slower in natural language processing (NLP) than in areas such as computer vision. This paper introduces a practical and efficient adversarial attack model called SSCAE for \textbf{S}emantic, \textbf{S}yntactic, and \textbf{C}ontext-aware natural language \textbf{AE}s generator. SSCAE identifies important words and uses a masked language model to generate an early set of substitutions. Next, two well-known language models are employed to evaluate the initial set in terms of semantic and syntactic characteristics. We introduce (1) a dynamic threshold to capture more efficient perturbations and (2) a local greedy search to generate high-quality AEs. As a black-box method, SSCAE generates humanly imperceptible and context-aware AEs that preserve semantic consistency and the source language's syntactical and grammatical requirements. The effectiveness and superiority of the proposed SSCAE model are illustrated with fifteen comparative experiments and extensive sensitivity analysis for parameter optimization. SSCAE outperforms the existing models in all experiments while maintaining a higher semantic consistency with a lower query number and a comparable perturbation rate.