Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of five commercial DNA extraction kits using Salmonella as a model for implementation of rapid Nanopore sequencing in routine diagnostic laboratories

Oxford Nanopore long-read sequencing offers advantages over Illumina short reads for the identification and characterization of bacterial pathogens for outbreak detection and surveillance activities within a diagnostic public health laboratory context. Compared to Illumina, Nanopore is more cost-effective for small batches, has a lower capital cost and has a faster turnaround time, in addition to the ability to assemble complete bacterial genomes. The quantity and quality of DNA required for Nanopore sequencing are greater than for Illumina, and the DNA extraction methods recommended for obtaining high-molecular-weight DNA are different from those typically used in diagnostic laboratories. Using a Salmonella isolate with a previously closed PacBio genome as a model Enterobacteriaceae organism, we evaluated the quantity, quality and fragmentation of five commercial DNA extraction kits. Nanopore sequencing performance was evaluated for the top three methods: Qiagen EZ1 DNA Tissue, Qiagen DNeasy Blood and Tissue, and a modified, in-house version of the MasterPure Complete DNA and RNA purification. To evaluate the effect of post-extraction DNA purification methods, we subjected extracted DNA from the three selected extraction methods to purification by AMPure beads or ethanol precipitation and compared these outputs with untreated DNA as a control. All methods are suitable for routine whole-genome sequencing (WGS), since all 60 replicates had very high genome recovery rates, with ≥98 % of the reference genome covered by mapped Nanopore reads. For 85 % of the replicates, assembly was able to produce a complete, circular chromosome using either Flye or Canu. In most cases, it is recommended to move directly from extraction to sequencing, as untreated DNA had the highest rates of genome closure regardless of extraction method. Using our evaluation criteria, the Qiagen DNeasy Blood and Tissue kit was found to be the best overall method due to its low cost, ability to scale from single tubes to 96-well plates, and high consistency in yield and sequencing performance.
Effects of baicalein with memantine on aluminium chloride-induced neurotoxicity in Wistar rats

Alzheimer’s disease is a progressive neurodegenerative condition. It is one of the most common 28 forms of dementia accounting for 60–80% of people suffering from dementia. There are very few medications that are approved for the treatment of Alzheimer’s disease. Baicalein, belonging to the flavone subclass of flavonoids, has been reported to have a neuroprotective effect by reducing oxidative stress and neuroinflammation, inhibiting the AChE enzyme, and reducing amyloid protein aggregation and toxicity. Memantine is one of the most important drugs used for treating Alzheimer’s disease. The purpose of this work was to study the effect of baicalein with memantine on aluminum chloride-induced neurotoxicity in Wistar rats. Aluminum chloride (100 mg/kg p.o.) was administered for 42 days in male Wistar rats to induce neurotoxicity. Baicalein alone (10 mg/kg) and a combination of baicalein (5 mg/kg and 10 mg/kg) with memantine (20 mg/kg) were administered for 42 days. Treatment of baicalein with memantine showed significant improvement in behavioral parameters. The combination reduced oxidative stress and the formation of β-Amyloid plaques and increased brain-derived neurotrophic factor (BDNF) expression. Based on findings, it can be concluded that treatment with baicalein and memantine may slow the progression of neurodegeneration in rats.
Online Identification Method of Tea Diseases in Complex Natural Environments

An intelligent Internet-of-Things (IoT) hardware system in the field tea plantations was built, comprising collection of tea images by HD zoom cameras in a cluster structure and deployment of the detection model by cluster-head edge computing nodes. Data was sent to customer premise equipment through edge nodes and gateways and then to cloud platforms, which provided a hardware platform for identifying remote tea disease online. Field-placed cameras were used as the main acquisition means to study various diseases on Yashixiang, a typical variety of Chaozhou Dancong tea, in different seasons and weather conditions and shooting angles in a natural year period with complex backgrounds. In turn, we constructed a natural environment high-quality dataset covering major diseases e.g., tea anthracnose, tea leaf blight, tea grey blight, Pseudocercospora theae, etc. and explored the feasibility of deep learning algorithms for automatic identification of Chaozhou Dancong tea diseases. Results showed that the recognition rate of Swim Transformer reached 94% in complex natural environments. This paper demonstrated the effectiveness of the dataset and the feasibility of deep learning algorithms applied to the automatic identification of diseases of Chaozhou Dancong tea, laying a foundation for the practical application of the technology in complex natural environments.
Neural Bypasses: Literature Review and Future Directions in Developing Artificial Neural Connections

Reported neuro-modulation schemes in the literature are typically classified as closed-loop or open-loop. A novel group of recently developed neuro-modulation devices may be better described as a neural bypass, which attempts to transmit neural data from one location of the nervous system to another. The most common form of neural bypasses in the literature utilize EEG recordings of cortical information paired with functional electrical stimulation for effector muscle output, most commonly for assistive applications and rehabilitation in spinal cord injury or stroke. Other neural bypass locations that have also been described, or may soon be in development, include cortical-spinal bypasses, cortical-cortical bypasses, autonomic bypasses, peripheral-central bypasses, and inter-subject bypasses. The most common recording devices include EEG, ECoG, and microelectrode arrays, while stimulation devices include both invasive and noninvasive electrodes. Several devices are in development to improve the temporal and spatial resolution and biocompatibility for neuronal recording and stimulation. A major barrier to entry includes neuroplasticity and current decoding mechanisms that regularly require retraining. Neural bypasses are a unique class of neuro-modulation. Continued advancement of neural recording and stimulating devices with high spatial and temporal resolution, combined with decoding mechanisms uninhibited by neuroplasticity, can expand the therapeutic capability of neural bypassing. Overall, neural bypasses are a promising modality to improve the treatment of common neurologic disorders, including stroke, spinal cord injury, peripheral nerve injury, brain injury and more.
Relationships between surrogate measures of mechanical and psychophysiological load, patellar tendon adaptations, and neuromuscular performance in NCAA division I men's volleyball athletes

Introduction Patellar tendon adaptations occur in response to mechanical load. Appropriate loading is necessary to elicit positive adaptations with increased risk of injury and decreased performance likely if loading exceeds the capacity of the tendon. The aim of the current study was to examine intra-individual associations between workloads and patellar tendon properties and neuromuscular performance in collegiate volleyball athletes. Methods National Collegiate Athletics Association Division I men's volleyball athletes (n = 16, age: 20.33 ± 1.15 years, height: 193.50 ± 6.50 cm, body mass: 84.32 ± 7.99 kg, bodyfat%: 13.18 ± 4.72%) competing across 9 weeks of in-season competition participated. Daily measurements of external workloads (i.e., jump count) and internal workloads [i.e., session rating of perceived exertion (sRPE)] were recorded. Weekly measurements included neuromuscular performance assessments (i.e., countermovement jump, drop jump), and ultrasound images of the patellar tendon to evaluate structural adaptations. Repeated measures correlations (r-rm) assessed intra-individual associations among performance and patellar tendon metrics. Results Workload measures exhibited significant negative small to moderate (r-rm =−0.26–0.31) associations with neuromuscular performance, negative (r-rm = −0.21–0.30), and positive (r-rm = 0.20–0.32) small to moderate associations with patellar tendon properties. Discussion Monitoring change in tendon composition and performance adaptations alongside workloads may inform evidence-based frameworks toward managing and reducing the risk of the development of patellar tendinopathy in collegiate men's volleyball athletes.
Incongruity between Ads and Consumer Expectations of Advertising

The effectiveness of advertising is a topic of interest to both marketing research and advertising practice. Many advertising theories specify that effective ads, i.e., ads that result in favorable brand attitudes, should match consumer brand expectations. Implicit in these theories is the assumption that consumers use their brand schemas in ad processing. Alternatively, however, consumers may use their ad schemas in ad processing. Especially in a cluttered media environment consumers have formed expectations of advertising in particular product categories. In this thesis, we consider both the origins of consumer expectations of advertising and study the effects of ads that are incongruent with such advertising expectations. We find that ads that match consumer brand expectations are only more effective than brand-mismatching ads if the brand schema is salient in ad processing. The requirement of schema salience is more strict than the brand awareness requirement that is part of the aforementioned advertising theories. If consumers use their ad schemas in processing advertising, brand-matching does not affect consumer evaluations of brands and ads. Contrary to incongruity with the brand schema, incongruity with the ad schema is evaluated favorably. This is explained by the way in which consumers determine incongruity with the brand schema and incongruity with the ad schema. Consumers only consider ad relevancy to the brand in case of incongruity with the brand schema. In line with this reasoning, we find that incongruity with the brand schema mainly has cognitive consequences, whereas incongruity with the ad schema predominantly has affective consequences.
Canonical and non‐canonical functions of STAT in germline stem cell maintenance

Maintenance of the Drosophila male germline stem cells (GSCs) requires activation of the Janus kinase/signal transducer and activators of transcription (JAK/STAT) pathway by niche signals. The precise role of JAK/STAT signaling in GSC maintenance, however, remains incompletely understood.
Truncation of NS1 Protein Enhances T Cell-Mediated Cross-Protection of a Live Attenuated Influenza Vaccine Virus Expressing Wild-Type Nucleoprotein

Current seasonal influenza vaccines have suboptimal effectiveness, especially in seasons dominated by viruses that do not match the vaccine. Therefore, finding new approaches to improve the immunogenicity and efficacy of traditional influenza vaccines is of high priority for public health. Licensed live attenuated influenza vaccine (LAIV) is a promising platform for designing broadly protective vaccines due to its ability to induce cross-reactive T-cell immunity. In this study, we tested the hypothesis that truncation of the nonstructural protein 1 (NS1) and the replacement of the nucleoprotein (NP) of the A/Leningrad/17 master donor virus with a recent NP, i.e., switching to 5:3 genome composition, could improve the cross-protective potential of the LAIV virus. We generated a panel of LAIV candidates differing from the classical vaccine by the source of NP gene and/or by the length of NS1 protein. We showed that NS1-modified LAIV viruses had reduced viral replication in the respiratory tract of mice, indicating a more attenuated phenotype compared to the LAIVs with full-length NS1. Most importantly, the LAIV candidate with both NP and NS genes modified induced a robust systemic and lung-localized memory CD8 T-cell response targeting more recent viruses, and better protected immunized mice against lethal challenge with a heterosubtypic influenza virus than the control LAIV variant. Overall, these data indicate that the 5:3 LAIVs with truncated NS1 may be beneficial for protection against heterologous influenza viruses and warrant further preclinical and clinical development.
Innovations in Cattle Farming: Application of Innovative Technologies and Sensors in the Diagnosis of Diseases

Simple Summary As the importance of farming continues to grow, innovative technology and sensors play an increasingly important role. Automation and robots in agriculture have the potential to play a significant role in helping society fulfill its future demands for food supply. Wearable sensors connected to or within cows can monitor eating, rumination, pH, body temperature, laying behavior, animal activity, animal position or placement, and more. Research concentrates on biosensing technologies that have the potential to improve livestock early disease detection, management, and operations. The goals of this study were to investigate the currently available knowledge regarding agricultural innovations and their application tactics, and we intended to give a critical perspective and advance the understanding of what is known and unknown about innovations and dairy cattle. Abstract Precision livestock farming has a crucial function as farming grows in significance. It will help farmers make better decisions, alter their roles and perspectives as farmers and managers, and allow for the tracking and monitoring of product quality and animal welfare as mandated by the government and industry. Farmers can improve productivity, sustainability, and animal care by gaining a deeper understanding of their farm systems as a result of the increased use of data generated by smart farming equipment. Automation and robots in agriculture have the potential to play a significant role in helping society fulfill its future demands for food supply. These technologies have already enabled significant cost reductions in production, as well as reductions in the amount of intensive manual labor, improvements in product quality, and enhancements in environmental management. Wearable sensors can monitor eating, rumination, rumen pH, rumen temperature, body temperature, laying behavior, animal activity, and animal position or placement. Detachable or imprinted biosensors that are adaptable and enable remote data transfer might be highly important in this quickly growing industry. There are already multiple gadgets to evaluate illnesses such as ketosis or mastitis in cattle. The objective evaluation of sensor methods and systems employed on the farm is one of the difficulties presented by the implementation of modern technologies on dairy farms. The availability of sensors and high-precision technology for real-time monitoring of cattle raises the question of how to objectively evaluate the contribution of these technologies to the long-term viability of farms (productivity, health monitoring, welfare evaluation, and environmental effects). This review focuses on biosensing technologies that have the potential to change early illness diagnosis, management, and operations for livestock.
EEG feature extraction methods in motor imagery brain computer interface

Brain-computer interface (BCI) is a link between the human brain and a computer or other peripheral devices for communication and control. The most frequently utilized BCI paradigms at the time are motor imagination (MI) BCI. In the procedure of MI-BCI, one of the most important roles is the feature extraction of EEG signals. This article examines various feature extraction approaches in four distinct domains: time, frequency, time-frequency, and spatial. Various approaches are introduced in each domain, including the ERD/ERS computation, the FFT method, the Wavelet Transform (WT), the Discrete Wavelet Transform (DWT), Common Spatial Patterns (CSP), and Sub-band Common Spatial Patterns (SBCSP). This paper also compares the advantages and disadvantages of different methods in practical application, which can provide reference for future research.
Construction, assembly and tests of the ATLAS electromagnetic end-cap calorimeters

The construction and the assembly of the two end-caps of the ATLAS liquid argon electromagnetic calorimeter as well as their test and qualification programs are described. The work described here started at the beginning of 2001 and lasted for approximately three years. The results of the qualification tests performed before installation in the LHC ATLAS pit are given. The detectors are now installed in the ATLAS cavern, full of liquid argon and being commissioned. The complete detectors coverage is powered with high voltage and readout.
Ultrasound Imaging and Guidance for Cervical Myofascial Pain: A Narrative Review

Cervical myofascial pain is a very common clinical condition in the daily practice of musculoskeletal physicians. Physical examination is currently the cornerstone for evaluating the cervical muscles and identifying the eventual presence of myofascial trigger points. Herein, the role of ultrasound assessment in precisely localizing them is progressively mounting in the pertinent literature. Moreover, using ultrasound, not only the muscle tissue but also the fascial and neural elements can be accurately located/evaluated. Indeed, several potential pain generators, in addition to paraspinal muscles, can be involved in the clinical scenario of cervical myofascial pain syndrome. In this article, the authors extensively reviewed the sonographic approach for cervical myofascial pain in order to better diagnose or guide different procedures that can be performed in the clinical practice of musculoskeletal physicians.
Additive Transformation Models for Recurrent Events

In this article, we propose a class of additive transformation models for recurrent event data, which includes the additive rates model as a special case. The new models offer great flexibility in formulating the effects of covariates on the mean function of recurrent events. Estimating equation approaches are developed for the model parameters, and asymptotic properties of the resulting estimators are established. In addition, a model checking procedure is presented to assess the adequacy of the model. The finite sample performance of the proposed estimators is examined through simulation studies, and an application to a bladder cancer study is presented.
Hemolysin Co-Regulatory Protein 1 Enhances the Virulence of Clinically Isolated Escherichia coli in KM Mice by Increasing Inflammation and Inducing Pyroptosis

Hemolysin-coregulated protein 1 (Hcp1) is an effector released by the type VI secretion system (T6SS) in certain pathogenic strains of Escherichia coli (E. coli) that causes apoptosis and contributes to the development of meningitis. The exact toxic consequences of Hcp1 and whether it intensifies the inflammatory response by triggering pyroptosis are yet unknown. Here, utilizing the CRISPR/Cas9 genome editing method, we removed the gene expressing Hcp1 from wild-type E. coli W24 and examined the impact of Hcp1 on E. coli virulence in Kunming (KM) mice. It was found that Hcp1-sufficient E. coli was more lethal, exacerbating acute liver injury (ALI) and acute kidney injury (AKI) or even systemic infections, structural organ damage, and inflammatory factor infiltration. These symptoms were alleviated in mice infected with W24Δhcp1. Additionally, we investigated the molecular mechanism by which Hcp1 worsens AKI and found that pyroptosis is involved, manifested as DNA breaks in many renal tubular epithelial cells. Genes or proteins closely related to pyroptosis are abundantly expressed in the kidney. Most importantly, Hcp1 promotes the activation of the NLRP3 inflammasome and the expression of active caspase-1, thereby cleaving GSDMD-N and accelerating the release of active IL-1β and ultimately leading to pyroptosis. In conclusion, Hcp1 enhances the virulence of E. coli, aggravates ALI and AKI, and promotes the inflammatory response; moreover, Hcp1-induced pyroptosis is one of the molecular mechanisms of AKI.
Additional Periodic Variables in NGC 2264

We present results from a second season of monitoring fields in the young cluster NGC 2264 at Van Vleck Observatory. In Paper I of this series, we reported the discovery of nine periodic variables—all interpreted as spotted pre–main-sequence stars. That has now been increased to 31, one of which is quite unusual. The preliminary result reported in Paper I—that the frequency distribution of rotation periods in NGC 2264 is significantly different from what is seen in the Orion Nebula cluster (ONC)—is confirmed. In particular, the distribution peaks at a period of about 4 days, precisely where there is a gap in the ONC distribution. There is also a good number of very rapidly rotating stars and a long tail of slow rotators. The distribution can be understood, at least qualitatively, in terms of a disk-locking model of rotational evolution. In this interpretation, the majority of stars in NGC 2264 must have unlocked from their disks by an age of about 1 million years, and spun up roughly in accordance with conservation of angular momentum. A minority (about 20%) are conserving angular velocity instead (i.e., locked to their disks). The unusual star, 15D, has an apparent period of about 48 days and a light curve indicative of an eclipse by a nonstellar object. Its amplitude exceeds 3 mag. Our fragmentary data suggest a complex structure for the eclipsing body. It could be a feature (protoplanet? ) in this star's circumstellar disk and, as such, deserves observational attention.