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Genome-wide investigation to assess copy number variants in the Italian local chicken population

Journal of Animal Science and Biotechnology 2024年第2期15卷 563-577页

作者： Filippo Cendron Martino Cassandro mauro Penasa Department of Agronomy FoodNatural ResourcesAnimals and Environment(DAFNAE)University of PadovaViale Dell’Universita 1635020 LegnaroPDItaly Federazione Delle Associazioni Nazionali Di Razza E Specie Via XXIV Maggio 4300187 RomeItaly

Background Copy number variants(CNV)hold significant functional and evolutionary *** ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of ***-density chips have enabled the detection of CNV with increased resolution,leading to the identification of even small *** study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the *** Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type *** majority of CNV in the investigated breeds were of types 0 and 1,and the minimum length of CNV was significantly larger than that reported in previous ***,a high proportion of the length of chromosome 16 was covered by copy number variation regions(CNVR),with the major histocompatibility complex being the likely *** the genes identified within CNVR,only those present in at least five animals across breeds(n=95)were discussed to reduce the focus on redundant *** of these genes have been associated to functional traits in ***,several CNVR on different chromosomes harbor genes related to muscle development,tissue-specific biological processes,heat stress resistance,and immune *** trait loci(QTL)were also analyzed to investigate potential overlapping with the identified CNVR:54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size,carcass characteristics,egg production,egg components,fat deposition,and feed *** The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources.

关键词： Chicken Copy number variant Conservation Local breed SNP

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Spatial sensitivity to absorption changes for various near-infrared spectroscopy methods:A compendium review

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Journal of Innovative Optical Health Sciences 2024年第4期17卷 1-115页

作者： Giles Blaney angelo Sassaroli Sergio Fantini Department of Biomedical Engineering Tufts University 4 Colby StreetMedfordMA 02155USA

This compendium review focuses on the spatial distribution of sensitivity to localized absorption changes in optically diffuse media,particularly for measurements relevant to near-infrared *** three temporal domains,continuous wave,frequency domain,and time domain,each obtain different optical data types whose changes may be related to effective homogeneous changes in the absorption *** is the relationship between a localized perturbation and the recovered effective homogeneous absorption ***,spatial sensitivity maps representing the perturbation location can be generated for the numerous optical data types in the three temporal *** review first presents a history of the past 30 years of work investigating this sensitivity in optically diffuse *** works are experimental and theoretical,presenting one-,two-,and three-dimensional sensitivity maps for different Near-Infrared Spectroscopy methods,domains,and data *** this history,we present a compendium of sensitivity maps organized by temporal domain and then data *** compendium provides a valuable tool to compare the spatial sensitivity of various measurement methods and parameters in one *** for one to generate these maps are provided in Appendix A,including the *** historical review and comprehensive sensitivity map compendium provides a single source researchers may use to visualize,investigate,compare,and generate sensitivity to localized absorption change maps.

关键词： Diffuse optics diffusion theory Monte Carlo spatial sensitivity absorption perturbations near-infrared spectroscopy continuous-wave frequency-domain time-domain

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Unveiling DNA methylation in Alzheimer’s disease:a review of array-based human brain studies

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Neural Regeneration Research 2024年第11期19卷 2365-2376页

作者： Victoria Cunha alves Eva Carro Joana Figueiro-Silva Neurodegenerative Diseases Group Hospital Universitario 12 de Octubre Research Institute(imas12)MadridSpain Network Center for Biomedical Research Neurodegenerative Diseases(CIBERNED)MadridSpain PhD Program in Neuroscience Autonoma de Madrid UniversityMadridSpain Neurotraumatology and Subarachnoid Hemorrhage Group Hospital Universitario 12 de Octubre Research Institute(imas12)MadridSpain Neurobiology of Alzheimer’s Disease Unit Functional Unit for Research Into Chronic DiseasesInstituto de Salud Carlos IIIMadridSpain Institute of Medical Genetics University of ZurichZurichSwitzerland Department of Molecular Life Science University of ZurichZurichSwitzerland

The intricacies of Alzheimer’s disease pathogenesis are being increasingly illuminated by the exploration of epigenetic mechanisms,particularly DNA *** review comprehensively surveys recent human-centered studies that investigate whole genome DNA methylation in Alzheimer’s disease *** examination of various brain regions reveals distinctive DNA methylation patterns that associate with the Braak stage and Alzheimer’s disease *** entorhinal cortex emerges as a focal point due to its early histological alterations and subsequent impact on downstream regions like the ***,ANK1 hypermethylation,a protein implicated in neurofibrillary tangle formation,was recurrently identified in the entorhinal ***,the middle temporal gyrus and prefrontal cortex were shown to exhibit significant hypermethylation of genes like HOXA3,RHBDF2,and MCF2L,potentially influencing neuroinflammatory *** complex role of BIN1 in late-onset Alzheimer’s disease is underscored by its association with altered methylation *** the disparities across studies,these findings highlight the intricate interplay between epigenetic modifications and Alzheimer’s disease *** research efforts should address methodological variations,incorporate diverse cohorts,and consider environmental factors to unravel the nuanced epigenetic landscape underlying Alzheimer’s disease progression.

关键词： Alzheimer’s disease ANK1 BIN1 DNA methylation epigenome-wide association studies HOXA3 MCF2L RHBDF2

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High-speed tracked vehicle model order reduction for static and dynamic simulations

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Defence Technology（防务技术） 2024年第8期38卷 89-110页

作者： Luca Dimauro Simone Venturini Antonio Tota Enrico Galvagno mauro Velardocchia Department of Mechanical and Aerospace Engineering Politecnico di TorinoCorso Duca degli Abruzzi2410129TorinoItaly

In this paper, a model order reduction strategy is adopted for the static and dynamic behaviour simulation of a high-speed tracked vehicle. The total number of degree of freedom of the structure is condensed through a selection of interface degrees of freedom and significant global mode shapes, for an approximated description of vehicle dynamic behaviour. The methodology is implemented in a customised open-source software to reduce the computational efforts. The modelled tracked vehicle includes the sprung mass, the unsprung masses, connected by means of torsional bars, and all the track assemblies, composing the track chain. The proposed research activity presents a comprehensive investigation of the influence of the track chain, combined with longitudinal vehicle speed, on statics and vehicle dynamics, focusing on vertical dynamics. The vehicle response has been investigated both in frequency and time domain. In this last case road-wheel displacements are assumed as inputs for the model, under different working conditions, hence considering several road profiles with different amplitudes and characteristic excitation frequencies. Simulation results have proven a high fidelity in model order reduction approach and a significant contribution of the track chain in the global dynamic behaviour of the tracked vehicle.

关键词： Tracked vehicle dynamics Rubber characteristics Component mode synthesis Modal analysis Open-source

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Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment

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Marine Life Science & Technology 2024年第1期6卷 126-142页

作者： Elisa Banchi Erwan Corre Paola Del Negro mauro Celussi Francesca Malfatti National Institute of Oceanography and Applied Geophysics OGS TriesteItaly FR2424 Station Biologique de RoscoffPlateforme ABiMS(Analysis and Bioinformatics for Marine Science)Sorbonne Universite CNRS29680 RoscoffFrance Department of Life Sciences University of TriesteTriesteItaly

Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from‘omics’***,we characterized metagenome-assembled-genomes(MAGs)from the surface sediment microbes of the Venice Lagoon(northern Adriatic Sea)in distinct sub-basins exposed to various natural and anthropogenic *** were explored for biodiversity,major marine metabolic processes,anthropogenic activity-related functions,adaptations at the microscale,and biosynthetic gene *** from 126 MAGs,a non-redundant dataset of 58 was compiled,the majority of which(35)belonged to(Alpha-and Gamma-)*** the broad microbial metabolic repertoire(including C,N,and S metabolisms)the potential to live without oxygen emerged as one of the most important *** was also found as a successful *** analysis showed that different MAGs encoded the same metabolic patterns(e.g.,C fixation,sulfate oxidation)thus suggesting metabolic *** and toxic compounds resistance genes were coupled,a condition that could promote the spreading of these genetic *** showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular *** results highlighted that bacteria living in an impacted environment,such as the surface sediments of the Venice Lagoon,may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites,promoting ecosystem resilience and stability toward environmental pressures.

关键词： Antibiotic resistance PAHs Biosynthetic gene clusters Microscale Mobilome Resistome

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Quartz-enhanced multiheterodyne resonant photoacoustic spectroscopy

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Light(Science & Applications) 2024年第4期13卷 696-705页

作者： Jiapeng Wang Hongpeng Wu angelo Sampaolo Pietro Patimisco Vincenzo Spagnolo Suotang Jia Lei Dong State Key Laboratory of Quantum Optics and Quantum Optics Devices Institute of Laser SpectroscopyShanxi UniversityTaiyuan 030006China. Collaborative Innovation Center of Extreme Optics Shanxi UniversityTaiyuan 030006China. PolySense Lab Dipartimento Interateneo di FisicaUniversity and Politecnico of BariCNR-IFNVia Amendola 17370126 BariItaly

The extension of dual-comb spectroscopy(DCS)to all wavelengths of light along with its ability to provide ultralarge dynamic range and ultra-high spectral resolution,renders it extremely useful for a diverse array of applications in physics,chemistry,atmospheric science,space science,as well as medical *** this work,we report on an innovative technique of quartz-enhanced multiheterodyne resonant photoacoustic spectroscopy(QEMR-PAS),in which the beat frequency response from a dual comb is frequency down-converted into the audio frequency *** this way,gas molecules act as an optical-acoustic converter through the photoacoustic effect,generating heterodyne sound *** conventional DCS,where the light wave is detected by a wavelengthdependent photoreceiver,QEMR-PAS employs a quartz tuning fork(QTF)as a high-Q sound transducer and works in conjunction with a phase-sensitive detector to extract the resonant sound component from the multiple heterodyne acoustic tones,resulting in a straightforward and low-cost hardware *** novel QEMRPAS technique enables wavelength-independent DCS detection for gas sensing,providing an unprecedented dynamic range of 63 dB,a remarkable spectral resolution of 43 MHz(or~0.3 pm),and a prominent noise equivalent absorption of 5.99×10^(-6)cm^(-1)·Hz-1/2.

关键词： Quartz hardware resonant

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Time-Series Embeddings from Language Models:A Tool for Wind Direction Nowcasting

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Journal of Meteorological Research 2024年第3期38卷 558-569页

作者： Decio alves Fabio MENDONCA Sheikh Shanawaz MOSTAFA Fernando MORGADO-DIAS University of Madeira Campus Universitário da Penteada9020-105FunchalPortugal Interactive Technologies Institute/Laboratory for Robotics and Engineering Systems and Agência Regional para o Desenvolvimento da Investigação Tecnologia e InovaçãoEdif.Madeira TecnopoloCaminho da Penteada piso-29020-105FunchalPortugal

Wind direction nowcasting is crucial in various sectors,particularly for ensuring aviation operations and *** this context,the TELMo(Time-series Embeddings from Language Models)model,a sophisticated deep learning architecture,has been introduced in this work for enhanced wind-direction *** by using three years of data from multiple stations in the complex terrain of an international airport,TELMo incorporates the horizontal u(east-west)and v(north-south)wind components to significantly reduce forecasting *** a day with high wind direction variability,TELMo achieved mean absolute error values of 5.66 for 2-min,10.59 for 10-min,and 14.79 for 20-min forecasts,processed within a swift 9-ms/step *** degree-based analysis,in comparison,yielded lower performance,emphasizing the effectiveness of the u and v *** contrast,a Vanilla neural network,representing a shallow-learning approach,underperformed in all analyses,highlighting the superiority of deep learning methodologies in wind direction *** is an efficient model,capable of accurately forecasting wind direction for air traffic operations,with an error less than 20°in 97.49%of the predictions,aligning with recommended international *** model design enables its applicability across various geographical locations,making it a versatile tool in global aviation meteorology.

关键词： wind nowcasting wind components wind direction time series prediction deep learning

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Ultra-highly sensitive dual gases detection based on photoacoustic spectroscopy by exploiting a long-wave,high-power,wide-tunable,singlelongitudinal-mode solid-state laser

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Light(Science & Applications) 2024年第5期13卷 941-956页

作者： Shunda Qiao Ying He Haiyue Sun Pietro Patimisco angelo Sampaolo Vincenzo Spagnolo Yufei Ma National Key Laboratory of Laser Spatial Information Harbin Institute of TechnologyHarbinChina PolySense Lab Dipartimento Interateneo di FisicaUniversity and Politecnico of BariVia AmendolaBariItaly

Photoacoustic spectroscopy(PAS)as a highly sensitive and selective trace gas detection technique has extremely broad application in many ***,the laser sources currently used in PAS limit the sensing *** to diode laser and quantum cascade laser,the solid-state laser has the merits of high optical power,excellent beam quality,and wide tuning *** we present a long-wave,high-power,wide-tunable,singlelongitudinal-mode solid-state laser used as light source in a PAS sensor for trace gas *** self-built solid-state laser had an emission wavelength of~2μm with Tm:YAP crystal as the gain material,with an excellent wavelength and optical power stability as well as a high beam *** wide wavelength tuning range of 9.44 nm covers the absorption spectra of water and ammonia,with a maximum optical power of~130 mW,allowing dual gas detection with a single laser *** solid-state laser was used as light source in three different photoacoustic detection techniques:standard PAS with microphone,and external-and intra-cavity quartz-enhanced photoacoustic spectroscopy(QEPAS),proving that solid-state laser is an attractive excitation source in photoacoustic spectroscopy.

关键词： power tunable tuning

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RepDNet:A re-parameterization despeckling network for autonomous underwater side-scan sonar imaging with prior-knowledge customized convolution

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Defence Technology（防务技术） 2024年第5期35卷 259-274页

作者： Zhuoyi Li Zhisen Wang Deshan Chen Tsz Leung Yip angelo P.Teixeira Department of Logistics and Maritime Studies The Hong Kong Polytechnic UniversityChina State Key Laboratory of Maritime Technology and Safety Wuhan University of TechnologyChina School of Transportation and Logistics Engineering Wuhan University of TechnologyChina National Engineering Research Center for Water Transport Safety Wuhan University of TechnologyChina Centre for Marine Technology and Ocean Engineering(CENTEC) Instituto Superior TecnicoUniversidade de LisboaPortugal

Side-scan sonar(SSS)is now a prevalent instrument for large-scale seafloor topography measurements,deployable on an autonomous underwater vehicle(AUV)to execute fully automated underwater acoustic scanning imaging along a predetermined ***,SSS images often suffer from speckle noise caused by mutual interference between echoes,and limited AUV computational resources further hinder noise *** approaches for SSS image processing and speckle noise reduction rely heavily on complex network structures and fail to combine the benefits of deep learning and domain *** address the problem,Rep DNet,a novel and effective despeckling convolutional neural network is *** DNet introduces two re-parameterized blocks:the Pixel Smoothing Block(PSB)and Edge Enhancement Block(EEB),preserving edge information while attenuating speckle *** training,PSB and EEB manifest as double-layered multi-branch structures,integrating first-order and secondorder derivatives and smoothing *** inference,the branches are re-parameterized into a 3×3 convolution,enabling efficient inference without sacrificing *** DNet comprises three computational operations:3×3 convolution,element-wise summation and Rectified Linear Unit *** on benchmark datasets,a real SSS dataset and Data collected at Lake Mulan aestablish Rep DNet as a well-balanced network,meeting the AUV computational constraints in terms of performance and latency.

关键词： Side-scan sonar Sonar image despeckling Domain knowledge Re-parameterization

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Plant community on a volcano mountaintop reveals unique high-altitude vegetation in southeastern Brazil

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Journal of Mountain Science 2024年第9期21卷 3018-3030页

作者： Igor Musauer KESSOUS Ruy JoséValka alves Nílber Gonçalves da SILVA Amilcar Walter SAPORETTI JUNIOR Biodiversity Laboratory Federal Institute of EducationScience and Technology of Southern Minas Gerais(IFSULDEMINAS)Av.Dirce Pereira Rosa300-Jardim Esperança37713-100Poços de CaldasMGBrazil Department of Botany National MuseumFederal University of Rio de JaneiroQuinta da Boa Vista s.n.São Cristóvão20949-040Rio de JaneiroRJBrazil Gothenburg Global Biodiversity Centre Carl Skottsbergs Gata 22BSE 41319GothenburgSweden

Mountains exhibit a high degree of endemism and diversity,however,quantifying their biodiversity can be *** to islands,species isolation in mountainous regions results in comparable patterns of evolution and extinction,rendering their biodiversity unique and highly susceptible to anthropogenic *** topographic relief in mountains plays a crucial role in creating habitat complexity,which in turn contribute to high plant ***,we investigated plant diversity in the volcano mountaintop vegetation on the Poços de Caldas Plateau,a region situated in the ecotone between the Atlantic Forest and Cerrado,characterized by natural radiation and significant anthropogenic *** employed an automated approach through the filtering of georeferenced and non-georeferenced data to obtain a list of plant species in the ***,we statistically investigated the similarity among different high-altitude vegetations belonging to the campos de altitude from the Atlantic Forest and campos rupestres from the *** plateau exhibits high plant diversity,including 1,659 specific and infraspecific taxa,especially belonging to Asteraceae and *** analyses suggest that geographical distance is a strong predictor of dissimilarity and that the Poços de Caldas Plateau is more floristically related to the campos rupestres,despite being associated with campos de *** region possesses a unique set of biodiversity,indicating that it may be a distinct ***,we hypothesize that Pleistocene events likely influenced the conformation of the current floristic composition in the region through species interchange between the Cerrado and Atlantic *** study also highlights the few taxa assessed for conservation status and anthropogenic threats that this habitat is facing.

关键词： Atlantic Forest Biogeography Cerrado Community ecology Grassland

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