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"Yao, Xin"
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الطب الصيني التقليدي كنز ثمين وعظيم بنته الأمة الصينية على مدى عصور طويلة من الإنتاج والممارسة، يرمي هذا الطب إلى الشفاء من الأمراض والتخفيف من الآلام والمعاناة، ويركز-بطبيعته-على التناغم بين الإنسان والطبيعة ويشكل إطاره النظري ليبني عليه أساليب ومنهجيات فريدة في التشخيص والعلاج، تستند إلى مفاهيم فلسفية قديمة.
Efficient assembly of nanopore reads via highly accurate and intact error correction
2021
Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.
Nanopore reads have been advantageous for de novo genome assembly; however these reads have high error rates. Here, the authors develop an error correction and de novo assembly tool, NECAT, which produces efficient, high quality assemblies of nanopore reads.
Journal Article
Generation of vascularized brain organoids to study neurovascular interactions
by
Zhou, Ying-Ying
,
Zeng, Peng-Ming
,
Chen, Yue-Jun
in
Angiogenesis
,
Blood vessels
,
Blood-brain barrier
2022
Brain organoids have been used to recapitulate the processes of brain development and related diseases. However, the lack of vasculatures, which regulate neurogenesis and brain disorders, limits the utility of brain organoids. In this study, we induced vessel and brain organoids, respectively, and then fused two types of organoids together to obtain vascularized brain organoids. The fused brain organoids were engrafted with robust vascular network-like structures and exhibited increased number of neural progenitors, in line with the possibility that vessels regulate neural development. Fusion organoids also contained functional blood–brain barrier-like structures, as well as microglial cells, a specific population of immune cells in the brain. The incorporated microglia responded actively to immune stimuli to the fused brain organoids and showed ability of engulfing synapses. Thus, the fusion organoids established in this study allow modeling interactions between the neuronal and non-neuronal components in vitro, particularly the vasculature and microglia niche. Understanding how the organs form and how their cells behave is essential to finding the causes and treatment for developmental disorders, as well as understanding certain diseases. However, studying most organs in live animals or humans is technically difficult, expensive and invasive. To address this issue, scientists have developed models called ‘organoids’ that recapitulate the development of organs using stem cells in the lab. These models are easier to study and manipulate than the live organs. Brain organoids have been used to recapitulate brain formation as well as developmental, degenerative and psychiatric brain conditions such as microcephaly, autism and Alzheimer’s disease. However, these brain organoids lack the vasculature (the network of blood vessels) that supplies a live brain with nutrients and regulates its development, and which has important roles in brain disorders. Partly due to this lack of blood vessels, brain organoids also do not develop a blood brain barrier, the structure that prevents certain contents of the blood, including pathogens, toxins and even certain drugs from entering the brain. These characteristics limit the utility of existing brain organoids. To overcome these limitations, Sun, Ju et al. developed brain organoids and blood vessel organoids independently, and then fused them together to obtain vascularized brain organoids. These fusion organoids developed a robust network of blood vessels that was well integrated with the brain cells, and produced more neural cell precursors than brain organoids that had not been fused. This result is consistent with the idea that blood vessels can regulate brain development. Analyzing the fusion organoids revealed that they contain structures similar to the blood-brain barrier, as well as microglial cells (immune cells specific to the brain). When exposed to lipopolysaccharide – a component of the cell wall of certain bacteria – these cells responded by initiating an immune response in the fusion organoids. Notably, the microglial cells were also able to engulf connections between brain cells, a process necessary for the brain to develop the correct structures and work normally. Sun, Ju et al. have developed a new organoid system that will be of broad interest to researchers studying interactions between the brain and the circulatory system. The development of brain-blood-barrier-like structures in the fusion organoids could also facilitate the development of drugs that can cross this barrier, making it easier to treat certain conditions that affect the brain. Refining this model to allow the fusion organoids to grow for longer times in the lab, and adding blood flow to the system will be the next steps to establish this system.
Journal Article
Landslide Detection and Mapping Based on SBAS-InSAR and PS-InSAR: A Case Study in Gongjue County, Tibet, China
2022
The rock mass along the Jinsha River is relatively broken under complex geological action. Many ancient landslides were distributed along the Jinsha River in Gongjue County, which is very dangerous under the action of gravity, tectonic stress and river erosion. Efficient and accurate identification and monitoring of landslides is important for disaster monitoring and early warning. Interferometric synthetic aperture radar (InSAR) technology has been proved to be an effective technology for landslide hazard identification and mapping. However, great uncertainty inevitably exists due to the single deformation observation method, resulting in wrong judgment during the process of landslide detection. Therefore, to address the uncertainties arising from single observations, a cross-comparison method is put forward using SBAS-InSAR (small baseline subset InSAR) and PS-InSAR (permanent scatterers InSAR) technology. Comparative analysis of the spatial complementarity of interference points and temporal deformation refined the deformation characteristics and verified the reliability of the InSAR results, aiding in the comprehensive identification and further mapping of landslides. Landslides along the Jinsha River in Gongjue County were studied in this paper. Firstly, 14 landslides with a total area of 20 km2 were identified by using two time-series InSAR methods. Then, the deformation characteristics of these landslides were validated by UAV (unmanned aerial vehicle) images, multiresource remote sensing data and field investigation. Further, the precipitation data were introduced to analyze the temporal deformation characteristics of two large landslides. Lastly, the influence of fault activity on landslide formation is further discussed. Our results demonstrate that the cross-comparison of the time-series InSAR method can effectively verify the accuracy of landslide identification.
Journal Article
Optical orbital-angular-momentum-multiplexed data transmission under high scattering
by
Yin-Mei, Li
,
Xin-Yao, Hu
,
Gong Lei
in
Data transmission
,
Energy transfer
,
Fiber optic communications
2019
Multiplexing multiple orbital angular momentum (OAM) channels enables high-capacity optical communication. However, optical scattering from ambient microparticles in the atmosphere or mode coupling in optical fibers significantly decreases the orthogonality between OAM channels for demultiplexing and eventually increases crosstalk in communication. Here, we propose a novel scattering-matrix-assisted retrieval technique (SMART) to demultiplex OAM channels from highly scattered optical fields and achieve an experimental crosstalk of –13.8 dB in the parallel sorting of 24 OAM channels after passing through a scattering medium. The SMART is implemented in a self-built data transmission system that employs a digital micromirror device to encode OAM channels and realize reference-free calibration simultaneously, thereby enabling a high tolerance to misalignment. We successfully demonstrate high-fidelity transmission of both gray and color images under scattering conditions at an error rate of <0.08%. This technique might open the door to high-performance optical communication in turbulent environments.Recovering scattered data from twisted lightTwisted light beams can be made to transmit higher quality data by decoding the information present in the ‘speckle patterns’ that arise when they pass through scattering media. Lei Gong of the University of Science and Technology of China and colleagues developed the ‘scattering-matrix-assisted retrieval technique’ (SMART) to recover scattered data from multiplexed multiple orbital angular momentum (OAM) channels. These multiple twisting light beams have the potential to carry unlimited data channels, but light scattering, caused by micro-particles in the atmosphere or by energy transfer between channels, reduces data quality. The SMART platform allowed high-fidelity transmission of images, reducing the error rate by 21 times compared to previous reports. Improvements on the technique could facilitate the transfer of high quality optical data in harsh atmospheric or underwater conditions.
Journal Article
Porous molybdenum carbide nano-octahedrons synthesized via confined carburization in metal-organic frameworks for efficient hydrogen production
by
Lou, Xiong Wen (David)
,
Yu, Le
,
Yu, Xin-Yao
in
639/301/299/1013
,
639/301/299/921
,
639/638/263/406/77/886
2015
Electrochemical water splitting has been considered as a promising approach to produce clean and sustainable hydrogen fuel. However, the lack of high-performance and low-cost electrocatalysts for hydrogen evolution reaction hinders the large-scale application. As a new class of porous materials with tunable structure and composition, metal-organic frameworks have been considered as promising candidates to synthesize various functional materials. Here we demonstrate a metal-organic frameworks-assisted strategy for synthesizing nanostructured transition metal carbides based on the confined carburization in metal-organic frameworks matrix. Starting from a compound consisting of copper-based metal-organic frameworks host and molybdenum-based polyoxometalates guest, mesoporous molybdenum carbide nano-octahedrons composed of ultrafine nanocrystallites are successfully prepared as a proof of concept, which exhibit remarkable electrocatalytic performance for hydrogen production from both acidic and basic solutions. The present study provides some guidelines for the design and synthesis of nanostructured electrocatalysts.
There is extensive research into non-platinum electrocatalysts for hydrogen evolution. Here, the authors report a molybdenum carbide catalyst, prepared via the carburization of a copper metal-organic framework host/molybdenum-based polyoxometalates guest system, and demonstrate its catalytic activity.
Journal Article
Superexchange and charge transfer in the nickelate superconductor La3Ni2O7 under pressure
2024
Recently, a bulk nickelate superconductor La
3
Ni
2
O
7
is discovered at pressures with a remarkable high transition temperature T
c
∼ 80 K. Here, we study a Hubbard model with tight-binding parameters derived from
ab initio
calculations of La
3
Ni
2
O
7
, by employing large scale determinant quantum Monte Carlo and cellular dynamical mean-field theory. Our result suggests that the superexchange couplings in this system are comparable to that of cuprates. The system is a charge transfer insulator as the hole concentration becomes four per site at large Hubbard
U
. Upon hole doping, two low-energy spin-singlet bands emerge in the system exhibiting distinct correlation properties: while the one composed of the out-of-plane
Ni-
d
3
z
2
−
r
2
and O-
p
z
orbitals demonstrates strong antiferromagnetic correlations and narrow effective bandwidth, the in-plane singlet band consisting of the
Ni-
d
x
2
−
y
2
and O-
p
x
/
p
y
orbitals is in general more itinerant. Over a broad range of hole doping, the doped holes occupy primarily the
d
x
2
−
y
2
and
p
x
/
p
y
orbitals, whereas the
d
3
z
2
−
r
2
and
p
z
orbitals retain underdoped. We propose an effective
t
-
J
model to capture the relevant physics and discuss the implications of our result for comprehending the La
3
Ni
2
O
7
superconductivity.
Journal Article
N-doped graphene layers encapsulated NiFe alloy nanoparticles derived from MOFs with superior electrochemical performance for oxygen evolution reaction
2016
Water splitting, an efficient approach for hydrogen production, is often hindered by unfavorable kinetics of oxygen evolution reaction (OER). In order to reduce the overpotential, noble metal oxides-based electrocatalysts like RuO
2
and IrO
2
are usually utilized. However, due to their scarcity, the development of cost-effective non-precious OER electrocatalysts with high efficiency and good stability is urgently required. Herein, we report a facile one-step annealing of metal-organic frameworks (MOFs) strategy to synthesize N-doped graphene layers encapsulated NiFe alloy nanoparticles (NiFe@C). Through tuning the nanoparticle size and calcination temperature, NiFe@C with an average size of around 16 nm obtained at 700 °C exhibits superior OER performance with an overpotential of only 281 mV at 10 mA cm
−2
and high durability. The facile synthesis method and excellent electrochemical performance show great potential of NiFe@C in replacing the precious metal-based electrocatalysts in the OER.
Journal Article
A self-destructive nanosweeper that captures and clears amyloid β-peptides
2018
Cerebral amyloid β-peptide (Aβ) accumulation resulting from an imbalance between Aβ production and clearance is one of the most important causes in the formation of Alzheimer’s disease (AD). In order to preserve the maintenance of Aβ homeostasis and have a notable AD therapy, achieving a method to clear up Aβ plaques becomes an emerging task. Herein, we describe a self-destructive nanosweeper based on multifunctional peptide-polymers that is capable of capturing and clearing Aβ for the effective treatment of AD. The nanosweeper recognize and bind Aβ via co-assembly through hydrogen bonding interactions. The Aβ-loaded nanosweeper enters cells and upregulates autophagy thus promoting the degradation of Aβ. As a result, the nanosweeper decreases the cytotoxicity of Aβ and rescues memory deficits of AD transgenic mice. We believe that this resourceful and synergistic approach has valuable potential as an AD treatment strategy.
Cerebral amyloid β-peptide accumulation is a causative factor in Alzheimer’s Disease. Here the authors design a 'nanosweeper' that binds amyloid β-peptide and induces autophagy to clear the accumulated plagues.
Journal Article