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1.
BMC Biol ; 22(1): 143, 2024 Jun 27.
Artigo em Inglês | MEDLINE | ID: mdl-38937802

RESUMO

BACKGROUND: The endothelial-to-hematopoietic transition (EHT) process during definitive hematopoiesis is highly conserved in vertebrates. Stage-specific expression of transposable elements (TEs) has been detected during zebrafish EHT and may promote hematopoietic stem cell (HSC) formation by activating inflammatory signaling. However, little is known about how TEs contribute to the EHT process in human and mouse. RESULTS: We reconstructed the single-cell EHT trajectories of human and mouse and resolved the dynamic expression patterns of TEs during EHT. Most TEs presented a transient co-upregulation pattern along the conserved EHT trajectories, coinciding with the temporal relaxation of epigenetic silencing systems. TE products can be sensed by multiple pattern recognition receptors, triggering inflammatory signaling to facilitate HSC emergence. Interestingly, we observed that hypoxia-related signals were enriched in cells with higher TE expression. Furthermore, we constructed the hematopoietic cis-regulatory network of accessible TEs and identified potential TE-derived enhancers that may boost the expression of specific EHT marker genes. CONCLUSIONS: Our study provides a systematic vision of how TEs are dynamically controlled to promote the hematopoietic fate decisions through transcriptional and cis-regulatory networks, and pre-train the immunity of nascent HSCs.


Assuntos
Elementos de DNA Transponíveis , Hematopoese , Células-Tronco Hematopoéticas , Análise de Célula Única , Animais , Elementos de DNA Transponíveis/genética , Análise de Célula Única/métodos , Camundongos , Hematopoese/genética , Humanos , Células-Tronco Hematopoéticas/metabolismo , Células Endoteliais/metabolismo
2.
BMC Plant Biol ; 24(1): 714, 2024 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-39060979

RESUMO

BACKGROUND: Festuca kryloviana is a significant native grass species in the Qinghai Lake region, and its low emergence rate is a primary factor limiting the successful establishment of cultivated grasslands. The region's arid and low-rainfall climate characteristics result in reduced soil moisture content at the surface. Despite the recognized impact of water availability on plant growth, the specific role of moisture in seedling development remains not fully elucidated. This study aims to investigate the germination rate and seedling growth velocity of F. kryloviana seeds under varying moisture conditions, and to integrate physiological and transcriptomic analyses of seedlings under these conditions to reveal the mechanisms by which water influences seedling development. RESULTS: The emergence rate of F. kryloviana seedlings exhibited an initial increase followed by a decrease with increasing moisture content. The highest emergence rate, reaching 75%, was observed under 20% soil moisture conditions. By the eighth day of the experiment, the lengths of the plumules and radicles under the optimal emergence rate (full water, FW) were 21.82% and 10.87% longer, respectively, than those under closely matching the soil moisture content during the background survey (stress water, SW). The differential development of seedlings under varying moisture regimes is attributed to sugar metabolism within the seeds and the accumulation of abscisic acid (ABA). At FW conditions, enhanced sugar metabolism, which generates more energy for seedling development, is facilitated by higher activities of α-amylase, sucrose synthase, and trehalose-6-phosphate synthase compared to SW conditions. This is reflected at the transcriptomic level with upregulated expression of the α-amylase (AMY2) gene and trehalose-6-phosphate synthase (TPS6), while genes associated with ABA signaling and transduction are downregulated. Additionally, under FW conditions, the expression of genes related to the chloroplast thylakoid photosystems, such as photosystem II (PSII) and photosystem I (PSI), is upregulated, enhancing the seedlings' light-capturing ability and photosynthetic efficiency, thereby improving their autotrophic capacity. Furthermore, FW treatment enhances the expression of the non-enzymatic antioxidant system, promoting metabolism within the seeds. In contrast, SW treatment increases the activity of the enzymatic antioxidant system, including peroxidase (POD), superoxide dismutase (SOD), and catalase (CAT), to cope with water stress. CONCLUSIONS: Our experiment systematically evaluated the impact of moisture conditions on the growth and development of F. kryloviana seedlings. Physiological and transcriptomic data collectively indicate that adequate water (20%) supply enhances seedling growth and development by reducing ABA levels and increasing α-amylase activity within seeds, thereby boosting sugar metabolism and promoting the growth of seedling, which in turn leads to an improved emergence rate. Considering water management in future cultivation practices may be a crucial strategy for enhancing the successful establishment of F. kryloviana in grassland ecosystems.


Assuntos
Festuca , Plântula , Água , Plântula/crescimento & desenvolvimento , Plântula/genética , Plântula/metabolismo , Festuca/genética , Festuca/crescimento & desenvolvimento , Festuca/metabolismo , Água/metabolismo , Transcriptoma , Germinação , Regulação da Expressão Gênica de Plantas , Perfilação da Expressão Gênica , Sementes/crescimento & desenvolvimento , Sementes/genética , Sementes/metabolismo
3.
Angew Chem Int Ed Engl ; : e202412368, 2024 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-39090033

RESUMO

Selective hydroboration of C-C single bonds presents a fundamental challenge in the chemical industry. Previously, only catalytic systems utilizing precious metals Ir and Rh, in conjunction with N- and P- ligands, could achieve this, ensuring bond cleavage and selectivity. In sharp contrast, we discovered an unprecedented and general transition-metal-free system for the hydroboration of C-C single bonds. This methodology is transition-metal and ligand-free and surpasses the transition-metal systems regarding chemo- and regioselectivities, substrate versatility, or yields. In addition, our system tolerates various functional groups such as Ar-X (X = halides), heterocyclic rings, ketones, esters, amides, nitro, nitriles, and C=C double bonds, which are typically susceptible to hydroboration in the presence of transition metals. As a result, a diverse range of γ-boronated amines with varied structures and functions has been readily obtained. Experimental mechanistic studies, density functional theory (DFT), and intrinsic bond orbital (IBO) calculations unveiled a hydroborane-promoted C-C bond cleavage and hydride-shift reaction pathway. The carbonyl group of the amide suppresses dehydrogenation between the free N-H and hydroborane. The lone pair on the nitrogen of the amide facilitates the cleavage of C-C bonds in cyclopropanes.

4.
Sensors (Basel) ; 22(9)2022 Apr 20.
Artigo em Inglês | MEDLINE | ID: mdl-35590831

RESUMO

Estimating the biomass of Phragmites australis (Cav.) Trin. ex Steud., i.e., a common wetland macrophyte, and the associated carbon sequestration capacity has attracted increasing attention. Hanshiqiao Wetland Nature Reserve (HWNR) is a large P. australis wetland in Beijing, China, and provides an ideal case study site for such purpose in an urban setting. In this study, an existing P. australis growth dynamics model was adapted to estimate the plant biomass, which was in turn converted to the associated carbon sequestration capacity in the HWNR throughout a typical year. To account for local differences, the modeling parameters were calibrated against the above-ground biomass (AGB) of P. australis retrieved from hyperspectral images of the study site. We also analyzed the sensitivity of the modeling parameters and the influence of environmental factors, particularly the nutrient availability, on the growth dynamics and carbon sequestration capacity of P. australis. Our results show that the maximum AGB and below-ground biomass (BGB) of P. australis in the HWNR are 2.93 × 103 and 2.49 × 103 g m-2, respectively, which are higher than the reported level from nearby sites with similar latitudes, presumably due to the relatively high nutrient availability and more suitable inundation conditions in the HWNR. The annual carbon sequestration capacity of P. australis in the HWNR was estimated to be 2040.73 gC m-2 yr-1, which was also found to be highly dependent on nutrient availability, with a 50% increase (decrease) in the constant of the nutrient availability KNP, resulting in a 12% increase (23% decrease) in the annual carbon sequestration capacity. This implies that a comprehensive management of urban wetlands that often encounter eutrophication problems to synergize the effects of nutrient control and carbon sequestration is worth considering in future practices.


Assuntos
Sequestro de Carbono , Áreas Alagadas , Pequim , Biomassa , China , Poaceae , Tecnologia de Sensoriamento Remoto
5.
Angew Chem Int Ed Engl ; 60(50): 26238-26245, 2021 Dec 06.
Artigo em Inglês | MEDLINE | ID: mdl-34536251

RESUMO

An unprecedented and general hydroboration of alkenes with BX3 (X=Br, Cl) as the boration reagent in the presence of i Pr2 NEt is reported. The addition of i Pr2 NEt not only suppresses alkene polymerization and haloboration side reactions but also provides an "H" source for hydroboration. More importantly, the site-fixed installation of a boryl group at the original position of the internal double bond is readily achieved in contrast to conventional transition-metal-catalyzed hydroboration processes. Further application to the synthesis of 1,n-diborylalkanes (n=3-10) is also demonstrated. Preliminary mechanistic studies reveal a major reaction pathway that involves radical species and operates through a frustrated Lewis pair type single-electron-transfer mechanism.

6.
Angew Chem Int Ed Engl ; 59(32): 13608-13612, 2020 Aug 03.
Artigo em Inglês | MEDLINE | ID: mdl-32297413

RESUMO

A general and atom-economical synthesis of 1,1-diborylalkanes from alkenes and a borane without the need for an additional H2 acceptor is reported for the first time. The key to our success is the use of an earth-abundant zirconium-based catalyst, which allows a balance of self-contradictory reactivities (dehydrogenative boration and hydroboration) to be achieved. Our method avoids using an excess amount of another alkene as an H2 acceptor, which was required in other reported systems. Furthermore, substrates such as simple long-chain aliphatic alkenes that did not react before also underwent 1,1-diboration in our system. Significantly, the unprecedented 1,1-diboration of internal alkenes enabled the preparation of 1,1-diborylalkanes.

7.
Opt Express ; 27(16): 22522-22531, 2019 Aug 05.
Artigo em Inglês | MEDLINE | ID: mdl-31510543

RESUMO

In this paper we demonstrate fast-response Pancharatnam-Berry (PB) phase optical elements (PBOEs) based on polymer-stabilized liquid crystal (PSLC). First, a non-interferometric photo-alignment technique is employed to generate PB patterns in a dye-doped liquid crystal by green laser light. Then the samples are exposed to UV light to form polymer networks. Due to the greatly increased elastic constant in PSLC, all PBOEs can achieve submillisecond response time, while maintaining high diffraction efficiency (>90%). Furthermore, a varifocus PB lens (PBL) is implemented based on two identical PB lens elements and its application in fatigue free augmented-reality (AR) displays is verified. The fast response PBOEs based on PSLC hold great potential for various display and photonics applications.

8.
Opt Express ; 27(6): 9054-9060, 2019 Mar 18.
Artigo em Inglês | MEDLINE | ID: mdl-31052714

RESUMO

We report a non-interferometric single-exposure technique for fabricating Pancharatnam-Berry (PB) devices with arbitrary wavefronts, via photo-patterning an azo-dye doped LC with a two-dimensional linear polarization field, whose local polarization direction can be controlled by a spatial light modulator (SLM) on the pixel level. Upon one exposure, different local LC orientations are generated simultaneously. The non-interferometric approach is insensitive to environmental disturbance, and moreover, the dynamic phase mask on the SLM can be conveniently reconfigured by a computer. Our fabricated PB gratings, q-plates and hologram exhibit good optical performances. Such a simple yet reconfigurable fabrication method enables new PB devices to be developed, and it would open a new gateway towards widespread applications.

9.
Org Biomol Chem ; 17(24): 5891-5896, 2019 06 28.
Artigo em Inglês | MEDLINE | ID: mdl-31166354

RESUMO

An efficient method for the synthesis of N-aryl carbamates from N-Boc-protected amines has been developed. The cobalt-catalyzed in situ generation of isocyanates from N-Boc-protected amines and benzyl alcohols from benzyl formates has been achieved for the first time, which in turn furnished the corresponding benzyl carbamates in moderate to high yields. The reaction was catalyzed by CoI2 with tris-(4-dimethylaminophenyl)-phosphine as the ligand and zinc powder as the reductant. The developed reaction conditions were found to be compatible for aromatic amines with both electron-donating and -withdrawing substituents.

10.
Angew Chem Int Ed Engl ; 58(45): 16167-16171, 2019 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-31486246

RESUMO

The first example of an efficient and direct dehydrogenative boration of alkenes for vinyl boronate ester synthesis was achieved using a zirconium catalyst. Our methodology avoids using precious transition metals, additional hydrogen acceptors, high temperatures, and long reaction times, which were required to overcome the reducing ability of borane, to give alkyl boronate esters. Detailed mechanistic studies revealed a reversible reaction pathway and further suggested applying the zirconium complex as a "shuttle catalyst" for transfer boration, which thus sidesteps the use of relatively sensitive borane.

11.
Nanotechnology ; 29(46): 465708, 2018 Nov 16.
Artigo em Inglês | MEDLINE | ID: mdl-30063216

RESUMO

A surface relaxation model is established to study the elastic properties of nanoscale structures. This model predicts coordination-dependent strain at the surface and thickness-dependent stiffness of a material. Several atomic layers at the surface endure a significant strain gradient, which is dominated by the intrinsic properties of the material. The stiffness of low-dimensional materials is enhanced by surface relaxation effect. Surface effects on strong structures, including honeycomb structure and octet-truss structure with a high stiffness-to-weight ratio, are discussed. For these structures assembled with nanobeams, the Young's modulus decreases with decreasing size of the struts. The coupling between Young's modulus and relative density can be scaled down by engineering tensile strain on the struts.

12.
Neurosurg Focus ; 36(1): E12, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24380478

RESUMO

OBJECT: Pediatric patients with sickle cell anemia (SCA) carry a significant risk of developing moyamoya syndrome (MMS) and brain ischemia. The authors sought to review the safety and efficacy of pial synangiosis in the treatment of MMS in children with SCA by performing a comprehensive review of all previously reported cases in the literature. METHODS: The authors retrospectively reviewed the clinical and radiographic records in 17 pediatric patients with SCA treated at the Morgan Stanley Children's Hospital of New York (MSCHONY) who developed radiological evidence of MMS and underwent pial synangiosis between 1996 and 2012. The authors then added any additional reported cases of pial synangiosis for this population in the literature for a combined analysis of clinical and radiographic outcomes. RESULTS: The combined data consisted of 48 pial synangiosis procedures performed in 30 patients. Of these, 27 patients (90%) presented with seizure, stroke, or transient ischemic attack, whereas 3 (10%) were referred after transcranial Doppler screening. At the time of surgery, the median age was 12 years. Thirteen patients (43%) suffered an ischemic stroke while on chronic transfusion therapy. Long-term follow-up imaging (MR angiography or catheter angiography) at a mean of 25 months postoperatively was available in 39 (81%) treated hemispheres. In 34 (87%) of those hemispheres there were demonstrable collateral vessels on imaging. There were 4 neurological events in 1590 cumulative months of follow-up, or 1 event per 33 patient-years. In the patients in whom complete data were available (MSCHONY series, n = 17), the postoperative stroke rate was reduced more than 6-fold from the preoperative rate (p = 0.0003). CONCLUSIONS: Pial synangiosis in patients with SCA, MMS, and brain ischemia appears to be a safe and effective treatment option. Transcranial Doppler and/or MRI screening in asymptomatic patients with SCA is recommended for the diagnosis of MMS.


Assuntos
Anemia Falciforme/complicações , Veias Cerebrais/cirurgia , Doença de Moyamoya/cirurgia , Procedimentos Neurocirúrgicos/métodos , Adolescente , Anemia Falciforme/fisiopatologia , Isquemia Encefálica/cirurgia , Angiografia Cerebral , Criança , Estudos de Coortes , Feminino , Humanos , Ataque Isquêmico Transitório/etiologia , Ataque Isquêmico Transitório/cirurgia , Angiografia por Ressonância Magnética , Imageamento por Ressonância Magnética , Masculino , Doença de Moyamoya/diagnóstico por imagem , Procedimentos Neurocirúrgicos/efeitos adversos , Complicações Pós-Operatórias/epidemiologia , Acidente Vascular Cerebral/etiologia , Acidente Vascular Cerebral/cirurgia , Resultado do Tratamento , Adulto Jovem
13.
Nat Commun ; 15(1): 1846, 2024 Feb 28.
Artigo em Inglês | MEDLINE | ID: mdl-38418499

RESUMO

Selective cleavage and subsequent functionalization of C-C single bonds present a fundamental challenge in synthetic organic chemistry. Traditionally, the activation of C-C single bonds has been achieved using stoichiometric transition-metal complexes. Recently, examples of catalytic processes were developed in which use is made of precious metals. However, the use of inexpensive and Earth-abundant group IV metals for catalytic C-C single-bond cleavage is largely underdeveloped. Herein, the zirconium-catalyzed C-C single-bond cleavage and subsequent hydroboration reactions is realized using Cp2ZrCl2 as a catalytic system. A series of structures of various γ-boronated amines are readily obtained, which are otherwise difficult to obtain. Mechanistic studies disclose the formation of a N-ZrIV species, and then a ß-carbon elimination route is responsible for C-C single bond activation. Besides zirconium, hafnium exhibits a similar performance for this transformation.

14.
Life Sci ; 345: 122580, 2024 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-38514005

RESUMO

Substance use disorder (SUD) affects over 48 million Americans aged 12 and over. Thus, identifying novel chemicals contributing to SUD will be critical for developing efficient prevention and mitigation strategies. Considering the complexity of the actions and effects of these substances on human behavior, a high-throughput platform using a living organism is ideal. We developed a quick and easy screening assay using Caenorhabditis elegans. C. elegans prefers high-quality food (Escherichia coli HB101) over low-quality food (Bacillus megaterium), with a food preference index of approximately 0.2, defined as the difference in the number of worms at E. coli HB101 and B. megaterium over the total worm number. The food preference index was significantly increased by loperamide, a µ-opioid receptor (MOPR) agonist, and decreased by naloxone, a MOPR antagonist. These changes depended on npr-17, a C. elegans homolog of opioid receptors. In addition, the food preference index was significantly increased by arachidonyl-2'-chloroethylamide, a cannabinoid 1 receptor (CB1R) agonist, and decreased by rimonabant, a CB1R inverse agonist. These changes depended on npr-19, a homolog of CB1R. These results suggest that the conserved opioid and endocannabinoid systems modulate the food preference behaviors of C. elegans. Finally, the humanoid C. elegans strains where npr-17 was replaced with human MOPR and where npr-19 was replaced with human CB1R phenocopied the changes in food preference by the drug treatment. Together, the current results show that this method can be used to rapidly screen the potential effectors of MOPR and CB1R to yield results highly translatable to humans.


Assuntos
Caenorhabditis elegans , Transtornos Relacionados ao Uso de Substâncias , Animais , Humanos , Preferências Alimentares , Escherichia coli , Agonismo Inverso de Drogas , Transtornos Relacionados ao Uso de Substâncias/tratamento farmacológico , Analgésicos Opioides/farmacologia
15.
Heliyon ; 10(15): e35116, 2024 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-39161831

RESUMO

Artificial grasslands of F. kryloviana in the region surrounding Qinghai Lake have been observed to a decline in productivity following three years of establishment. Traditional fertilization practices, aimed at maintaining ecological balance, have predominantly focused on the application of phosphorus. However, it remains unclear whether phosphorus fertilizers offer a superior advantage over nitrogen fertilizers in sustaining productivity. Consequently, from 2017 to 2019, we conducted an experimental to assess the impact of nitrogen and phosphorus fertilization on forage yield and quality. We designed with four levels of phosphorus and two levels of nitrogen, resulting in eight distinct fertilizer combinations. Our experimental findings indicate that the degradation of artificial grasslands leads to a shift in the allocation pattern of aboveground biomass. There was a respective decrease of 68.2 % and 62.5 % in the biomass proportions of stems and ears, contrasted by a greater than 200 % increase in the biomass proportion of leaves. The application of nitrogen not only elevated the total aboveground biomass but also promoted a preferential allocation of biomass to stems and leaves, consequently enhancing the forage's crude protein content. Nitrogen fertilization significantly increased aboveground biomass, and crude protein content by 63.21 %, and 6 %, respectively. Phosphorus fertilization's impact varied annually but favored the distribution of biomass to stems and ears. The net photosynthetic rate improved by over 53.12 % with fertilizer application, although the differences among treatments were not statistically significant. The balanced application of nitrogen and phosphorus fertilizers significantly bolstered the aboveground biomass, ear biomass, stem biomass, leaf biomass, and crude protein content in varying years by 17.25 %-209.83 %, 34.7 %-438.9 %, 25.5 %-250.2 %, 18.4 %-133.3 %, and 10.21 %-25.62 %, respectively. Our analysis revealed that nitrogen-only fertilization exhibited the most optimal fertilizer use efficiency and economic returns. In conclusion, nitrogen fertilization is crucial for sustaining the productivity and quality of F. kryloviana artificial grasslands. The local practice of 75 kg ha-1 phosphorus fertilizer is detrimental to the maintenance of productivity in F. kryloviana artificial grasslands. This study offers valuable insights into the optimization of fertilization strategies for sustainable forage production within alpine regions.

16.
Food Chem Toxicol ; 186: 114560, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38432440

RESUMO

Alpha lipoic acid (ALA) is a dietary supplement that has been used to treat a wide range of diseases, including obesity and diabetes, and have lipid-lowering effects, making it a potential candidate for mitigating dyslipidemia resulting from exposures to the per- and polyfluoroalkyl substance (PFAS) family member perfluorooctanesulfonic acid (PFOS). ALA can be considered a non-fluorinated structural analog to PFOS due to their similar 8-carbon chain and amphipathic structure, but, unlike PFOS, is rapidly metabolized. PFOS has been shown to reduce pancreatic islet area and induce ß-cell lipotoxicity, indicating that changes in ß-cell lipid microenvironment is a mechanism contributing to hypomorphic islets. Due to structural similarities, we hypothesized that ALA may compete with PFOS for binding to proteins and distribution throughout the body to mitigate the effects of PFOS exposure. However, ALA alone reduced islet area and fish length, with several morphological endpoints indicating additive toxicity in the co-exposures. Individually, ALA and PFOS increased fatty acid uptake from the yolk. ALA alone increased liver lipid accumulation, altered fatty acid profiling and modulated PPARÉ£ pathway signaling. Together, this work demonstrates that ALA and PFOS have similar effects on lipid uptake and metabolism during embryonic development in zebrafish.


Assuntos
Ácidos Alcanossulfônicos , Fluorocarbonos , Ácido Tióctico , Poluentes Químicos da Água , Animais , Peixe-Zebra , Ácido Tióctico/farmacologia , Ácidos Alcanossulfônicos/toxicidade , Fluorocarbonos/toxicidade , Ácidos Graxos , Poluentes Químicos da Água/toxicidade
17.
Front Plant Sci ; 15: 1370593, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38742217

RESUMO

Establishing cultivated grassland in the Qinghai-Tibet Plateau region is an effective method to address the conflict between vegetation and livestock. However, the high altitude, low temperature, and arid climate in the region result in slow regeneration and susceptibility to degradation of mixed cultivation grassland containing perennial legumes and gramineous plants. Therefore, we aim to through field experiments, explore the feasibility of establishing mixed cultivation grassland of Poaceae species in the region by utilizing two grass species, Poa pratensis L. and Puccinellia tenuiflora. By employing a mixture of P. pratensis and P. tenuiflora to establish cultivated grassland, we observed significant changes in forage yield over time. Specifically, during the 3rd to 6th years of cultivation, the yield in the mixed grassland was higher than in monocultures. It exceeded the yield of monoculture P. tenuiflora by 19.38% to 29.14% and surpassed the monoculture of P. pratensis by 17.18% to 62.98%. Through the analysis of soil physicochemical properties and soil microbial communities in the cultivated grassland, the study suggests that the mixed grassland with Poaceae species can enhance soil enzyme activity and improve soil microbial communities. Consequently, this leads to increased soil nutrient levels, enhanced nitrogen fixation efficiency, and improved organic phosphorus conversion efficiency. Therefore, establishing mixed grasslands with Poaceae species in the Qinghai-Tibet Plateau region is deemed feasible.

18.
Comput Struct Biotechnol J ; 23: 801-812, 2024 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-38328004

RESUMO

Many pathogenic bacteria use type IV secretion systems (T4SSs) to deliver effectors (T4SEs) into the cytoplasm of eukaryotic cells, causing diseases. The identification of effectors is a crucial step in understanding the mechanisms of bacterial pathogenicity, but this remains a major challenge. In this study, we used the full-length embedding features generated by six pre-trained protein language models to train classifiers predicting T4SEs and compared their performance. We integrated three modules into a model called T4SEpp. The first module searched for full-length homologs of known T4SEs, signal sequences, and effector domains; the second module fine-tuned a machine learning model using data for a signal sequence feature; and the third module used the three best-performing pre-trained protein language models. T4SEpp outperformed other state-of-the-art (SOTA) software tools, achieving ∼0.98 accuracy at a high specificity of ∼0.99, based on the assessment of an independent validation dataset. T4SEpp predicted 13 T4SEs from Helicobacter pylori, including the well-known CagA and 12 other potential ones, among which eleven could potentially interact with human proteins. This suggests that these potential T4SEs may be associated with the pathogenicity of H. pylori. Overall, T4SEpp provides a better solution to assist in the identification of bacterial T4SEs and facilitates studies of bacterial pathogenicity. T4SEpp is freely accessible at https://bis.zju.edu.cn/T4SEpp.

19.
IEEE Trans Vis Comput Graph ; 30(5): 2767-2775, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38564356

RESUMO

High-precision virtual environments are increasingly important for various education, simulation, training, performance, and entertainment applications. We present HoloCamera, an innovative volumetric capture instrument to rapidly acquire, process, and create cinematic-quality virtual avatars and scenarios. The HoloCamera consists of a custom-designed free-standing structure with 300 high-resolution RGB cameras mounted with uniform spacing spanning the four sides and the ceiling of a room-sized studio. The light field acquired from these cameras is streamed through a distributed array of GPUs that interleave the processing and transmission of 4K resolution images. The distributed compute infrastructure that powers these RGB cameras consists of 50 Jetson AGX Xavier boards, with each processing unit dedicated to driving and processing imagery from six cameras. A high-speed Gigabit Ethernet network fabric seamlessly interconnects all computing boards. In this systems paper, we provide an in-depth description of the steps involved and lessons learned in constructing such a cutting-edge volumetric capture facility that can be generalized to other such facilities. We delve into the techniques employed to achieve precise frame synchronization and spatial calibration of cameras, careful determination of angled camera mounts, image processing from the camera sensors, and the need for a resilient and robust network infrastructure. To advance the field of volumetric capture, we are releasing a high-fidelity static light-field dataset, which will serve as a benchmark for further research and applications of cinematic-quality volumetric light fields.

20.
Front Oncol ; 14: 1364627, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-38854732

RESUMO

Purpose: Bulky tumor remains as a challenge to surgery, chemotherapy and conventional radiation therapy. Hence, in efforts to overcome this challenge, we designed a novel therapeutic paradigm via strategy of Stereotactic Central/Core Ablative Radiation Therapy (SCART).), which is based on the principles of SBRT (stereotactic body radiation therapy and spatially fractionated radiation therapy (SFRT). We intend to safely deliver an ablative dose to the core of the tumor and with a low dose at tumor edge. The purpose of the phase 1 study was to determine dose-limiting toxicities (DLT)s and the Maximum Tolerated Dose (MTD) of SCART. Methods and materials: We defined a SCART-plan volume inside the tumor, which is proportional to the dimension of tumor. VMAT/Cyberknife technique was adopted. In the current clinical trial; Patients with biopsy proven recurrent or metastatic bulky cancers were enrolled. The five dose levels were 15 Gy X1, 15Gy X3, 18GyX3, 21GyX3 and 24GyX3, while keeping the whole tumor GTV's border dose at 5Gy each fraction. There was no restriction on concurrent systemic chemotherapy agents. Results: 21 patients were enrolled and underwent SCART. All 21 patients have eligible data for study follow-up. Radiotherapy was well tolerated with all treatment completed as scheduled. The dose was escalated for two patients to 24GyX3. No grade 3 or higher toxicity was observed in any of the enrolled patients. The average age of patients was 66 years (range: 14-85) and 13 (62%) patients were male. The median SCART dose was 18Gy (range: 15 - 24). Six out of the 18 patients with data for overall survival (OS) died, and the median time to death was 16.3 months (range: 1 - 25.6). The mean percent change for tumor shrinkage between first visit volumes and post-SCART volumes was 49.5% (SD: 40.89, p-value:0.009). Conclusion: SCART was safely escalated to 24 GyX 3 fractions, which is the maximum Tolerated Dose (MTD) for SCART. This regimen will be used in future phase II trials.

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