Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species.

Ghost introgression, or the transfer of genetic material from extinct or unsampled lineages to sampled species, has attracted much attention. However, conclusive evidence for ghost introgression, especially in plant species, remains scarce. Here, we newly assembled chromosome-level genomes for both Carya sinensis and Carya cathayensis, and additionally re-sequenced the whole genomes of 43 C. sinensis individuals as well as 11 individuals representing 11 diploid hickory species. These genomic datasets were used to investigate the reticulation and bifurcation patterns within the genus Carya (Juglandaceae), with a particular focus on the beaked hickory C. sinensis. By combining the D-statistic and BPP methods, we obtained compelling evidence that supports the occurrence of ghost introgression in C. sinensis from an extinct ancestral hickory lineage. This conclusion was reinforced through the phylogenetic network analysis and a genome scan method VolcanoFinder, the latter of which can detect signatures of adaptive introgression from unknown donors. Our results not only dispel certain misconceptions about the phylogenetic history of C. sinensis but also further refine our understanding of Carya's biogeography via divergence estimates. Moreover, the successful integration of the D-statistic and BPP methods demonstrates their efficacy in facilitating a more precise identification of introgression types.

Detection of Ghost Introgression Requires Exploiting Topological and Branch Length Information.

In recent years, the study of hybridization and introgression has made significant progress, with ghost introgression-the transfer of genetic material from extinct or unsampled lineages to extant species-emerging as a key area for research. Accurately identifying ghost introgression, however, presents a challenge. To address this issue, we focused on simple cases involving 3 species with a known phylogenetic tree. Using mathematical analyses and simulations, we evaluated the performance of popular phylogenetic methods, including HyDe and PhyloNet/MPL, and the full-likelihood method, Bayesian Phylogenetics and Phylogeography (BPP), in detecting ghost introgression. Our findings suggest that heuristic approaches relying on site-pattern counts or gene-tree topologies struggle to differentiate ghost introgression from introgression between sampled non-sister species, frequently leading to incorrect identification of donor and recipient species. The full-likelihood method BPP uses multilocus sequence alignments directly-hence taking into account both gene-tree topologies and branch lengths, by contrast, is capable of detecting ghost introgression in phylogenomic datasets. We analyzed a real-world phylogenomic dataset of 14 species of Jaltomata (Solanaceae) to showcase the potential of full-likelihood methods for accurate inference of introgression.

Hybrid Ghost Phonon Polaritons in Thin-Film Heterostructure.

Ghost phonon polaritons (g-PhPs), a unique class of phonon polaritons in the infrared, feature ultralong diffractionless propagation (>20 µm) across the surface and tilted wavefronts in the bulk. Here, we study hybrid g-PhPs in a heterostructure of calcite and an ultrathin film of the phase change material (PCM) In3SbTe2, where the optical field is bound in the PCM film with enhanced confinement compared with conventional g-PhPs. Near-field optical images for hybrid g-PhPs reveal a lemniscate pattern in the momentum distribution. We fabricated In3SbTe2 gratings and investigated how different orientations and periodicities of gratings impact the propagation of hybrid g-PhPs. As the grating period decreases to zero, the wavefront of hybrid g-PhPs can be dynamically steered by varying the grating orientation. Our results highlight the promise of hybrid g-PhPs with tunable functionalities for nanophotonic studies.

Calcifying Odontogenic Cyst Demonstrates Recurrent WNT Pathway Mutations and So-Called Adenoid Ameloblastoma-Like Histology: Evidence Supporting Its Classification as a Neoplasm.

Calcifying odontogenic cyst (COC), once called calcifying cystic odontogenic tumor, is classified under the category of odontogenic cysts. However, the proliferative capacity of the lesional epithelium and consistent nuclear ß-catenin expression raise questions about its current classification. This study aimed to determine whether COC would be better classified as a neoplasm in the histologic and molecular context. Eleven odontogenic lesions diagnosed as COC or calcifying cystic odontogenic tumor were included in this study. The growth patterns of the lesional epithelium were analyzed histologically in all cases. ß-catenin immunohistochemistry and molecular profiling using Sanger sequencing and whole-exome sequencing were performed in 10 cases. Of the 11 cases studied, histologic features reminiscent of so-called adenoid ameloblastoma were observed in 72.7% (8/11), and small islands of clear cells extended into the wall in 36.4% (4/11). Intraluminal and/or mural epithelial proliferation was found in 72.7% of the cases (8/11). Nuclear ß-catenin expression was observed focally in all 10 cases studied, mainly highlighting epithelial cells forming morules and adjacent to dentinoid. CTNNB1 hotspot mutations were detected in 60.0% of the cases (6/10). All the remaining cases had frameshift mutations in tumor-suppressor genes involved in the WNT pathway, including APC and NEDD4L. Recurrent WNT pathway mutations leading to nuclear translocation of ß-catenin and distinct epithelial growth patterns found in COC are the neoplastic features shared by its solid counterpart, dentinogenic ghost cell tumor, supporting its classification as a tumor rather than a cyst.

Referenceless Nyquist ghost correction outperforms standard navigator-based method and improves efficiency of in vivo diffusion tensor cardiovascular magnetic resonance.

PURPOSE: The study aims to assess the potential of referenceless methods of EPI ghost correction to accelerate the acquisition of in vivo diffusion tensor cardiovascular magnetic resonance (DT-CMR) data using both computational simulations and data from in vivo experiments. METHODS: Three referenceless EPI ghost correction methods were evaluated on mid-ventricular short axis DT-CMR spin echo and STEAM datasets from 20 healthy subjects at 3T. The reduced field of view excitation technique was used to automatically quantify the Nyquist ghosts, and DT-CMR images were fit to a linear ghost model for correction. RESULTS: Numerical simulation showed the singular value decomposition (SVD) method is the least sensitive to noise, followed by Ghost/Object method and entropy-based method. In vivo experiments showed significant ghost reduction for all correction methods, with referenceless methods outperforming navigator methods for both spin echo and STEAM sequences at b = 32, 150, 450, and 600 smm - 2 $$ {\mathrm{smm}}^{-2} $$ . It is worth noting that as the strength of the diffusion encoding increases, the performance gap between the referenceless method and the navigator-based method diminishes. CONCLUSION: Referenceless ghost correction effectively reduces Nyquist ghost in DT-CMR data, showing promise for enhancing the accuracy and efficiency of measurements in clinical practice without the need for any additional reference scans.

Label-free cell detection of acute leukemia using ghost cytometry.

Early diagnosis and prompt initiation of appropriate treatment are critical for improving the prognosis of acute leukemia. Acute leukemia is diagnosed by microscopic morphological examination of bone marrow smears and flow cytometric immunophenotyping of bone marrow cells stained with fluorophore-conjugated antibodies. However, these diagnostic processes require trained professionals and are time and resource-intensive. Here, we present a novel diagnostic approach using ghost cytometry, a recently developed high-content flow cytometric approach, which enables machine vision-based, stain-free, high-speed analysis of cells, leveraging their detailed morphological information. We demonstrate that ghost cytometry can detect leukemic cells from the bone marrow cells of patients diagnosed with acute lymphoblastic leukemia and acute myeloid leukemia without relying on biological staining. The approach presented here holds promise as a precise, simple, swift, and cost-effective diagnostic method for acute leukemia in clinical practice.

The evolving molecular characterisation, histological criteria and nomenclature of adenoid ameloblastoma as a World Health Organisation tumour type.

Adenoid ameloblastoma (AA) was recently recognised as a separate tumour type in the most recent World Health Organisation (WHO) classification of head and neck tumours. This decision has been considered controversial by several groups, who have described AA as a subtype of ameloblastoma, a hybrid odontogenic tumour or to fall within the spectrum of other recognised odontogenic tumours, including dentinogenic ghost cell tumour and adenomatoid odontogenic tumour. Here we review the reasons for the WHO decision to classify AA as a separate tumour type. We also critique molecular and histological findings from recent reports published since the WHO classification. While acknowledging that the classification of tumours is constantly evolving, the balance of current evidence suggests that AA should remain a distinct tumour type, and not a subtype of ameloblastoma, pending further molecular characterisation.

Energy Transfer on Cytoskeleton of Red Blood Cell Ghosts and their Efficiency Control by KCl Concentration-induced Cell Shrinkage.

Lipid bilayer membranes such as liposomes have been utilized as platforms for bioinspired artificial photosynthesis. Embedding functional compounds, including chromophores and catalysts, into two-dimensional lipid membranes allows their high local concentration and proximity, resulting in enhanced reactivity compared to that of homogeneous solutions. The control of photoreactions by the physical and chemical properties of membranes, such as fluidity and phase separation, has also been well studied in recent years. In contrast, it remains difficult to control chemical reactions via dynamic membrane deformation. Here, we report on the control of excitation energy transfer using red blood cell ghosts (RBCGs) as scaffolds, relying on their asymmetric lipid membranes and inherent and unique deformability. RBCGs, in which donor and acceptor molecules were chemically conjugated to a two-dimensional cytoskeleton located beneath the inner membrane, exhibited energy transfer, and their efficiency varied depending on the amount and ratio of donor and acceptor modifications, as confirmed by experimental and theoretical analysis. Furthermore, the KCl concentration-induced RBCG shrinkage enhanced the energy transfer efficiency. Our proposed method is expected to facilitate the construction of photoreaction systems that can be controlled via membrane deformation.

Demonstrating the immunostimulatory and cytokine-augmentation effects of bacterial ghosts on natural killer cells and Caenorhabditis Elegans.

The potential of bacteria-based immunotherapy lies in its ability to inherently enhance immune responses. However, the "liveness" of bacteria poses risks of bacterial escape, nonspecific immuno-stimulation, and ethical concerns, limiting their acceptability in immunotherapy. In this scenario, nonliving empty bacterial-cell envelopes, named bacterial ghosts (BGs), have emerged as immuno-stimulants with the potential to side-step the limitations of live bacterial therapies. This study demonstrates the capability of BGs in modulating the functionality of NK-92 cells and Caenorhabditis elegans (C. elegans), as well as perform as cytokine-therapy adjuvants. BGs were obtained through a pH-driven culture method, and were validated for their structural and chemical integrity via electron microscopy and spectroscopy. In NK-92 cells, BGs have shown significant immuno-stimulation by boosting the gene-expression of perforin, granzyme-B, Fas-L, and interferon-gamma by factors of 3.5-, 1.5-, 12.5-, and 8.6-folds, respectively. Combined BG and IL-12 treatment yielded a notable 10.2-fold increase in interferon-gamma protein expression in 24 h. The BGs also significantly influenced the innate immune response in C. elegans through the upregulation of lysozyme genes viz., ilys-3 (8.8-fold) and lys-2 (3.1-fold). Our investigation into the impact of BGs on natural killer cells and C. elegans highlights its potential as a valid alternative approach for new-age immunotherapy and cytokine augmentation.

A bacterial ghost vaccine against Aeromonas salmonicida infection in turbot (Scophthalmus maximus).

Aeromonas salmonicida is one of the most prevalent pathogens that causes huge economic losses to aquaculture. Effective vaccination is the first choice for preventing infection. Bacterial ghost (BG), an empty bacterial shell devoid of cytoplasm, is a promising vaccine antigen with distinct advantages. Herein, we established strategies for producing a substantial yield of A. salmonicida ghost (ASG) and investigated the immune-protective properties of it. As a result, 2.84 mg/ml NaOH was discovered to be capable of inducing considerable amounts of ASG. Furthermore, the ASG vaccine elicited adaptive immunity in turbots after rapid activation of innate immunity. Even though formalin-killed cells (FKC) produced a few more antibodies than ASG, ASG ultimately provided a much stronger immune protection effect because it strengthened cellular immunity, with a relative percentage survival (RPS) of 50.1 % compared to FKC. These findings demonstrated that ASG effectively activated cell-mediated immunity, which helped get rid of microorganisms inside cells. Therefore, this study presented novel perspectives for future research on furunculosis vaccine products based on ASG as an antigen.

Simulating drifting fish aggregating device trajectories to identify potential interactions with endangered sea turtles.

Purse-seine fishers using drifting fish aggregating devices (dFADs), mainly built with bamboo, plastic buoys, and plastic netting, to aggregate and catch tropical tuna, deploy 46,000-65,000 dFADs per year in the Pacific Ocean. Some of the major concerns associated with this widespread fishing device are potential entanglement of sea turtles and other marine fauna in dFAD netting; marine debris and pollution; and potential ecological damage via stranding on coral reefs, beaches, and other essential habitats for marine fauna. To assess and quantify the potential connectivity (number of dFADs deployed in an area and arriving in another area) between dFAD deployment areas and important oceanic or coastal habitat of critically endangered leatherback (Dermochelys coriacea) and hawksbill (Eretmochelys imbricata) sea turtles in the Pacific Ocean, we conducted passive-drift Lagrangian experiments with simulated dFAD drift profiles and compared them with known important sea turtle areas. Up to 60% of dFADs from equatorial areas were arriving in essential sea turtle habitats. Connectivity was less when only areas where dFADs are currently deployed were used. Our simulations identified potential regions of dFAD interactions with migration and feeding habitats of the east Pacific leatherback turtle in the tropical southeastern Pacific Ocean; coastal habitats of leatherback and hawksbill in the western Pacific (e.g., archipelagic zones of Indonesia, Papua New Guinea, and Solomon Islands); and foraging habitat of leatherback in a large equatorial area south of Hawaii. Additional research is needed to estimate entanglements of sea turtles with dFADs at sea and to quantify the likely changes in connectivity and distribution of dFADs under new management measures, such as use of alternative nonentangling dFAD designs that biodegrade, or changes in deployment strategies, such as shifting locations.

Simulación de las trayectorias de dispositivos de concentración de peces a la deriva para identificar las interacciones potenciales con las tortugas marinas en peligro de extinción Resumen Los pescadores que usan redes de cerco con dispositivos de concentración de peces a la deriva (dFADs), hechos principalmente con bambú, boyas de plástico y redes de plástico, para concentrar y capturar atún, instalan entre 46,000 y 65,000 dFADs al año en el Océano Pacífico. Algunas de las problemáticas principales asociadas con este dispositivo de pesca de uso extenso son el enredamiento potencial de tortugas marinas y otras especies marinas en las redes de los dFADs; los desechos marinos y la contaminación; y el potencial daño ecológico por el varamiento en los arrecifes de coral, playas y otros hábitats esenciales para la fauna marina. Realizamos experimentos lagrangianos de deriva pasiva con la simulación de perfiles de deriva de los dFADs y los comparamos con áreas conocidas de importancia para las tortugas marinas. Esto fue con el objetivo de evaluar y cuantificar la conectividad potencial (número de dFADs instalados en un área que llegan a otra área) entre las áreas de instalación de dFADs y los hábitats oceánicos o costeros importantes para la tortuga laúd (Dermochelys coriacea) y la tortuga de carey (Eretmochelys imbricata), ambas en peligro crítico de extinción, en el Océano Pacífico. Hasta el 60% de los dFADs de las áreas ecuatoriales llegaron a los hábitats esenciales para las tortugas marinas. La conectividad fue menor sólo cuando se usaron áreas en donde actualmente hay dFADs instalados. Nuestras simulaciones identificaron regiones potenciales de interacción entre los dFADs y los hábitats de migración y alimentación de la tortuga laúd en el sureste tropical del Océano Pacífico; los hábitats costeros de ambas especies en el Pacífico occidental (p. ej.: zonas de archipiélagos en Indonesia, Papúa Nueva Guinea y en las Islas Salomón); y en el hábitat de forrajeo de la tortuga laúd en una gran área ecuatorial al sur de Hawái. Se requiere de mayor investigación para estimar el enredamiento de las tortugas marinas con los dFADs en el mar y para cuantificar los cambios probables en la conectividad y la distribución de los dFADs bajo nuevas medidas de manejo, como el uso alternativo de diseños que eviten el enredamiento y sean biodegradables, o cambios en las estrategias de instalación, como la reubicación.

Detection and molecular characterization of chicken parvovirus and chicken megrivirus in layer breeders affected by intestinal dilatation syndrome.

RESEARCH HIGHLIGHTS: IDS presented pathognomonic dilatation of the jejunum up to Meckel's diverticulum.IDS caused weight loss, decreased egg production, and increased culling and mortality.Chicken parvovirus (ChPV) was consistently detected through PCR assays.Chicken megrivirus (ChMV) was consistently detected through viral metagenomics.

First Passage Times of Long Transient Dynamics in Ecology.

Long transient dynamics in ecological models are characterized by extended periods in one state or regime before an eventual, and often abrupt, transition. One mechanism leading to long transient dynamics is the presence of ghost attractors, states where system dynamics slow down and the system lingers before eventually transitioning to the true attractor. This transition results solely from system dynamics rather than external factors. This paper investigates the dynamics of a classical herbivore-grazer model with the potential for ghost attractors or alternative stable states. We propose an intuitive threshold for first passage time analysis applicable to both bistable and ghost attractor regimes. By formulating the first passage time problem as a backward Kolmogorov equation, we examine how the mean first passage time changes as parameters are varied from the ghost attractor regime to the bistable one, through a saddle-node bifurcation. Our results reveal that the mean and variance of first passage times vary smoothly across the bifurcation threshold, eliminating the deterministic distinction between ghost attractors and bistable regimes. This work suggests that first passage time analysis can be an informative way to classify the length of a long transient. A better understanding of the duration of long transients may contribute to greater ecological understanding and more effective environmental management.

A W-Shaped Self-Supervised Computational Ghost Imaging Restoration Method for Occluded Targets.

We developed a novel method based on self-supervised learning to improve the ghost imaging of occluded objects. In particular, we introduced a W-shaped neural network to preprocess the input image and enhance the overall quality and efficiency of the reconstruction method. We verified the superiority of our W-shaped self-supervised computational ghost imaging (WSCGI) method through numerical simulations and experimental validations. Our results underscore the potential of self-supervised learning in advancing ghost imaging.

Application of the Five-Step Phase-Shifting Method in Reflective Ghost Imaging for Efficient Phase Reconstruction.

The conventional approach to phase reconstruction in Reflective Ghost Imaging (RGI) typically involves the introduction of three reference screens into the reference path, deeming the Fourier transform step indispensable. However, this method introduces complexity to the system and raises concerns regarding potential errors in phase retrieval. In response to these challenges, we advocate for adopting the Five-Step Phase-Shifting (FSPS) method in the RGI system. This method presents two key advantages over traditional approaches: (1) It streamlines the phase reconstruction process by eliminating the requirement for a Fourier inverse transform. (2) It avoids the need to insert objects into the reference optical path, simplifying the computation of reference optical path intensity and enabling seamless application to Computational Ghost Imaging (CGI), overcoming the constraints of Dual-Arm Ghost Imaging (DAGI). We substantiate the theoretical proposition through numerical simulations involving two intricate objects. Furthermore, our discussion delves into exploring the influence of varying reflective angles on the phase reconstruction performance.

A Method to Correct the Temporal Drift of Single-Photon Detectors Based on Asynchronous Quantum Ghost Imaging.

Single-photon detection and timing has attracted increasing interest in recent years due to their necessity in the field of quantum sensing and the advantages of single-quanta detection in the field of low-level light imaging. While simple bucket detectors are mature enough for commercial applications, more complex imaging detectors are still a field of research comprising mostly prototype-level detectors. A major problem in these detectors is the implementation of in-pixel timing circuitry, especially for two-dimensional imagers. One of the most promising approaches is the use of voltage-controlled ring resonators in every pixel. Each of these runs independently based on a voltage supplied by a global reference. However, this yields the problem that the supply voltage can change across the chip which, in turn, changes the period of the ring resonator. Due to additional parasitic effects, this problem can worsen with increasing measurement time, leading to drift in the timing information. We present here a method to identify and correct such temporal drifts in single-photon detectors based on asynchronous quantum ghost imaging. We also show the effect of this correction on recent quantum ghost imaging (QGI) measurement from our group.

Challenging pitfalls in frozen section pathology: a case of mandible ghost cell odontogenic carcinoma and the literature review.

BACKGROUND: Ghost cell odontogenic carcinoma (GCOC) is a rare malignancy characterized by the presence of ghost cells, preferably in the maxilla. Only slightly more than 50 case reports of GCOC have been documented to date. Due to the rarity of this tumor and its nonspecific clinical criteria, there is a heightened risk of misdiagnosis in clinical examination, imaging findings, and pathology interpretation. CASE PRESENTATION: A 50-year-old male patient presented to the hospital due to experiencing pain in his lower front teeth while eating for the past 2 months. Upon examination, a red, hard, painless mass was found in his left lower jaw, measuring approximately 4.0 cm × 3.5 cm. Based on the malignant histological morphology of the tumor and the abundant red-stained keratinized material, the preoperative frozen section pathology misdiagnosed it as squamous cell carcinoma (SCC). The surgical resection specimen pathology via paraffin section revealed that the tumor was characterized by round-like epithelial islands within the fibrous interstitium, accompanied by a large number of ghost cells and some dysplastic dentin with infiltrative growth. The malignant components displayed marked heterogeneity and mitotic activity. Additionally, a calcified cystic tumor component of odontogenic origin was observed. Hemorrhage, necrosis, and calcifications were present, with a foreign body reaction around ghost cells. Immunoreactivity for ß-catenin showed strong nuclear positivity in tumor cells, while immunostaining was completely negative for p53. The Ki67 proliferation index was approximately 30-40%. The tumor cells exhibited diffuse CK5/6, p63, and p40 immunoreactivity, with varying immunopositivity for EMA. Furthermore, no BRAFV600E mutation was identified by ARMS-PCR. The final pathology confirmed that the tumor was a mandible GCOC. CONCLUSION: We have reported and summarized for the first time the specific manifestations of GCOC in frozen section pathology and possible pitfalls in misdiagnosis. We also reviewed and summarized the etiology, pathological features, molecular characteristics, differential diagnosis, imaging features, and current main treatment options for GCOC. Due to its rarity, the diagnosis and treatment of this disease still face certain challenges. A correct understanding of the pathological morphology of GCOC, distinguishing the ghost cells and the secondary stromal reaction around them, is crucial for reducing misdiagnosis rates.

The Religious Dimensions of Epidemic Disease: Cholera, the Ghost Rite, and Missionary Medicine in Nineteenth-Century Korea.

One of the most catastrophic pandemics in human history was the repeated spread of cholera in the nineteenth century. In spite of its historical significance, few scholars have studied cholera's influence in East Asia. This paper illustrates how cholera was considered, conceptualized, and treated by Korean people prior to contact with North American medical missionaries in 1885. In particular, the article compares the government-ordered public health measures during the Joseon dynasty, focusing on the "ghost rite" performed during outbreaks of epidemic disease with the work of medical missionaries in the late nineteenth century. This study finds that even after the introduction of Western biomedicine, the Korean people persisted with a religious-based etiology of cholera and other infectious diseases until the twentieth century.

Adenoid Ameloblastoma Shares Clinical, Histologic, and Molecular Features With Dentinogenic Ghost Cell Tumor: The Histologic Spectrum of WNT Pathway-Altered Benign Odontogenic Tumors.

An epithelial odontogenic tumor called adenoid ameloblastoma (AA) has recently been included in the new WHO classification. However, AA has considerable overlapping features with a preexisting entity, dentinogenic ghost cell tumor (DGCT). This study compared the clinical, histologic, and molecular characteristics of AA and DGCT. Eight cases of odontogenic tumors initially diagnosed as AA or DGCT were included in this study. Quantitative histologic analysis, ß-catenin immunohistochemistry, and molecular profiling using next generation sequencing were performed. Additionally, accumulated clinical data of AA and DGCT were statistically analyzed. Nuclear ß-catenin accumulation was detected in all cases in common, although the tumors studied histologically consisted of varying combinations of the AA-like phenotype, ghost cells, and dentinoid. However, CTNNB1 hotspot mutations were not found in any case. Instead, loss-of-function mutations in tumor suppressor genes involved in the WNT pathway, including the APC, SMURF1, and NEDD4L genes, were found regardless of histologic type. In addition, KRT13 mutations were detected in 2 cases with a high proportion of ghost cells. Finally, a literature analysis revealed clinical similarities between the previously reported cases of AA and DGCT. These findings suggest that from a clinical and molecular point of view, AA and DGCT represent a histologic spectrum of WNT pathway-altered benign odontogenic tumors rather than 2 distinct tumors. Moreover, previously unidentified keratin mutations may be associated with ghost cell formation found in specific types of odontogenic lesions.

Reconstruction for 7T high-resolution whole-brain diffusion MRI using two-stage N/2 ghost correction and L1-SPIRiT without single-band reference.

PURPOSE: To combine a new two-stage N/2 ghost correction and an adapted L1-SPIRiT method for reconstruction of 7T highly accelerated whole-brain diffusion MRI (dMRI) using only autocalibration scans (ACS) without the need of additional single-band reference (SBref) scans. METHODS: The proposed ghost correction consisted of a 3-line reference approach in stage 1 and the reference-free entropy method in stage 2. The adapted L1-SPIRiT method was formulated within the 3D k-space framework. Its efficacy was examined by acquiring two dMRI data sets at 1.05-mm isotropic resolutions with a total acceleration of 6 or 9 (i.e., 2-fold or 3-fold slice and 3-fold in-plane acceleration). Diffusion analysis was performed to derive DTI metrics and estimate fiber orientation distribution functions (fODFs). The results were compared with those of 3D k-space GRAPPA using only ACS, all in reference to 3D k-space GRAPPA using both ACS and SBref (serving as a reference). RESULTS: The proposed ghost correction eliminated artifacts more robustly than conventional approaches. Our adapted L1-SPIRiT method outperformed 3D k-space GRAPPA when using only ACS, improving image quality to what was achievable with 3D k-space GRAPPA using both ACS and SBref scans. The improvement in image quality further resulted in an improvement in estimation performances for DTI and fODFs. CONCLUSION: The combination of our new ghost correction and adapted L1-SPIRiT method can reliably reconstruct 7T highly accelerated whole-brain dMRI without the need of SBref scans, increasing acquisition efficiency and reducing motion sensitivity.