A systematic review of automated methods to perform white matter tract segmentation.

White matter tract segmentation is a pivotal research area that leverages diffusion-weighted magnetic resonance imaging (dMRI) for the identification and mapping of individual white matter tracts and their trajectories. This study aims to provide a comprehensive systematic literature review on automated methods for white matter tract segmentation in brain dMRI scans. Articles on PubMed, ScienceDirect [NeuroImage, NeuroImage (Clinical), Medical Image Analysis], Scopus and IEEEXplore databases and Conference proceedings of Medical Imaging Computing and Computer Assisted Intervention Society (MICCAI) and International Symposium on Biomedical Imaging (ISBI), were searched in the range from January 2013 until September 2023. This systematic search and review identified 619 articles. Adhering to the specified search criteria using the query, "white matter tract segmentation OR fiber tract identification OR fiber bundle segmentation OR tractography dissection OR white matter parcellation OR tract segmentation," 59 published studies were selected. Among these, 27% employed direct voxel-based methods, 25% applied streamline-based clustering methods, 20% used streamline-based classification methods, 14% implemented atlas-based methods, and 14% utilized hybrid approaches. The paper delves into the research gaps and challenges associated with each of these categories. Additionally, this review paper illuminates the most frequently utilized public datasets for tract segmentation along with their specific characteristics. Furthermore, it presents evaluation strategies and their key attributes. The review concludes with a detailed discussion of the challenges and future directions in this field.

Unique case of vascularization: superficial brachial artery and radial persistent median artery.

During a routine cadaveric dissection of a 93-year-old male donor, unique arterial variations were observed in the right upper extremity. This rare arterial branching pattern began at the third part of the axillary artery (AA), where it gave off a large superficial brachial artery (SBA) before bifurcating into the subscapular artery and a common stem. The common stem then gave off a division for the anterior and posterior circumflex humeral arteries, before continuing as a small brachial artery (BA). The BA terminated as a muscular branch to the brachialis muscle. The SBA bifurcated into a large radial artery (RA) and small ulnar artery (UA) in the cubital fossa. The UA branching pattern was atypical, giving off only muscular branches in the forearm and a deep UA before contributing to the superficial palmar arch (SPA). The RA provided the radial recurrent artery and a common trunk (CT) proximally before continuing its course to the hand. The CT from the RA gave off a branch that divided into anterior and posterior ulnar recurrent arteries, as well as muscular branches, before it bifurcated into the persistent median artery (PMA) and the common interosseous artery. The PMA anastomosed with the UA before entering the carpal tunnel and contributed to the SPA. This case presents a unique combination of arterial variations in the upper extremity and is clinically and pathologically relevant.

R2Net: Efficient and flexible diffeomorphic image registration using Lipschitz continuous residual networks.

Classical diffeomorphic image registration methods, while being accurate, face the challenges of high computational costs. Deep learning based approaches provide a fast alternative to address these issues; however, most existing deep solutions either lose the good property of diffeomorphism or have limited flexibility to capture large deformations, under the assumption that deformations are driven by stationary velocity fields (SVFs). Also, the adopted squaring and scaling technique for integrating SVFs is time- and memory-consuming, hindering deep methods from handling large image volumes. In this paper, we present an unsupervised diffeomorphic image registration framework, which uses deep residual networks (ResNets) as numerical approximations of the underlying continuous diffeomorphic setting governed by ordinary differential equations, which is parameterized by either SVFs or time-varying (non-stationary) velocity fields. This flexible parameterization in our Residual Registration Network (R2Net) not only provides the model's ability to capture large deformation but also reduces the time and memory cost when integrating velocity fields for deformation generation. Also, we introduce a Lipschitz continuity constraint into the ResNet block to help achieve diffeomorphic deformations. To enhance the ability of our model for handling images with large volume sizes, we employ a hierarchical extension with a multi-phase learning strategy to solve the image registration task in a coarse-to-fine fashion. We demonstrate our models on four 3D image registration tasks with a wide range of anatomies, including brain MRIs, cine cardiac MRIs, and lung CT scans. Compared to classical methods SyN and diffeomorphic VoxelMorph, our models achieve comparable or better registration accuracy with much smoother deformations. Our source code is available online at https://github.com/ankitajoshi15/R2Net.

Sth1, the ATPase subunit of the RSC chromatin remodeler has important roles in stress response and DNA damage repair in the pathogenic fungi Candida albicans.

Candida albicans, the most prevalent fungal pathogen, exists as a commensal in the human host. It is subjected to myriad physiological stress conditions in different host niches, which jeopardizes its fitness to survive and propagate as an established commensal. C. albicans has highly labile chromatin which gets remodeled in response to the stress conditions to facilitate the expression of several stress-responsive genes. Several epigenetic factors including histone variants, histone modifiers and chromatin remodelers that define the chromatin architecture play crucial roles in the regulation of the stress-responsive genes in this organism. Here we investigated the roles of the ATP-dependent chromatin remodeler RSC (Remodel the Structure of Chromatin) in several stress responses in C. albicans, by targeting the key ATPase component, Sth1, given its profound and similar roles exist in Saccharomyces cerevisiae. We have unraveled the crucial roles of the RSC complex (Sth1) in maintaining cell wall integrity and fighting against osmotic and oxidative stresses. We found that the mutant conditionally depleted of Sth1 was sensitive to the cell wall disrupting agents, and the mutant without exposure to any stressor accumulated higher chitin content in the cell wall as a defense mechanism to restore the cell wall integrity. Further, this was supported by the phosphorylation of MAPK1 protein Mkc1, which happens due to activation of the cell wall integrity pathway PKC1. We also observed the Sth1 mutant to be sensitive to oxidative and osmotic stresses in vitro, which are very important and imparted by the host defense mechanism. This suggests that the mutant could get attenuated and hence become less virulent than the wild-type when loss of function of Sth1 happens. We also found that Sth1 has a crucial role in maintaining genomic integrity as sth1 mutant cells accumulate extensive DNA damages and show the loss in cell viability. Overall this work suggests that Sth1 has an important role in fighting against some of the clinically relevant and physiologically important stresses. It also has a crucial role in fighting against stress to the genomic integrity and hence functions in DNA damage repair.

Switching the charge transfer characteristics of quaterthiophene from p-type to n-type via interactions with carbon nanotubes.

Carbon nanotube-based semiconductors are of great interest for optoelectronic applications at the nanoscale. The present study investigates the structural, optoelectronic and charge transport properties of non-covalent complexes formed between carbon nanotubes (CNTs) and quaterthiophene (4T) by employing dispersion-corrected density functional methods. The effect of different functionals viz., B97-D, B3LYP-GD3 and ωB97X-D on the properties of endo- and exohedral complexes is examined. The endohedral complex (4T@CNT) is found to be energetically more stable than the exohedral one (4T-CNT). Electronic properties such as the ionization energy, electron affinity and energy gap between the frontier molecular orbitals of the CNT are not significantly changed by the adsorption or the encapsulation of 4T. Contrary to the p-type characteristics of 4T, its complexes formed with CNTs exhibit n-type characteristics due to the higher electron mobility than the hole mobility. Among the endo- and exohedral complexes, the former one shows the highest electron mobility of 3.79 cm2 V-1 s-1. The absorption properties of all the systems were studied by time-dependent density functional theory (TD-DFT). It is found that the complexes undergo several charge transfer transitions in the visible region of the electromagnetic spectrum. The above results unequivocally suggest that the charge-transfer characteristics of 4T can be altered on forming complexes with CNTs.

Vitexin alleviates non-alcoholic fatty liver disease by activating AMPK in high fat diet fed mice.

Non-alcoholic fatty liver disease (NAFLD) is a most common liver disorder characterized by accumulation of fat in the liver and currently there is no approved treatment for it. Obesity and diabetes being leading cause of NAFLD, compounds having anti-obesity activity and potential to reduce insulin resistance are considered suitable candidate for NAFLD treatment. In this study, we checked effect of vitexin, a naturally occurring flavonoid, on high fat diet (HFD) induced NAFLD in C57BL/6J mice. In presence of vitexin, significant reduction in body and liver weight, triglyceride and cholesterol content in serum and liver was observed. Serum Alanine aminotransferase (ALT) and Aspartate aminotransferase (AST) levels were reduced significantly by vitexin which were elevated in HFD group whereas serum lipase activity remained unchanged. Vitexin suppressed de novo lipogenesis by downregulating expression of Peroxisome proliferator-activated receptor γ (PPARγ), CCAAT/enhancer-binding protein-α (C/EBP-α), sterol regulatory element-binding protein-1c (SREBP-1c), Fatty acid synthase (FAS) and Acetyl-CoA Carboxylase (ACC). Additionally, it also enhanced fatty acid oxidation and lipolysis by upregulating Peroxisome proliferator-activated receptor α (PPAR-α), carnitine palmitoyltransferase-1a (CPT-1a) and Adipose triglyceride lipase (ATGL). Inhibition of lipogenesis and activation of lipolysis and fatty acid oxidation by vitexin was found to be mediated by activation of AMP-activated protein kinase (AMPK). Vitexin also improved insulin signalling by activating insulin receptor substrate-1 (IRS-1) and its downstream target AKT. AMPK activation of vitexin was possibly through binding of vitexin to leptin receptor (LepR) which was confirmed by molecular docking studies and by observed enhanced expression of LepR. Thus, we propose that vitexin alleviates NAFLD by activating AMPK possibly by binding to LepR.

Structural, optoelectronic and charge transport properties of the complexes of indigo encapsulated in carbon nanotubes.

Using the dispersion-corrected density functional B97D and 6-31g(d,p) basis set, the structural, stability, electronic, optical and charge transport properties of the complexes formed by encapsulating indigo inside carbon nanotubes (CNTs) of varying diameters are investigated. Based on the stabilization energy of the complexes indigo@(n,n)CNT (where n = 6, 7 and 8), indigo@(7,7)CNT is shown to be the most stable owing to the ideal diameter of (7,7)CNT for encapsulating indigo. The nature of the interaction between the guest and the host is investigated by means of energy decomposition analysis employing the symmetry adapted perturbation theory. Electronic properties such as the ionization energy, the electron affinity and the energy gap between the highest occupied and lowest unoccupied molecular orbitals (ΔEH-L) of the complexes are determined. The low values of ΔEH-L (<1 eV) for the complexes suggest that they can act as narrow energy gap semiconductors. All the complexes exhibit high hole and electron mobilities which vary inversely with respect to the diameter of the CNT. Using the time-dependent density functional theoretical method, the absorption properties are predicted for the most stable complex indigo@(7,7)CNT. The presence of charge transfer peaks in the visible and near-infrared regions of the electromagnetic spectrum suggests that the complexes are suitable for optoelectronic devices such as solar cells.

Charge transport and optical properties of the complexes of indigo wrapped over carbon nanotubes.

A new molecular system comprising the non-covalently functionalized complexes of single walled (6,6) carbon nanotubes (SWCNTs) of finite length with indigo is proposed based on the dispersion-corrected density functional theory calculations. In the complexes viz. the dyad and triad, indigo is wrapped over carbon nanotubes in the ratio of 1 : 1 and 2 : 1, respectively. A comprehensive study of stabilization energy, ionization energy, electron affinity, the energy gap between the highest occupied and lowest unoccupied molecular orbitals (ΔELUMO-HOMO), and absorption spectra unravels the structure-property relationship of the complexes. The energy gap of ∼1 eV between the HOMO and the LUMO of the complexes suggests that they can be semiconductive. The energy levels of the frontier molecular orbitals of indigo and CNT suggest the possibility of the photoinduced charge transfer between them. Using the charge hopping rate based on Marcus theory, a hole mobility as high as 8.77 cm(2) V(-1) s(-1) is obtained for the dyad. For both the dyad and triad, a higher value of hole mobility than electron mobility is observed, thereby suggesting them to be useful for p-type semiconductor devices. The time-dependent density functional theory (TD-DFT) calculations predict that the absorption of indigo-CNT complexes occurs in the visible and the near-infrared regions finding applications in organic light emitting diodes (OLEDs). Furthermore, the effects of the length and the capping of CNTs as well as the orientation of indigo over the CNTs on the charge transport properties are also discussed.

Studies on nutritional requirement for the culture of lichen Ramalina nervulosa and Ramalina pacifica to enhance the production of antioxidant metabolites.

In the present report, nutritional requirement for the culture of two lichen species Ramalina nervulosa and Ramalina pacifica were studied in order to enhance their growth rate and antioxidant metabolite production. Extract of R. nervulosa cultured in Bold's basal medium (BBM) showed higher antioxidant activity than R. pacifica cultured in Murashige and Skoog (MS) medium. The lichen species were sub-cultured in standardized nutrient media. R. nervulosa in BBM (1% glucose, 50 ppb asparagines, pH 6.5) yielded 2.76 g biomass with 26.18 mg sekikaic acid, 24.32 mg usnic acid/g dry biomass in a period of 60 days. R. pacifica in MS media (3% sucrose, 100 ppb thiamine, pH 5.9) yielded 3.54 g biomass and 58.92 mg salazinic acid, 40.16 mg usnic acid in the same time period. The standardized culture conditions implemented on bioreactor, R. nervulosa yielded 17.7 g biomass with the production of sekikaic acid 122.8 mg, usnic acid 75.4 mg in 4.5 days. R. pacifica produced 10.3 g biomass along with salazinic acid 200 mg and usnic acid 136.8 mg in the same duration. Lichen secondary metabolites produced in bioreactor showed moderate antioxidant activity; sekikaic acid 42% to 56.4%; salazinic acid 33.6% to 41.9% and usnic acid 19.9% to 29.5%.