Global prevalence of organohalide-respiring bacteria dechlorinating polychlorinated biphenyls in sewage sludge.

BACKGROUND: Massive amounts of sewage sludge are generated during biological sewage treatment and are commonly subjected to anaerobic digestion, land application, and landfill disposal. Concurrently, persistent organic pollutants (POPs) are frequently found in sludge treatment and disposal systems, posing significant risks to both human health and wildlife. Metabolically versatile microorganisms originating from sewage sludge are inevitably introduced to sludge treatment and disposal systems, potentially affecting the fate of POPs. However, there is currently a dearth of comprehensive assessments regarding the capability of sewage sludge microbiota from geographically disparate regions to attenuate POPs and the underpinning microbiomes. RESULTS: Here we report the global prevalence of organohalide-respiring bacteria (OHRB) known for their capacity to attenuate POPs in sewage sludge, with an occurrence frequency of ~50% in the investigated samples (605 of 1186). Subsequent laboratory tests revealed microbial reductive dechlorination of polychlorinated biphenyls (PCBs), one of the most notorious categories of POPs, in 80 out of 84 sludge microcosms via various pathways. Most chlorines were removed from the para- and meta-positions of PCBs; nevertheless, ortho-dechlorination of PCBs also occurred widely, although to lower extents. Abundances of several well-characterized OHRB genera (Dehalococcoides, Dehalogenimonas, and Dehalobacter) and uncultivated Dehalococcoidia lineages increased during incubation and were positively correlated with PCB dechlorination, suggesting their involvement in dechlorinating PCBs. The previously identified PCB reductive dehalogenase (RDase) genes pcbA4 and pcbA5 tended to coexist in most sludge microcosms, but the low ratios of these RDase genes to OHRB abundance also indicated the existence of currently undescribed RDases in sewage sludge. Microbial community analyses revealed a positive correlation between biodiversity and PCB dechlorination activity although there was an apparent threshold of community co-occurrence network complexity beyond which dechlorination activity decreased. CONCLUSIONS: Our findings that sludge microbiota exhibited nearly ubiquitous dechlorination of PCBs indicate widespread and nonnegligible impacts of sludge microbiota on the fate of POPs in sludge treatment and disposal systems. The existence of diverse OHRB also suggests sewage sludge as an alternative source to obtain POP-attenuating consortia and calls for further exploration of OHRB populations in sewage sludge. Video Abstract.

Combatting multiple aromatic organohalide pollutants in sediments by bioaugmentation with a single Dehalococcoides.

Dehalococcoides are capable of dehalogenating various organohalide pollutants under anaerobic conditions, and they have been applied in bioremediation. However, the presence of multiple aromatic organohalides, including polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), and tetrabromobisphenol A (TBBPA), at contaminated sites may pose challenges to Dehalococcoides-mediated bioremediation due to the lack of knowledge about the influence of co-contamination on bioremediation. In this study, we investigated the bioremediation of aromatic organohalides present as individual and co-contaminants in sediments by bioaugmentation with a single population of Dehalococcoides. Bioaugmentation with Dehalococcoides significantly increased the dehalogenation rate of PCBs, PBDEs, and TBBPA in sediments contaminated with individual pollutants, being up to 19.7, 27.4 and 2.1 times as that in the controls not receiving bioinoculants. For sediments containing all the three classes of pollutants, bioaugmentation with Dehalococcoides also effectively enhanced dehalogenation, and the extent of enhancement depended on the bioinoculants and types of pollutants. Interestingly, in many cases co-contaminated sediments bioaugmented with Dehalococcoides mccartyi strain CG1 displayed a greater enhancement in dehalogenation rates compared to the sediments polluted with individual pollutant. For instance, when augmented with a low quantity of strain CG1, the dehalogenation rates of Aroclor1260 and PBDEs in co-contaminated sediments were approximately two times as that in sediments containing individual pollutants (0.428 and 9.03 vs. 0.195 and 4.20 × 10-3d-1). Additionally, D. mccartyi CG1 grew to higher abundances in co-contaminated sediments. These findings demonstrate that a single Dehalococcoides population can sustain dehalogenation of multiple aromatic organohalides in contaminated sediments, suggesting that co-contamination does not necessarily impede the use of Dehalococcoides for bioremediation. The study also underscores the significance of anaerobic organohalide respiration for effective bioremediation.

Interspecies Mobility of Organohalide Respiration Gene Clusters Enables Genetic Bioaugmentation.

Anthropogenic organohalide pollutants pose a severe threat to public health and ecosystems. In situ bioremediation using organohalide respiring bacteria (OHRB) offers an environmentally friendly and cost-efficient strategy for decontaminating organohalide-polluted sites. The genomic structures of many OHRB suggest that dehalogenation traits can be horizontally transferred among microbial populations, but their occurrence among anaerobic OHRB has not yet been demonstrated experimentally. This study isolates and characterizes a novel tetrachloroethene (PCE)-dechlorinating Sulfurospirillum sp. strain SP, distinguishing itself among anaerobic OHRB by showcasing a mechanism essential for horizontal dissemination of reductive dehalogenation capabilities within microbial populations. Its genetic characterization identifies a unique plasmid (pSULSP), harboring reductive dehalogenase and de novo corrinoid biosynthesis operons, functions critical to organohalide respiration, flanked by mobile elements. The active mobility of these elements was demonstrated through genetic analyses of spontaneously emerging nondehalogenating variants of strain SP. More importantly, bioaugmentation of nondehalogenating microcosms with pSULSP DNA triggered anaerobic PCE dechlorination in taxonomically diverse bacterial populations. Our results directly support the hypothesis that exposure to anthropogenic organohalide pollutants can drive the emergence of dehalogenating microbial populations via horizontal gene transfer and demonstrate a mechanism by which genetic bioaugmentation for remediation of organohalide pollutants could be achieved in anaerobic environments.

Tractography-based automated identification of the retinogeniculate visual pathway with novel microstructure-informed supervised contrastive learning.

The retinogeniculate visual pathway (RGVP) is responsible for carrying visual information from the retina to the lateral geniculate nucleus. Identification and visualization of the RGVP are important in studying the anatomy of the visual system and can inform the treatment of related brain diseases. Diffusion MRI (dMRI) tractography is an advanced imaging method that uniquely enables in vivo mapping of the 3D trajectory of the RGVP. Currently, identification of the RGVP from tractography data relies on expert (manual) selection of tractography streamlines, which is time-consuming, has high clinical and expert labor costs, and is affected by inter-observer variability. In this paper, we present a novel deep learning framework, DeepRGVP , to enable fast and accurate identification of the RGVP from dMRI tractography data. We design a novel microstructure-informed supervised contrastive learning method that leverages both streamline label and tissue microstructure information to determine positive and negative pairs. We propose a simple and successful streamline-level data augmentation method to address highly imbalanced training data, where the number of RGVP streamlines is much lower than that of non-RGVP streamlines. We perform comparisons with several state-of-the-art deep learning methods that were designed for tractography parcellation, and we show superior RGVP identification results using DeepRGVP. In addition, we demonstrate a good generalizability of DeepRGVP to dMRI tractography data from neurosurgical patients with pituitary tumors and we show DeepRGVP can successfully identify RGVPs despite the effect of lesions affecting the RGVPs. Overall, our study shows the high potential of using deep learning to automatically identify the RGVP.

Metabolic Synergy of Dehalococcoides Populations Leading to Greater Reductive Dechlorination of Polychlorinated Biphenyls.

Polychlorinated biphenyls (PCBs) are dioxin-like pollutants that cause persistent harm to life. Organohalide-respiring bacteria (OHRB) can detoxify PCBs via reductive dechlorination, but individual OHRB are potent in dechlorinating only specific PCB congeners, restricting the extent of PCB dechlorination. Moreover, the low biomass of OHRB frequently leads to the slow natural attenuation of PCBs at contaminated sites. Here we constructed defined microbial consortia comprising various combinations of PCB-dechlorinating Dehalococcoides strains (CG1, CG4, and CG5) to successfully enhance PCB dechlorination. Specifically, the defined consortia consisting of strains CG1 and CG4 removed 0.28-0.44 and 0.23-0.25 more chlorine per PCB from Aroclor1260 and Aroclor1254, respectively, compared to individual strains, which was attributed to the emergence of new PCB dechlorination pathways in defined consortia. Notably, different Dehalococcoides populations exhibited similar growth when cocultivated, but temporal differences in the expression of PCB reductive dehalogenase genes indicated their metabolic synergy. Bioaugmentation with individual strains (CG1, CG4, and CG5) or defined consortia led to greater PCB dechlorination in wetland sediments, and augmentation with the consortium comprising strains CG1 and CG4 resulted in the greatest PCB dechlorination. These findings collectively suggest that simultaneous application of multiple Dehalococcoides strains, which catalyze complementary dechlorination pathways, is an effective strategy to accelerate PCB dechlorination.

B4GALNT1 promotes hepatocellular carcinoma stemness and progression via integrin α2ß1-mediated FAK and AKT activation.

Background & Aims: ß-1,4-N-Acetyl-galactosaminyltransferase 1 (B4GALNT1) has been reported to contribute to the development of human malignancies. However, its role in hepatocellular carcinoma (HCC) remains uncharacterised. In this study, we aimed to elucidate the role of B4GALNT1 in HCC stemness and progression. Methods: Immunohistochemical staining was used to evaluate B4GALNT1 expression in HCC tissues and adjacent normal liver tissues. Flow cytometry analysis and sphere formation analysis were performed to investigate the role of B4GALNT1 in HCC stemness. Colony formation, Incucyte, wound-healing, Transwell migration, and invasion assays, and an animal model were used to study the role of B4GALNT1 in HCC progression. RNA-sequencing and co-immunoprecipitation were used to investigate the downstream targets of B4GALNT1. Results: B4GALNT1 was upregulated in HCC and associated with poor clinical outcome of patients with the disease. Moreover, B4GALNT1 promoted HCC stemness, migration, invasion, and growth. Mechanistically, B4GALNT1 not only promoted the expression of the integrin α2ß1 ligand THBS4, but also directly interacted with the ß subunit of integrin α2ß1 ITGB1 to inhibit its ubiquitin-independent proteasomal degradation, resulting in activation of FAK and AKT. Ophiopogonin D inhibited HCC stemness and progression by reducing ITGB1 and THBS4 expression and inhibiting FAK and AKT activation. Conclusions: Our study suggests the B4GALNT1/integrin α2ß1/FAK/PI3K/AKT axis as a therapeutic target for the inhibition of HCC stemness and tumour progression. Impact and implications: The role and regulatory mechanism of B4GALNT1 in HCC have not been studied previously. Here, we reveal that B4GALNT1 has a crucial role in HCC stemness and progression by activating the integrin α2ß1/FAK/PI3K/AKT axis, providing a potential target for HCC therapy. In addition, we find Ophiopogonin D as a potential therapeutic drug for patients with HCC.

Reconstructing the somatotopic organization of the corticospinal tract remains a challenge for modern tractography methods.

The corticospinal tract (CST) is a critically important white matter fiber tract in the human brain that enables control of voluntary movements of the body. The CST exhibits a somatotopic organization, which means that the motor neurons that control specific body parts are arranged in order within the CST. Diffusion magnetic resonance imaging (MRI) tractography is increasingly used to study the anatomy of the CST. However, despite many advances in tractography algorithms over the past decade, modern, state-of-the-art methods still face challenges. In this study, we compare the performance of six widely used tractography methods for reconstructing the CST and its somatotopic organization. These methods include constrained spherical deconvolution (CSD) based probabilistic (iFOD1) and deterministic (SD-Stream) methods, unscented Kalman filter (UKF) tractography methods including multi-fiber (UKF2T) and single-fiber (UKF1T) models, the generalized q-sampling imaging (GQI) based deterministic tractography method, and the TractSeg method. We investigate CST somatotopy by dividing the CST into four subdivisions per hemisphere that originate in the leg, trunk, hand, and face areas of the primary motor cortex. A quantitative and visual comparison is performed using diffusion MRI data (N = 100 subjects) from the Human Connectome Project. Quantitative evaluations include the reconstruction rate of the eight anatomical subdivisions, the percentage of streamlines in each subdivision, and the coverage of the white matter-gray matter (WM-GM) interface. CST somatotopy is further evaluated by comparing the percentage of streamlines in each subdivision to the cortical volumes for the leg, trunk, hand, and face areas. Overall, UKF2T has the highest reconstruction rate and cortical coverage. It is the only method with a significant positive correlation between the percentage of streamlines in each subdivision and the volume of the corresponding motor cortex. However, our experimental results show that all compared tractography methods are biased toward generating many trunk streamlines (ranging from 35.10% to 71.66% of total streamlines across methods). Furthermore, the coverage of the WM-GM interface in the largest motor area (face) is generally low (under 40%) for all compared tractography methods. Different tractography methods give conflicting results regarding the percentage of streamlines in each subdivision and the volume of the corresponding motor cortex, indicating that there is generally no clear relationship, and that reconstruction of CST somatotopy is still a large challenge. Overall, we conclude that while current tractography methods have made progress toward the well-known challenge of improving the reconstruction of the lateral projections of the CST, the overall problem of performing a comprehensive CST reconstruction, including clinically important projections in the lateral (hand and face areas) and medial portions (leg area), remains an important challenge for diffusion MRI tractography.

Substrate-dependent strategies to mitigate sulfate inhibition on microbial reductive dechlorination of polychlorinated biphenyls.

Sulfate widely co-exists with polychlorinated biphenyls (PCBs) at various concentrations in the subsurface environment. Previous studies have suggested that sulfate often hampers microbial degradation of aliphatic chlorinated solvents such as chloroethenes. However, the impact of sulfate on microbial reductive dechlorination of aromatic PCBs and the underlying mechanisms have received limited attention. Likewise, strategies to mitigate such inhibition remain scarce. Here we found that the mechanisms and mitigation strategies of sulfate inhibition on PCB dechlorination were substrate-dependent. Under electron donor-limiting conditions, even a low concentration of sulfate (2 mM) resulted in a decreased PCB dechlorination rate by 88.7% in a co-culture comprising Dehalococcoides mccartyi CG1 and the sulfate-reducing bacterium Desulfovibrio desulfuricans F1, an inhibition which was attributed to the competition for electron donor between sulfate reduction and PCB dechlorination. As expected, re-amendment of 5 mM lactate effectively re-initiated PCB dechlorination. However, in the presence of a higher concentration of sulfate (5 mM), the PCB dechlorination rate in the co-culture was 77.7% lower than in the control, even with excessive electron donor supply. This inhibition was linked to high concentration of sulfide (∼5 mM) produced from sulfate reduction, as suggested by high availability of electron donor, recovery of dechlorination activity after removal of sulfide, and negligible influence of sulfate on PCB dechlorination in the axenic culture of D. mccartyi CG1. Indeed, sulfide (>5 mM) was found to directly suppress expression of PCB-dechlorinating reductive dehalogenase gene. The highest transcriptional level of pcbA1 was 2.9 ± 0.3 transcripts·cell-1 in the presence of ∼5 mM sulfide, which was increased to 37.4 ± 5.0 transcripts·cell-1 when sulfide was removed. Under this scenario, introduction of ferrous salts (5 mM) efficiently alleviated sulfide inhibition on PCB dechlorination. Interestingly, the augmentation of methanogens in the co-culture was also effective in mitigating sulfide inhibition on PCB dechlorination, offering a new approach to protect Dehalococcoides under sulfide stress. Collectively, these findings deepen our understanding of the influence of sulfate on microbial reductive dechlorination of PCBs and contribute to developing appropriate strategies based on geochemical conditions to alleviate sulfate inhibition during bioremediation of PCB-contaminated sites.

Expression of ACE2, TMPRSS2, and SARS-CoV-2 nucleocapsid protein in gastrointestinal tissues from COVID-19 patients and association with gastrointestinal symptoms.

BACKGROUND: Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can infect the gastrointestinal (GI) tract in coronavirus disease 2019 (COVID-19) patients, the mechanism of GI tract injury is largely unknown. We aimed to study the potential factors that cause COVID-19 GI symptoms. METHODS: We investigated the expression and co-localization of angiotensin converting enzyme 2 (ACE2), transmembrane serine protease 2 (TMPRSS2), SARS-CoV-2 nucleocapsid protein (NP), and the severity of inflammation in GI tissues from COVID-19 patients (n = 19) by immunofluorescence and histopathologic staining, and then studied their associations with GI symptoms. RESULTS: Infected stomach tissues showed significantly higher ACE2 expression than uninfected ones, while infected duodenum tissues showed significantly higher TMPRSS2 expression than uninfected ones. The expression of TMPRSS2 exhibited a moderate correlation with viral NP across different GI tissues, while no significant association was observed between ACE2 and viral NP. Some GI symptoms such as diarrhea and nausea, were related to the expression level of ACE2, TMPRSS2 or the severity of inflammation. Furthermore, age and elevated aspartate transaminase were major risk factors for disease progression. CONCLUSIONS: ACE2 and TMPRSS2 were essential proteins in the SARS-CoV-2 infection of GI tract, while TMPRSS2 rather than ACE2 may play a more important role. GI symptoms may derive from the host receptor expression level and pro-inflammatory response in COVID-19 patients after viral infection of GI tissues, and further exacerbate the disease. So targeting TMPRSS2 and inflammation may represent an effective strategy for treating COVID-19 patients with GI symptoms.

Alleviating Chlorinated Alkane Inhibition on Dehalococcoides to Achieve Detoxification of Chlorinated Aliphatic Cocontaminants.

Cocontamination by multiple chlorinated solvents is a prevalent issue in groundwater, presenting a formidable challenge for effective remediation. Despite the recognition of this issue, a comprehensive assessment of microbial detoxification processes involving chloroethenes and associated cocontaminants, along with the underpinning microbiome, remains absent. Moreover, strategies to mitigate the inhibitory effects of cocontaminants have not been reported. Here, we revealed that chloroform exhibited the most potent inhibitory effects, followed by 1,1,1-trichloroethane and 1,1,2-trichloroethane, on dechlorination of dichloroethenes (DCEs) in Dehalococcoides-containing consortia. The observed inhibition could be attributed to suppression of biosynthesis and enzymatic activity of reductive dehalogenases and growth of Dehalococcoides. Notably, cocontaminants more profoundly inhibited Dehalococcoides populations harboring the vcrA gene than those possessing the tceA gene, thereby explaining the accumulation of vinyl chloride under cocontaminant stress. Nonetheless, we successfully ameliorated cocontaminant inhibition by augmentation with Desulfitobacterium sp. strain PR owing to its ability to attenuate cocontaminants, resulting in concurrent detoxification of DCEs, trichloroethanes, and chloroform. Microbial community analyses demonstrated obvious alterations in taxonomic composition, structure, and assembly of the dechlorinating microbiome in the presence of cocontaminants, and introduction of strain PR reshaped the dechlorinating microbiome to be similar to its original state in the absence of cocontaminants. Altogether, these findings contribute to developing bioremediation technologies to clean up challenging sites polluted with multiple chlorinated solvents.

Learning Background-Suppressed Dual-Regression Correlation Filters for Visual Tracking.

The discriminative correlation filter (DCF)-based tracking method has shown good accuracy and efficiency in visual tracking. However, the periodic assumption of sample space causes unwanted boundary effects, restricting the tracker's ability to distinguish between the target and background. Additionally, in the real tracking environment, interference factors such as occlusion, background clutter, and illumination changes cause response aberration and, thus, tracking failure. To address these issues, this work proposed a novel tracking method named the background-suppressed dual-regression correlation filter (BSDCF) for visual tracking. First, we utilize the background-suppressed function to crop out the target features from the global features. In the training step, while introducing the spatial regularity constraint and background response suppression regularization, we construct a dual regression structure to train the target and global filters separately. The aim is to exploit the difference between the output response maps for mutual constraint to highlight the target and suppress the background interference. Furthermore, in the detection step, the global response can be enhanced by a weighted fusion of the target response to further improve the tracking performance in complex scenes. Finally, extensive experiments are conducted on three public benchmarks (including OTB100, TC128, and UAVDT), and the experimental results indicate that the proposed BSDCF tracker achieves tracking performance comparable to many state-of-the-art (SOTA) trackers in a variety of complex situations.

GSK3ß-driven SOX2 overexpression is a targetable vulnerability in esophageal squamous cell carcinoma.

Esophageal squamous cell carcinoma (ESCC) is one of the deadliest forms of human malignancy that currently lacks approved targeted therapeutics. Accumulating evidence suggests that SOX2 overexpression is a key driving factor for ESCC and various squamous cell carcinoma. Here, through screening a small-molecule kinase inhibitor library, we identified GSK3ß as a kinase that is critically required for robust SOX2 expression in ESCC cells. GSK3ß did not promote SOX2 transcriptionally but was required for SOX2 protein stability. We demonstrated that GSK3ß interacts with and phosphorylates SOX2 at residue S251, which blocks SOX2 from ubiquitination and proteasome-dependent degradation instigated by ubiquitin E3 ligase CUL4ADET1-COP1. Pharmacological inhibition or knockdown of GSK3ß by RNA interference selectively impaired SOX2-positive ESCC cell proliferation, cancer stemness, and tumor growth in mouse xenograft model, suggesting that GSK3ß promotes ESCC tumorigenesis primarily by driving SOX2 overexpression. GSK3ß was found to be frequently overexpressed in clinical esophageal tumors, and there was a positive correlation between GSK3ß and SOX2 protein levels. Notably, we found that SOX2 enhanced GSK3ß expression transcriptionally, suggesting the existence of a vicious cycle that drives a coordinated GSK3ß and SOX2 overexpression in ESCC cells. Finally, we demonstrated in tumor xenograft model that GSK3ß inhibitor AR-A014418 was effective in suppressing SOX2-positive ESCC tumor progression and inhibited tumor progression cooperatively with chemotherapeutic agent carboplatin. In conclusion, we uncovered a novel role for GSK3ß in driving SOX2 overexpression and tumorigenesis and provided evidence that targeting GSK3ß may hold promise for the treatment of recalcitrant ESCCs.

Control of SOX2 protein stability and tumorigenic activity by E3 ligase CHIP in esophageal cancer cells.

SOX2 is highly expressed and controls tumor initiation and cancer stem cell function in various squamous cell carcinomas including esophageal squamous cancer. However, the molecular mechanism leading to SOX2 overexpression in cancer is incompletely understood. Here, we identified CHIP, a chaperone-associated ubiquitin E3 ligase, as a novel negative regulator of SOX2 protein stability and tumorigenic activity in esophageal squamous carcinoma cells. We showed that CHIP interacted with SOX2 primarily via chaperone HSP70, together they catalyzed SOX2 ubiquitination and degradation via proteasome. In contrast, HSP90 promoted SOX2 stability and inhibition of HSP90 activity induced SOX2 ubiquitination and degradation. Notably, unlike the case in normal esophageal tissues where CHIP was detected in both the cytoplasm and nucleus, CHIP in clinical esophageal tumor specimens was predominantly localized in the cytoplasm. Consistent with this observation, we observed increased expression of exportin-1/CRM-1 in clinical esophageal tumor specimens. We further demonstrated that CHIP catalyzed SOX2 ubiquitination and degradation primarily in the nuclear compartment. Taken together, our study has identified CHIP as a key suppressor of SOX2 protein stability and tumorigenic activity and revealed CHIP nuclear exclusion as a potential mechanism for aberrant SOX2 overexpression in esophageal cancer. Our study also suggests HSP90 inhibitors as potential therapeutic agents for SOX2-positive cancers.

Fiber-specific white matter alterations in Parkinson's disease patients with freezing of gait.

Freezing of gait (FOG) is a gait disorder that usually occurs in advanced stages of Parkinson's disease (PD). Understanding the underlying mechanism of FOG is important for treatment and prevention. Previous studies have investigated white matter (WM) structure to explore the pathology of FOG. However, the pathology is still unclear, possibly due to the methodological limitation in identifying specific fiber tracts. This study aimed to investigate tract-specific WM structural changes in FOG patients and their relationships with clinical characteristics. We enrolled 19 PD patients with FOG (PD-FOG), 19 without FOG (PD-woFOG) and 21 controls. Fixel-based analysis is a novel framework to avoid the effect of crossing fibers, which provides the metrics to assess WM morphology. By combining a method for segmenting fibers, we identified abnormalities in the specific fiber tracts. Compared to PD-woFOG, PD-FOG showed significant increased fiber-bundle cross-section (FC) in the corpus callosum (CC), fornix (FX), inferior longitudinal fasciculus (ILF), striato-premotor (ST_PREM), superior thalamic radiation (STR), thalamo-premotor (T_PREM), increased fiber density and cross-section (FDC) in the STR, and decreased fiber density (FD) in the CC and ILF. Additionally, the ILF was correlated with motor, cognition and memory, the CC was correlated with anxiety, and the T_PREM was also correlated with cognition. In conclusion, in addition to impairments of WM found in PD-FOG, we found enhancements in WM, which may imply compensatory mechanisms. Furthermore, multiple fiber tracts were correlated with clinical characteristics, especially the ILF, validating the involvement of transmission circuits of multiple distinct information in mechanisms of FOG.

Spatial analysis of stromal signatures identifies invasive front carcinoma-associated fibroblasts as suppressors of anti-tumor immune response in esophageal cancer.

BACKGROUND: Increasing evidence indicates that the tumor microenvironment (TME) is a crucial determinant of cancer progression. However, the clinical and pathobiological significance of stromal signatures in the TME, as a complex dynamic entity, is still unclear in esophageal squamous cell carcinoma (ESCC). METHODS: Herein, we used single-cell transcriptome sequencing data, imaging mass cytometry (IMC) and multiplex immunofluorescence staining to characterize the stromal signatures in ESCC and evaluate their prognostic values in this aggressive disease. An automated quantitative pathology imaging system determined the locations of the lamina propria, stroma, and invasive front. Subsequently, IMC spatial analyses further uncovered spatial interaction and distribution. Additionally, bioinformatics analysis was performed to explore the TME remodeling mechanism in ESCC. To define a new molecular prognostic model, we calculated the risk score of each patient based on their TME signatures and pTNM stages. RESULTS: We demonstrate that the presence of fibroblasts at the tumor invasive front was associated with the invasive depth and poor prognosis. Furthermore, the amount of α-smooth muscle actin (α-SMA)+ fibroblasts at the tumor invasive front positively correlated with the number of macrophages (MØs), but negatively correlated with that of tumor-infiltrating granzyme B+ immune cells, and CD4+ and CD8+ T cells. Spatial analyses uncovered a significant spatial interaction between α-SMA+ fibroblasts and CD163+ MØs in the TME, which resulted in spatially exclusive interactions to anti-tumor immune cells. We further validated the laminin and collagen signaling network contributions to TME remodeling. Moreover, compared with pTNM staging, a molecular prognostic model, based on expression of α-SMA+ fibroblasts at the invasive front, and CD163+ MØs, showed higher accuracy in predicting survival or recurrence in ESCC patients. Regression analysis confirmed this model is an independent predictor for survival, which also identifies a high-risk group of ESCC patients that can benefit from adjuvant therapy. CONCLUSIONS: Our newly defined biomarker signature may serve as a complement for current clinical risk stratification approaches and provide potential therapeutic targets for reversing the fibroblast-mediated immunosuppressive microenvironment.

Directionally encoded color track density imaging in brain tumor patients: A potential application to neuro-oncology surgical planning.

BACKGROUND: Diffusion magnetic resonance imaging white matter tractography, an increasingly popular preoperative planning modality used for pre-surgical planning in brain tumor patients, is employed with the goal of maximizing tumor resection while sparing postoperative neurological function. Clinical translation of white matter tractography has been limited by several shortcomings of standard diffusion tensor imaging (DTI), including poor modeling of fibers crossing through regions of peritumoral edema and low spatial resolution for typical clinical diffusion MRI (dMRI) sequences. Track density imaging (TDI) is a post-tractography technique that uses the number of tractography streamlines and their long-range continuity to map the white matter connections of the brain with enhanced image resolution relative to the acquired dMRI data, potentially offering improved white matter visualization in patients with brain tumors. The aim of this study was to assess the utility of TDI-based white matter maps in a neurosurgical planning context compared to the current clinical standard of DTI-based white matter maps. METHODS: Fourteen consecutive brain tumor patients from a single institution were retrospectively selected for the study. Each patient underwent 3-Tesla dMRI scanning with 30 gradient directions and a b-value of 1000 s/mm2. For each patient, two directionally encoded color (DEC) maps were produced as follows. DTI-based DEC-fractional anisotropy maps (DEC-FA) were generated on the scanner, while DEC-track density images (DEC-TDI) were generated using constrained spherical deconvolution based tractography. The potential clinical utility of each map was assessed by five practicing neurosurgeons, who rated the maps according to four clinical utility statements regarding different clinical aspects of pre-surgical planning. The neurosurgeons rated each map according to their agreement with four clinical utility statements regarding if the map 1 identified clinically relevant tracts, (2) helped establish a goal resection margin, (3) influenced a planned surgical route, and (4) was useful overall. Cumulative link mixed effect modeling and analysis of variance were performed to test the primary effect of map type (DEC-TDI vs. DEC-FA) on rater score. Pairwise comparisons using estimated marginal means were then calculated to determine the magnitude and directionality of differences in rater scores by map type. RESULTS: A majority of rater responses agreed with the four clinical utility statements, indicating that neurosurgeons found both DEC maps to be useful. Across all four investigated clinical utility statements, the DEC map type significantly influenced rater score. Rater scores were significantly higher for DEC-TDI maps compared to DEC-FA maps. The largest effect size in rater scores in favor of DEC-TDI maps was observed for clinical utility statement 2, which assessed establishing a goal resection margin. CONCLUSION: We observed a significant neurosurgeon preference for DEC-TDI maps, indicating their potential utility for neurosurgical planning.

Mechanistic and microbial ecological insights into the impacts of micro- and nano- plastics on microbial reductive dehalogenation of organohalide pollutants.

Micro- and nano-plastics are prevalent in diverse ecosystems, but their impacts on biotransformation of organohalide pollutants and underpinning microbial communities remain poorly understood. Here we investigated the influence of micro- and nano-plastics on microbial reductive dehalogenation at strain and community levels. Generally, microplastics including polyethylene (PE), polystyrene (PS), polylactic acid (PLA), and a weathered microplastic mixture increased dehalogenation rate by 10 - 217% in both the Dehalococcoides isolate and enrichment culture, whereas the effects of polyvinyl chloride (PVC) and a defined microplastic mixture depended on their concentrations and cultures. Contrarily, nano-PS (80 nm) consistently inhibited dehalogenation due to increased production of reactive oxygen species. Nevertheless, the enrichment culture showed higher tolerance to nano-PS inhibition, implying crucial roles of non-dehalogenating populations in ameliorating nanoplastic inhibition. The variation in dehalogenation activity was linked to altered organohalide-respiring bacteria (OHRB) growth and reductive dehalogenase (RDase) gene transcription. Moreover, microplastics changed the community structure and benefited the enrichment of OHRB, favoring the proliferation of Dehalogenimonas. More broadly, the assembly of microbial communities on plastic biofilms was more deterministic than that in the planktonic cells, with more complex co-occurrence networks in the former. Collectively, these findings contribute to better understanding the fate of organohalides in changing environments with increasing plastic pollution.

Salinity determines performance, functional populations, and microbial ecology in consortia attenuating organohalide pollutants.

Organohalide pollutants are prevalent in coastal regions due to extensive intervention by anthropogenic activities, threatening public health and ecosystems. Gradients in salinity are a natural feature of coasts, but their impacts on the environmental fate of organohalides and the underlying microbial communities remain poorly understood. Here we report the effects of salinity on microbial reductive dechlorination of tetrachloroethene (PCE) and polychlorinated biphenyls (PCBs) in consortia derived from distinct environments (freshwater and marine sediments). Marine-derived microcosms exhibited higher halotolerance during PCE and PCB dechlorination, and a halotolerant dechlorinating culture was enriched from these microcosms. The organohalide-respiring bacteria (OHRB) responsible for PCE and PCB dechlorination in marine microcosms shifted from Dehalococcoides to Dehalobium when salinity increased. Broadly, lower microbial diversity, simpler co-occurrence networks, and more deterministic microbial community assemblages were observed under higher salinity. Separately, we observed that inhibition of dechlorination by high salinity could be attributed to suppressed viability of Dehalococcoides rather than reduced provision of substrates by syntrophic microorganisms. Additionally, the high activity of PCE dechlorinating reductive dehalogenases (RDases) in in vitro tests under high salinity suggests that high salinity likely disrupted cellular components other than RDases in Dehalococcoides. Genomic analyses indicated that the capability of Dehalobium to perform dehalogenation under high salinity was likely owing to the presence of genes associated with halotolerance in its genomes. Collectively, these mechanistic and ecological insights contribute to understanding the fate and bioremediation of organohalide pollutants in environments with changing salinity.

A unified global tractography framework for automatic visual pathway reconstruction.

The human visual pathway starts from the retina, passes through the retinogeniculate visual pathway, the optic radiation, and finally connects to the primary visual cortex. Diffusion MRI tractography is the only technology that can noninvasively reconstruct the visual pathway. However, complete and accurate visual pathway reconstruction is challenging because of the skull base environment and complex fiber geometries. Specifically, the optic nerve within the complex skull base environment can cause abnormal diffusion signals. The crossing and fanning fibers at the optic chiasm, and a sharp turn of Meyer's loop at the optic radiation, contribute to complex fiber geometries of the visual pathway. A fiber trajectory distribution (FTD) function-based tractography method of our previous work and several high sensitivity tractography methods can reveal these complex fiber geometries, but are accompanied by false-positive fibers. Thus, the related studies of the visual pathway mostly applied the expert region of interest selection strategy. However, interobserver variability is an issue in reconstructing an accurate visual pathway. In this paper, we propose a unified global tractography framework to automatically reconstruct the visual pathway. We first extend the FTD function to a high-order streamline differential equation for global trajectory estimation. At the global level, the tractography process is simplified as the estimation of global trajectory distribution coefficients by minimizing the cost between trajectory distribution and the selected directions under the prior guidance by introducing the tractography template as anatomic priors. Furthermore, we use a deep learning-based method and tractography template prior information to automatically generate the mask for tractography. The experimental results demonstrate that our proposed method can successfully reconstruct the visual pathway with high accuracy.