OBJECTIVE: The prone transpsoas approach is a single-position alternative to traditional lateral lumbar interbody fusion (LLIF). Earlier prone LLIF studies have focused on technique, feasibility, perioperative efficiencies, and immediate postoperative radiographic alignment. This study was undertaken to report longer-term clinical and radiographic outcomes, and to identify learnings from experiential evolution of the prone LLIF procedure.
METHODS: All consecutive patients undergoing prone LLIF for any indication at one institution were included (n = 120). Demographic, diagnostic, treatment, and outcomes data were captured via prospective institutional registry. Retrospective analysis identified 31 \'pre-proceduralization\' and 89 \'post-proceduralization\' prone LLIF approaches, enabling comparison across early and later cohorts.
RESULTS: 187 instrumented LLIF levels were performed. Operative time, retraction time, LLIF blood loss, and hospital stay averaged 150 min, 17 min, 50 ml, and 2.2 days, respectively. 79% of cases were without complication. Postoperative hip flexion weakness was identified in 14%, transient lower extremity weakness in 12%, and sensory deficits in 10%. At last follow-up, back pain, worst-leg pain, Oswestry, and EQ-5D health state improved by 55%, 46%, 48%, and 51%, respectively. 99% improved or maintained sagittal alignment with an average 6.5° segmental lordosis gain at LLIF levels. Only intra-psoas retraction time differed between pre- and post-proceduralization; proceduralization saved an average 3.4 min/level (p = 0.0371).
CONCLUSIONS: The largest single-center prone LLIF experience with the longest follow-up to-date shows that it results in few complications, quick recovery, improvements in pain and function, high patient satisfaction, and improved sagittal alignment at an average one year and up to four years postoperatively.

Glioblastoma multiforme (GBM)is the most common and aggressive primary brain tumor. Although temozolomide (TMZ)-based radiochemotherapy improves overall GBM patients\' survival, it also increases the frequency of false positive post-treatment magnetic resonance imaging (MRI) assessments for tumor progression. Pseudo-progression (PsP) is a treatment-related reaction with an increased contrast-enhancing lesion size at the tumor site or resection margins miming tumor recurrence on MRI. The accurate and reliable prognostication of GBM progression is urgently needed in the clinical management of GBM patients. Clinical data analysis indicates that the patients with PsP had superior overall and progression-free survival rates. In this study, we aimed to develop a prognostic model to evaluate the tumor progression potential of GBM patients following standard therapies. We applied a dictionary learning scheme to obtain imaging features of GBM patients with PsP or true tumor progression (TTP) from the Wake dataset. Based on these radiographic features, we conducted a radiogenomics analysis to identify the significantly associated genes. These significantly associated genes were used as features to construct a 2YS (2-year survival rate) logistic regression model. GBM patients were classified into low- and high-survival risk groups based on the individual 2YS scores derived from this model. We tested our model using an independent The Cancer Genome Atlas Program (TCGA) dataset and found that 2YS scores were significantly associated with the patient\'s overall survival. We used two cohorts of the TCGA data to train and test our model. Our results show that the 2YS scores-based classification results from the training and testing TCGA datasets were significantly associated with the overall survival of patients. We also analyzed the survival prediction ability of other clinical factors (gender, age, KPS (Karnofsky performance status), normal cell ratio) and found that these factors were unrelated or weakly correlated with patients\' survival. Overall, our studies have demonstrated the effectiveness and robustness of the 2YS model in predicting the clinical outcomes of GBM patients after standard therapies.

DNA sequences are increasingly used for large-scale biodiversity inventories. Because these genetic data avoid the time-consuming initial sorting of specimens based on their phenotypic attributes, they have been recently incorporated into taxonomic workflows for overlooked and diverse taxa. Major statistical developments have accompanied this new practice, and several models have been proposed to delimit species with single-locus DNA sequences. However, proposed approaches to date make different assumptions regarding taxon lineage history, leading to strong discordance whenever comparisons are made among methods. Distance-based methods, such as Automatic Barcode Gap Discovery (ABGD) and Assemble Species by Automatic Partitioning (ASAP), rely on the detection of a barcode gap (i.e., the lack of overlap in the distributions of intraspecific and interspecific genetic distances) and the associated threshold in genetic distances. Network-based methods, as exemplified by the REfined Single Linkage (RESL) algorithm for the generation of Barcode Index Numbers (BINs), use connectivity statistics to hierarchically cluster-related haplotypes into molecular operational taxonomic units (MOTUs) which serve as species proxies. Tree-based methods, including Poisson Tree Processes (PTP) and the General Mixed Yule Coalescent (GMYC), fit statistical models to phylogenetic trees by maximum likelihood or Bayesian frameworks.Multiple webservers and stand-alone versions of these methods are now available, complicating decision-making regarding the most appropriate approach to use for a given taxon of interest. For instance, tree-based methods require an initial phylogenetic reconstruction, and multiple options are now available for this purpose such as RAxML and BEAST. Across all examined species delimitation methods, judicious parameter setting is paramount, as different model parameterizations can lead to differing conclusions. The objective of this chapter is to guide users step-by-step through all the procedures involved for each of these methods, while aggregating all necessary information required to conduct these analyses. The \"Materials\" section details how to prepare and format input files, including options to align sequences and conduct tree reconstruction with Maximum Likelihood and Bayesian inference. The Methods section presents the procedure and options available to conduct species delimitation analyses, including distance-, network-, and tree-based models. Finally, limits and future developments are discussed in the Notes section. Most importantly, species delimitation methods discussed herein are categorized based on five indicators: reliability, availability, scalability, understandability, and usability, all of which are fundamental properties needed for any approach to gain unanimous adoption within the DNA barcoding community moving forward.

BACKGROUND: Protein tyrosine phosphatase non-receptor type 7 (PTPN7) is a signaling molecule that regulates a multitude of cellular processes, spanning cell proliferation, cellular differentiation, the mitotic cycle, and oncogenic metamorphosis. However, the characteristic of PTPN7 in the glioma microenvironment has yet to be elucidated.
METHODS: The prognostic value, genomic features, immune characteristics, chemotherapy prediction, and immunotherapy prediction of PTPN7 were systematically explored at the bulk sequencing level. The cell evolution trajectory, cell communication pattern, and cell metabolic activity related to PTPN7 were systematically explored at the single-cell sequencing level. HMC3 and M0 cells were cocultured with U251 and T98G cells, and flow cytometry was carried out to investigate the polarization of HMC3 and M0. Transwell assay and CCK-8 assay were performed to explore the migration and proliferation activity of U251 and T98G.
RESULTS: The expression level of PTPN7 is significantly elevated in glioma and indicates malignant features. PTPN7 expression predicts worse prognosis of glioma patients. PTPN7 is associated with genome alteration and immune infiltration. Besides, PTPN7 plays a crucial role in modulating metabolic and immunogenic processes, particularly by influencing the activity of microglia and macrophages through multiple signaling pathways involved in cellular communication. Specifically, PTPN7 actively mediates inflammation-resolving-polarization of macrophages and microglia and protects glioma from immune attack. PTPN7 could also predict the response of immunotherapy.
CONCLUSIONS: PTPN7 is critically involved in inflammation-resolving-polarization mediated by macrophage and microglia and promotes the immune escape of glioma cells.

The Prone Transpsoas (PTP) approach to lumbar spine surgery, emerging as an evolution of lateral lumbar interbody fusion (LLIF), offers significant advantages over traditional methods. PTP has demonstrated increased lumbar lordosis gains compared to LLIF, owing to the natural increase in lordosis afforded by prone positioning. Additionally, the prone position offers anatomical advantages, with shifts in the psoas muscle and lumbar plexus, reducing the likelihood of postoperative femoral plexopathy and moving critical peritoneal contents away from the approach. Furthermore, operative efficiency is a notable benefit of PTP. By eliminating the need for intraoperative position changes, PTP reduces surgical time, which in turn decreases the risk of complications and operative costs. Finally, its versatility extends to various lumbar pathologies, including degeneration, adjacent segment disease, and deformities. The growing body of evidence indicates that PTP is at least as safe as traditional approaches, with a potentially better complication profile. In this narrative review, we review the historical evolution of lateral interbody fusion, culminating in the prone transpsoas approach. We also describe several adjuncts of PTP, including robotics and radiation-reduction methods. Finally, we illustrate the versatility of PTP and its uses, ranging from \'simple\' degenerative cases to complex deformity surgeries.

Phosphotyrosine biomimetics are starting points for potent inhibitors of protein tyrosine phosphatases (PTPs) and, thus, crucial for drug development. Their identification, however, has been heavily driven by rational design, limiting the discovery of diverse, novel, and improved mimetics. In this chapter, we describe two screening approaches utilizing fragment ligation methods: one to identify new mimetics and the other to optimize existing mimetics into more potent and selective inhibitors.

The formation of a reversible disulfide bond between the catalytic cysteine and a spatially neighboring cysteine (backdoor) in protein tyrosine phosphatases (PTPs) serves as a critical regulatory mechanism for maintaining the activity of protein tyrosine phosphatases. The failure of such protection results in the formation of irreversibly oxidized cysteines into sulfonic acid in a highly oxidative cellular environment in the presence of free radicals. Hence, it is important to develop methods to interconvert PTPs into reduced and oxidized forms to understand their catalytic function in vitro. Protein tyrosine phosphatase 4A type 1 (PTP4A1), a dual-specificity phosphatase, is catalytically active in the reduced form. Unexpectedly, also its oxidized form performs a key biological function in systemic sclerosis (SSc) by forming a kinase-phosphatase complex with Src kinases. Thus, we developed simple and efficient protocols for producing oxidized and reduced PTP4A1 to elucidate their biological function, which can be extended to study other protein tyrosine phosphatases and other recombinantly produced proteins.

The zebrafish is an ideal model for functional analysis of genes at the molecular, protein, cell, organ, and organism levels. We have used zebrafish to analyze the function of members of the protein tyrosine phosphatase (PTP) superfamily for more than two decades. The molecular genetic toolbox has significantly improved over the years. Currently, generating mutant lines that lack the function of a PTP gene is relatively straightforward by CRISPR/Cas9 technology-mediated generation of insertions or deletions in the target gene. In addition, generating point mutations using CRISPR/Cas9 technology and homology-directed repair (HDR) is feasible, albeit the success rate could be higher. Here, we describe the methods, including the tips and tricks, that we have used to generate knock-out and knock-in zebrafish lines in PTP genes successfully.

An accurate species delimitation is critical for biological studies. In this context, the use of molecular techniques along with species delimitation methods would help to a rapid and accurate biodiversity assessment. The species delimitation methods cluster data sets of orthologous sequences in molecular operational taxonomic units (MOTU). In particular, the methods based on a single gene are easily integrated with the widely used DNA barcoding approach. We developed SPdel a user-friendly pipeline to integrate different single-gene species delimitation methods. SPdel is designed to calculate and compare MOTUs obtained by different species delimitation approaches. SPdel also outputs diverse ready-to-publish quality figures, that facilitate the interpretation of results. SPdel aims to help researchers use species delimitation methods that would improve biodiversity studies.

Introduction The retroperitoneal approach for lateral lumbar interbody fusion (LLIF) originally described an initial posterolateral fascial incision enabling finger dissection from behind the peritoneum and guidance of instruments through a second direct-lateral fascial incision. It has since become common for single direct-lateral incisional access to the retroperitoneum. This study attempted to quantify the distance of the peritoneum from posterior landmarks in the space, assess the risk of peritoneal violation in each access trajectory (i.e., posterolateral versus direct lateral retroperitoneal dissection), and determine whether there are differences based on patient position (prone versus lateral decubitus). Methods In three prone cadaveric torsos, Steinman pins were percutaneously placed mid-disc at each level L2-5 bilaterally (for a total of 18 prone approaches). Open dissections exposed the retroperitoneum including the quadratus lumborum and psoas muscles, maintaining the natural reflection of the peritoneum. Visual assessment qualified whether any pin violated any retroperitoneal structure. Distance from the anterior border of the quadratus lumborum to the posterior-most reflection of the peritoneum was measured. For comparison, three additional torsos were positioned in lateral decubitus, and the above steps were repeated, only unilaterally (for a total of nine lateral decubitus approaches). Results In prone, no pin violated the peritoneum; three (3/18 total approaches) violated the kidney, all at L2-3 (3/6 approaches at L2-3). In lateral decubitus, all three L2-3 pins violated the kidney (3/3 approaches at L2-3); five of the six remaining pins from L3-5 violated the peritoneum (totaling eight violations in the nine total approaches). The incidence of any violation was significantly greater in lateral decubitus vs. prone (8/9 vs. 3/18, p=0.0006). The structure at risk (kidney vs. peritoneum) was significantly associated with disc level (p=0.0041): all kidney violations occurred at L2-3 and all peritoneal violations occurred at L3-4 or L4-5. Distance from the quadratus lumborum to the posterior-most reflection of the peritoneum averaged 8.7 cm (range: 6-10) in prone, and 2.9 cm (range: 2.5-3.2) in lateral decubitus (p=0.0129). Conclusion A cadaveric study of retroperitoneal anatomy demonstrates that there is an increased distance from the quadratus lumborum to the peritoneum in prone versus lateral decubitus and that the trajectory of approach to the lumbar discs risks violation of the peritoneum more frequently when accessing directly laterally versus posterolaterally. In either approach, care should be taken to identify and release the peritoneal reflection to create a safe passage to the lumbar discs.