Miracle-dz/UniFAR-FTUs huggingface dataset:
Differential Gene Expression Profiles between N-Terminal Domain and Ligand-Binding Domain Inhibitors of Androgen Receptor Reveal Ralaniten Induction of Metallothionein by a Mechanism Dependent on MTF1

Simple Summary Inhibition of the androgen receptor (AR) remains the mainstay treatment for prostate cancer. All current therapies involving AR inhibition either directly or indirectly target its ligand-binding domain (LBD). We have developed the first novel compounds which target the N-terminal domain, (NTD) a region which is essential for AR transcriptional activity. First-generation ralaniten (NCT02606123), and second-generation EPI-7386 (NCT04421222) remain the only AR-NTD inhibitors to progress to clinical trials. Here we aim to characterize differences between different classes of AR antagonists targeting the AR-LBD and the AR-NTD, as well as next generation AR-NTD inhibitors. An incidental finding was that ralaniten was uniquely associated with increased metallothionein expression which was independent of AR activity. Instead, expression of metallothionein genes was driven by MTF-1 indicating a potential off-target effect. Neither AR-LBD inhibitor enzalutamide nor second-generation AR-NTD inhibitor EPI-7170 had this effect. This work has important implications for the development of novel AR-NTD inhibitors. Abstract Hormonal therapies for prostate cancer target the androgen receptor (AR) ligand-binding domain (LBD). Clinical development for inhibitors that bind to the N-terminal domain (NTD) of AR has yielded ralaniten and its analogues. Ralaniten acetate is well tolerated in patients at 3600 mgs/day. Clinical trials are ongoing with a second-generation analogue of ralaniten. Binding sites on different AR domains could result in differential effects on AR-regulated gene expression. Here, we provide the first comparison between AR-NTD inhibitors and AR-LBD inhibitors on androgen-regulated gene expression in prostate cancer cells using cDNA arrays, GSEA, and RT-PCR. LBD inhibitors and NTD inhibitors largely overlapped in the profile of androgen-induced genes that they each inhibited. However, androgen also represses gene expression by various mechanisms, many of which involve protein–protein interactions. De-repression of the transcriptome of androgen-repressed genes showed profound variance between these two classes of inhibitors. In addition, these studies revealed a unique and strong induction of expression of the metallothionein family of genes by ralaniten by a mechanism independent of AR and dependent on MTF1, thereby suggesting this may be an off-target. Due to the relatively high doses that may be encountered clinically with AR-NTD inhibitors, identification of off-targets may provide insight into potential adverse events, contraindications, or poor efficacy.
Subdividing Stress Groups into Eustress and Distress Groups Using Laterality Index Calculated from Brain Hemodynamic Response

A stress group should be subdivided into eustress (low-stress) and distress (high-stress) groups to better evaluate personal cognitive abilities and mental/physical health. However, it is challenging because of the inconsistent pattern in brain activation. We aimed to ascertain the necessity of subdividing the stress groups. The stress group was screened by salivary alpha-amylase (sAA) and then, the brain’s hemodynamic reactions were measured by functional near-infrared spectroscopy (fNIRS) based on the near-infrared biosensor. We compared the two stress subgroups categorized by sAA using a newly designed emotional stimulus-response paradigm with an international affective picture system (IAPS) to enhance hemodynamic signals induced by the target effect. We calculated the laterality index for stress (LIS) from the measured signals to identify the dominantly activated cortex in both the subgroups. Both the stress groups exhibited brain activity in the right frontal cortex. Specifically, the eustress group exhibited the largest brain activity, whereas the distress group exhibited recessive brain activity, regardless of positive or negative stimuli. LIS values were larger in the order of the eustress, control, and distress groups; this indicates that the stress group can be divided into eustress and distress groups. We built a foundation for subdividing stress groups into eustress and distress groups using fNIRS.
Synchronous Generative Development amidst Situated Entropy

The Sustainable Development Goals have been criticized for not providing sufficient balance between human well-being and environmental well-being. By contrast, joint agent-environment systems theory is focused on reciprocal synchronous generative development. The purpose of this paper is to extend this theory towards practical application in sustainable development projects. This purpose is fulfilled through three interrelated contributions. First, a practitioner description of the theory is provided. Then, the theory is extended through reference to research concerned with multilevel pragmatics, competing signals, commitment processes, technological mediation, and psychomotor functioning. In addition, the theory is related to human-driven biosocial-technical innovation through the example of digital twins for agroecological urban farming. Digital twins being digital models that mirror physical processes; that are connected to physical processes through, for example, sensors and actuators; and which carry out analyses of physical processes in order to improve their performance. Together, these contributions extend extant theory towards application for synchronous generative development that balances human well-being and environmental well-being. However, the practical examples in the paper indicate that counterproductive complexity can arise from situated entropy amidst biosocial-technical innovations: even when those innovations are compatible with synchronous generative development.
Novel Risk Classification Based on Pyroptosis-Related Genes Defines Immune Microenvironment and Pharmaceutical Landscape for Hepatocellular Carcinoma

Simple Summary It has been indicated that pyroptosis functions in the development of cancer as well as the orchestration of cancer cell death. Nonetheless, specific roles of pyroptosis-related genes in tumor progression, immune response, prognosis and immunotherapy have, to date, not been thoroughly elucidated. After a comprehensive evaluation of pyroptosis patterns, unsupervised clustering was performed to generate three distinct clusters of 26-gene profiles from HCC. We aimed to establish an efficiency criterion for classifying and predicting patients’ prognosis. After comprehensive analysis of the clustering and risk scoring system, satisfactory sensitivity and specificity are demonstrated, and new insights into the molecular characterization of pyroptosis-related subtypes are contributed. Abstract Growing evidence has indicated that pyroptosis functions in the development of cancer. Nonetheless, specific roles of pyroptosis-related genes in tumor progression, immune response, prognosis, and immunotherapy have not been thoroughly elucidated. After a comprehensive evaluation of pyroptosis genes, unsupervised clustering was performed to generate three distinct clusters from hepatocellular carcinoma (HCC) samples. Three distinct pyroptosis-related molecular subtypes comprising three gene clusters that had differential prognostic effects on patient survival were then identified. Immune characteristics analyses revealed diversified immune cell infiltration among the subtypes. Two clusters served as immune-hot phenotypes associated with significantly poorer survival compared to a remaining third immune-cold cluster. Among these, the immune-hot clusters were characterized by abundant adaptive immune cell infiltration, active CD4+ and CD8+ T cells, high total leukocyte counts and tumor growth status, and lower Th17 cell and M2 macrophage densities. Then, risk scores indicated that low-risk patients were more sensitive to anti-tumor therapy. Subsequently, we found a significant correlation between pyroptosis and prognosis in HCC and that pyroptosis genes drive the heterogeneity of the tumor microenvironment. The risk scoring system, based on pyroptosis-related differentially expressed genes, was established to evaluate the individual outcomes and contribute to new insights into the molecular characterization of pyroptosis-related subtypes.
A high density of PD-L1-expressing immune cells is significantly correlated with favorable disease free survival in nonmetastatic colorectal cancer

Abstract The impact of immune cells (ICs) expressing various markers remains poorly understood in nonmetastatic colorectal cancer patients who have undergone colectomy. Here, we aimed to clarify the correlation between IC density and clinical parameters and survival. Programmed death protein-1 (PD-1), programmed cell death protein ligand-1 (PD-L1), clusters of differentiation (CD)-3, CD-8, and CD45RO immunostaining was performed for 421 patients using tissue microarray and automatic counting. Tumor stroma area immune density was assessed in comparison to clinical histological factors and surgical outcomes. High-density CD-8 expression was significantly associated with current smoking habits or a smoking history (P = .006). High-density of PD-1 expression was correlated with Lynch syndrome patients (P < .001) and with patients who did not consume alcohol (P = .034). A significant decrease in CR45RO expression density was associated with aging (P = .002 and r = –0.014), and high-density CD-3, CD-8, and PD-1 expression was significantly associated with right colon tumor location (P < .001). High CD-3 and PD-L1 expression was significantly associated with early tumor T-staging (P = .018 and P = .002). High-density PD-1 expression was significantly correlated with mucinous type adenocarcinoma (P = .027) and poor differentiation (P < .001). For treatment outcomes, multivariate analysis confirmed that patients exhibiting high-density PD-L1 expression possessed significantly longer disease free survival (adjusted hazard ratio: 0.752, 95% confidence interval [CI]: 0.61–0.92, P = .006) and overall survival (adjusted hazard ratio: 0.872, 95% CI: 0.75–1.91, P = .064) Significantly varied density in IC subsets was related to distinct demographic or clinic-histological factors. The presence of high-density PD-L1-expressing ICs is an independent favorable prognostic factor for disease free survival and overall survival among stage I to III colorectal cancer patients.
A Structural Perspective on the RNA Editing of Plant Respiratory Complexes

The last steps of respiration, a core energy-harvesting process, are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. Several essential subunits of the respiratory complexes are RNA-edited in plants, frequently leading to changes in the encoded amino acids. While the impact of RNA editing is clear at the sequence and phenotypic levels, the underlying biochemical explanations for these effects have remained obscure. Here, we used the structures of plant respiratory complex I, complex III2 and complex IV to analyze the impact of the amino acid changes of RNA editing in terms of their location and biochemical features. Through specific examples, we demonstrate how the structural information can explain the phenotypes of RNA-editing mutants. This work shows how the structural perspective can bridge the gap between sequence and phenotype and provides a framework for the continued analysis of RNA-editing mutants in plant mitochondria and, by extension, in chloroplasts.
Prevalence and Management of Cancer of the Rectal Stump after Total Colectomy and Rectal Sparing in Patients with Familial Polyposis: Results from a Registry-Based Study

Simple Summary Prophylactic total colectomy with ileo-rectal anastomosis (IRA) is the surgical approach that guarantees a better quality of life compared to proctocolectomy and ileo-anal anastomosis (IPAA) in familial adenomatous polyposis (FAP) patients. However, previous studies have warned about the high risk of cancer of the rectal stump, especially considering the young age of these patients. This is a retrospective study whose aim was to assess both clinical and surgical features of patients who developed cancer of the rectal stump. The data reported show that IRA is a safe approach from an oncological perspective. Since early tumors of the rectal stump may be easily detected via endoscopic or minimally invasive approaches, strict surveillance is necessary. Abstract Background: The balance between quality of life and colorectal cancer risk in familial adenomatous polyposis (FAP) patients is of primary importance. A cut-off of less than 30 polyps under 1 cm of diameter in the rectum has been used as an indication for performing ileo-rectal anastomosis (IRA) in terms of lower rectal cancer risk. This study aimed to assess clinical and surgical features of FAP patients who developed cancer of the rectal stump. Methods: This retrospective study included all FAP patients who underwent total colectomy/IRA from 1977 to 2021 and developed subsequent rectal cancer. Patients’ features were reported using descriptive statistics by considering the overall case series and within pre-specified classes of age (<20, 20–30, and >30 years) at first surgery. Results: Among the 715 FAP patients, 47 (6.57%, 95% confidence interval: 4.87; 8.65) developed cancer in the rectal stump during follow-up. In total, 57.45% of the population were male and 38.30% were proband. The median interval between surgery and the occurrence of rectal cancer was 13 years. This interval was wider in the youngest group (p-value: 0.012) than the oldest ones. Twelve patients (25.53%) received an endoscopic or minimally invasive resection. Amongst them, 61.70% were Dukes stage A cancers. Conclusions: There is a definite risk of rectal cancer after total colectomy/IRA; however, the time interval from the index procedure to cancer developing is long. Minimally invasive and endoscopic treatments should be the procedures of choice in patients with early stage cancers.
Cell Cycle Regulation by Heat Shock Transcription Factors

Cell division and cell cycle mechanism has been studied for 70 years. This research has revealed that the cell cycle is regulated by many factors, including cyclins and cyclin-dependent kinases (CDKs). Heat shock transcription factors (HSFs) have been noted as critical proteins for cell survival against various stresses; however, recent studies suggest that HSFs also have important roles in cell cycle regulation-independent cell-protective functions. During cell cycle progression, HSF1, and HSF2 bind to condensed chromatin to provide immediate precise gene expression after cell division. This review focuses on the function of these HSFs in cell cycle progression, cell cycle arrest, gene bookmarking, mitosis and meiosis.
Association of TyG Index with CT Features in Patients with Tuberculosis and Diabetes Mellitus

Background The purpose of this study was to investigate the association of the triglyceride glucose (TyG) index, a surrogate marker of insulin resistance (IR) with a high sensitivity of 96.5% and a specificity of 85.0% for the diagnosis of IR, with computed tomography (CT) features in patients with tuberculosis and diabetes mellitus. Methods A total of 247 subjects were enrolled from July, 2020 to May, 2021. The basic clinical features and CT features were analyzed. In addition, multivariate logistic regression analysis models were employed to evaluate the association of the TyG indicator with CT features in participants. Results In the quartile groups of TyG index, air bronchial sign detection rate was 11.7%, 14.5%, 23.2%, and 44.1%; large segmented leafy shadow detection rate was 27.9%, 40.6%, 46.4%, and 66.2%; thick-walled cavity was found in 38.2%, 43.4%, 57.9%, and 69.1%; the rate of multiple cavities was 17.6%, 27.5%, 36.2%, 52.9%; the rate of lymph node enlargement was 22.1%, 17.4%, 28.9%, and 38.2%, respectively. In addition, the positive relation with the TyG index and the prevalence of abnormal CT signs was observed in the fully adjusted model: TyG, per one-unit increase: air bronchial sign: adjusted odds ratio (AOR) 3.92, 95% CI 1–15.35, P = 0.049; multiple cavities: AOR 4.1, 95% CI 1.26–13.31, P = 0.019; thick-walled cavity: AOR 2.89, 95% CI 1.05–8.03, P = 0.041. In quartile of TyG index, compared with patients in quartile 1, the AOR (95% CI) values for air bronchial sign in quartile 4 was 8.1 (1.7–44), p = 0.011; multiple cavities was 7.1 (1.7–32), p = 0.008; thick-walled cavity was 7.8 (1.9–34.7), p = 0.005. Conclusion The present study showed that an increased TyG index was positively related to the severity of patients with T2DM-PTB.
Does diabetes affect paraneoplastic thrombocytosis in colorectal cancer?

Abstract Background A large variety of factors can affect colorectal cancer (CRC) survival, including type 2 diabetes mellitus (T2DM) and paraneoplastic thrombocytosis. Although several common factors play a role in their development and platelets are damaged in both diseases, the combined relationship of the three conditions was never investigated previously. Methods A prospective, real-life observational cohort study was conducted with the inclusion of 108 CRC patients and 166 voluntary non-CRC subjects. Plasma interleukin-6 and thrombopoietin levels were measured. Results Study participants were divided into cohorts based on the presence of T2DM. Platelet count (p < 0.0500) and interleukin-6 (p < 0.0100) level were significantly higher in the CRC groups. Thrombopoietin level was higher in the T2DM, CRC, and CRC + T2DM groups (p < 0.0500). Analysis of parameter changes over time and survival models revealed that neither platelet count, interleukin-6, nor thrombopoietin levels were affected by T2DM. Death of patients was associated with higher baseline platelet count (p = 0.0042) and interleukin-6 level (p < 0.0001). Conclusion Although the independent, disease-worsening effect of paraneoplastic thrombocytosis and T2DM is known, the coexistence of the two did not further impair the survival of CRC patients, suggesting that T2DM has no significant effect over paraneoplastic thrombocytosis.
SPR Analysis of SUMO-Murine Rap1-Interacting Factor 1 C-Terminal Domain Interaction with G4

One of the advantages of surface plasmon resonance is its sensitivity and real-time analyses performed by this method. These characteristics allow us to further investigate the interactions of challenging proteins like Rap1-interacting factor 1 (Rif1). Rif1 is a crucial protein responsible for regulating different cellular processes including DNA replication, repair, and transcription. Mammalian Rif1 is yet to be fully characterized, partly because it is predicted to be intrinsically disordered for a large portion of its polypeptide. This protein has recently been the target of research as a potential biomarker in many cancers. Therefore, finding its most potent interacting partner is of utmost importance. Previous studies showed Rif1’s affinity towards structured DNAs and amongst them, T6G24 was superior. Recent studies have shown mouse Rif1 (muRif1) C-terminal domain’s (CTD) role in binding to G-quadruplexes (G4). There were many concerns in investigating the Rif1 and G4 interaction, which can be minimized using SPR. Therefore, for the first time, we have assessed its binding with G4 at nano-molar concentrations with SPR which seems to be crucial for its binding analyses. Our results indicate that muRif1-CTD has a high affinity for this G4 sequence as it shows a very low KD (6 ± 1 nM).
Differential Expression and Localization of EHBP1L1 during the First Wave of Rat Spermatogenesis Suggest Its Involvement in Acrosome Biogenesis

The identification and characterization of new proteins involved in spermatogenesis is fundamental, considering that good-quality gametes are basic in ensuring proper reproduction. Here, we further analyzed the temporal and spatial localization during the first spermatogenic wave of rat testis of EHBP1L1, which is involved in vesicular trafficking due to the CH and bMERB domains, which bind to actin and Rab8/10, respectively. Western blot and immunofluorescence analyses showed that EHBP1L1 protein expression started at 21 days post-partum (dpp) concomitantly with the appearance of primary spermatocytes (I SPC). In subsequent stages, EHBP1L1 specifically localized together with actin in the perinuclear cytoplasm close to the acrosomal and Golgian regions of spermatids (SPT) during the different phases of acrosome biogenesis (AB). Moreover, it was completely absent in elongated SPT and in mature spermatozoa, suggesting that its role was completed in previous stages. The combined data, also supported by our previous report demonstrating that EHBP1L1 mRNA was expressed by primary (I) and secondary (II) SPC, lead us to hypothesize its specific role during AB. Although these results are suggestive, further studies are needed to better clarify the underlying molecular mechanisms of AB, with the aim to use EHBP1L1 as a potential new marker for spermatogenesis.
Acceptance of COVID-19 Vaccines among Patients with Inflammatory Bowel Disease in Japan

Coronavirus disease 2019 (COVID-19) vaccination is recommended for patients with inflammatory bowel disease (IBD). However, the acceptance of COVID-19 vaccines has not been sufficiently evaluated in patients with IBD. We aimed to assess the acceptance and hesitancy of COVID-19 vaccination and related factors among these patients. A retrospective cohort study using a self-reported questionnaire was performed among patients with IBD between 22 June 2021 and 30 August 2021. Of the 187 participants, 10.2% (n = 19) were hesitant to be vaccinated. Patients in the vaccine-hesitant group were younger (p = 0.009) and had a shorter disease duration (p = 0.020). Vedolizumab was prescribed more frequently (p = 0.024) and immunomodulators were less frequently used (p = 0.027) in this group. Multivariable logistic regression analysis identified age (odds ratio [OR]: 0.96, 95% confidence interval [CI]: 0.92–1.00, p = 0.042) and the use of immunomodulators (OR: 0.08, 95% CI: 0.01–0.66, p = 0.019) as independent significant factors for vaccine hesitancy. The COVID-19 vaccine hesitancy rate in patients with IBD in Japan was 10% in this study. The Japanese COVID-19 vaccination campaign appears to be successful. The risk of COVID-19 among patients with IBD requires adequate measures to ensure that vaccines are accepted by vaccine-hesitant patients. These findings may be helpful in achieving adequate vaccination rates.