Miracle-dz/UniFAR-FTUs huggingface dataset:
The Dynamic Proteome of Oligodendrocyte Lineage Differentiation Features Planar Cell Polarity and Macroautophagy Pathways

Abstract Background Generation of oligodendrocytes is a sophisticated multistep process, the mechanistic underpinnings of which are not fully understood and demand further investigation. To systematically profile proteome dynamics during human embryonic stem cell differentiation into oligodendrocytes, we applied in-depth quantitative proteomics at different developmental stages and monitored changes in protein abundance using a multiplexed tandem mass tag-based proteomics approach. Findings Our proteome data provided a comprehensive protein expression profile that highlighted specific expression clusters based on the protein abundances over the course of human oligodendrocyte lineage differentiation. We identified the eminence of the planar cell polarity signalling and autophagy (particularly macroautophagy) in the progression of oligodendrocyte lineage differentiation—the cooperation of which is assisted by 106 and 77 proteins, respectively, that showed significant expression changes in this differentiation process. Furthermore, differentially expressed protein analysis of the proteome profile of oligodendrocyte lineage cells revealed 378 proteins that were specifically upregulated only in 1 differentiation stage. In addition, comparative pairwise analysis of differentiation stages demonstrated that abundances of 352 proteins differentially changed between consecutive differentiation time points. Conclusions Our study provides a comprehensive systematic proteomics profile of oligodendrocyte lineage cells that can serve as a resource for identifying novel biomarkers from these cells and for indicating numerous proteins that may contribute to regulating the development of myelinating oligodendrocytes and other cells of oligodendrocyte lineage. We showed the importance of planar cell polarity signalling in oligodendrocyte lineage differentiation and revealed the autophagy-related proteins that participate in oligodendrocyte lineage differentiation.
Clinical implications and nomogram prediction of long noncoding RNA FRGCA as diagnostic and prognostic indicators in colon adenocarcinoma

Supplemental Digital Content is available in the text Abstract Colorectal cancer, especially colon adenocarcinoma (COAD), is associated with significant morbidity and mortality worldwide. Long noncoding RNA (lncRNA) has been implicated in tumorigenesis. The aim of the present study was to elucidate the potential diagnostic and prognostic values of lncRNA FRGCA in COAD. The data of 438 COAD patients were retrieved for analysis. Diagnostic significance was evaluated using tumor and nontumor tissues. Prognostic significance was evaluated using a Cox proportional regression model. Stratified analysis was performed to identify associations between clinical factors and lncRNA FRGCA expression. A nomogram was constructed using the clinical factors and lncRNA FRGCA for survival prediction. Enrichment analysis identified gene ontologies and metabolic pathways of mRNAs with high Pearson correlation coefficients with lncRNA FRGCA. lncRNA FRGCA was highly expressed in tumor tissues of COAD and demonstrated diagnostic value (area under curve = 0.763, P < .0001). Prognostic significance analysis indicated that lncRNA FRGCA had prognostic value in COAD [adjusted P < . 001, hazard ratio (HR) = 0.444, 95% confidence interval (95% CI) = 0.288–0.685] and high expression of lncRNA FRGCA indicated better survival in COAD. A nomogram was evaluated for prediction of survival at 1, 3, and 5 years. Enrichment analysis revealed many mRNAs involved in the structural constituents of the mitochondrial inner membrane and translational termination, protein binding, translation, ribosome, oxidative phosphorylation, and metabolic pathways, especially the nucleoplasm. Differentially expressed in tumor vs nontumor tissues, lncRNA FRGCA had both diagnostic and prognostic implications in COAD, which may be associated with ribosome metabolism, oxidative phosphorylation, and nucleoplasm-related metabolic pathways.
Intraprostatic Tumor Segmentation on PSMA PET Images in Patients with Primary Prostate Cancer with a Convolutional Neural Network

Accurate delineation of the intraprostatic gross tumor volume (GTV) is a prerequisite for treatment approaches in patients with primary prostate cancer (PCa). Prostate-specific membrane antigen PET (PSMA PET) may outperform MRI in GTV detection. However, visual GTV delineation underlies interobserver heterogeneity and is time consuming. The aim of this study was to develop a convolutional neural network (CNN) for automated segmentation of intraprostatic tumor (GTV-CNN) in PSMA PET. Methods: The CNN (3D U-Net) was trained on the 68Ga-PSMA PET images of 152 patients from 2 different institutions, and the training labels were generated manually using a validated technique. The CNN was tested on 2 independent internal (cohort 1: 68Ga-PSMA PET, n = 18 and cohort 2: 18F-PSMA PET, n = 19) and 1 external (cohort 3: 68Ga-PSMA PET, n = 20) test datasets. Accordance between manual contours and GTV-CNN was assessed with the Dice-Sørensen coefficient (DSC). Sensitivity and specificity were calculated for the 2 internal test datasets (cohort 1: n = 18, cohort 2: n = 11) using whole-mount histology. Results: The median DSCs for cohorts 1–3 were 0.84 (range: 0.32–0.95), 0.81 (range: 0.28–0.93), and 0.83 (range: 0.32–0.93), respectively. Sensitivities and specificities for the GTV-CNN were comparable with manual expert contours: 0.98 and 0.76 (cohort 1) and 1 and 0.57 (cohort 2), respectively. Computation time was around 6 s for a standard dataset. Conclusion: The application of a CNN for automated contouring of intraprostatic GTV in 68Ga-PSMA and 18F-PSMA PET images resulted in a high concordance with expert contours and in high sensitivities and specificities in comparison with histology as a reference. This robust, accurate and fast technique may be implemented for treatment concepts in primary prostate cancer. The trained model and the study’s source code are available in an open source repository.
Dental Diagnosis and Treatment Assessments: Between X-rays Radiography and Optical Coherence Tomography

A correct diagnosis in dental medicine is typically provided only after clinical and radiological evaluations. They are also required for treatment assessments. The aim of this study is to establish the boundaries from which a modern, although established, imaging technique, Optical Coherence Tomography (OCT), is more suitable than the common X-ray radiography to assess dental issues and treatments. The most common methods for daily-basis clinical imaging are utilized in this study for extracted teeth (but also for other dental samples and materials), i.e., panoramic, intraoral radiography, and three-dimensional (3D) cone beam computed tomography (CBCT). The advantages of using OCT as an imaging method in dentistry are discussed, with a focus on its superior image resolution. Drawbacks related to its limited penetration depth and Field-of-View (FOV) are pointed out. High-quality radiological investigations are performed, measurements are done, and data collected. The same teeth and samples are also imaged (mostly) with an in-house developed Swept Source (SS)-OCT system, Master-Slave enhanced. Some of the OCT investigations employed two other in-house developed OCT systems, Spectral Domain (SD) and Time Domain (TD). Dedicated toolbars from Romexis software (Planmeca, Helsinki, Finland) are used to perform measurements using both radiography and OCT. Clinical conclusions are drawn from the investigations. Upsides and downsides of the two medical imaging techniques are concluded for each type of considered diagnosis. For treatment assessments, it is concluded that OCT is more appropriate than radiography in all applications, except bone-related investigations and periodontitis that demand data from higher-penetration depths than possible with the current level of OCT technology.
Opportunistic Infections and Efficacy Following Conversion to Belatacept-Based Therapy after Kidney Transplantation: A French Multicenter Cohort

Conversion from calcineurin-inhibitors (CNIs) to belatacept can help kidney-transplant (KT) recipients avoid CNI-related nephrotoxicity. The risk of associated opportunistic infections (OPIs) is ill-defined. We conducted a multicentric cohort study across 15 French KT-centers in a real-life setting. Between 07-2010 and 07-2019, 453 KT recipients were converted from CNI- to belatacept-based therapy at 19 [0.13–431] months post-transplantation. Most patients, i.e., 332 (79.3%), were converted after 6-months post-transplantation. Follow-up time after conversion was 20.1 +/− 13 months. OPIs developed in 42(9.3%) patients after 14 +/− 12 months post-conversion. Eight patients (19%) had two OPI episodes during follow-up. Incidences of CMV DNAemia and CMV disease were significantly higher in patients converted before 6-months post-KT compared to those converted later (i.e., 31.6% vs. 11.5%; p < 0.001; and 11.6% vs. 2.4%, p < 0.001, respectively). Cumulative incidence of OPIs was 6.5 OPIs/100 person–years. Incidence of CMV disease was 2.8/100 person–years, of pneumocystis pneumonia 1.6/100 person–years, and of aspergillosis 0.2/100 person–years. Multivariate analyses showed that estimated glomerular filtration (eGFR) < 25 mL/min/1.73 m2 at conversion was independently associated with OPIs (HR = 4.7 (2.2 − 10.3), p < 0.001). The incidence of EBV DNAemia was 17.3 events /100 person–years. At 1-year post-conversion, mean eGFR had significantly increased from 32.0 +/− 18 mL/min/1.73 m2 to 42.2 +/− 18 mL/min/1.73 m2 (p < 0.0001). Conversion to belatacept is an effective strategy with a low infectious risk.
Costing the impact of interventions during pregnancy in the UK: a systematic review of economic evaluations

Objective The aim of this review was to summarise the current evidence on the costing of resource use within UK maternity care, in order to facilitate the estimation of incremental resource and cost impacts potentially attributable to maternity care interventions. Methods A systematic review of economic evaluations was conducted by searching Medline, the Health Management Information Consortium, the National Health Service (NHS) Economic Evaluations Database, CINAHL and National Institute for Health and Care Excellence (NICE) guidelines for economic evaluations within UK maternity care, published between January 2010 and August 2019 in the English language. Unit costs for healthcare activities provided to women within the antenatal, intrapartum and postnatal period were inflated to 2018–2019 prices. Assessment of study quality was performed using the Quality of Health Economic Analyses checklist. Results Of 5084 titles or full texts screened, 37 papers were included in the final review (27 primary research articles, 7 review articles and 3 economic evaluations from NICE guidelines). Of the 27 primary research articles, 21 were scored as high quality, 3 as medium quality and 3 were low quality. Variation was noted in cost estimates for healthcare activities throughout the maternity care pathway: for midwife-led outpatient appointment, the range was £27.34–£146.25 (mean £81.78), emergency caesarean section, range was £1056.44–£4982.21 (mean £3508.93) and postnatal admission, range was £103.00–£870.10 per day (mean £469.55). Conclusions Wide variation exists in costs applied to maternity healthcare activities, resulting in challenges in attributing cost to maternity activities. The level of variation in cost calculations is likely to reflect the uncertainty within the system and must be dealt with by conducting sensitivity analyses. Nationally agreed prices for granular unit costs are needed to standardise cost-effectiveness evaluations of new interventions within maternity care, to be used either for research purposes or decisions regarding national intervention uptake. PROSPERO registration number CRD42019145309.
New Insights into Potocki-Shaffer Syndrome: Report of Two Novel Cases and Literature Review

Potocki-Shaffer syndrome (PSS) is a rare non-recurrent contiguous gene deletion syndrome involving chromosome 11p11.2. Current literature implies a minimal region with haploinsufficiency of three genes, ALX4 (parietal foramina), EXT2 (multiple exostoses), and PHF21A (craniofacial anomalies, and intellectual disability). The rest of the PSS phenotype is still not associated with a specific gene. We report a systematic review of the literature and included two novel cases. Because deletions are highly variable in size, we defined three groups of patients considering the PSS-genes involved. We found 23 full PSS cases (ALX4, EXT2, and PHF21A), 14 cases with EXT2-ALX4, and three with PHF21A only. Among the latter, we describe a novel male child showing developmental delay, café-au-lait spots, liner postnatal overgrowth and West-like epileptic encephalopathy. We suggest PSS cases may have epileptic spasms early in life, and PHF21A is likely to be the causative gene. Given their subtle presentation these may be overlooked and if left untreated could lead to a severe type or deterioration in the developmental plateau. If our hypothesis is correct, a timely therapy may ameliorate PSS phenotype and improve patients’ outcomes. Our analysis also shows PHF21A is a candidate for the overgrowth phenotype.
Sex-related interannual plasticity in wing morphological design in Heliconius charithonia enhances flight metabolic performance

Flight morphological variations and its consequences on animal performance are common in winged insects. In the butterfly Heliconius charithonia, sex-related differences in the wing morphological design have been described resulting in differences in foraging behavior, daily flight distances and flight aerodynamics. It has been suggested that these differences should be reflected in the metabolic capacities and energetic budgets associated with flight in both sexes. In this study, we analyzed the relationship between wing morphological variation and metabolic performance, flight aerodynamics and energetic reserves in females and males of Heliconius charithonia over two years. The results confirm the presence of wing shape sexual dimorphism, but also show an unexpected sex-related annual variation in wing shape, mirrored in the metabolic condition (resting metabolic rate) of individuals. However, contrary to expectation, intersexual variations in wing shape are not related to differences between the sexes in terms of flight aerodynamics, flight metabolic rates, or energetic reserves (carbohydrates, lipids and proteins). Our results indicate a considerable plasticity in H. charithonia wing shape, which we suggest is determined by a trade-off between environmental pressures and reproductive restriction of each sex, maintaining an optimum flight design. Finally, similarities in metabolic rates between young and older males and females in both years may be a consequence of the ability of Heliconius species to feed on pollen.
Structural equation modeling test of the pre-intentional phase of the health action process approach (HAPA) model on condom use intention among senior high school students in Tianjin, China

Supplemental Digital Content is available in the text Abstract Based on the Theory of Health Action Process Approach (HAPA) Model, this study aimed to investigate factors associated with condom use intention in Chinese adolescents. In 2017, we conducted a cross-sectional study using stratified cluster, convenience sampling method to assess condom use intention among senior high school students in Tianjin, China. One thousand eighty two senior high school students were anonymously surveyed through self-administered questionnaires. Structural equation modelling was used to assess the pre-intentional phase of HAPA model. Among the participants, 41.5% (449/1082) were male, 54.1% (585/1082) were female, 4.4% (48/1082) were gender-deficient. The average age was 16.7 years. The final pre-intentional phase of HAPA model was acceptable (CFI = 0.95; GFI = 0.94; RMSEA = 0.06). Action self-efficacy (r = 0.60) had a strong direct effect on condom use intention. The pre-intentional phase of HAPA model is valid to assess condom use intention among Chinese senior high school students. The pre-intention phase of the HAPA model could be applied to guide AIDS health educations of students, and further research is needed to evaluate the effect.
Characteristics and clinical outcomes in pituitary incidentalomas and non-incidental pituitary tumors treated with endoscopic transsphenoidal surgery

Abstract Purpose: In this retrospective study, we investigated the status and validity of endoscopic transsphenoidal surgery (eTSS) for pituitary incidentalomas (PIs) as well as the value of basing the indication for surgery on the PI guidelines. Methods: Patients who underwent eTSS at Fukuoka University Chikushi Hospital between 2012 and 2018 were divided into the PI group and the non-PI group in accordance with the PI guideline of the Endocrine Society and their clinicopathological characteristics and outcomes were compared and analyzed. Results: A total of 59 patients were enrolled, with 35 patients in the PI group and 24 patients in the non-PI group. The diagnoses in the PI group were of non-functioning pituitary adenoma (NFPA) (n = 12, 34%), gonadotropin-producing pituitary adenoma (n = 8, 23%), Rathke cleft cyst (n = 7, 20%), meningioma (n = 4, 11%), and growth hormone-producing pituitary adenoma (n = 3, 9%); those in the non-PI group were of NFPA (n = 6, 25%), gonadotropin-producing pituitary adenoma (n = 3, 13%), Rathke cleft cyst (n = 3, 13%), growth hormone-producing pituitary adenoma (n = 3, 13%), and prolactin producing pituitary adenoma (n = 3, 13%). Regarding the preoperative factors, 1 patient in the PI group with panhypopituitarism was diagnosed with pituitary apoplexy (pure infarction) of an NFPA. The rates of postoperative anterior pituitary hormonal deficiencies (14% vs 46%, P = .015), residual tumor size (2 ± 5 vs 6 ± 7 mm, P = .008), and reoperation (n = 0, 0% vs n = 5, 21%, P = .005) were significantly different between the PI and non-PI groups. Conclusions: This study showed that, postoperatively, the incidence of anterior pituitary hormonal deficiencies was lower in the PI than in the non-PI group, although it was comparable between the 2 groups before the operation. The patients in the PI group also had smaller residual tumors and a lower risk of reoperation than those in non-PI group. PIs could have a better postoperative clinical outcome than non-PIs when the indication for eTSS is based on preoperative scrutiny according to the PI guidelines and eTSS is performed by an experienced pituitary surgeon. Hence, more aggressive scrutiny and treatment for PIs might be desirable.
The Scissors Effect in Action: The Fox-Flory Relationship between the Glass Transition Temperature of Crosslinked Poly(Methyl Methacrylate) and Mc in Nanophase Separated Poly(Methyl Methacrylate)-l-Polyisobutylene Conetworks

The glass transition temperature (Tg) is one of the most important properties of polymeric materials. In order to reveal whether the scissors effect, i.e., the Fox–Flory relationship between Tg and the average molecular weight between crosslinking points (Mc), reported only in one case for polymer conetworks so far, is more generally effective or valid only for a single case, a series of poly(methyl methacrylate)-l-polyisobutylene (PMMA-l-PIB) conetworks was prepared and investigated. Two Tgs were found for the conetworks by DSC. Fox–Flory type dependence between Tg and Mc of the PMMA component (Tg = Tg,∞ − K/Mc) was observed. The K constants for the PMMA homopolymer and for the PMMA in the conetworks were the same in the margin of error. AFM images indicated disordered bicontinuous, mutually nanoconfined morphology with average domain sizes of 5–20 nm, but the correlation between Tg and domain sizes was not found. These new results indicate that the macrocrosslinkers act like molecular scissors (scissors effect), and the Tg of PMMA depend exclusively on the Mc in the conetworks. Consequently, these findings mean that the scissors effect is presumably a general phenomenon in nanophase-separated polymer conetworks, and this finding could be utilized in designing, processing, and applications of these novel materials.
High-yield synthesis of a tau PET radioligand and its non-radioactive ligand using an alternative protection and deprotection strategy.

Recently developed tau imaging radiopharmaceuticals show specific uptake in tau protein-rich regions in human brains without off-target binding. These radiopharmaceuticals and their non-radioactive reference ligands are generally obtained in low (radio)chemical yields. In the present study, we investigated high-yield synthesis of 18 F-RO948 ([18 F]1) and its non-radioactive ligand (1). The ligand 1 was synthesized by a Suzuki-Miyaura coupling reaction between 9-(4-methoxybenzyl)-9H-pyrrolo[2,3-b:4,5-c']dipyridin-2-yl trifluoromethanesulfonate (3) and 2-fluoro-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine (4), followed by oxidative removal of the para-methoxybenzyl (PMB) group with ceric ammonium nitrate (CAN). This two-step reaction gave 1 in 55.8% yield. The precursor for [18 F]1 was synthesized from 3 and 2-nitro-5-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)pyridine (6). The resulting PMB-protected precursor 8 was obtained in 74.5% yield. [18 F]1 was synthesized by radiofluorination of 8 (radiochemical conversion (RCC): 95.7 ± 1.7%), followed by deprotection under mild conditions with CAN. This one-pot, two-step radiochemical synthesis followed by HPLC purification gave [18 F]1 in high decay-corrected radiochemical yield (54-60%). The RCC of [18 F]fluoride to [18 F]1 in our two-step synthesis method was similar to that in a one-step radiofluorination reaction of a tert-butoxycarbonyl (BOC)-protected precursor 10 that proceeds with concomitant thermal deprotection of the BOC group. This one-pot, two-step synthesis method will be useful for the synthesis of 18 F-labeled (NH)heteroarene compounds.
Development of Methods Derived from Iodine-Induced Specific Cleavage for Identification and Quantitation of DNA Phosphorothioate Modifications

DNA phosphorothioate (PT) modification is a novel modification that occurs on the DNA backbone, which refers to a non-bridging phosphate oxygen replaced by sulfur. This exclusive DNA modification widely distributes in bacteria but has not been found in eukaryotes to date. PT modification renders DNA nuclease tolerance and serves as a constitute element of bacterial restriction–modification (R–M) defensive system and more biological functions are awaiting exploration. Identification and quantification of the bacterial PT modifications are thus critical to better understanding their biological functions. This work describes three detailed methods derived from iodine-induced specific cleavage-an iodine-induced cleavage assay (ICA), a deep sequencing of iodine-induced cleavage at PT site (ICDS) and an iodine-induced cleavage PT sequencing (PT-IC-Seq)-for the investigation of PT modifications. Using these approaches, we have identified the presence of PT modifications and quantized the frequency of PT modifications in bacteria. These characterizations contributed to the high-resolution genomic mapping of PT modifications, in which the distribution of PT modification sites on the genome was marked accurately and the frequency of the specific modified sites was reliably obtained. Here, we provide time-saving and less labor-consuming methods for both of qualitative and quantitative analysis of genomic PT modifications. The application of these methodologies will offer great potential for better understanding the biology of the PT modifications and open the door to future further systematical study.