Miracle-dz/UniFAR-FTUs huggingface dataset:
Textured-Based Deep Learning in Prostate Cancer Classification with 3T Multiparametric MRI: Comparison with PI-RADS-Based Classification

The current standardized scheme for interpreting MRI requires a high level of expertise and exhibits a significant degree of inter-reader and intra-reader variability. An automated prostate cancer (PCa) classification can improve the ability of MRI to assess the spectrum of PCa. The purpose of the study was to evaluate the performance of a texture-based deep learning model (Textured-DL) for differentiating between clinically significant PCa (csPCa) and non-csPCa and to compare the Textured-DL with Prostate Imaging Reporting and Data System (PI-RADS)-based classification (PI-RADS-CLA), where a threshold of PI-RADS ≥ 4, representing highly suspicious lesions for csPCa, was applied. The study cohort included 402 patients (60% (n = 239) of patients for training, 10% (n = 42) for validation, and 30% (n = 121) for testing) with 3T multiparametric MRI matched with whole-mount histopathology after radical prostatectomy. For a given suspicious prostate lesion, the volumetric patches of T2-Weighted MRI and apparent diffusion coefficient images were cropped and used as the input to Textured-DL, consisting of a 3D gray-level co-occurrence matrix extractor and a CNN. PI-RADS-CLA by an expert reader served as a baseline to compare classification performance with Textured-DL in differentiating csPCa from non-csPCa. Sensitivity and specificity comparisons were performed using Mcnemar’s test. Bootstrapping with 1000 samples was performed to estimate the 95% confidence interval (CI) for AUC. CIs of sensitivity and specificity were calculated by the Wald method. The Textured-DL model achieved an AUC of 0.85 (CI [0.79, 0.91]), which was significantly higher than the PI-RADS-CLA (AUC of 0.73 (CI [0.65, 0.80]); p < 0.05) for PCa classification, and the specificity was significantly different between Textured-DL and PI-RADS-CLA (0.70 (CI [0.59, 0.82]) vs. 0.47 (CI [0.35, 0.59]); p < 0.05). In sub-analyses, Textured-DL demonstrated significantly higher specificities in the peripheral zone (PZ) and solitary tumor lesions compared to the PI-RADS-CLA (0.78 (CI [0.66, 0.90]) vs. 0.42 (CI [0.28, 0.57]); 0.75 (CI [0.54, 0.96]) vs. 0.38 [0.14, 0.61]; all p values < 0.05). Moreover, Textured-DL demonstrated a high negative predictive value of 92% while maintaining a high positive predictive value of 58% among the lesions with a PI-RADS score of 3. In conclusion, the Textured-DL model was superior to the PI-RADS-CLA in the classification of PCa. In addition, Textured-DL demonstrated superior performance in the specificities for the peripheral zone and solitary tumors compared with PI-RADS-based risk assessment.
Heterogeneity in conservation of multifunctional partner enzymes with meiotic importance, CDK2 kinase and BRCA1 ubiquitin ligase

The evolution of proteins can be accompanied by changes not only to their amino acid sequences, but also their structural and spatial molecular organization. Comparison of the protein conservation within different taxonomic groups (multifunctional, or highly specific) allows to clarify their specificity and the direction of evolution. Two multifunctional enzymes, cyclin-dependent kinase 2 (CDK2) and BRCA1 ubiquitin ligase, that are partners in some mitotic and meiotic processes were investigated in the present work. Two research methods, bioinformatics and immunocytochemical, were combined to examine the conservation levels of the two enzymes. It has been established that CDK2 is a highly conserved protein in different taxonomic lineages of the eukaryotic tree. Immunocytochemically, a conserved CDK2 pattern was revealed in the meiotic autosomes of five rodent species and partially in domestic turkey and clawed frog. Nevertheless, variable CDK2 distribution was detected at the unsynapsed segments of the rodent X chromosomes. BRCA1 was shown to be highly conserved only within certain mammalian taxa. It was also noted that in those rodent nuclei, where BRCA1 specifically binds to antigens, asynaptic regions of sex chromosomes were positive. BRCA1 staining was not always accompanied by specific binding, and a high nonspecificity in the nucleoplasm was observed. Thus, the studies revealed different conservation of the two enzymes at the level of protein structure as well as at the level of chromosome behavior. This suggests variable rates of evolution due to both size and configuration of the protein molecules and their multifunctionality.
Perfusion Patterns in Patients with Chronic Limb-Threatening Ischemia versus Control Patients Using Near-Infrared Fluorescence Imaging with Indocyanine Green

In assessing the severity of lower extremity arterial disease (LEAD), physicians rely on clinical judgements supported by conventional measurements of macrovascular blood flow. However, current diagnostic techniques provide no information about regional tissue perfusion and are of limited value in patients with chronic limb-threatening ischemia (CLTI). Near-infrared (NIR) fluorescence imaging using indocyanine green (ICG) has been used extensively in perfusion studies and is a possible modality for tissue perfusion measurement in patients with CLTI. In this prospective cohort study, ICG NIR fluorescence imaging was performed in patients with CLTI and control patients using the Quest Spectrum Platform® (Middenmeer, The Netherlands). The time–intensity curves were analyzed using the Quest Research Framework. Fourteen parameters were extracted. Successful ICG NIR fluorescence imaging was performed in 19 patients with CLTI and in 16 control patients. The time to maximum intensity (seconds) was lower for CLTI patients (90.5 vs. 143.3, p = 0.002). For the inflow parameters, the maximum slope, the normalized maximum slope and the ingress rate were all significantly higher in the CLTI group. The inflow parameters observed in patients with CLTI were superior to the control group. Possible explanations for the increased inflow include damage to the regulatory mechanisms of the microcirculation, arterial stiffness, and transcapillary leakage.
SARS-CoV-2 Reinfection Is a New Challenge for the Effectiveness of Global Vaccination Campaign: A Systematic Review of Cases Reported in Literature

Reinfection with SARS-CoV-2 seems to be a rare phenomenon. The objective of this study is to carry out a systematic search of literature on the SARS-CoV-2 reinfection in order to understand the success of the global vaccine campaigns. A systematic search was performed. Inclusion criteria included a positive RT-PCR test of more than 90 days after the initial test and the confirmed recovery or a positive RT-PCR test of more than 45 days after the initial test that is accompanied by compatible symptoms or epidemiological exposure, naturally after the confirmed recovery. Only 117 articles were included in the final review with 260 confirmed cases. The severity of the reinfection episode was more severe in 92/260 (35.3%) with death only in 14 cases. The observation that many reinfection cases were less severe than initial cases is interesting because it may suggest partial protection from disease. Another interesting line of data is the detection of different clades or lineages by genome sequencing between initial infection and reinfection in 52/260 cases (20%). The findings are useful and contribute towards the role of vaccination in response to the COVID-19 infections. Due to the reinfection cases with SARS-CoV-2, it is evident that the level of immunity is not 100% for all individuals. These data highlight how it is necessary to continue to observe all the prescriptions recently indicated in the literature in order to avoid new contagion for all people after healing from COVID-19 or becoming asymptomatic positive.
Genetic Relatedness of 5-Year Isolates of Clostridioides difficile Polymerase Chain Reaction Ribotype 017 Strains in a Hospital

The objective of this study was to analyse the genetic relatedness of Clostridioides difficile polymerase chain reaction ribotype 017 (RT017) strains from patients with hospital-acquired C. difficile infection (HA-CDI) in a hospital with a high RT017 prevalence. From 2009 to 2013, 200 RT017 strains (26.8%) were collected from 745 HA-CDI patient isolates. They comprised 64 MLVA types, and 197 (98.5%) strains were genetically related to 5 clonal complexes (CCs). The largest cluster, CC-A, included 163 isolates of 40 MLVA types. CC-A accounted for 20% of RT017 strains in 2009 and sharply increased to 94.9% in 2010, 94% in 2011, 86.2% in 2012, and 73.5% in 2013. The other 4 CCs included 20 isolates with 7 MLVA types. The resistance rates of antimicrobials were as follows: clindamycin 100%, moxifloxacin 99%, rifaximin 88.5%, and vancomycin 1%. All isolates were susceptible to metronidazole and piperacillin/tazobactam. Comparing antibiotic resistance among CCs, the geometric mean of the minimum inhibitory concentrations of moxifloxacin, vancomycin, and piperacillin/tazobactam were significantly higher for CC-A isolates than for the other CCs. RT017 clones constantly evolved over the 5 years studied with regard to genetic relatedness. The levels of antibiotic resistance may contribute to the persistence of organisms in the institution.
Clinical and Histopathological Factors Influencing IgA Nephropathy Outcome

IgA nephropathy (IgAN) is the most frequent primary glomerulonephritis worldwide. Due to its heterogenicity, there is a need to establish robust biomarkers for IgAN, to support treatment decisions and evaluate the risk of progression to end-stage renal disease. Using both clinical and histopathological data, derived from renal biopsies, we aimed to find predictors of renal function deterioration and proteinuria reduction. Clinical and histopathological data of 80 patients with biopsy proven IgAN were analyzed. In a multivariate logarithmic regression model, the presence of endocapillary hypercellularity (E1) predicted a decline in estimated glomerular filtration rate (eGFR)of at least 50% with an odds ratio (OR) of 15.2, whereas serum albumin concentration had a negative influence on eGFR deterioration (OR 0.2). In the second multivariate model, the extent of interstitial fibrosis predicted the worsening of eGFR by 50% (OR 1.1) and serum albumin concentration had a protective impact (OR 0.1). In the univariate logarithmic regression, both the extent of interstitial fibrosis and the presence of endocapillary hypercellularity negatively correlated with the reduction in proteinuria below 1.0 g/24 h with an OR of 0.2 and 0.9, respectively. In our paper, we confirmed the utility of histopathological variables, especially endocapillary hypercellularity and interstitial fibrosis, and clinical parameters, particularly serum albumin concentration, in the prediction of both a decline in eGFR and a reduction in proteinuria in IgA nephropathy.
Identification of Novel Endogenous Controls for qPCR Normalization in SK-BR-3 Breast Cancer Cell Line

Normalization of gene expression using internal controls or reference genes (RGs) has been the method of choice for standardizing the technical variations in reverse transcription quantitative polymerase chain reactions (RT-qPCR). Conventionally, ACTB and GAPDH have been used as reference genes despite evidence from literature discouraging their use. Hence, in the present study we identified and investigated novel reference genes in SK-BR-3, an HER2-enriched breast cancer cell line. Transcriptomic data of 82 HER2-E breast cancer samples from TCGA database were analyzed to identify twelve novel genes with stable expression. Additionally, thirteen RGs from the literature were analyzed. The expression variations of the candidate genes were studied over five successive passages (p) in two parallel cultures S1 and S2 and in acute and chronic hypoxia using various algorithms. Finally, the most stable RGs were selected and validated for normalization of the expression of three genes of interest (GOIs) in normoxia and hypoxia. Our results indicate that HSP90AB1, DAD1, PFN1 and PUM1 can be used in any combination of three (triplets) for optimizing intra- and inter-assay gene expression differences in the SK-BR-3 cell line. Additionally, we discourage the use of conventional RGs (ACTB, GAPDH, RPL13A, RNA18S and RNA28S) as internal controls for RT-qPCR in SK-BR-3 cell line.
Temporal and Geographical Variation of Intestinal Ulcers in Grey Seals (Halichoerus grypus) and Environmental Contaminants in Baltic Biota during Four Decades

Simple Summary In the 1970s it was discovered that seal populations in the Baltic Sea had decreased severely due to hunting and high levels of contaminants. Lesions were found in several organs and many of the females became sterile. Since then, most of the organ lesions have decreased and so have the levels of some pollutants. However, ulcers in the large intestines of the grey seals increased in the early 1980s and decreased after the mid-1990s. The aims of this study were to: (1) describe the ulcers and investigate if there is a trend over time that coincides with concentrations of some pollutants in Baltic biota; (2) evaluate the significance of different sea areas in the Baltic, grade of parasite intensity, as well as the sex and age of the seals. The results show that seals with ulcers had, in general, higher parasite intensity. Ulcers were more common in older seals and in the Bothnian Sea. The time trend of ulcers coincides with the trend of certain contaminant levels (BDE-47, PFOS and cadmium). The high prevalence of intestinal ulcers and the high intensity of acanthocephalan parasites appear to be unique to the Baltic population of grey seals. Abstract The prevalence of intestinal ulcers and parasites was investigated in 2172 grey seals (Halichoerus grypus) collected in the Baltic Sea and 49 grey seals collected outside the Baltic Sea (i.e., the Atlantic). An increase in frequency of ileocaeco-colonic ulcers was observed in the early 1980s, followed by a decrease in the mid-1990s. At the same time, there was an increase followed by a decrease in brominated flame retardants, Perfluorooctanesulfonic acid (PFOS) and cadmium levels in herring (Clupea harengus), the most common prey item in Baltic grey seal diet, as well as in another top predator in the Baltic, the common guillemot (Uria aalge). The frequency of intestinal ulcers was significantly related to the intensity of acanthocephalan parasites, the age of the seal and the region of the Baltic Sea. Perforation of the intestinal wall was the cause of death in 26 of the investigated Baltic grey seals. In contrast, none of the investigated Atlantic grey seals had intestinal ulcers. They showed a thin colonic wall and very few acanthocephalan parasites. The high prevalence of intestinal ulcers and the high parasite intensity appear to be unique to the Baltic population of grey seals.
Computed Tomography Angiography (CTA) before Reconstructive Jaw Surgery Using Fibula Free Flap: Retrospective Analysis of Vascular Architecture

Computed tomography angiography (CTA) is widely used in preoperative evaluation of the lower limbs’ vascular system for virtual surgical planning (VSP) of fibula free flap (FFF) for jaw reconstruction. The present retrospective clinical study analysed n = 72 computed tomography angiographies (CTA) of lower limbs for virtual surgical planning (VSP) for jaw reconstruction. The purpose of the investigation was to evaluate the morphology of the fibular bone and its vascular supply in CTA imaging, and further, the amount and distribution of periosteal branches (PB) and septo-cutaneous perforators (SCPs) of the fibular artery. A total of 144 lower limbs was assessed (mean age: 58.5 ± 15.3 years; 28 females, 38.9%; 44 males, 61.1%). The vascular system was categorized as regular (type I-A to II-C) in 140 cases (97.2%) regarding the classification by Kim. Absent anterior tibial artery (type III-A, n = 2) and posterior tibial artery (type III-B, n = 2) were detected in the left leg. Stenoses were observed mostly in the fibular artery (n = 11), once in the anterior tibial artery, and twice in the posterior tibial artery. In total, n = 361 periosteal branches (PBs) and n = 231 septo-cutaneous perforators (SCPs) were recorded. While a distribution pattern for PBs was separated into two clusters, a more tripartite distribution pattern for SCPs was found. We conclude that conventional CTA for VSP of free fibula flap (FFF) is capable of imaging and distinguishing SCPs and PBs.
Training Early Childhood Teachers to Support Children’s Social and Emotional Learning: A Preliminary Evaluation of Roundies Program

(1) Background: Implementing social-emotional learning (SEL) programs in Early Childhood Education (ECE) settings is a promising approach that can strengthen overall development and well-being during childhood and into adolescence and adulthood. This study described the development, implementation, and preliminary evaluation of a universal SEL program, i.e., Roundies, in the Finnish ECE context to address the need for professional development opportunities. (2) Methods: The Roundies program was a quasi-experimental pre-test/post-test with intervention and control design. A total of 194 children were assigned to either the intervention group (n = 136) or control group (n = 58) (MAGE = 60.35 months at pre-test; 48% boys). Teachers rated the children’s behaviors using the Strength and Difficulties Questionnaire (SDQ) at the pre-and post-test. (3) Results: Feedback collected by teachers on the program suggested that teachers were highly satisfied with the overall program and the components. Multilevel models showed significantly increased prosocial behaviors and reduced SDQ total difficulties in the intervention group compared to the control group. (4) Conclusions: These preliminary findings provide evidence of the effectiveness of the Roundies program in improving teachers’ capacity to support early SEL.
Can we use the internet to study speech production? Yes we can! Evidence contrasting online versus laboratory naming latencies and errors

The closure of cognitive psychology labs around the world due to the COVID-19 pandemic has prevented in-person testing. This has caused a particular challenge for speech production researchers, as before the pandemic there were no studies demonstrating that reliable overt speech production data could be collected via the internet. Here, we present evidence that both accurate and reliable overt articulation data can be collected from internet-based speech production experiments. We tested 100 participants in a picture naming paradigm, where we manipulated the word and phonotactic frequency of the picture names. We compared our results to a lab-based study conducted on different participants which used the same materials and design. We found a significant word frequency effect but no phonotactic frequency effect, fully replicating the lab-based results. Effect sizes were similar between experiments, but with significantly longer latencies in the internet-collected data. We found no evidence that internet upload or download speed affected either naming latencies or errors. In addition, we carried out a permutation-style analysis which recommends a minimum sample size of 40 participants for online production paradigms. In sum, our study demonstrates that internet-based testing of speech production is a feasible and promising endeavour, with less challenges than many researchers (anecdotally) assumed.
Single-Breath-Hold MRI-SPACE Cholangiopancreatography with Compressed Sensing versus Conventional Respiratory-Triggered MRI-SPACE Cholangiopancreatography at 3Tesla: Comparison of Image Quality and Diagnostic Confidence

To compare two magnetic resonance cholangiopancreatography (MRCP) sequences at 3 Tesla (3T): the conventional 3D Respiratory-Triggered SPACE sequence (RT-MRCP) and a prototype 3D Compressed-Sensing Breath-Hold SPACE sequence (CS-BH-MRCP), in terms of qualitative and quantitative image quality and radiologist’s diagnostic confidence for detecting common bile duct (CBD) lithiasis, biliary anastomosis stenosis in liver-transplant recipients, and communication of pancreatic cyst with the main pancreatic duct (MPD). Sixty-eight patients with suspicion of choledocholithiasis or biliary anastomosis stenosis after liver transplant, or branch-duct intraductal papillary mucinous neoplasm of the pancreas (BD-IPMN), were included. The relative CBD to peri-biliary tissues (PBT) contrast ratio (CR) was assessed. Overall image quality, presence of artefacts, background noise suppression and the visualization of 12 separated segments of the pancreatic and bile ducts were evaluated by two observers working independently on a five-point scale. Diagnostic confidence was scored on a 1–3 scale. The CS-BH-MRCP presented significantly better CRs (p < 0.0001), image quality (p = 0.004), background noise suppression (p = 0.011), fewer artefacts (p = 0.004) and better visualization of pancreatic and bile ducts segments with the exception of the proximal CBD (p = 0.054), cystic duct confluence (p = 0.459), the four secondary intrahepatic bile ducts, and central part of the MPD (p = 0.885) for which no significant differences were found. Overall, diagnostic confidence was significantly better with the CS-BH-MRCP sequence for both readers (p = 0.038 and p = 0.038, respectively). This study shows that the CS-BH-MRCP sequence presents overall better image quality and bile and pancreatic ducts visualization compared to the conventional RT-MRCP sequence at 3T.
DBtRend: A Web-Server of tRNA Expression Profiles from Small RNA Sequencing Data in Humans

Transfer RNA (tRNA), a key component of the translation machinery, plays critical roles in stress conditions and various diseases. While knowledge regarding the importance of tRNA function is increasing, its biological roles are still not well understood. There is currently no comprehensive database or web server providing the expression landscape of tRNAs across a variety of human tissues and diseases. Here, we constructed a user-friendly and interactive database, DBtRend, which provides a profile of mature tRNA expression across various biological conditions by reanalyzing the small RNA or microRNA sequencing data from the Cancer Genome Atlas (TCGA) and NCBI’s Gene Expression Omnibus (GEO) in humans. Users can explore not only the expression values of mature individual tRNAs in the human genome, but also those of isodecoders and isoacceptors based on our specific pipelines. DBtRend provides the expressed patterns of tRNAs, the differentially expressed tRNAs in different biological conditions, and the information of samples or patients, tissue types, and molecular subtype of cancers. The database is expected to help researchers interested in functional discoveries of tRNAs.