Miracle-dz/UniFAR-FTUs huggingface dataset:
Subgrid-scale physical parameterization in atmospheric modeling: How can we make it consistent?

Approaches to subgrid-scale physical parameterization in atmospheric modeling are reviewed by taking turbulent combustion flow research as a point of reference. Three major general approaches are considered for its consistent development: moment, distribution density function (DDF), and mode decomposition. The moment expansion is a standard method for describing the subgrid-scale turbulent flows both in geophysics and engineering. The DDF (commonly called PDF) approach is intuitively appealing as it deals with a distribution of variables in subgrid scale in a more direct manner. Mode decomposition was originally applied by Aubry et al (1988 J. Fluid Mech. 192 115-73) in the context of wall boundary-layer turbulence. It is specifically designed to represent coherencies in compact manner by a low-dimensional dynamical system. Their original proposal adopts the proper orthogonal decomposition (empirical orthogonal functions) as their mode-decomposition basis. However, the methodology can easily be generalized into any decomposition basis. Among those, wavelet is a particularly attractive alternative. The mass-flux formulation that is currently adopted in the majority of atmospheric models for parameterizing convection can also be considered a special case of mode decomposition, adopting segmentally constant modes for the expansion basis. This perspective further identifies a very basic but also general geometrical constraint imposed on the massflux formulation: the segmentally-constant approximation. Mode decomposition can, furthermore, be understood by analogy with a Galerkin method in numerically modeling. This analogy suggests that the subgrid parameterization may be re-interpreted as a type of mesh-refinement in numerical modeling. A link between the subgrid parameterization and downscaling problems is also pointed out.
Wind tunnel test of airfoil with erosion and leading edge protection

This paper describes wind tunnel tests of a NACA 633 – 418 airfoil with erosion and leading edge protection. Measurements are carried out at high Reynolds number (Re = 5 million) representing modern wind turbines. Three examples of deviations from the perfect airfoil surface are shown. It is seen how the presence of a roughness mesh degrades the aerodynamics and that the presence of the mesh is more important than the actual topology of the mesh. That is also the case for the stall strips where a small strip influences the performance slightly less than a big stall strip, but the presence of the stall strip alone is influencing the performance significantly. Finally, a simulated leading edge protection (LEP), represented by a sheet of paper, can influence the performance significantly as the paper leads to a backward facing step. Furthermore, the measurements showed that correct mounting of LEP is important to avoid too big losses in aerodynamic performance. Investigating the impact of reduced airfoil performance for the rotor performance showed losses in annual energy production of between 0.3% and 4.0%. All in all the wind tunnel tests reflected that leading edge damages have a significant impact on the aerodynamic performance.
Neurofeedback-enabled beta power control with a fully implanted DBS system in patients with Parkinson's disease

Parkinsonian motor symptoms are linked to pathologically increased beta oscillations in the basal ganglia. Studies with externalised deep brain stimulation electrodes showed that Parkinson patients were able to rapidly gain control over these pathological basal ganglia signals through neurofeedback. Studies with fully implanted deep brain stimulation systems duplicating these promising results are required to grant transferability to daily application. In this study, seven patients with idiopathic Parkinson's disease and one with familial Parkinson's disease were included. In a postoperative setting, beta oscillations from the subthalamic nucleus were recorded with a fully implanted deep brain stimulation system and converted to a real-time visual feedback signal. Participants were instructed to perform bidirectional neurofeedback tasks with the aim to modulate these oscillations. While receiving regular medication and deep brain stimulation, participants were able to significantly improve their neurofeedback ability and achieved a significant decrease of subthalamic beta power (median reduc- tion of 31% in the final neurofeedback block). We could demonstrate that a fully implanted deep brain stimulation system can provide visual neurofeedback enabling patients with Parkinson's disease to rapidly control pathological subthalamic beta oscillations.
Synthetic data for privacy-preserving clinical risk prediction

Synthetic data promise privacy-preserving data sharing for healthcare research and development. Compared with other privacy-enhancing approaches - such as federated learning - analyses performed on synthetic data can be applied downstream without modification, such that synthetic data can act in place of real data for a wide range of use cases. However, the role that synthetic data might play in all aspects of clinical model development remains unknown. In this work, we used state-of-the-art generators explicitly designed for privacy preservation to create a synthetic version of the UK Biobank before building prognostic models for lung cancer under several data release assumptions. We demonstrate that synthetic data can be effectively used throughout the modelling pipeline even without eventual access to the real data. Furthermore, we show the implications of different data release approaches on how synthetic data could be deployed within the healthcare system.
Large tandem duplications in cancer result from transcription and DNA replication collisions

Despite the abundance of somatic structural variations (SVs) in cancer, the underlying molecular mechanisms of their formation remain unclear. Here, we use 6,193 whole-genome sequenced tumors to study the contributions of transcription and DNA replication collisions to genome instability. After deconvoluting robust SV signatures in three independent pan-cancer cohorts, we detect transcription-dependent replicated-strand bias, the expected footprint of transcription-replication collision (TRC), in large tandem duplications (TDs). Large TDs are abundant in female-enriched, upper gastrointestinal tract and prostate cancers. They are associated with poor patient survival and mutations in TP53, CDK12, and SPOP. Upon inactivating or suppressing CDK12, cells display significantly more TRCs and R-loops. Inhibition of WEE1, a cell cycle regulator that promotes DNA repair, selectively inhibits the growth of cells with loss of CDK12. Our data suggest that large TDs in cancer form due to TRC, and their presence can be used as a biomarker for prognosis and treatment.
eoPred: Predicting the placental phenotype of early-onset preeclampsia using DNA methylation

Background: A growing body of literature has reported molecular and histological changes in the human placenta in association with preeclampsia (PE). Placental DNA methylation (DNAme) and transcriptomic patterns have revealed molecular subgroups of PE that are associated with placental histopathology and clinical phenotypes of the disease. However, the heterogeneity of PE both across and within subtypes, whether defined clinically or molecularly, complicates the study of this disease. PE is most strongly associated with placental pathology and adverse fetal and maternal outcomes when it develops early in pregnancy. We focused on placentae from pregnancies affected by preeclampsia that were delivered before 34 weeks of gestation to develop eoPred, a predictor of the DNAme signature associated with the placental phenotype of early-onset preeclampsia (EOPE). Results: Public data from 83 placental samples (HM450K), consisting of 42 EOPE and 41 normotensive preterm birth (nPTB) cases, was used to develop eoPred - a supervised model that relies on a highly discriminative 45 CpG DNAme signature of EOPE in the placenta. The performance of eoPred was assessed using cross-validation (AUC=0.95) and tested in an independent validation cohort (n=49, AUC=0.725). A subset of fetal growth restriction (FGR) and late-PE cases showed a similar DNAme profile at the 45 predictive CpGs, consistent with the overlap in placental pathology between these conditions. The relationship between the EOPE probability generated by eoPred and various phenotypic variables was also assessed, revealing that it is associated with gestational age, and it is not driven by cell composition differences. Conclusions: eoPred relies on a 45 CpG DNAme signature to predict EOPE, and it can be used in a discrete or continuous manner. Using this classifier should 1) improve the consistency of future placental DNAme studies of PE and placental insufficiency, 2) facilitate identifying cases of EOPE in public data sets and 3) importantly, standardize the placental diagnosis to allow better cross-cohort comparisons. Lastly, classification of cases with eoPred should be useful for testing associations between placental pathology and genetic or environmental variables.
Rare diagnosis of coexistent antiphospholipid syndrome and systemic lupus erythematosus in a male patient with successful management: a case report

Introduction: Antiphospholipid syndrome (APS) and systemic lupus erythematosus (SLE) are two autoimmune disorders that can develop together or separately. Similarities in the pathogenesis have been discovered, including the production of autoantibodies that target subcellular antigens and shared elevated risk of cardiovascular morbidity, which may be caused by common pathologic pathways. Case presentation: A 28-year-old male, referred to our hospital for the assessment of chest pain. Past medical history was significant for extensive deep venous thrombosis despite the appropriate management with a therapeutic dose of direct-acting oral anticoagulant. Prolonged partial thromboplastin time was not corrected by mixing study along with positive lupus anticoagulant, anticardiolipin, and B-2 glycoprotein antibodies. In addition, antinuclear antibodies, anti-DNA antibodies, and direct Coombs were positive with decreased levels of C3. The patient was diagnosed with SLE with brain, heart, and kidney involvement in the setting of antiphospholipid antibody syndrome. He was treated successfully with full recovery. Discussion: SLE and APS both have sneaky ways of manifestation. Ineffective diagnosis and therapy could cause irreversible organ damage. Clinicians should have a high index of suspicion for APS, particularly in young patients who approach with spontaneous or unprovoked thromboses or unexplained recurrent early or late pregnancy loss. Anticoagulation, modifying cardiovascular risk factors, and identifying and treating any underlying inflammatory diseases are all part of the multidisciplinary care that is needed for management. Conclusion: Although male affection is rare, SLE and APS should be considered in male patients as these conditions tend to be more aggressive than in the female.
An unusual association between Burkitt’s lymphoma and a Carcinoid tumor in a Syrian boy: a rare case report

Introduction: Burkitt’s lymphoma (BL), an aggressive kind of non-Hodgkin’s B-cell lymphoma. On the other hand, appendiceal carcinoid tumors are uncommon neuroendocrine neoplasms. Case presentation: The authors report a case of a 15-year-old Syrian adolescent who was admitted to our hospital due to a persistent, severe generalized abdomen pain accompanied by nausea, vomiting, loss of appetite, and inability to pass stool or gas. An abdominal radiograph revealed dilated intestinal loops with air-fluid levels. The patient underwent emergency surgery through which a retroperitoneal mass was removed as well as part of the ileum and the appendix. The final diagnosis was consistent with intestinal BL associated with an appendiceal carcinoid tumor. Discussion: The correlation between gastrointestinal carcinoids and other types of tumors was frequently reported. However, there have been few reports of carcinoid tumors being associated with lymphoreticular system cancers. BLs were classified into three variants: endemic, sporadic, and acquired immunodeficiency-associated BL while appendiceal neuroendocrine tumors were classified as the following: well-differentiated neuroendocrine tumors with benign or uncertain malignant potential; well-differentiated neuroendocrine carcinoma with low malignant potential; and mixed exocrine-neuroendocrine carcinoma. Conclusion: Our article demonstrates an unusual association between BL and an appendiceal carcinoid tumor that highlights the significant role of histological and immunohistochemical staining in confirming the diagnosis, as well as the role of surgery in treating the complications of intestinal BLs.
Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides

Abstract Genomic studies of bacteria have long pointed toward widespread prevalence of small open reading frames (sORFs) encoding for short proteins, <100 amino acids in length. Despite the mounting genomic evidence of their robust expression, relatively little progress has been made in their mass spectrometry-based detection and various blanket statements have been used to explain this observed discrepancy. In this study, we provide a large-scale riboproteogenomics investigation of the challenging nature of proteomic detection of such small proteins as informed by conditional translation data. A panel of physiochemical properties alongside recently developed mass spectrometry detectability metrics was interrogated to provide a comprehensive evidence-based assessment of sORF-encoded polypeptide (SEP) detectability. Moreover, a large-scale proteomics and translatomics compendium of proteins produced by Salmonella Typhimurium (S. Typhimurium), a model human pathogen, across a panel of growth conditions is presented and used in support of our in silico SEP detectability analysis. This integrative approach is used to provide a data-driven census of small proteins expressed by S. Typhimurium across growth phases and infection-relevant conditions. Taken together, our study pinpoints current limitations in proteomics-based detection of novel small proteins currently missing from bacterial genome annotations.
A study on measuring the 222Rn in the Buriganga River and tap water of the megacity Dhaka

Radon (222Rn), an inert gas, is considered a silent killer due to its carcinogenic characteristics. Dhaka city is situated on the banks of the Buriganga River, which is regarded as the lifeline of Dhaka city because it serves as a significant source of the city’s water supply for domestic and industrial purposes. Thirty water samples (10 tap water from Dhaka city and 20 surface samples from the Buriganga River) were collected and analyzed using a RAD H2O accessory for 222Rn concentration. The average 222Rn concentration in tap and river water was 1.54 ± 0.38 Bq/L and 0.68 ± 0.29 Bq/L, respectively. All the values were found below the maximum contamination limit (MCL) of 11.1 Bq/L set by the USEPA, the WHO-recommended safe limit of 100 Bq/L, and the UNSCEAR suggested range of 4–40 Bq/L. The mean values of the total annual effective doses due to inhalation and ingestion were calculated to be 9.77 μSv/y and 4.29 μSv/y for tap water and river water, respectively. Although all these values were well below the permissible limit of 100 μSv/y proposed by WHO, they cannot be neglected because of the hazardous nature of 222Rn, especially considering their entry to the human body via inhalation and ingestion pathways. The obtained data may serve as a reference for future 222Rn-related works.
Combined action observation and motor imagery improves learning of activities of daily living in children with Developmental Coordination Disorder

Developmental coordination disorder (DCD) is characterised by poor motor coordination, which interferes with the ability to execute activities of daily living (ADLs). Combined action observation and motor imagery (AOMI) involves observing movement videos whilst imagining simultaneously the sensations of executing the same movement. Laboratory-based research indicates that AOMI can help improve movement coordination in children with DCD, but no previous research had investigated the efficacy of AOMI interventions for learning ADLs. This study investigated the efficacy of a home-based, parent-led, AOMI intervention for learning ADLs in children with DCD. Children with confirmed (n = 23) or suspected (n = 5) DCD (total sample n = 28), aged 7–12 years, were assigned to either an AOMI intervention or a control intervention (both n = 14). Participants attempted the following ADLs at pre-test (week 1), post-test (week 4), and retention test (week 6): shoelace tying, cutlery use, shirt buttoning, and cup stacking. Task completion times and movement techniques were recorded. The AOMI intervention produced significantly faster task completion times than the control intervention at post-test for shoelace tying, and significantly improved movement techniques for shoelace tying and cup stacking. Importantly, for children who could not tie shoelaces at pre-test (n = 9 per group), 89% of those following the AOMI intervention learnt the skill successfully by the end of the study, compared to only 44% of those following the control intervention. The findings indicate that home-based, parent-led, AOMI interventions can aid the learning of complex ADLs in children with DCD, and may be particularly effective for facilitating the learning of motor skills that do not currently exist within these children’s motor repertoire.
A 2-Tuple Fuzzy Time Series and Fuzzy Modeling Inference Method

Abstract This study proposes a 2-tuple fuzzy time series forecasting method. The 2-tuple linguistic representation was first proposed by Herrera and Martínez [14], and was mainly applied for computing with words, decision making and decision analysis problems. This study applies the 2-tuple concept to the fuzzy time series, and the historical data is fuzzified to 2-tuple linguistic representation. The advantage of 2-tuple linguistic representation is that the data can be fuzzified more accurately and the loss of information is reduced. In addition, the 2-tuple fuzzy logical relationship can be established. A new fuzzy inference process based on proportional shift is also proposed. Finally, this study applies the 2-tuple fuzzy time series method to forecast the enrollments at the University of Alabama. Compared to several other methods, the forecasting results of the present method show better accuracy. For verification, another dataset is also used. This study applies the present method to forecast Taiwan tourists to Europe. Compared to Chen's method[4], the forecasting results of the present method show better accuracy.
Detection of FLAD1 mutations and lipid storage myopathy in a 5-year-old boy: a case report study

Introduction and importance: Lipid storage myopathy due to flavin adenine dinucleotide synthetase 1 (FLAD1) deficiency is an autosomal recessive error of metabolism that causes variable mitochondrial dysfunction. Case presentation: At the age of 3, the patient was found to have movement problems, such as difficulty rising from a chair (Gower’s sign) and climbing stairs, which led to hospital admission and diagnosis. At the age of 4, carrier detection for spinal muscular atrophy was normal; however, at the age of 5, whole-exome sequencing revealed a pathogenic variant of Chr1: 154960762: A>T c.A554T:p.D185V in exon-2 of FLAD1 gene was identified as homozygous. Clinical discussion: In general, it is expected that the treatment of type 2 FLAD1 gene mutation with riboflavin has a better prognosis, but these interventions may not be sufficient for the survival of the patient. Treatment with riboflavin has increased various functions, including skeletal-muscular, and cardiovascular function. As a result, like the patient in our study, the mutation in exon-2 is more severe and less responsive to riboflavin treatment. Conclusion: Checking the FLAD1 gene is recommended in all people with multiple acyl-CoA dehydrogenase deficiency.
Long-term efficacy of penile rehabilitation with low-intensity extracorporeal shock wave therapy for sexual and erectile function recovery following robotic-assisted radical prostatectomy: a single-cohort pilot study

Abstract Background The long-term efficacy of low-intensity extracorporeal shock wave therapy (LIESWT) for penile rehabilitation after robot-assisted radical prostatectomy (RARP) has not yet been reported. Aim To assess the long-term efficacy of LIESWT for penile rehabilitation after RARP by evaluating the postoperative recovery of sexual and erectile functions following RARP. Methods Patients who underwent RARP at our institution were categorized into 2 groups: those who received LIESWT and those who underwent penile rehabilitation with a phosphodiesterase type 5 inhibitor (PDE5i). The control group included patients who did not undergo penile rehabilitation. Potency and scores on the Expanded Prostate Cancer Index Composite for sexual function and 5-item International Index of Erectile Function (IIEF-5) were evaluated preoperatively and over 60 months after RARP. Outcomes The LIESWT group had significantly higher postoperative sexual function and total IIEF-5 scores and potency than the control group over the long term, and its results were not inferior to those of the PDE5i group. Results The LIESWT, PDE5i, and control groups comprised 16, 13, and 139 patients, respectively. As compared with the control group, the LIESWT group had significantly higher sexual function scores at 6, 12, and 60 months after surgery (P < .05) and total IIEF-5 scores at 24 and 60 months (P < .05). The LIESWT group also had a significantly higher potency rate than the control group at 60 months (P < .05). For all time points after surgery, there were no significant differences between the LIESWT and PDE5i groups in terms of sexual function and total IIEF-5 scores and potency. Clinical Implications LIESWT may be a new option for penile rehabilitation in patients with erectile dysfunction after RARP. Strengths and Limitations This pilot study was performed at a single center and involved relatively few patients, which may have led to selection bias. Furthermore, the selection of this study for penile rehabilitation was not made randomly but by the patient’s choice. Despite these limitations, our results provide evidence in support of LIESWT for penile rehabilitation after RARP because this is the first study to assess the long-term efficacy of LIESWT. Conclusion LIESWT can improve sexual and erectile functions in patients with erectile dysfunction after RARP, and its efficacy can be maintained over a long period after surgery.
Gut-brain axis: altered microbiome and depression – review

The concept of a ‘gut-brain axis’ was recently developed when the complex communications between the brain and the gut became evident. The interaction may affect emotions, motivation, mood, and higher cognitive functions as well as gut homeostasis. Human microbe symbiosis’s merits are now acknowledged to transcend human mental health. Research has recently indicated that the gut-brain axis plays a vital role in brain health maintenance. The term ‘gut-brain axis’ can only partially capture the intricacy of these interactions. Dysbiosis of the gut commensals has been seen in patients with psychiatric diseases, such as depression. Major depressive disorder is caused by complicated interactions between the individual gene and the environment. In a forced swimming test, P. Zheng et al. discovered that germ-free mice with no gut microbiota had a shorter immobility duration than healthy mice. More radical effects were expressed on the use of probiotics rather than prebiotics and postbiotics in reducing the symptoms of depression in patients with major depressive disorder. One of prime importance can be given to exploring more microbiota to investigate the better therapeutic effects of probiotics, prebiotics, and postbiotics.