Miracle-dz/UniFAR-FTUs huggingface dataset:
Polarization and magneto-optical properties of excitonic emission from wurtzite CdTe/(Cd,Mg)Te core/shell nanowires

Wurtzite CdTe and (Cd,Mn)Te nanowires embedded in (Cd,Mg)Te shells are grown by employing vapour–liquid–solid growth mechanism in a system for molecular beam epitaxy. A combined study involving cathodoluminescence, transmission electron microscopy and micro-photoluminescence is used to correlate optical and structural properties in these structures. Typical features of excitonic emission from individual wurtzite nanowires are highlighted including the emission energy of 1.65 eV, polarization properties and the appearance B-exciton related emission at high excitation densities. Angle dependent magneto-optical study performed on individual (Cd,Mn)Te nanowires reveals heavy-hole-like character of A-excitons typical for wurtzite structure and allows to determine the crystal field splitting, ΔCR. The impact of the strain originating from the lattice mismatched shell is discussed and supported by theoretical calculations.
Local structure and phase change behavior in interfacial intermixing GeTe–Sb2Te3 superlattices

Ge/Sb atomic intermixing in interfacial cationic layers is a common phenomenon for GeTe–Sb2Te3 superlattice (GST-SL) used in memory devices. In this paper, we explored the effect of Ge/Sb intermixing on the phase change behavior of GST-SL upon the heating-quenching procedure. Four interfacial intermixing models of Kooi, Ferro, Petrov and inverted Petrov with different Ge/Sb intermixing ratios (25/75, 50/50 and 75/25) were developed based on the ab initio molecular dynamics. The structural evolution indicated that the Ge/Sb interfacial intermixing could facilitate the structure changes especially for 50/50 Ge/Sb intermixed models. When quenching from 1500 K, more 4-fold Ge-centered octahedrons were produced than tetrahedrons, and the electron localization function further proved that the distorted of Ge(Sb)-centered 6-fold octahedrons were caused by the asymmetrical interactions of Ge–Ge/Sb and Ge–Te. A relatively large Te p orbital contribution in coexisted Ge/Te layer led to a narrower bandgap. In addition, different Ge/Sb atom intermixed ratio which affected the electronic local structure, led to the discrepancy in the initial atom movement of Sb or Ge movement near the gap. The present studies enrich the understanding of Ge/Sb interfacial atomic intermixing effects in GST-SL structural changes.
Estimating the fiscal impact of three vaccination strategies in Italy

Abstract Objectives When assessing the economic value of vaccines, decision makers should adopt a full societal perspective. One approach for estimation of the fiscal impact of a disease is to use the human capital method to determine productivity losses. The aim of this study was to test an analytical framework developed for the estimation of the fiscal impacts of vaccination programs for influenza (FLU), pneumococcus (PC), and herpes zoster (HZ), in Italy. Methods We tested the framework in a two-stage analysis. First, we estimated the fiscal impact of the disease, second we performed a cost–benefit analysis of the individual benefits of vaccination against the cost of the vaccine. To estimate the fiscal impact of the diseases, the human capital approach was used. Epidemiological data were extrapolated from the literature. A Monte Carlo simulation enabled exploration of the uncertainty in the model variables. Results For FLU, assuming 2.1 million people infected, the total expected impact was EUR 999,371,520; the estimated fiscal impact was EUR 159,563,520. For PC, assuming 90,000 people infected, the total impact was EUR 148,055,040 and the estimated fiscal impact was EUR 23,639,040. For HZ, assuming 6,400 people infected, the total impact was EUR 4,777,200, with EUR 630,000 resulting from a decrease in fiscal taxation. Conclusions In conclusion, our work shows how traditional methods aimed at estimating the cost of illness from a social perspective can be improved by additionally considering the fiscal impact, which accounts for the decrease in fiscal revenues due to illness.
Plasmonic Effects on the Growth of Ag Nanocrystals in Solution.

The light-stimulated transformation of ensembles of spherical nanoparticles into anisotropic metal nanostructures mediated by localized surface plasmon resonance (LSPR) excitation is an elegant way of synthesizing triangular silver nanoprisms with extraordinary control over size and shape. Usually the transformation occurs in oxidizing environments along a pathway that involves the oxidative etching of small pre-existing Ag seeds, followed by plasmon-mediated reduction of the resulting Ag ions and Ag0 incorporation into the anisotropic nanocrystals. Here, we investigate pathways toward Ag nanoprisms from initially homogeneous AgNO3 solutions held at reducing conditions. Observations by in-situ electron microscopy show that reducing environments and high Ag precursor concentrations in the presence of sodium citrate favor two alternative transformation routes of initial spherical nuclei into anisotropic nanoprisms: (i) the aggregation of spherical nanoparticles and plasmon-mediated conversion of small clusters into triangular prisms; and (ii) shape fluctuations of individual small nanoparticles. Simulated field distributions confirm that the coupling of the LSPR excitation between closely spaced nanoparticles causes significant field enhancements near local plasmonic hot spots, which can drive accelerated Ag incorporation and thus supports the transformation into nanoprisms.
scBatch: batch-effect correction of RNA-seq data through sample distance matrix adjustment

MOTIVATION Batch effect is a frequent challenge in deep sequencing data analysis that can lead to misleading conclusions. Existing methods do not correct batch effects satisfactorily, especially with single cell RNA sequencing (RNA-seq) data. RESULTS We present scBatch, a numerical algorithm for batch effect correction on bulk and single cell RNA-seq data with emphasis on improving both clustering and gene differential expression analysis. scBatch is not restricted by assumptions on the mechanism of batch effect generation. As shown in simulations and real data analyses, scBatch outperforms benchmark batch effect correction methods. AVAILABILITY The R package is available at github.com/tengfei-emory/scBatch. The code to generate results and figures in this paper is available at github.com/tengfei-emory/scBatch-paper-scripts. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Identifying a new microRNA signature as a prognostic biomarker in colon cancer

Background The aim was to identify a novel prognostic miRNA signature for colon cancer (CC) in silico. Methods Data on the expression of miRNAs and relevant clinical information for 407 patients were obtained from The Cancer Genome Atlas (TCGA), and the samples were randomly split into a validation set (n = 203) and training set (n = 204). The differential expression of miRNAs between normal tissues and patients with CC was analyzed. We detected a miRNA expression signature in the training dataset by using a Cox proportional hazard regression model. Then, we verified the signature in the validation set. Association of the miRNA signature with overall survival was assessed in the validation cohort and combined cohort by log-rank test and based on Kaplan-Meier curves. The receiver operating characteristic and disease-free survival analyses were performed to evaluate the miRNA signature of CC in the combined cohort. Multivariate and univariate Cox analyses related to survival for the miRNA signature were performed, and a nomogram was built as a prognostic model for CC. To explore the function of target genes of the miRNA signature, Gene Ontology analysis and Kyoto Encyclopedia of Genes and Genomes pathway analysis were used. Results Between the matched normal tissues and colon cancer tissues, 267 differentially expressed miRNAs were detected, and a single-factor CoxPH model showed that 13 miRNAs were related to overall survival in the training cohort. Then, a five-miRNA signature was identified using a CoxPH regression model with multiple factors. The five-miRNA signature had significant prognostic value in the training cohort and was validated in the validation cohort and combined cohort. A total of 193 target genes of the miRNA signature were identified. According to the results of functional analysis of the target genes, the signaling pathways MAPK, AMPK and PI3K-Akt, focal adhesion, and microRNAs in cancer were remarkably enriched. Conclusion A five-miRNA signature had increased prognostic value for CC, which may provide important biological insights for the discovery and development of molecular predictors to improve the prognosis of patients with CC.
Diagnosis of Complex Regional Pain Syndrome I Following Traumatic Axonal Injury of the Corticospinal Tract in a Patient with Mild Traumatic Brain Injury

A 54-year-old male suffered from direct head trauma resulting from a fall while working. At approximately two months after the accident, he began to feel pain (burning sensation) and swelling of the dorsum of the right hand and wrist. He showed the following clinical features among the clinical signs and symptoms of revised diagnostic criteria for complex regional pain syndrome (CRPS): spontaneous pain, mechanical hyperalgesia, vasodilation, skin temperature asymmetries, skin color changes, swelling, motor weakness. No specific lesion was observed on brain MRI taken at ten weeks after onset. Plain X-ray, electromyography, and nerve conduction studies for the right upper extremity detected no abnormality. A three-phase bone scan showed hot uptake in the right wrist in the delayed image. On two-month diffusion tensor tractography, partial tearing of the corticospinal tract (CST) was observed at the subcortical white matter in both hemispheres (much more severe in the left CST). In addition, the fiber number of the right CST was significantly decreased than that of seven normal control subjects. CRPS I of the right hand in this patient appeared to be related to traumatic axonal injury of the left CST following mild traumatic brain injury.
Bodily changes and sensory sensitivity in complex regional pain syndrome and fibromyalgia.

Complex regional pain syndrome (CRPS) and fibromyalgia are chronic pain conditions of unexplained origins. In addition to symptoms in the diagnostic criteria, patients can report changes to vision and other sensations or bodily functions. It is unclear whether these are greater than would be expected due to normal ageing, living with chronic pain generally, or common co-morbidities of chronic pain such as depression or anxiety. We administered an on-line survey evaluating the frequencies and types of self-reported somatic symptoms, bodily changes, and sensory sensitivity in respondents with CRPS (n=390), fibromyalgia (n=425), and both CRPS and fibromyalgia ('CRPS+fibromyalgia'; n=88) compared to respondents with other chronic pain conditions (n=331) and pain-free controls (n=441). The survey assessed somatic symptoms (Patient Health Questionnaire-15), bodily changes, pain/discomfort/distress triggers, and pain intensifiers. We conducted ANCOVA's with age, sex, Patient Health Questionnaire-9 (measuring depression), Generalized Anxiety Disorder-7, pain duration in years, hours of pain per day, and number of pain-related medical diagnoses as covariates. After controlling for covariates, respondents with CRPS and/or fibromyalgia reported more somatic symptoms, changes in movement and biological responses, pain/discomfort/distress triggers, and pain intensifiers than pain(-free) control groups. Fibromyalgia specifically related to changes in vision and hearing; urinary/intestinal function; and drinking and eating. CRPS changes related to changes in hair, skin, and nails; and infection and healing. The CRPS+fibromyalgia group presented with features of both disorders with minimal additional stressors or symptoms over and above these. Our findings suggest CRPS and fibromyalgia share underlying pathophysiologies, although specific mechanisms might be different.
Dynamic pulmonary CT perfusion using first-pass analysis technique with only two volume scans: Validation in a swine model

Purpose To evaluate the accuracy of a low-dose first-pass analysis (FPA) CT pulmonary perfusion technique in comparison to fluorescent microsphere measurement as the reference standard. Method The first-pass analysis CT perfusion technique was validated in six swine (41.7 ± 10.2 kg) for a total of 39 successful perfusion measurements. Different perfusion conditions were generated in each animal using serial balloon occlusions in the pulmonary artery. For each occlusion, over 20 contrast-enhanced CT images were acquired within one breath (320 x 0.5mm collimation, 100kVp, 200mA or 400mA, 350ms gantry rotation time). All volume scans were used for maximum slope model (MSM) perfusion measurement, but only two volume scans were used for the FPA measurement. Both MSM and FPA perfusion measurements were then compared to the reference fluorescent microsphere measurements. Results The mean lung perfusion of MSM, FPA, and microsphere measurements were 6.21 ± 3.08 (p = 0.008), 6.59 ± 3.41 (p = 0.44) and 6.68 ± 3.89 ml/min/g, respectively. The MSM (PMSM) and FPA (PFPA) perfusion measurements were related to the corresponding reference microsphere measurement (PMIC) by PMSM = 0.51PMIC + 2.78 (r = 0.64) and PFPA = 0.79PMIC + 1.32 (r = 0.90). The root-mean-square-error for the MSM and FPA techniques were 3.09 and 1.72 ml/min/g, respectively. The root-mean-square-deviation for the MSM and FPA techniques were 2.38 and 1.50 ml/min/g, respectively. The CT dose index for MSM and FPA techniques were 138.7 and 8.4mGy, respectively. Conclusions The first-pass analysis technique can accurately measure regional pulmonary perfusion and has the potential to reduce the radiation dose associated with dynamic CT perfusion for assessment of pulmonary disease.
Risk Factors for Diabetic Peripheral Neuropathy and Cardiovascular Autonomic Neuropathy in the Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) Study

The Diabetes Control and Complications Trial/Epidemiology of Diabetes Interventions and Complications (DCCT/EDIC) study demonstrated that intensive glucose control reduced the risk of developing diabetic peripheral neuropathy (DPN) and cardiovascular autonomic neuropathy (CAN). We evaluated multiple risk factors and phenotypes associated with DPN and CAN in this large, well-characterized cohort of participants with type 1 diabetes, followed for >23 years. DPN was defined by symptoms, signs, and nerve conduction study abnormalities in ≥2 nerves; CAN was assessed using standardized cardiovascular reflex tests. Generalized estimating equation models assessed the association of DPN and CAN with individual risk factors measured repeatedly. During DCCT/EDIC, 33% of participants developed DPN and 44% CAN. Higher mean HbA1c was the most significant risk factor for DPN, followed by older age, longer duration, greater height, macroalbuminuria, higher mean pulse rate, β-blocker use, and sustained albuminuria. The most significant risk factor for CAN was older age, followed by higher mean HbA1c, sustained albuminuria, longer duration of type 1 diabetes, higher mean pulse rate, higher mean systolic blood pressure, β-blocker use, estimated glomerular filtration rate <60 mL/min/1.73 m2, higher most recent pulse rate, and cigarette smoking. These findings identify risk factors and phenotypes of participants with diabetic neuropathy that can be used in the design of new interventional trials and for personalized approaches to neuropathy prevention.
Contributions and prognostic values of m6A RNA methylation regulators in non‐small‐cell lung cancer

N6‐methyladenosine (m6A) RNA modification can alter gene expression and function by regulating RNA splicing, stability, translocation, and translation. Deregulation of m6A has been involved in various types of cancer. However, its implications in non‐small‐cell lung cancer (NSCLC) are mostly unknown. This posttranscriptional modification is dynamically and reversibly mediated by different regulators, including methyltransferase, demethylases, and m6A binding proteins. In this study, we comprehensively investigated the contributions and prognostic values of 13 common m6A RNA modification regulators using The Cancer Genome Atlas database. We found that the expression levels of most of the studied genes were significantly altered in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Using consensus clustering, the gene‐expression profiles of 13 m6A regulators could classify patients with LUAD into two subgroups with significantly distinct clinical outcomes, but not the LUSC cohort or the combination of the two cohorts. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set enrichment analysis were applied to explore differential signaling pathways and cellular processes between the two LUAD subgroups. Moreover, we found that this gene‐expression signature could better predict prognosis in the late‐stage (III + IV) than in the early‐stage (I + II) LUAD. Finally, we developed an optimal prognostic gene signature by using the least absolute shrinkage and selection operator Cox regression algorithm and compute risk score. In conclusion, our study unveiled the implication of m6A RNA modification regulators in NSCLC and identified the m6A gene expression classifiers for predicting the prognosis of NSCLC.
Echocardiographic Assessment of Right Ventriculo-arterial Coupling: Clinical Correlates and Prognostic Impact in Heart Failure Patients Undergoing Cardiac Resynchronization Therapy

BACKGROUND Right ventriculo-arterial coupling (RV-PA) can be estimated by echocardiography using the ratio between tricuspid annular plane systolic excursion (TAPSE) and pulmonary artery systolic pressure (PASP) and it has prognostic value in the general heart failure (HF) population. We aimed to study the clinical correlates and prognostic value of RV-PA in HF patients undergoing cardiac resynchronization therapy (CRT). METHODS We retrospectively studied 70 HF patients undergoing CRT implantation. RESULTS RV-PA coupling was estimated by TAPSE/PASP ratio using baseline echocardiography. Non-response to CRT was defined as improvement of left ventricular ejection fraction < 5% in a follow-up echo 6-12 months after CRT. Those with lower TAPSE/PASP ratios (worse RV-PA coupling) had higher NT-proBNP concentrations and increased E/e′ ratio. TAPSE/PASP ratio and PASP, but not TAPSE, predicted nonresponse to CRT with TAPSE/PASP ratio showing the best discriminative ability with a sensitivity of 76% and specificity of 71%. Among these parameters, PASP independently predicted all-cause mortality. CONCLUSIONS RV-PA coupling estimated by TAPSE/PASP ratio was associated with established prognostic markers in HF. It numerically outperformed PASP and TAPSE in predicting the response to CRT. Our data suggest that this simple and widely available echocardiographic parameter conveys significant pathophysiological and prognostic meaning in HF patients undergoing CRT.
Sphenoid Wing Meningioma Presenting as Sudden Sensorineural Hearing Loss: A Case Report and Literature Review

Sphenoid wing meningiomas are tumors that typically present with vision deterioration and neurological changes due to their proximity to the sella, cavernous sinus, and other vital structures. Some unusual symptoms have also been described in the literature, such as cognitive dysfunction, parkinsonism, and intracerebral hemorrhage. In this report, we detail another unusual case of sphenoid wing meningioma in a 63-year-old female who presented with left sudden sensorineural hearing loss. A brief review of the literature is also included.
Autologous platelet concentrates in maxillofacial regenerative therapy

Platelet concentrates have emerged as innovative autologous blood products that enhance tissue healing and regeneration in regenerative therapy. A common feature of these products is their higher than baseline platelet concentration, which improves wound healing and tissue repair. Four main categories of products can be easily defined, based on their leukocyte content and fibrin architecture: pure platelet‐rich plasma, such as Cell Separator PRP or Anitua' PRGF; leukocyte‐ and platelet‐rich plasma (L‐PRP), such as PCCS or Ace PRP; pure platelet‐rich fibrin (P‐PRF), such as Fibrinet PRFM; and leukocyte‐ and platelet‐rich fibrin (L‐PRF), such as Choukroun's PRF. Two families contain significant concentrations of leukocytes: L‐PRP and L‐PRF. These four families of products have different biological signatures and mechanisms and obviously different clinical applications. An L‐PRF membrane releases growth factors and matrix proteins over a period longer than 7 days, whereas a PRP gel matrix releases and disperses its growth factors in a relatively quick download. In the near future, simple and inexpensive products such as L‐PRF are expected to have applications in oral‐maxillofacial surgery, periodontal surgery, plastic surgery, orthopedic surgery, and sports medicine. Leukocytes substantially affect the intrinsic biology and properties of platelet concentrates, not only because they enhance immune function and antibacterial potential, but also because they have essential roles in the wound healing process. Unfortunately, their impact has been almost completely neglected in the literature. Improved understanding of the effects of leukocytes in wound healing is essential for development of new clinical applications of platelet concentrates.
Parent and Clinician Perspectives on the Participation of Children with Cerebral Palsy in Community-Based Football: A Qualitative Exploration in a Regional Setting

The current study aimed to qualitatively explore parent and clinician perspectives on the factors influencing participation in a community-based Australian-Rules Football program for five to 12-year-old children with cerebral palsy (CP) in a regional setting. Six allied-health clinicians and two parents of children with CP participated in focus groups exploring factors influencing participation. Thematic analysis indicated seven key factors influencing participation—of which, six were environmental factors and one was related to child characteristics. Environmental factors included resources, communication, knowledge and previous experience, attitudes and expectations, game factors and community relevance. Child characteristics included age, preferences, confidence, as well and cognitive and physical functioning. Notwithstanding limitations, the current study highlights the central role of ‘people factors’ in the child’s environment, in facilitating participation in community-based physical activity.