Miracle-dz/UniFAR-FTUs huggingface dataset:
Phosflow assessment of PDGFRA phosphorylation state: A guide for tyrosine kinase inhibitor targeted therapy in hypereosinophilia patients

Clonal eosinophilia is a hematologic disorder caused by translocation in growth factor receptor (GFR) genes. Despite the identified molecular mechanisms underlying clonal hypereosinophilia, the distinction between clonal and reactive eosinophilia has remained challenging due to the diversity of partner genes for translocated GFRs. This study aimed to examine the feasibility of phosphoflow cytometry in the diagnosis of clonal hypereosinophilia through evaluating the level of platelet‐derived growth factor receptor alpha (PDGFRA) phosphorylation and its correlation with PDGFRA genetic aberration. Blood samples were collected from 45 hypereosinophilia patients and 10 healthy controls. Using phosphoflow cytometry method, the phosphorylation state of PDGFRA was assessed. The specificity of phosflow results was confirmed by western blotting and eventually compared with qRT‐PCR expression analysis of 3′‐region of PDGFRA. To detect the genetic aberration of PDGFRA, 5′‐rapid amplification of cDNA ends (5′‐RACE) was performed. Phosflow analysis illustrated that 9 of 45 hypereosinophilic patients had higher level of PDGFRA phosphorylation while sequence analysis of 5′‐RACE‐PCR fragments confirmed that in seven cases of them, there was a PDGFRA‐FIP1L1 fusion. We also verified that two of nine patients with hyperposphorylated PDGFRA hold ETV6‐PDGFRA and STRN‐PDGFRA rearrangements. Importantly, nine cases also had significantly higher levels of PDGFRA mRNA expression when compared with healthy controls, and cases with no PDGFRA rearrangement. These findings highlight a robust correlation between hyperphosphorylation state of PDGFRA and aberrant PDGFRA gene fusions. This implicates phosflow as an efficient and reliable technique raising an intriguing possibility that it could replace other genomic and cDNA‐amplification‐based diagnostic approaches with limited effectiveness.
Decolorization of Basic Red 46 and Methylene Blue by anaerobic sludge: Biotic and abiotic processes

Decolorization of Basic Red 46 (Maxilon Red GRL) (BR46; azo dye) and Methylene Blue (MB.; cationic dye) was studied by using anaerobic sludge taken from upflow anaerobic sludge blanket bed (UASB) reactor treating wastewaters of Pakmaya Yeast Factory in Izmit, Turkey. Experiments were carried out under abiotic and biotic conditions. Abiotic tests were carried out without living biomass in order to determine color removal by non-biological process. The biotic tests were achieved at two cases as dye main carbon source without co-substrate (glucose) and using different concentrations of glucose (500-1000-1500-2000-3000 mg/l). For first case; the concentration of dyes was 25(B1), 50(B2), 100(B3) mg/l. In the other case; dye concentration was kept constant as 100 mg/l for changing glucose concentrations. MB removal (40%) was better than BR46 removal (25%) physically as physically in abiotic conditions. In biotic tests without glucose, color removal for both dyes were achieved at almost within in the 120 h. The .
Clinical Pharmacogenetics Implementation Consortium Guideline for CYP2D6, OPRM1, and COMT Genotypes and Select Opioid Therapy

Opioids are mainly used to treat both acute and chronic pain. Several opioids are metabolized to some extent by CYP2D6 (codeine, tramadol, hydrocodone, oxycodone, and methadone). Polymorphisms in CYP2D6 have been studied for an association with the clinical effect and safety of these drugs. Other genes that have been studied for their association with opioid clinical effect or adverse events include OPRM1 (mu receptor) and COMT (catechol‐O‐methyltransferase). This guideline updates and expands the 2014 Clinical Pharmacogenetics Implementation Consortium (CPIC) guideline for CYP2D6 genotype and codeine therapy and includes a summation of the evidence describing the impact of CYP2D6, OPRM1, and COMT on opioid analgesia and adverse events. We provide therapeutic recommendations for the use of CYP2D6 genotype results for prescribing codeine and tramadol and describe the limited and/or weak data for CYP2D6 and hydrocodone, oxycodone, and methadone, and for OPRM1 and COMT for clinical use.
Magnetic field enhancement of water vaporization

The water vaporization rate, an essential process for all the biological processes, was found to be significantly influenced under static magnetic fields up to 8 T in air and oxygen. The magnitude of the effect depended on the field–field gradient product B⋅dB/dx rather than on B itself. Under forced flow conditions of the atmosphere, both enhancement and suppression of the vaporization rate were observed depending upon the direction of the gas flow relative to the field gradient. A mechanism is proposed to explain the results in a systematic manner based on the assumption of the creation of magnetic wind driven by the gradient susceptibility distribution caused by water content distribution in the atmosphere. It is discussed that this magneto enhancement of vaporization may be the indirect cause of frequently reported field effects on living organisms.
Determinants of in-hospital mortality in COVID-19; a prospective cohort study from Pakistan

A prospective cohort study was conducted at the Indus Hospital Karachi, Pakistan between March and June 2020 to describe the determinants of mortality among hospitalized COVID-19 patients. 186 adult patients were enrolled and all-cause mortality was found to be 36% (67/186). Those who died were older and more likely to be males (p<0.05). Temperature and respiratory rate were higher among non-survivors while Oxygen saturation was lower (p<0.05). Serum CRP, D-dimer and IL-6 were higher while SpO2 was lower on admission among non-survivors (p<0.05). Non-survivors had higher SOFA and CURB-65 scores while thrombocytopenia, lymphopenia and severe ARDS was more prevalent among them (p<0.05). Use of non-invasive ventilation in emergency room, ICU admission and invasive ventilation were associated with mortality in our cohort (p<0.05). Length of hospital stay and days of intubation were longer in non-survivors (p<0.05). Use of azithromycin, hydroxychloroquine, steroids, tocilizumab, antibiotics, IVIG or anticoagulation showed no mortality benefit (p>0.05). Multivariable logistic regression showed that age > 60 years, oxygen saturation <93% on admission, pro-calcitonin > 2 ng/ml, unit rise in temperature and SOFA score, ICU admission and sepsis during hospital stay were associated with higher odds of mortality. Larger prospective studies are needed to further strengthen these findings.
Development of a saliva-optimized RT-LAMP assay for SARS-CoV-2

Conventional reverse transcription quantitative polymerase chain reaction (RT-qPCR) technology has struggled to fulfill the unprecedented need for diagnostic testing created by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Complexity and cost hinder access to testing, and long turnaround-time decreases its utility. To ameliorate these issues, we focus on saliva and introduce several advances to colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) technology; RT-LAMP offers a minimal equipment alternative to RT-qPCR. First, we validated the use of the novel dye LAMPShade Violet (LSV), which improves the visual clarity and contrast of the colorimetric readout. Second, we compared different inactivation conditions on infectivity and RNA yield from saliva. Third, we developed a ten-minute RNA purification protocol from saliva. We call this magnetic bead protocol SalivaBeads. Finally, we developed a magnetic stick, StickLAMP, which provides reliable bead-based RNA purification as well as simple and low-cost access to scalable testing from saliva.
Electron injection and transport mechanism in organic devices based on electron transport materials

Electron injection and transport in organic devices based on electron transport (ET) materials, such as 4,7- diphyenyl-1,10-phenanthroline (Bathophenanthroline BPhen), 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline (Bathocuproine BCP) and bipyridyl oxadiazole compound 1,3-bis [2-(2,2′-bipyridin-6-yl)-1,3,4-oxadiazol-5-yl]benzene (Bpy-OXD), have been reported. The devices are composed of ITO/ET materials (BPhen, BCP Bpy-OXD)/cathodes, where cathodes = Au, Al and Ca. Current–voltage characteristics of each ET material are performed as a function of cathodes. We have found that Ca and Al exhibit quite different J–V characteristics compared with the gold (Au) cathode. The current is more than one order of magnitude higher for the Al cathode and more than three orders of magnitude higher for Ca compared with that of the Au cathode at ∼8 V for all ET materials. This is because of the relatively low energy barrier at the organic/metal interface for Ca and Al cathodes. Electron-only devices with the Au cathode show that the electron transfer limitation is located at the organic/cathode interface and the Fowler–Nordheim mechanism is qualitatively consistent with experimental data at high voltages. With Ca and Al cathodes, electron conduction is preponderant and is bulk limited. A power law dependence J ∼ Vm with m > 2 is consistent with the model of trap-charge limited conduction. The total electron trap density is estimated to be ∼5 × 1018 cm−3. The critical voltage (Vc) is found to be ∼45 V and is almost independent of the materials.
Early hearing loss induces plasticity within extra‐striate visual cortex

Supranormal perceptual performance has been observed within the intact senses of early‐deaf or blind humans and animals. For cortical areas deprived of their normal sensory input, numerous studies have shown that the lesioned modality is replaced by that of the intact sensory modalities through a process termed crossmodal plasticity. In contrast, little is known about the effects of loss of a particular sensory modality on the cortical representations of the remaining, intact sensory modalities. In the present study, an area of extrastriate visual cortex from early‐deaf adult cats was examined for features of dendritic plasticity known to occur after early‐deafness. Using light‐microscopy of Golgi‐stained pyramidal neurons from the posterolateral lateral suprasylvian (PLLS) cortex, dendritic spine density significantly increased (~19%), while spine head size was slightly but significantly decreased (~9%) following early hearing loss. Curiously, these changes were not localized to regions of the visual PLLS known to receive auditory inputs, but instead showed a broad pattern more reflective of the distribution of the area's visual features. Whereas hearing loss results in crossmodal plasticity in auditory cortices, the same peripheral lesion can also induce intramodal plasticity within representations of the intact sensory systems that may also contribute to supranormal performance.
Anti‐apoptotic effects of human gingival mesenchymal stromal cells on polymorphonuclear leucocytes

Abstract Objectives Polymorphonuclear leucocytes (PMNs) constitute the first line of host defence and are crucial in maintaining periodontal health. Their survival and function are modulated by mesenchymal stromal cells (MSCs) from different origin. Gingival MSCs (GMSCs) play an important role in maintaining oral health and in the initial inflammatory response. The present study aimed to investigate the effects of GMSCs on PMNs apoptosis and reactive oxygen species (ROS) production. Methods PMNs were either directly incubated with untreated, interleukin (IL)‐1β‐ or tumour necrosis factor (TNF)‐α‐treated GMSCs or stimulated with their conditioned media. Resulting ROS production was evaluated by dichlorofluorescin diacetate staining, whereas PMNs apoptosis was assessed by Annexin V staining, followed by flow cytometry analysis. Results While conditioned media of untreated and TNF‐α‐treated GMSCs did not affect apoptosis of PMNs, it was significantly delayed by conditioned media of GMSCs treated with IL‐1β. In direct co‐culture, GMSCs exerted anti‐apoptotic effects on PMNs independently of the previous stimulation. However, the strongest impact was observed by IL‐1β‐treated GMSCs. ROS production of PMNs was not influenced by GMSCs or their conditioned media. Conclusion This study demonstrates for the first time the immunomodulatory properties of GMSCs towards PMNs, revealing that IL‐1β enhances anti‐apoptotic effects of GMSCs.
Research progress on deep learning in magnetic resonance imaging–based diagnosis and treatment of prostate cancer: a review on the current status and perspectives

Multiparametric magnetic resonance imaging (mpMRI) has emerged as a first-line screening and diagnostic tool for prostate cancer, aiding in treatment selection and noninvasive radiotherapy guidance. However, the manual interpretation of MRI data is challenging and time-consuming, which may impact sensitivity and specificity. With recent technological advances, artificial intelligence (AI) in the form of computer-aided diagnosis (CAD) based on MRI data has been applied to prostate cancer diagnosis and treatment. Among AI techniques, deep learning involving convolutional neural networks contributes to detection, segmentation, scoring, grading, and prognostic evaluation of prostate cancer. CAD systems have automatic operation, rapid processing, and accuracy, incorporating multiple sequences of multiparametric MRI data of the prostate gland into the deep learning model. Thus, they have become a research direction of great interest, especially in smart healthcare. This review highlights the current progress of deep learning technology in MRI-based diagnosis and treatment of prostate cancer. The key elements of deep learning-based MRI image processing in CAD systems and radiotherapy of prostate cancer are briefly described, making it understandable not only for radiologists but also for general physicians without specialized imaging interpretation training. Deep learning technology enables lesion identification, detection, and segmentation, grading and scoring of prostate cancer, and prediction of postoperative recurrence and prognostic outcomes. The diagnostic accuracy of deep learning can be improved by optimizing models and algorithms, expanding medical database resources, and combining multi-omics data and comprehensive analysis of various morphological data. Deep learning has the potential to become the key diagnostic method in prostate cancer diagnosis and treatment in the future.
The Initial State of Optically Polarized 8Li+ from the β-NMR in Bismuth

Unlike the positive muon, β-NMR probe nuclei must be actively polarized. At the TRIUMF ISAC facility this is accomplished by in-flight collinear optical pumping with resonant circularly polarized laser light. This reliably produces a high degree of polarization, but the detailed state populations in the beam emerging from the optical polarizer are not well known. These populations are significant as they represent the initial state of the ensemble of probe spins implanted in a β-NMR experiment. Here we use the well-resolved quadrupolar split spectrum of 8Li+ in a high purity single crystal of bismuth to extract the sublevel populations under typical polarizer operating conditions, accounting for the spin relaxation in this semimetal.
Teacher identity formation through classroom practices in the post-method era: A systematic review

Abstract This paper presents a systematic review of 37 empirical studies that explored English teacher identity, and its formation through classroom practices from 1997 to 2020. After excluding 26 non-relevant studies from 63 articles, the remaining research has been analyzed through a systematic process to get salient themes that can be best cognized in terms of identity (re)construction issues among English language teachers, how they implement critical and post-method pedagogy, and reflect it in their classroom practices. More specifically, the following themes emerged: classroom practice as a reflection of teacher identity, native/non-native English speakers’ (NES/NNES) dichotomy, emotional tensions in identity formation, teachers’ knowledge of post-method pedagogy, and post-method barriers. This review also provided practical teaching tips for novice English teachers and teacher educators to better manage their identity tensions as teachers, improve their classroom practices and teacher education programs, and propose areas of investigation for future research. It calls for more in-depth qualitative and quantitative longitudinal studies that employ a positivist psychometric approach to measure and examine different facets of teacher identity development.
Serum phospholipid fatty acid composition and insulin action in type 2 diabetic patients.

Relationships have been demonstrated between insulin sensitivity and the fatty acid (FA) composition of serum and tissue lipids in adult humans. The present study aimed to investigate the above relationships in different groups of type 2 diabetic patients (DM2). The FA composition of serum phospholipids (S-PL) measured by gas liquid chromatography and insulin action during a 2-step hyperinsulinemic isoglycemic clamp (1 and 10 mU/kg. min) were determined in 21 newly diagnosed DM2 subjects (DMN), in groups of long-term DM2 patients treated with hypoglycemic agents (DMH; n = 21) or diet alone (DMD; n = 11), and in 24 healthy subjects (HS). In diabetics, the metabolic clearance rates of glucose at both insulin levels (MCR(glu)submax and MCR(glu)max) were significantly reduced compared with HS (MCR(glu)submax DMN, 5.35 +/- 2.7 mL x kg(-1) x min(-1), DMH, 5.38 +/- 2.17 mL x kg(-1) x min(-1); DMD, 5.48 +/- 2.35 mL x kg(-1) x min(-1) v HS, 10.9 +/- 3.3 mL x kg(-1) x min(-1); P <. 01; MCR(glu)max DMN, 13.3 +/- 3.3 mL x kg(-1) x min(-1); DMH, 12.5 +/- 3.0 mL x kg(-1) x min(-1); DMD, 13.3 +/- 3.0 mL x kg(-1) x min(-1) v HS, 17.4 +/- 3.8 mL x kg(-1) x min(-1); P <. 05). Increased contents of highly unsaturated n-6 family FA (P <.01), arachidonic acid in particular (DMN, 10.98% +/- 1.79%; DMD, 10.78% +/- 1.64%; DMH, 10.97% +/- 1.7% v HS, 8.51% +/- 1.53%; P <.001), were found in all groups of diabetics compared with HS, while lower levels of linoleic acid were seen in DMN (P <.001) and DMH (P <.05). The contents of saturated FA and monounsaturated FA were comparable in HS, DMN, and DMD. While in HS there were significant negative correlations between MCR(glu) and the contents of saturated FA and a positive association between insulin action and proportions of linoleic and arachidonic acids, no significant relationships were found in diabetic subjects. Different groups of DM2 patients show an altered FA pattern of S-PL, which is not related to insulin action. The above data support the hypothesis that changes in FA composition may play a role in modulating insulin action in peripheral tissues, but cannot explain the insulin resistance (IR) in DM2 patients.
Microphase separation versus the vapor-liquid transition in systems of spherical particles

The conditions, i.e., the interparticle potentials, for which vapor–liquid coexistence is supplanted by microphase separation are examined. The liquid phase is found for potentials with a steeply repulsive core and an attraction of not-too-short a range. To this potential we add a repulsion of longer range than the attraction and find that it breaks up and mixes coexisting bulk vapor and liquid to form a single microphase-separated phase. Our spherical particles are perhaps the simplest continuum model to show a Lifshitz point and microphase separation. In the microphase-separated phase the density is modulated with a period typically ten times the size of the particle’s core. Microphase separation, apart from providing a rich and interesting phase behavior, may have a potential use in nanoelectronic applications.
Elastic and electronic properties of hexagonal and cubic polymorphs of tungsten monocarbide WC and mononitride WN from first‐principles calculations

We have performed accurate ab‐initio total energy calculations using the full‐potential linearized augmented plane wave (FP‐LAPW) method with the generalized gradient approximation (GGA) for the exchange‐correlation potential to investigate the elastic, electronic and cohesive properties of hexagonal and cubic polymorphs of WC and WN. The optimized lattice parameters, independent elastic constants (Cij), bulk moduli (B), shear moduli (G), as well as band structure, density of states, electron density distribution and cohesive energies are obtained and analyzed in comparison with the available theoretical and experimental data. In addition, for the first time, the numerical estimates are made for some elastic parameters of the polycrystalline WC and WN ceramics (in the framework of the Voigt–Reuss–Hill approximation), namely bulk and shear moduli, compressibility (β), Young's moduli (Y), Poisson's ratio (ν) and Lamé's coefficients (μ, λ). (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Hydrophilicity and polarity of cubic silicon carbide nanocrystals identified from photoluminescence emissions in various solvents

Abstract. Since the surface-structure-related state dominates the photoluminescence (PL) emissions of cubic silicon carbide (3C-SiC) nanocrystals (NCs) with a diameter lower than 3.0 nm, the PL lines of 3C-SiC NCs in deionized water with different pH values, methanol, ethanol, chloroform, and toluene are characterized at the excitation of 300 to 360 nm. The position and intensity of the PL peaks provide experimental evidence that the surface of 3C-SiC is hydrophilic and hydroxyl bonding on the surface decreases the energy gap of the NCs. The PL emission wavelength of 3C-SiC NCs can be adjusted by adjusting the pH value of the solvent. The polar 3C-SiC NCs prefer to precipitate in chloroform and toluene.
Research on blood oxygen activity in cerebral cortical motor function areas with adjustment intention during gait.

BACKGROUND The study of the neural mechanism of human gait control can provide a theoretical basis for the treatment of walking disorders or the improvement of rehabilitation strategies, and further promote the functional rehabilitation of patients with movement disorders. However, the performance and changes of cerebral cortex activity corresponding to gait adjustment intentions are still not clear. OBJECTIVE The purpose of this study was to detect the blood oxygen activation characterization of the cerebral cortex motor function area when people have the intention to adjust gait during walking. METHODS Thirty young volunteers (21 ± 1 years old) performed normal walking, speed increase, speed reduction, step increase, and step reduction, during which oxygenated hemoglobin (HbO), deoxygenated hemoglobin (HbR), and total oxyhemoglobin (HbT) information in the prefrontal cortex (PFC), premotor cortex (PMC), supplementary motor area (SMA) was continuous monitored using near-infrared brain functional imaging. RESULTS (1) With the intention to adjust gait, the HbO concentration in the SMA increased significantly, while the HbT concentration in the medial-PFC decreased significantly. (2) In the HbO concentration, step reduction is more activated than the step increase in the left-PMC (p= 0.0130); step adjustment is more activated than speed adjustment in the right-PMC (p= 0.0067). In the HbR concentration, the speed reduction is more activated than the speed increase in the left-PFC (p= 0.0103). CONCLUSIONS When the intention of gait adjustment occurs, the increase of HbO concentration in the SMA indicates the initial stage of gait adjustment will increase the cognitive-locomotor demand of the brain. The left brain area meets the additional nerve needs of speed adjustment. The preliminary findings of this study can lay an important theoretical foundation for the realization of gait control based on fNIRS-BCI technology.