Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparison of Polymerase Chain Reaction–Restriction Fragment Length Polymorphism, Immunohistochemistry, and DNA Sequencing for the Detection of IDH1 Mutations in Gliomas

Background: IDH1 mutation shows diagnostic, prognostic, and predictive value in gliomas. Direct Sanger sequencing is considered the gold standard to detect IDH1 mutation. However, this technology is not available in most neuropathological centers in developing countries such as Indonesia. Immunohistochemistry (IHC) and polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) have also been used to detect IDH1 mutation. This study aimed to compare DNA sequencing, IHC, and PCR–RFLP in detecting IDH1 mutations in gliomas. Methods: Research subjects were recruited from Dr. Sardjito Hospital. Genomic DNA was extracted from fresh or formalin-fixed paraffin-embedded samples of tumor tissue. DNA sequencing, PCR–RFLP and IHC were performed to detect IDH1 mutation. Sensitivity, specificity, and accuracy of PCR–RFLP and IHC were calculated by comparing them to DNA sequencing as the gold standard. Results: Among 61 recruited patients, 13 (21.3%) of them carried a mutation in codon 132 of the IDH1 gene, as shown by DNA sequencing. PCR–RFLP and DNA sequencing have a concordance value of 100%. Meanwhile, the concordance value between IDH1 R132H IHC and DNA sequencing was 96.7%. The sensitivity, specificity, positive predictive values, negative predictive values, and accuracy for PCR–RFLP were all 100%. On the other hand, the sensitivity, specificity, and accuracy of IHC were 92.3%, 97.9%, and 96.7%, respectively. Conclusion: This study showed that both PCR–RFLP and IHC have high accuracy in detecting IDH1 mutation. We recommend a combination of PCR–RFLP and IHC to detect IDH1 mutation in resource-limited settings.
Efficacy of personal protective equipment and H2O2‐based spray against coronavirus in dental setting

We detected very low viral loads on the external targets compared to the inoculum, suggesting that the aerosol generated by dental handpieces may have low viral content. Unsurprisingly, we found the highest viral loads over the external surfaces of mask and respirators when a face shield was not worn, confirming that great attention has to be paid when disposing of used masks and respirators. Conversely, when the shield was on, viral loads on masks/respirators surfaces were under the detection limit, demonstrating shield efficacy. Importantly, inside the operator's mouth, the viral was under the detection limit using any PPE, with no differences between surgical masks and respirators, all of which showing protection against the These data agree with the findings of Loeb who did not found differences in the efficacy of surgical masks compared to N95 respirators against influenza the the of
Assessment of Tumor Angiogenesis by Expression of CD 105 in Ameloblastoma, Odontogenic Keratocyst and Central Giant Cell Lesion

Background: Angiogenesis is critical for tumor growth and reflects the aggressive behavior of invasive odontogenic lesions [like amelogenesis (AM) (AM), Odontogenic Keratocyst (OKC) and Central giant cell lesion (CGCL)]. Mean vascular density (MVD) shows the angiogenic potential and CD105 is an ideal endothelial biomarker due to its specificity to new blood vessels for MVD detection. The aim of the study was to compare the MVD (angiogenic potential) among AM, OKC and CGCL in comparison to Pyogenic Granuloma (PG) using CD105 biomarker. Methods: Sixty-four primary cases of odontogenic invasive tumors (AM, OKC and CGCL) and PG, diagnosed clinically and histologically were included in the study, with 16 samples in each group. Tissue samples of peripheral AM, Peripheral GCL of jaws, malignant AM, and specimen with insufficient tissue were excluded. Tissue sections were embedded, processed and stained using Hematoxylin and Eosin (H and E). Immunohistochemistry was performed using antibodies against CD105, with positive brown cytoplasmic staining in the endothelial cells of neo-vasculature. Distinct countable, positively stained endothelial cell or clusters were evaluated under light microscope for identification of MVD. ANOVA and t-test were applied for statistical analysis of data. Results: Highest MVD was displayed in CGCL (32.99±0.77) and the minimum was observed in OKC (7.21± 0.75) respectively. CGCL showed significantly higher MVD to AM, OKC and PG lesions (p<0.05). AM (8.07± 0.36) and Odontogenic Keratocyst (7.21± 0.75) showed comparable MVD, which was lower than PG (14.7± 0.96) and CGCL vascular density (p < 0.01) respectively. Conclusion: CGCL was most aggressive, with highest MVD among the investigated odontogenic lesions (OKC, AM and PG). The proliferative aggressive behavior of Odontogenic Keratocyst is comparable to AM due to comparable mean vascular density.
Rayleigh-Taylor mixing: confinement by stratification and geometry

Rayleigh-Taylor instability has been an area of active research in fluid dynamics for the last twenty years, but relatively little attention has been paid to the dynamics of problems where Rayleigh-Taylor instability plays a role, but is only one component of a more complex system. Here, Rayleigh-Taylor instability between miscible fluids is examined in situations where it is confined by various means: by geometric restriction, by penetration into a stable linear stratification, and by impingement on a stable density interface. Water-based experiments are modelled using a variety of techniques, ranging from simple hand calculation of energy exchange to full three-dimensional numerical simulation. Since there are well known difficulties in modelling unconfined Rayleigh-Taylor instability, the confined test cases have been sequenced to begin with dynamically simple benchmark systems on which existing modelling approaches perform well, then they progress to more complex systems and explore the limitations of the various models. Some work on the phenomenology of turbulent mixing is also presented, including a new experimental technique that allows mixed fluid to be visualised directly, and an analysis of energy transport and mixing efficiency in variable density flows dominated by mixing.
Selectivity in hydrocarbon conversions and methanol decomposition on a Pd/Fe3O4 model catalyst. A molecular beam study

One of the most important objectives in chemistry is to understand and control the selectivity towards a desired reaction pathway. In catalysis, selectivity is thought to be governed by the catalyst’s structure; many practical catalysts, however, have an inherently complex structure that obstructs their detailed understanding; therefore, simplified materials are studied instead. In order to advance the understanding of catalysis, we have applied a combination of surface science experimental techniques, centered around molecular beam methods to study surface reactions under vacuum on a wellcharacterized Pd/Fe3O4 model catalyst; the reactions were followed by massspectrometric rate measurement and infrared-spectroscopic detection of adsorbates. Our experiments focussed on the origins of selectivity in two reactions, the decomposition of methanol and the conversion of 2-butene with coadsorbed deuterium; additionally, both reactants may decompose on the Pd metal to carbonaceous species or carbon. Methanol decomposition is a well-established model reaction in surface science and of high interest for application per se. We show in this work that methanol is dehydrogenated to formaldehyde and water by reaction with surface oxygen on pristine Fe3O4 with high selectivity; the surface oxygen consumed by this reaction has to be replenished in order to sustain the reactivity. In the presence of Pd nanoparticles, support-related methanol and methoxy migrate quickly to the metal particles before formaldehyde could be formed on the oxide; on the Pd metal surface methanol decomposes in two pathways, forming carbon monoxide and hydrogen in the main pathway, and carbon in the minor pathway, which accumulates slowly on the Pd surface and poisons its catalytic activity. 2-butene conversion was studied as a model for hydrocarbon conversion reactions, focussing on mechanisms that induce selectivity between the three reaction pathways (hydrogenation, H/D-exchange/isomerization and decomposition). This work demonstrates that sustained reactivity can be obtained on the Pd/Fe3O4 model catalyst at elevated temperatures (around 250 K); isomerization proceeds with sustained rates already on a clean catalyst, but sustained hydrogenation can only be induced in the presence of previously deposited, strongly dehydrogenated carbonaceous deposits (carbon); this induction of hydrogenation was explained by the ability of carbon to facilitate the formation of subsurface hydrogen under reaction conditions, which is necessary for hydrogenation. Additionally, we have compared the conversion rates with cisand trans-2-butene; selectivity occurs under conditions where the reaction rates seem to be limited by the availability of butene; cis2-butene gives higher yields in those cases, presumably because it reaches higher alkene surface coverages in adsorption-desorption equilibrium.
TGF-β Enhances the Anti-inflammatory Effect of Tumor-Infiltrating CD33+11b+HLA-DR Myeloid-Derived Suppressor Cells in Gastric Cancer: A Possible Relation to MicroRNA-494

Background: Accumulation of myeloid-derived suppressor cells (MDSCs) constitutes a key mechanism of tumor immune evasion in gastric cancer (GC). Therefore, searching for more accurate prognostic factors affecting their immunosuppressive role has become a growing interest in cancer immunotherapy research. Increased expression of microRNA-494 was noticed in MDSCs from tumor-bearing mice, suggesting another new therapeutic objective for cancer treatment. It was also discovered that tumor-derived transforming growth factor beta (TGF-β) is responsible for the up-regulation of microRNA-494 in MDSCs. The purpose of this study was to address the effect of recombinant (rTGF-β) on the anti-inflammatory activity of MDSCs in GC and its possible association with micro-RNA-494 expression in tumor tissue. Methods: Freshly obtained GC tumor tissue samples and peripheral blood were used for isolation of CD33+11b+HLADR- MDSCs cells from 40 GC patients and 31 corresponding controls using flow cytometry. MDSCs were co-cultured with isolated autologous T cells to assess proliferation and cytokine production in the presence and absence of rTGF-β. Real-time PCR and Enzyme linked immunosorbent assay were used to evaluate tumor expression of miRNA-494 and TGF-β respectively. Results: Results showed that rTGF-β markedly increased the suppressive ability of tumor MDSCs on proliferation of autologous T cells and interferon gamma production. However, no inhibitory effect was observed for MDSCs from circulation. In addition, infiltration of MDSCs in tumors is associated with the prognosis of GC. MiRNA-494 was also extensively expressed in tumor samples with a significant correlation to MDSCs. Conclusion: These results indicate that tumor-derived MDSCs but not circulatory MDSCs have an immunosuppressive effect on T cells, potentially involving TGF-β mediated stimulation. Results also suggest a role for miRNA-494 in GC progression. Therefore, control of TGF-β and miRNA-494 may be used as a treatment strategy to downregulate the immunosuppressive effect of MDSCs.
The mechanisms of atmospheric oxidation of aromatic hydrocarbons

A leading cause of polluted air in urban atmospheres is the interaction of sunlight with an air mixture containing nitrogen oxides and reactive hydrocarbons. Several classes of hydrocarbons are highly reactive hydrocarbons; one is the alkenes, the subject of "The Mechanisms of the Atmospheric Oxidation of the Alkenes" (Calvert, et al., OUP, 2000). This book, the second in a series of comprehensive studies of these compounds, will review and evaluate existing literature on the mechanisms of the aromatic hydrocarbons, which have a particularly high potential for ozone generation. The focus of the text will be on problem solving and clarifying uncertain aspects of the chemistry of these compounds.
I-KCKT allows dissection-free RNA profiling of adult Drosophila intestinal progenitor cells

ABSTRACT The adult Drosophila intestinal epithelium is a model system for stem cell biology, but its utility is limited by current biochemical methods that lack cell type resolution. Here, we describe a new proximity-based profiling method that relies upon a GAL4 driver, termed intestinal-kickout-GAL4 (I-KCKT-GAL4), that is exclusively expressed in intestinal progenitor cells. This method uses UV crosslinked whole animal frozen powder as its starting material to immunoprecipitate the RNA cargoes of transgenic epitope-tagged RNA binding proteins driven by I-KCKT-GAL4. When applied to the general mRNA-binder, poly(A)-binding protein, the RNA profile obtained by this method identifies 98.8% of transcripts found after progenitor cell sorting, and has low background noise despite being derived from whole animal lysate. We also mapped the targets of the more selective RNA binder, Fragile X mental retardation protein (FMRP), using enhanced crosslinking and immunoprecipitation (eCLIP), and report for the first time its binding motif in Drosophila cells. This method will therefore enable the RNA profiling of wild-type and mutant intestinal progenitor cells from intact flies exposed to normal and altered environments, as well as the identification of RNA-protein interactions crucial for stem cell function. Summary: A dissection-free method to identify proximity-based RNA-protein interactions in an in vivo stem cell population, enabling molecular analysis of these cells at unprecedented speed and resolution.
Retrospective cohort study of clinical characteristics of 2199 hospitalised patients with COVID-19 in New York City

Objective The COVID-19 pandemic is a global public health crisis, with over 33 million cases and 999 000 deaths worldwide. Data are needed regarding the clinical course of hospitalised patients, particularly in the USA. We aimed to compare clinical characteristic of patients with COVID-19 who had in-hospital mortality with those who were discharged alive. Design Demographic, clinical and outcomes data for patients admitted to five Mount Sinai Health System hospitals with confirmed COVID-19 between 27 February and 2 April 2020 were identified through institutional electronic health records. We performed a retrospective comparative analysis of patients who had in-hospital mortality or were discharged alive. Setting All patients were admitted to the Mount Sinai Health System, a large quaternary care urban hospital system. Participants Participants over the age of 18 years were included. Primary outcomes We investigated in-hospital mortality during the study period. Results A total of 2199 patients with COVID-19 were hospitalised during the study period. As of 2 April, 1121 (51%) patients remained hospitalised, and 1078 (49%) completed their hospital course. Of the latter, the overall mortality was 29%, and 36% required intensive care. The median age was 65 years overall and 75 years in those who died. Pre-existing conditions were present in 65% of those who died and 46% of those discharged. In those who died, the admission median lymphocyte percentage was 11.7%, D-dimer was 2.4 μg/mL, C reactive protein was 162 mg/L and procalcitonin was 0.44 ng/mL. In those discharged, the admission median lymphocyte percentage was 16.6%, D-dimer was 0.93 μg/mL, C reactive protein was 79 mg/L and procalcitonin was 0.09 ng/mL. Conclusions In our cohort of hospitalised patients, requirement of intensive care and mortality were high. Patients who died typically had more pre-existing conditions and greater perturbations in inflammatory markers as compared with those who were discharged.
Mandibulofacial dysostosis with microcephaly: An expansion of the phenotype via parental survey

Mandibulofacial dysostosis with microcephaly (MFDM) is due to haploinsufficiency of spliceosomal GTPase EFTUD2. Features include microcephaly, craniofacial dysmorphology, developmental disability, and other anomalies. We surveyed parents of individuals with MFDM to expand knowledge about health, development, and parental concerns. Participants included attendees of the inaugural MFDM family conference in June 2019 and members of the MFDM online group. To explore MFDM variable expressivity, we offered targeted Sanger sequencing for untested parents. Forty‐seven parents participated in the survey. 59% of individuals with MFDM were male, with mean age 6.4 years (range 8 months to 49 years). Similar to the literature (n = 123), common features include microcephaly, cleft palate, choanal stenosis, tracheoesophageal fistula, heart problems, and seizures. New information includes airway intervention details, age‐based developmental outcomes, rate of vision refractive errors, and lower incidences of prematurity and IUGR. Family concerns focused on development, communication, and increased support. Targeted Sanger sequencing for families of seven individuals demonstrated de novo variants, for a total of 91.9% de novo EFTUD2 variants (n = 34/37). This study reports the largest single cohort of individuals with MFDM, expands phenotypic spectrum and inheritance patterns, improves understanding of developmental outcomes and care needs, and identifies development as the biggest concern for parents.
The Syndromic Spectrum of COVID-19 and Correlates of Admission Parameters with Severity-outcome Gradients: A Retrospective Study.

Background Clinical and laboratory features of COVID-19 may have regional variations. This study aimed to discern their association with severity of illness and mortality in tertiary setup of Delhi, India. Methods Retrospective data of hospitalised COVID-19 patients over 3 months (end March to June 2020) were evaluated for symptom profile, blood investigations and chest radiograph data and classified according to COVID-19 severity and as survivors and non-survivors. Results Average age (n=182) was 46.1 years, male to female ratio 1.4:1. Fever (51.1%), cough (49.4%) and breathlessness (48.3%) were the commonest symptoms, and frequency of all the three increased with severity of COVID-19. Fever duration, leucocytosis, neutrophilia, elevated blood urea, transaminitis and higher Brixia score on chest X-ray were also more in severe COVID-19 compared to mild and moderate categories. Higher age, more comorbidities, fever, breathlessness and chest pain; longer duration of fever, leucocytosis, neutrophilia, lymphopenia, high neutrophil to lymphocyte ratio, elevated serum urea, creatinine, transaminases and hyperglycemia, and higher radiographic Brixia score were observed in non-survivors compared to survivors. Conclusion Greater prevalence of symptoms (alone and in combination) and derangements in blood biochemistry are seen in severe COVID-19 compared to mild or moderate cases, and also in non-survivors compared to survivors.
Autonomous motivation explains interprofessional education outcomes

In response to the observations that interprofessional education (IPE) is seemingly atheoretical or under‐theorised, this quantitative research seeks to uncover students’ motivational mechanisms which could explain their behavioural and collaborative outcomes using self‐determination theory (SDT). While SDT has been studied in various contexts, its applicability to IPE remains underexplored. This study aims to integrate a new perspective in understanding students’ motivation in IPE by exploring how the fulfilment of a need for sense of autonomy, competence and relatedness is linked to desirable IPE outcomes.
A second attempt at pulp revascularisation on an immature traumatised anterior tooth: a case report with two-year follow-up.

This report describes the second attempt at pulp revascularisation, using an association between 2% chlorhexidine (CHX) and calcium hydroxide (CH) as intracanal dressing, in an immature traumatised anterior tooth with pulp necrosis. A 21-year-old woman complained of pain and dental crown darkening of a permanent maxillary right central incisor. Her medical records presented a history of dental trauma, and at age 15, the first attempt at revascularisation was performed, using triple antibiotic paste (TAP) as the intracanal dressing. Recent radiographs then showed a periapical lesion associated with an immature root, which demonstrated the failure of the first attempt. The second pulp revascularisation was performed, using an association between CHX and CH as intracanal medication. The case was followed up for 24 months. Observations showed evidence of root development, dentinal wall thickening and periapical healing. In this case, the association between CHX and CH showed favourable results as an intracanal medication.
Feasibility and accuracy of pathological diagnosis in en‐bloc transurethral resection specimens versus conventional transurethral resection specimens of bladder tumour: evaluation with pT1 substaging by 10 pathologists

En‐bloc transurethral resection (TUR) of bladder tumour (ERBT) is designed to provide more accurate pathological diagnosis of specimens than conventional TUR of bladder tumour (cTURBT). Some studies have reported that T1 bladder cancer substage could be a prognostic factor in assessing tumour progression, but such substaging has not been widely adopted because of problems with pathological diagnosis using cTURBT specimens. The aim of this study was to evaluate the possible advantages of en‐bloc TUR specimens in T1 substaging following assessment by a panel of 10 pathologists.
Investigating the Metabolic Model in Preterm Neonates by Tandem Mass Spectrometry: A Cohort Study

Abstract The changes of metabolite profiles in preterm birth have been demonstrated using newborn screening data. However, little is known about the holistic metabolic model in preterm neonates. The aim was to investigate the holistic metabolic model in preterm neonates. All metabolite values were obtained from a cohort data of routine newborn screening. A total of 261 758 newborns were recruited and randomly divided into a training subset and a testing subset. Using the training subset, 949 variates were considered to establish a logistic regression model for identifying preterm birth (<37 weeks) from term birth (≥37 weeks). Sventy-two variates (age at collection, TSH, 17α-OHP, proline, tyrosine, C16:1-OH, C18:2, and 65 ratios) entered into the final metabolic model for identifying preterm birth from term birth. Among the variates entering into the final model of PTB [Leucine+Isoleucine+Proline-OH)/Valine (OR=38.36], (C3DC+C4-OH)/C12 (OR=15.58), Valine/C5 (OR=6.32), [Leucine+isoleucine+Proline-OH)/Ornithine (OR=2.509)], and Proline/C18:1 (OR=2.465) have the top five OR values, and [Leucine+Isoleucine+Proline-OH)/C5 (OR=0.05)], [Leucine+Isoleucine+Proline-OH)/Phenylalanine (OR=0.214)], proline/valine (OR=0.230), C16/C18 (OR=0.259), and Alanine/free carnitine (OR=0.279) have the five lowest OR values. The final metabolic model had a capacity of identifying preterm infants with >80% accuracy in both the training and testing subsets. When identifying neonates ≤32 weeks from those >32 weeks, it had a robust performance with nearly 95% accuracy in both subsets. In summary, we have established an excellent metabolic model in preterm neonates. These findings could provide new insights for more efficient nutrient supplements and etiology of preterm birth.