Miracle-dz/UniFAR-FTUs huggingface dataset:
Artificial Intelligence-Based Diagnosis of Cardiac and Related Diseases

Automatic chest anatomy segmentation plays a key role in computer-aided disease diagnosis, such as for cardiomegaly, pleural effusion, emphysema, and pneumothorax. Among these diseases, cardiomegaly is considered a perilous disease, involving a high risk of sudden cardiac death. It can be diagnosed early by an expert medical practitioner using a chest X-Ray (CXR) analysis. The cardiothoracic ratio (CTR) and transverse cardiac diameter (TCD) are the clinical criteria used to estimate the heart size for diagnosing cardiomegaly. Manual estimation of CTR and other diseases is a time-consuming process and requires significant work by the medical expert. Cardiomegaly and related diseases can be automatically estimated by accurate anatomical semantic segmentation of CXRs using artificial intelligence. Automatic segmentation of the lungs and heart from the CXRs is considered an intensive task owing to inferior quality images and intensity variations using nonideal imaging conditions. Although there are a few deep learning-based techniques for chest anatomy segmentation, most of them only consider single class lung segmentation with deep complex architectures that require a lot of trainable parameters. To address these issues, this study presents two multiclass residual mesh-based CXR segmentation networks, X-RayNet-1 and X-RayNet-2, which are specifically designed to provide fine segmentation performance with a few trainable parameters compared to conventional deep learning schemes. The proposed methods utilize semantic segmentation to support the diagnostic procedure of related diseases. To evaluate X-RayNet-1 and X-RayNet-2, experiments were performed with a publicly available Japanese Society of Radiological Technology (JSRT) dataset for multiclass segmentation of the lungs, heart, and clavicle bones; two other publicly available datasets, Montgomery County (MC) and Shenzhen X-Ray sets (SC), were evaluated for lung segmentation. The experimental results showed that X-RayNet-1 achieved fine performance for all datasets and X-RayNet-2 achieved competitive performance with a 75% parameter reduction.
Is Respiratory Epithelial Adenomatoid Hamartoma Related to Central Compartment Atopic Disease?

Background Respiratory epithelial adenomatoid hamartoma (REAH) is a benign lesion of the sinonasal tract that may mimic more concerning pathology. Clinical factors associated with REAH have not been well characterized. Objective To report our findings on patients with this pathologic diagnosis. Methods A retrospective chart review of patients with REAH between September 2006 and November 2019 was conducted. Data collected included clinical allergic rhinitis and asthma history, additional sinonasal diagnoses, prior sinus surgery, and the location of the REAH within the sinonasal cavity. Results Twenty-six patients were identified (53.8% male, mean age 62 years [range, 29–93]). Bilateral REAH occurred in 50%. REAH was located at the superior nasal septum in 84.6% cases, with the remainder identified in sinus contents submitted for pathology, making definitive site uncertain. Concurrent sinonasal inflammatory disorders were identified in 18 patients (69.2%), including chronic rhinosinusitis with nasal polyps—not otherwise specified (6), chronic rhinosinusitis without nasal polyps (4), aspirin-exacerbated respiratory disease (2), allergic fungal rhinosinusitis (1), central compartment atopic disease (5), and IgG4-related sclerosing disease (1). Eight patients had isolated REAH. Adequate allergy records were available for 19 patients, of which 18 of 19 (94.7%) had clinical allergic rhinitis. Conclusions REAH is a benign sinonasal lesion commonly located within the central compartment of the nasal cavity, a site of significant allergen exposure. Affected patients have a high incidence of allergy along with chronic inflammatory conditions. The coexistence of REAH within inflammatory nasal mucosa in a consistent anatomic location, suggests REAH may have a similar etiology to central compartment atopic disease, with resultant respiratory glandular ingrowth within long-standing reactive changes of mucosa derived from ethmoid embryologic origin.
Relation of serum melatonin levels to postoperative delirium in older patients undergoing major abdominal surgery

Objective Postoperative delirium (POD) is a perennial and distressing complication in older patients, and it may be caused by various factors. This study aimed to determine whether serum melatonin levels are associated with POD in older patients who undergo major abdominal surgery. Methods We collected serum samples from patients undergoing major abdominal surgery. Melatonin was measured by enzyme-linked immunosorbent assay and delirium was assessed by the Confusion Assessment Method after surgery. We classified the patients into the POD group and non-POD group. Results A total of 120 patients met the inclusion criteria and 104 patients were included in the analysis. Postoperative serum melatonin levels were significantly lower than preoperative levels. Multivariate analyses showed that a longer duration of anesthesia (odds ratio [OR] = 1.29, 95% confidence interval [CI] = 1.02–1.64), advanced age (OR = 3.36, 95% CI = 1.37–8.22), and lower postoperative levels of melatonin (OR = 0.50, 95% CI = 0.25–1.00) were associated with POD. Conclusions Serum melatonin levels significantly decline after surgery and anesthesia. Significantly decreased serum melatonin concentrations postoperatively may be a biomarker for predicting POD in older patients undergoing major abdominal surgery with general anesthesia.
f90wrap: an automated tool for constructing deep Python interfaces to modern Fortran codes

f90wrap is a tool to automatically generate Python extension modules which interface to Fortran libraries that makes use of derived types. It builds on the capabilities of the popular f2py utility by generating a simpler Fortran 90 interface to the original Fortran code which is then suitable for wrapping with f2py, together with a higher-level Pythonic wrapper that makes the existance of an additional layer transparent to the final user. f90wrap has been used to wrap a number of large software packages of relevance to the condensed matter physics community, including the QUIP molecular dynamics code and the CASTEP density functional theory code.
Depletion of Blautia Species in the Microbiota of Obese Children Relates to Intestinal Inflammation and Metabolic Phenotype Worsening

Child obesity constitutes a risk factor for developing insulin resistance which, if sustained, could lead to more severe conditions like type 2 diabetes (T2D) in adulthood. Our study identified previously unknown species whose depletion (Blautia luti and Blautia wexlerae) is associated with insulin resistance in obese individuals. Our results also indicate that these bacterial species might help to reduce inflammation causally linked to obesity-related complications. Childhood is considered a window of opportunity to tackle obesity. These new findings provide, therefore, valuable information for the future design of microbiota-based strategies for the early prevention of obesity-related complications. ABSTRACT Cross-sectional studies conducted with obese and control subjects have suggested associations between gut microbiota alterations and obesity, but the links with specific disease phenotypes and proofs of causality are still scarce. The present study aimed to profile the gut microbiota of lean and obese children with and without insulin resistance to characterize associations with specific obesity-related complications and understand the role played in metabolic inflammation. Through massive sequencing of 16S rRNA gene amplicons and data analysis using a novel permutation approach, we have detected decreased incidence of Blautia species, especially Blautia luti and B. wexlerae, in the gut microbiota of obese children, which was even more pronounced in cases with both obesity and insulin resistance. There was also a parallel increase in proinflammatory cytokines and chemokines (gamma interferon [IFN-γ], tumor necrosis factor alpha [TNF-α], and monocyte chemoattractant protein 1 [MCP-1]) in feces of obese children compared to those of lean ones. B. luti and B. wexlerae were also shown to exert an anti-inflammatory effect in peripheral blood mononuclear cell cultures in vitro, compared to non-obesity-associated species. We suggest that the depletion of B. luti and B. wexlerae species in the gut ecosystem may occur in cases of obesity and contribute to metabolic inflammation leading to insulin resistance. IMPORTANCE Child obesity constitutes a risk factor for developing insulin resistance which, if sustained, could lead to more severe conditions like type 2 diabetes (T2D) in adulthood. Our study identified previously unknown species whose depletion (Blautia luti and Blautia wexlerae) is associated with insulin resistance in obese individuals. Our results also indicate that these bacterial species might help to reduce inflammation causally linked to obesity-related complications. Childhood is considered a window of opportunity to tackle obesity. These new findings provide, therefore, valuable information for the future design of microbiota-based strategies for the early prevention of obesity-related complications.
Consensus mutagenesis and ancestral reconstruction provide insight into the substrate specificity and evolution of the front-end Δ6-desaturase family

Marine algae are a major source of omega (ω)-3 long-chain polyunsaturated fatty acids (ω3-LCPUFAs), which are conditionally essential nutrients in humans and a target for industrial production. The biosynthesis of these molecules in marine algae begins with the desaturation of fatty acids by Δ6-desaturases and enzymes from different species display a range of specificities towards ω3 and ω6 LCPUFAs. In the absence of a molecular structure, the structural basis for the variable substrate specificity of Δ6-desaturases is poorly understood. Here we have conducted a consensus mutagenesis and ancestral protein reconstruction-based analysis of the Δ6-desaturase family, focusing on the ω3-specific Δ6-desaturase from Micromonas pusilla (MpΔ6des) and the bispecific (ω3/ω6) Δ6-desaturase from Ostreococcus tauri (OtΔ6des). Our characterization of consensus amino acid substitutions in MpΔ6des revealed that residues in diverse regions of the protein, such as the N-terminal cytochrome b5 domain, can make important contributions to determining substrate specificity. Ancestral protein reconstruction also suggests that some extant Δ6-desaturases, such as OtΔ6des, could have adapted to different environmental conditions by losing specificity for ω3-LCPUFAs. This dataset provides a map of regions within Δ6-desaturases that contribute to substrate specificity and could facilitate future attempts to engineer these proteins for use in biotechnology.
Site-directed MT1-MMP trafficking and surface insertion regulate AChR clustering and remodeling at developing NMJs

At vertebrate neuromuscular junctions (NMJs), the synaptic basal lamina contains different extracellular matrix (ECM) proteins and synaptogenic factors that induce and maintain synaptic specializations. Here, we report that podosome-like structures (PLSs) induced by ubiquitous ECM proteins regulate the formation and remodeling of acetylcholine receptor (AChR) clusters via focal ECM degradation. Mechanistically, ECM degradation is mediated by PLS-directed trafficking and surface insertion of membrane-type 1 matrix metalloproteinase (MT1-MMP) to AChR clusters through microtubule-capturing mechanisms. Upon synaptic induction, MT1-MMP plays a crucial role in the recruitment of aneural AChR clusters for the assembly of postsynaptic specializations. Lastly, the structural defects of NMJs in embryonic MT1-MMP-/- mice further demonstrate the physiological role of MT1-MMP in normal NMJ development. Collectively, this study suggests that postsynaptic MT1-MMP serves as a molecular switch to synaptogenesis by modulating local ECM environment for the deposition of synaptogenic signals that regulate postsynaptic differentiation at developing NMJs.
Healthcare utilisation patterns among older people with intellectual disability and with affective and anxiety diagnoses in comparison with the general population

Abstract Objectives This study investigates specialist healthcare visits of older people with intellectual disability ID having affective and anxiety diagnoses in comparison with the general population, as well as across different levels of ID, behavioural impairment, and living in special housing in Sweden. Method The study is a retrospective national-register-based study from 2002–2012 of people with ID 55 years and older (n = 7936) and a control group the same size matched by birth year and sex from the general population at the end of study. The study groups comprised those with affective (n = 918) and anxiety (n = 825) diagnoses who visited specialist healthcare, including data about living in special housing at the end of study in 2012. Results Older people with ID and with affective and anxiety diagnoses have a higher risk of inpatient and unplanned visits to psychiatric and somatic healthcare than the general population. The average length of stay in inpatient psychiatric healthcare was higher in older people with ID and anxiety diagnoses than in the general population. Within the ID group, more inpatient and unplanned visits were made by those with moderate and severe levels of ID, behavioural impairment, and living in special housing. Conclusion Older people with ID and affective and anxiety diagnoses are more likely to have inpatient and unplanned visits for specialist healthcare than the general population. Future research should explore the quality of healthcare services delivered by healthcare providers to older people with ID and with affective and anxiety diagnoses.
Physicians’ Attitudes and Ethical Obligations to Pharmacogenetic Testing

Introduction Despite the increased utilization of pharmacogenetic (PGt) testing to guide drug therapy, little is known about the ethical challenges posed by the use of these genetic tools. Methods This cross-sectional study aimed to address ethical issues related to ancillary genetic information, consent forms, and potential confidentiality breaches from physicians’ perspectives. A questionnaire was administered to all practicing physicians working in KAUH. Results Almost 49% and 65% of physicians were willing to recommend PGt testing for adult and pediatric patients, respectively. The findings showed that physicians attitudes towards the clinical utility of PGt testing became more preceptive. The majority (73.7%) indicated that PGt testing should not be treated as other routine laboratory tests. The finding also focused on potential conflicts regarding ancillary genetic information, in which 78.8% indicated that they would like to preserve the confidentiality and privacy of the patients and only 14.4% of physicians did not feel obligated to let patients know about any future risk that might be uncovered using PGt testing. The findings showed that collecting both verbal and written consents was imperative prior to testing. Seriousness and predictability of the diseases were reported to be legitimate circumstances that allow disclosure of genetic information. Discussion Unless the field of PGt testing addresses the ethical challenges that might be encountered during PGt treatment, these issues might influence its acceptance in routine clinical settings. Establishing a minimal set of ethical standards may help emphasize the role of physicians and thus facilitate the implementation of PGt tests.
Eight Million Years of Satellite DNA Evolution in Grasshoppers of the Genus Schistocerca Illuminate the Ins and Outs of the Library Hypothesis

Abstract Satellite DNA (satDNA) is an abundant class of tandemly repeated noncoding sequences, showing high rate of change in sequence, abundance, and physical location. However, the mechanisms promoting these changes are still controversial. The library model was put forward to explain the conservation of some satDNAs for long periods, predicting that related species share a common collection of satDNAs, which mostly experience quantitative changes. Here, we tested the library model by analyzing three satDNAs in ten species of Schistocerca grasshoppers. This group represents a valuable material because it diversified during the last 7.9 Myr across the American continent from the African desert locust (Schistocerca gregaria), and this thus illuminates the direction of evolutionary changes. By combining bioinformatic and cytogenetic, we tested whether these three satDNA families found in S. gregaria are also present in nine American species, and whether differential gains and/or losses have occurred in the lineages. We found that the three satDNAs are present in all species but display remarkable interspecies differences in their abundance and sequences while being highly consistent with genus phylogeny. The number of chromosomal loci where satDNA is present was also consistent with phylogeny for two satDNA families but not for the other. Our results suggest eminently chance events for satDNA evolution. Several evolutionary trends clearly imply either massive amplifications or contractions, thus closely fitting the library model prediction that changes are mostly quantitative. Finally, we found that satDNA amplifications or contractions may influence the evolution of monomer consensus sequences and by chance playing a major role in driftlike dynamics.
Tracheal resection: the team brief in multi‐stage airway surgery

The multidisciplinary team brief and effective clinical decision‐making are critical to airway surgery. To illustrate this, we present the case of a 58‐year‐old female with papillary thyroid cancer invading the trachea. We describe a basic framework that was used to aid planning the management of this patient. Tracheal resection is a complex airway operation requiring the evaluation of airway obstruction risk, the formulation of strategies for complex airway management and lung ventilation during complete resection of the tracheal segment and a handover plan for safe tracheal extubation. We suggest that team performance is facilitated by a standardised structure for consideration of anticipated events and important decisions to be made before the operation. Furthermore, it can provide a platform to engage the team when unanticipated events occur and alternate plans have to be made in a time‐critical manner.
Imaging of neuroinflammation in adult Niemann-Pick type C disease

Objective To test the hypothesis that neuroinflammation is a key process in adult Niemann-Pick type C (NPC) disease, we undertook PET scanning utilizing a ligand binding activated microglia on 9 patients and 9 age- and sex-matched controls. Method We scanned all participants with the PET radioligand 11C-(R)-PK-11195 and undertook structural MRI to measure gray matter volume and white matter fractional anisotropy (FA). Results We found increased binding of 11C-(R)-PK-11195 in total white matter compared to controls (p < 0.01), but not in gray matter regions, and this did not correlate with illness severity or duration. Gray matter was reduced in the thalamus (p < 0.0001) in patients, who also showed widespread reductions in FA across the brain compared to controls (p < 0.001). A significant correlation between 11C-(R)-PK11195 binding and FA was shown (p = 0.002), driven by the NPC patient group. Conclusions Our findings suggest that neuroinflammation—particularly in white matter—may underpin some structural and degenerative changes in patients with NPC.
Effects of Diabetes Mellitus on the Disposition of Tofacitinib, a Janus Kinase Inhibitor, in Rats

Tofacitinib, a Janus kinase inhibitor, was developed for the treatment of rheumatoid arthritis. Recently, it has been associated with an increased change in arthritis development in patients with diabetes. Herein, we evaluated the pharmacokinetics of tofacitinib after intravenous (10 mg/kg) and oral (20 mg/kg) administration to rats with streptozotocin-induced diabetes mellitus and control rats. Following intravenous administration of tofacitinib to rats with streptozotocin-induced diabetes mellitus, area under the plasma concentration-time curve from time zero to infinity of tofacitinib was significantly smaller (33.6%) than that of control rats. This might be due to the faster hepatic intrinsic clearance (112%) caused by an increase in the hepatic cytochrome P450 (CYP) 3A1(23) and the faster hepatic blood flow rate in rats with streptozotocin-induced diabetes mellitus than in control rats. Following oral administration, area under the plasma concentration-time curve from time zero to infinity of tofacitinib was also significantly smaller (55.5%) in rats with streptozotocin-induced diabetes mellitus than that in control rats. This might be due to decreased absorption caused by the higher expression of P-glycoprotein and the faster intestinal metabolism caused by the higher expression of intestinal CYP3A1(23), which resulted in the decreased bioavailability of tofacitinib (33.0%) in rats with streptozotocin-induced diabetes mellitus. In summary, our findings indicate that diabetes mellitus affects the absorption and metabolism of tofacitinib, causing faster metabolism and decreased intestinal absorption in rats with streptozotocin-induced diabetes mellitus.
Feeding and developmental outcomes of infants in a South African community

Abstract Background: Prevalent environmental risk factors place infants in lower-middle-income countries (LMICs) at an increased risk for feeding and developmental difficulties. Aim: This study aimed to determine the relationship between feeding and developmental outcomes in infants, as early feeding difficulties may have a cascading effect on developmental outcomes and vice versa. Methods: Data on 144 infants’ feeding and development [mean age (standard deviation) = 8.8 months (2.2)] from a primary health care clinic in Gauteng, South Africa were retrospectively analysed. Results: Early introduction of cup feeding was found to be a predictor of possible expressive language and articulation difficulties. Gagging, spitting, or vomiting, pocketing, the use of force feeding, and poor sucking and chewing abilities were significantly associated with behavioural and social–emotional difficulties. Breastfeeding was found to be a protective factor for language development. The results emphasise the importance of primary prevention and early identification of risks in late infancy in LMIC.