Miracle-dz/UniFAR-FTUs huggingface dataset:
Morphosyntactic Tagging with Pre-trained Language Models for Arabic and its Dialects

We present state-of-the-art results on morphosyntactic tagging across different varieties of Arabic using fine-tuned pre-trained transformer language models. Our models consistently outperform existing systems in Modern Standard Arabic and all the Arabic dialects we study, achieving 2.6% absolute improvement over the previous state-of-the-art in Modern Standard Arabic, 2.8% in Gulf, 1.6% in Egyptian, and 8.3% in Levantine. We explore different training setups for fine-tuning pre-trained transformer language models, including training data size, the use of external linguistic resources, and the use of annotated data from other dialects in a low-resource scenario. Our results show that strategic fine-tuning using datasets from other high-resource dialects is beneficial for a low-resource dialect. Additionally, we show that high-quality morphological analyzers as external linguistic resources are beneficial especially in low-resource settings.
Analytical Ultracentrifugation as a Matrix-Free Probe for the Study of Kinase Related Cellular and Bacterial Membrane Proteins and Glycans

Analytical ultracentrifugation is a versatile approach for analysing the molecular mass, molecular integrity (degradation/aggregation), oligomeric state and association/dissociation constants for self-association, and assay of ligand binding of kinase related membrane proteins and glycans. It has the great property of being matrix free—providing separation and analysis of macromolecular species without the need of a separation matrix or membrane or immobilisation onto a surface. This short review—designed for the non-hydrodynamic expert—examines the potential of modern sedimentation velocity and sedimentation equilibrium and the challenges posed for these molecules particularly those which have significant cytoplasmic or extracellular domains in addition to the transmembrane region. These different regions can generate different optimal requirements in terms of choice of the appropriate solvent (aqueous/detergent). We compare how analytical ultracentrifugation has contributed to our understanding of two kinase related cellular or bacterial protein/glycan systems (i) the membrane erythrocyte band 3 protein system—studied in aqueous and detergent based solvent systems—and (ii) what it has contributed so far to our understanding of the enterococcal VanS, the glycan ligand vancomycin and interactions of vancomycin with mucins from the gastrointestinal tract.
On Measuring Implant Fixation Stability in ACL Reconstruction

Numerous methods and devices are available for implant fixation in anterior cruciate ligament (ACL) reconstruction. Biomechanical data indicate high variability in fixation stability across different devices. This study aims to provide a better insight into measuring the structural characteristics and mechanical behavior of ACL implant fixations. Fourteen human tibial specimens with reconstructed ACLs were subjected to progressively increasing dynamic loading until failure. The motions of the tibia, the proximal and distal graft ends, as well as the testing frame and actuator, were continuously recorded via a motion tracking system. Significantly higher displacements of the machine actuator (1.0 mm at graft slippage onset, and 12.2 mm at ultimate load) were measured compared to the displacements of the proximal (0.8 and 4.3 mm, respectively) and distal graft (0.1 and 3.4 mm, respectively) ends. The displacements measured at different sites showed significant correlations. The provided data suggest significant and systematic inaccuracies in the stiffness and slippage of the fixation when using machine displacement, as commonly reported in the literature. The assessment of the distal graft displacement excludes the artifactual graft elongation, and most accurately reflects the graft slippage onset indicating clinical failure. Considering the high displacement at the ultimate load, the ultimate load could be used as a standardized variable to compare different fixation methods. However, the ultimate load alone is not sufficient to qualitatively describe fixation stability.
Risk of Pyogenic Liver Abscess in Proton Pump Inhibitor Users: New Inventory of Proton Pump Inhibitor Induced Complications?

c 2021 The Korean Society of Neurogastroenterology and Motility J Neurogastroenterol Motil, Vol. 27 No. 4 October, 2021 www.jnmjournal. org Proton pump inhibitors (PPIs) are widely used to manage acid-related gastrointestinal diseases, and the use of PPIs is increasing worldwide. Since the introduction of omeprazole in the 1980s, PPIs have gained popularity due to their proven efficacy and safety profile. In the United Kingdom, increasing prevalence of PPI use was reported in general practice from 0.2% to 15.0% between 1990 and 2014. In France, approximately one-third of the estimated adult population used PPIs in 2015. In the United States, 8.0% to 10.0% of ambulatory adults have been prescribed PPIs in the past 30 days. PPIs suppress acid secretion by irreversibly inhibiting gastric H/K-adenosine triphosphatase. They are effective for the management of gastroesophageal reflux disease, peptic ulcer disease, and are used as first-line therapy for functional dyspepsia. Even higher doses of PPIs are used for the control of extraesophageal symptoms and Helicobacter pylori eradication therapy. Moreover, long-term management in patients with Barrett’s esophagus is recommended to reduce the occurrence of dysplasia. In addition, concomitant administration of PPIs for the prevention of peptic ulcer disease in chronic users of NSAIDs and maintenance treatment in patients with gastroesophageal reflux disease is a common clinical practice. With the increasing use of PPIs, concerns regarding the adverse effects of PPIs have been raised in recent epidemiologic studies. Complications associated with PPI use have been reported in various organs, including fundic gland polyps, microscopic colitis, acute interstitial nephritis, chronic kidney disease, myocardial infarction, fracture, community-acquired pneumonia, bacterial enteric infection with Clostridium difficile, hepatic encephalopathy, and spontaneous bacterial peritonitis in patients with cirrhosis, dementia, and gastrointestinal malignancies. Most evidence on complications related to PPI use is not based on well-designed studies. Confounding factors and causal relationships remain unresolved. Also, the reported risk of an adverse event is relatively low. However, it has been reported constantly through epidemiologic studies. Of these, increasing susceptibility to infection induced by PPI use has relatively strong clinical relevance. Several plausible pathophysiologic mechanisms of PPI-induced complications have been postulated. Most of the convincing adverse effects of PPIs are related to reduced gastric acid secretion. PPI-induced hypochondria can induce intestinal dysbiosis, enteric infection, and JNM J Neurogastroenterol Motil, Vol. 27 No. 4 October, 2021 pISSN: 2093-0879 eISSN: 2093-0887 https://doi.org/10.5056/jnm21177 Editorial Journal of Neurogastroenterology and Motility
Synthesis of Proposed Structure of Aaptoline A, a Marine Sponge-Derived 7,8-Dihydroxyquinoline, and Its Neuroprotective Properties in C. elegans

A concise and efficient synthesis of the proposed structure of aaptoline A, a 7,8-dihydroxyquinoline derived from a marine sponge, was accomplished in seven steps with a 52% overall yield. A key feature of the synthesis is the high-yielding Ag(I)-catalyzed cycloisomerization of the N-propargylaniline precursor to afford the quinoline carboxylate skeleton from acid-labile methyl aminobenzoate. However, the spectral data of the synthesized aaptoline A were not consistent with those of previous studies. The structure of the synthesized aaptoline A was confirmed by combined 2D NMR analysis. Additional studies on the bioactivity of the synthesized aaptoline A revealed that it has the ability to protect dopaminergic neurons against MPP+-induced neurotoxicity in C. elegans. In addition, impaired food-sensing ability and travel distance capability in C. elegans were significantly ameliorated by aaptoline A treatment, suggesting that aaptoline A can protect dopaminergic neurons both morphologically and functionally.
Effects of sex and APOE on Parkinson's Disease-related cognitive decline.

INTRODUCTION Cognitive impairment is common in Parkinson's Disease, but the impact of predictive factors on incidence and rate of cognitive decline is incompletely understood. We aimed to determine the effects of sex and APOE allele status on cognitive performance in patients with Parkinson's Disease (PD). MATERIAL AND METHODS We conducted a retrospective analysis of 325 clinically diagnosed PD patients who underwent one or more cognitive screenings with a Mini-Mental Status Examination (MMSE) or Mattis Dementia Rating Scale (DRS-2). We used proportional odds regression models to estimate odds ratios for higher versus lower cognitive scores in association with age, sex, education, disease duration, and APOE allele status. RESULTS Higher cognitive scores were independently associated with female sex on the MMSE (OR 2.43; 95% CI 1.14, 5.14) and DRS-2 total (OR 4.14; 95% CI 2.01, 8.53). APOE ε4 dose was associated with lower DRS-2 totals (OR 0.42; 95% CI 0.22, 0.81), but there was no evidence of association with MMSE. Higher education level was also associated with higher scores on the MMSE (OR 1.22; 95% CI 1.07, 1.38) and DRS-2 total (OR 1.31; 95% CI 1.15, 1.50). Disease duration was not associated with cognitive performance on any measure when adjusting for age. CONCLUSION Male sex and APOE ε4, along with age and lower education level, were associated with poorer cognitive performance among a population of predominantly non-demented PD patients.
The Application of Hollow Carbon Nanofibers Prepared by Electrospinning to Carbon Dioxide Capture

Coaxial electrospinning has been considered a straightforward and convenient method for producing hollow nanofibers. Therefore, the objective of this study was to develop hollow activated carbon nanofibers (HACNFs) for CO2 capture in order to reduce emissions of CO2 to the atmosphere and mitigate global warming. Results showed that the sacrificing core could be decomposed at carbonization temperatures above 900 °C, allowing the formation of hollow nanofibers. The average outer diameters of HACNFs ranged from 550 to 750 nm, with a shell thickness of 75 nm. During the carbonization stage, the denitrogenation reactions were significant, while in the CO2 activation process, the release of carbon oxides became prominent. Therefore, the CO2 activation could increase the percentages of N=C and quaternary N groups. The major nitrogen functionalities on most samples were O=C–NH and quaternary N. However, =C and quaternary N groups were found to be crucial in determining the CO2 adsorption performance. CO2 adsorption on HACNFs occurred due to physical adsorption and was an exothermic reaction. The optimal CO2 adsorption performance was observed for HACNFs carbonized at 900 °C, where 3.03 mmol/g (1 atm) and 0.99 mmol/g (0.15 atm) were measured at 25 °C. The degradation of CO2 uptakes after 10 adsorption−desorption cyclic runs could be maintained within 8.9%.
Interest in artificial intelligence for the diagnosis of non-melanoma skin cancer: a survey among French general practitioners

General practitioners (GPs) are playing a key role in skin cancer screening. Non-melanoma skin cancer is frequent and difficult to diagnose. We aimed to assess whether GPs are facing difficulties in diagnosing non-pigmented skin tumours (NPSTs) and whether they would be interested in artificial intelligence (AI) software that could help them with this task. A questionnaire addressing the difficulties in diagnosing NPST and the potential interest in AI as a tool to help diagnose these tumours was emailed to GPs working in two French regions. In total, 147 respondents (98%) had faced difficulties diagnosing NPSTs; 86% agreed that an AI diagnostic tool could be useful in a GP’s office and 83% agreed that it could change their practice. Nevertheless, 68% would not be willing to pay for this kind of software. GPs are facing difficulties in diagnosing NPSTs and would be interested in an AI tool that could help them achieve this. As referral to dermatology practices can be trying, AI diagnostic aids should be developed to help GPs in their gatekeeping task, however at limited cost to the GP.
The Choice of Either Quetiapine or Aripiprazole as Augmentation Treatment in a European Naturalistic Sample of Patients With Major Depressive Disorder

Abstract Background Augmentation with second-generation antipsychotics (SGAs) represents an evidence-based psychopharmacotherapeutic strategy recommended in case of insufficient response to the first-line antidepressant (AD) treatment in major depressive disorder (MDD). Comparative evidence regarding efficacy and prescription preferences of the individual SGAs is scarce. Methods In the scope of this European, multi-site, naturalistic cross-sectional investigation with retrospective assessment of treatment outcome, we compared sociodemographic and clinical characteristics of 187 MDD patients receiving either quetiapine (n = 150) or aripiprazole (n = 37) as augmentation of their first-line AD psychopharmacotherapy. Results Comorbid posttraumatic stress disorder and diabetes were significantly associated with aripiprazole augmentation in our primary and post-hoc binary logistic regression analyses. Furthermore, we identified an association between aripiprazole co-administration and the presence of additional psychotic features, higher rates of AD combination treatment, and a longer duration of psychiatric hospitalizations during the lifetime, which, however, lost significance after correcting for multiple comparisons. Regarding treatment outcome, we found a trend of higher response rates and greater reductions in severity of depressive symptoms in MDD patients dispensed quetiapine. Conclusions Factors associated with a more chronic and severe profile of MDD seem to encourage clinicians to choose aripiprazole over quetiapine, that was, however, administered in the majority of our MDD patients, which might reflect the current approval situation allowing to prescribe exclusively quetiapine as on-label augmentation in MDD in Europe. Given the retrospective assessment of treatment response, the markedly smaller proportion of patients receiving aripiprazole augmentation generally showing an unfavorable disease profile, and the partially heterogeneous statistical robustness of our findings, further studies are required to elaborate on our observation and to generate unambiguous recommendations regarding the choice of first-line SGA augmentation in MDD.
Metastasis Suppressor Genes in Pancreatic Cancer

Abstract Pancreatic cancer, especially pancreatic ductal adenocarcinoma (PDAC), has for long remained a deadly form of cancer characterized by high mortality rates resulting from metastasis to multiple organs. Several factors, including the late manifestation of the disease, partly amplified by lack of efficient screening methods, have hampered the drive to design an effective therapeutic strategy to treat this deadly cancer. Understanding the biology of PDAC progression and identifying critical genes regulating these processes are essential to overcome the barriers toward effective treatment. Metastasis suppressor genes have been shown to inhibit multiple steps in the metastatic cascade without affecting primary tumor formation and are considered to hold promise for treating metastatic cancers. In this review, we catalog the bona fide metastasis suppressor genes reported in PDAC and discuss their known mechanism of action.
Visualizing the phenotype diversity: a case study of Alexander disease

Since only a small number of patients have a rare disease, it is difficult to identify all of the features of these diseases. This is especially true for patients uncommonly presenting with rare diseases. It can also be difficult for the patient, their families, and even clinicians to know which one of a number of disease phenotypes the patient is exhibiting. To address this issue, during Biomedical Linked Annotation Hackathon 7 (BLAH7), we tried to extract Alexander disease patient data in Portable Document Format. We then visualized the phenotypic diversity of those Alexander disease patients with uncommon presentations. This led to us identifying several issues that we need to overcome in our future work.
Optical Detection of SARS-CoV-2 Utilizing Antigen-Antibody Binding Interactions

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for the coronavirus disease (COVID-19) pandemic, is sweeping the world today. This study investigates the optical detection of SARS-CoV-2, utilizing the antigen-antibody binding interactions utilizing a light source from a smart phone and a portable spectrophotometer. The proof-of-concept is shown by detecting soluble preparations of spike protein subunits from SARS-CoV-2, followed by detection of the actual binding potential of the SARS-CoV-2 proteins with their corresponding antigens. The measured binding interactions for RBD and NCP proteins with their corresponding antibodies under different conditions have been measured and analyzed. Based on these observations, a “hump or spike” in light intensity is observed when a specific molecular interaction takes place between two proteins. The optical responses could further be analyzed using the principle component analysis technique to enhance and allows precise detection of the specific target in a multi-protein mixture.
Neutrophil-Derived Proteases Contribute to the Pathogenesis of Early Diabetic Retinopathy

Purpose Previous studies indicate that leukocytes, notably neutrophils, play a causal role in the capillary degeneration observed in diabetic retinopathy (DR), however, the mechanism by which they cause such degeneration is unknown. Neutrophil elastase (NE) is a protease released by neutrophils which participates in a variety of inflammatory diseases. In the present work, we investigated the potential involvement of NE in the development of early DR. Methods Experimental diabetes was induced in NE-deficient mice (Elane−/−), in mice treated daily with the NE inhibitor, sivelestat, and in mice overexpressing human alpha-1 antitrypsin (hAAT+). Mice were assessed for diabetes-induced retinal superoxide generation, inflammation, leukostasis, and capillary degeneration. Results In mice diabetic for 2 months, deletion of NE or selective inhibition of NE inhibited diabetes-induced retinal superoxide levels and inflammation, and inhibited leukocyte-mediated cytotoxicity of retinal endothelial cells. In mice diabetic for 8 months, genetic deletion of NE significantly inhibited diabetes-induced retinal capillary degeneration. Conclusions These results suggest that a protease released from neutrophils contributes to the development of DR, and that blocking NE activity could be a novel therapy to inhibit DR.
Comparison between PtCO2 and PaCO2 and Derived Parameters in Heart Failure Patients during Exercise: A Preliminary Study

Evaluation of arterial carbon dioxide pressure (PaCO2) and dead space to tidal volume ratio (VD/VT) during exercise is important for the identification of exercise limitation causes in heart failure (HF). However, repeated sampling of arterial or arterialized ear lobe capillary blood may be clumsy. The aim of our study was to estimate PaCO2 by means of a non-invasive technique, transcutaneous PCO2 (PtCO2), and to verify the correlation between PtCO2 and PaCO2 and between their derived parameters, such as VD/VT, during exercise in HF patients. 29 cardiopulmonary exercise tests (CPET) performed on a bike with a ramp protocol aimed at achieving maximal effort in ≈10 min were analyzed. PaCO2 and PtCO2 values were collected at rest and every 2 min during active pedaling. The uncertainty of PCO2 and VD/VT measurements were determined by analyzing the error between the two methods. The accuracy of PtCO2 measurements vs. PaCO2 decreases towards the end of exercise. Therefore, a correction to PtCO2 that keeps into account the time of the measurement was implemented with a multiple regression model. PtCO2 and VD/VT changes at 6, 8 and 10 min vs. 2 min data were evaluated before and after PtCO2 correction. PtCO2 overestimates PaCO2 for high timestamps (median error 2.45, IQR −0.635–5.405, at 10 min vs. 2 min, p-value = 0.011), while the error is negligible after correction (median error 0.50, IQR = −2.21–3.19, p-value > 0.05). The correction allows removing differences also in PCO2 and VD/VT changes. In HF patients PtCO2 is a reliable PaCO2 estimation at rest and at low exercise intensity. At high exercise intensity the overall response appears delayed but reproducible and the error can be overcome by mathematical modeling allowing an accurate estimation by PtCO2 of PaCO2 and VD/VT.
Pharmaceuticals and Their Main Metabolites in Treated Sewage Sludge and Sludge-Amended Soil: Availability and Sorption Behaviour

This work evaluated the availability and sorption behaviour of four pharmaceuticals and eight of their metabolites in sewage sludge and sludge-amended soil. Digested sludge and compost were evaluated. The highest levels found in digested sludge corresponded to caffeine (up to 115 ng g−1 dm), ibuprofen (45 ng g−1 dm) and carbamazepine (9.3 ng g−1 dm). The concentrations measured in compost were even lower than in digested sludge. No compound was detected in sludge-amended soils. This fact could be due to the dilution effect after sludge application to soil. Different adsorption capacities in sludge–soil mixtures were measured for the studied compounds at the same spike concentration. In general, except for paraxanthine and 3-hydroxycarbamazepine, the metabolite concentrations measured in the mixtures were almost two-fold lower than those of their parent compounds, which can be explained by their mobility and lixiviation tendency. The log Kd ranged from −1.55 to 1.71 in sludge samples and from −0.29 to 1.18 in soil–sludge mixtures. The log Kd values calculated for compost were higher than those calculated for digested sludge. The obtained results implied that the higher organic carbon content of compost could influence soil contamination when it is applied to soil.
Evidence for an Ordering Transition near 120 K in an Intrinsically Disordered Protein, Casein

Intrinsically disordered proteins (IDPs) are proteins that possess large unstructured regions. Their importance is increasingly recognized in biology but their characterization remains a challenging task. We employed field swept Electron Spin Echoes in pulsed EPR to investigate low-temperature stochastic molecular librations in a spin-labeled IDP, casein (the main protein of milk). For comparison, a spin-labeled globular protein, hen egg white lysozyme, is also investigated. For casein these motions were found to start at 100 K while for lysozyme only above 130 K, which was ascribed to a denser and more ordered molecular packing in lysozyme. However, above 120 K, the motions in casein were found to depend on temperature much slower than those in lysozyme. This abrupt change in casein was assigned to an ordering transition in which peptide residues rearrange making the molecular packing more rigid and/or more cohesive. The found features of molecular motions in these two proteins turned out to be very similar to those known for gel-phase lipid bilayers composed of conformationally ordered and conformationally disordered lipids. This analogy with a simpler molecular system may appear helpful for elucidation properties of molecular packing in IDPs.