Miracle-dz/UniFAR-FTUs huggingface dataset:
It’s gone, it’s back: A prospective study on the COVID-19 pandemic-related shortages and mental health of Australian families

ABSTRACT Our aim was to explore the association between COVID-19 pandemic-related product shortages and symptoms of stress, anxiety, and depression in Australian families, concurrently and longitudinally, while controlling for demographic, health, and psychological characteristics. This prospective study used two waves of data (baseline, Time 0 = April 2020; Time 1 = May 2020) from a longitudinal cohort study of Australian parents of a child aged 0‐18 years. Parents were surveyed at baseline about whether they had experienced product shortages related to COVID-19. DASS21 was used to measure symptoms of depression, anxiety, and stress at both waves. The sample included 2,110 participants (N = 1,701, 80.6% mothers). About 68.6% of the respondents reported being impacted by one or more shortages. Product shortages correlated significantly with higher combined and individual scores for anxiety, depression, and stress (r = 0.007 to 0.18, all p < 0.001) at baseline. At Time 1, parental emotion regulation explained 4.0% of the variance (p < .001). Our findings suggest a role for improving parental emotion regulation in coping with stressors, such as shortages and lockdowns.
Surface cleaning from laser-induced cavitation bubbles

When bubbles expand and collapse close to boundaries, a shear flow is generated which is able to remove particles from the surface, thus locally cleaning it. Here the authors demonstrate experimentally with microparticle tracking velocimetry that the strongest forcing of particles occurs during a very brief time interval of the bubble oscillation period. During this interval a jet flow impacts and spreads radially along the surface, thus transporting the particles with it.
Numerical simulation of periodic surface structures created by direct laser interference patterning

Surface structuring using nano-second lasers can be used to enhance certain properties of a material or even to introduce new ones. One way to create these structures efficiently is direct laser interference patterning using different polarization vector orientations of the interfering beams. However, experimentally measuring the fabrication process of these structures is very challenging due to small length and time scales. Therefore, a numerical model is developed and presented for resolving the physical effects during formation the predicting the resolidified surface structures. This three-dimensional, compressible computational fluid dynamics model considers the gas, liquid, and solid material phase and includes various physical effects, such as heating due to the laser beam for both parallel and radial polarization vector orientations, melting, solidification, and evaporation, Marangoni convection, and volumetric expansion. The numerical results reveal a very good qualitatively and quantitatively agreement with experimental reference data. Resolidified surface structures match both in overall shape as well as crater diameter and height, respectively. Furthermore, this model gives valuable insight on different quantities during the formation of these surface structures, such as velocity and temperature. In future, this model can be used to predict surface structures based on various process input parameters.
Endolysosomal impairment by binding of amyloid beta or MAPT/Tau to V-ATPase and rescue via the HYAL-CD44 axis in Alzheimer disease

ABSTRACT Impaired activities and abnormally enlarged structures of endolysosomes are frequently observed in Alzheimer disease (AD) brains. However, little is known about whether and how endolysosomal dysregulation is triggered and associated with AD. Here, we show that vacuolar ATPase (V-ATPase) is a hub that mediates proteopathy of oligomeric amyloid beta (Aβ) and hyperphosphorylated MAPT/Tau (p-MAPT/Tau). Endolysosomal integrity was largely destroyed in Aβ-overloaded or p-MAPT/Tau-positive neurons in culture and AD brains, which was a necessary step for triggering neurotoxicity, and treatments with acidic nanoparticles or endocytosis inhibitors rescued the endolysosomal impairment and neurotoxicity. Interestingly, we found that the lumenal ATP6V0C and cytosolic ATP6V1B2 subunits of the V-ATPase complex bound to the internalized Aβ and cytosolic PHF-1-reactive MAPT/Tau, respectively. Their interactions disrupted V-ATPase activity and accompanying endolysosomal activity in vitro and induced neurodegeneration. Using a genome-wide functional screen, we isolated a suppressor, HYAL (hyaluronidase), which reversed the endolysosomal dysfunction and proteopathy and alleviated the memory impairment in 3xTg-AD mice. Further, we found that its metabolite hyaluronic acid (HA) and HA receptor CD44 attenuated neurotoxicity in affected neurons via V-ATPase. We propose that endolysosomal V-ATPase is a bona fide proteotoxic receptor that binds to pathogenic proteins and deteriorates endolysosomal function in AD, leading to neurodegeneration in proteopathy. Abbreviations: AAV, adeno-associated virus; Aβ, amyloid beta; AD, Alzheimer disease; APP, amyloid beta precursor protein; ATP6V0C, ATPase H+ transporting V0 subunit c; ATP6V1A, ATPase H+ transporting V1 subunit A; ATP6V1B2, ATPase H+ transporting V1 subunit B2; CD44.Fc, CD44-mouse immunoglobulin Fc fusion construct; Co-IP, co-immunoprecipitation; CTSD, cathepsin D; HA, hyaluronic acid; HMWHA, high-molecular-weight hyaluronic acid; HYAL, hyaluronidase; i.c. v, intracerebroventricular; LMWHA, low-molecular-weight hyaluronic acid; NPs, nanoparticles; p-MAPT/Tau, hyperphosphorylated microtubule associated protein tau; PI3K, phosphoinositide 3-kinase; V-ATPase, vacuolar-type H+-translocating ATPase; WT, wild-type
Validation of the PCL-5, PHQ-9, and GAD-7 in a Sample of First Responders

Mental health professionals working with first responder can conceptualize PTSD by the 7-factor hybrid configuration, depression with two factors (cognitive affective and somatic), and generalized anxiety is a unidimensional construct. Objective First responders (FRs) commonly present for treatment with complex symptom constellations that frequently include posttraumatic stress disorder, depression, and generalized anxiety. To date, no FR study has validated these measures on a treatment-seeking sample. Methods Confirmatory factor analysis was utilized to validate measures that assess these constructs (Posttraumatic Stress Disorder Checklist for DSM-5, Patient Health Questionnaire-9, and Generalized Anxiety Disorder-7) on a treatment-seeking sample of FRs (N = 390). Results The seven-factor posttraumatic stress disorder hybrid configuration was the best fit. The best fitting factor model of the depression measure was a two-factor structure, cognitive-affective and somatic depression. Lastly, generalized anxiety was a unidimensional construct. Limitations Follow-up studies should validate these measures on each FR subtype. Conclusion We position these findings within the FR literature, review clinical implications for providers, and offer recommendations for future research.
Rare diseases presenting with hemophagocytic lymphohistiocytosis

Hemophagocytic lymphohistiocytosis (HLH) is a potentially fatal hyperinflammatory disorder characterized by hypercytokinemia caused by excessive activation of cytotoxic T cells and macrophages. HLH is caused by a variety of factors and is classified into primary and secondary HLH. Familial HLH (FHL) types 1–5, X‐linked lymphoproliferative syndrome types 1 and 2, and FHL syndrome with hypopigmentation are all examples of primary HLH. Secondary HLH, on the other hand, is linked to infections, malignant tumors, autoimmune diseases, and other diseases. The causes of HLH vary, and finding the underlying disease is critical for diagnosis and treatment. The majority of HLH is caused by the aforementioned conditions; however, approximately 10% of cases are caused by rare diseases such as inborn errors of immunity (IEI) and inborn errors of metabolism (IEM). Novel IEI, such as RhoG, MAP kinase activating death domain, TIM3, and ZNFX1 deficiencies, have recently been identified as causes of HLH. IEM patients are rarely associated with HLH. Surprisingly, children with lysinuric protein intolerance and lysosomal acid lipase deficiency (Wolman disease) frequently develop HLH. This review focuses on the most recent knowledge of HLH caused by rare diseases such as IEI and IEM.
Impact of DFT properties on the inherent resolution of compressed sensing reconstructed images

Compressed sensing (CS) algorithms exploit sparseness properties to reconstruct high spatial resolution magnetic resonance (MR) images from k-space data acquisitions significantly under sampled to reduce imaging times. CS algorithm effectiveness is frequently shown using under-sampled k-space data from NxN simulated images. These demonstration reconstructions are near perfect with quality higher than reconstructions using under-sampled NxN experimental k-space data sets. These differences are explained in terms of the interaction between the explicit transform domain sparsity requirement employed during iterative CS reconstruction and an inherent frequency domain property of the discrete Fourier transform (DFT). We report on experiments to overcome the limitations imposed by this DFT property by modifying the CS objective function to use a sparseness transform with a resolution higher that the standard transform related to the acquired NxN data matrix size. We demonstrate the relative effectiveness and limitations of standard CS and our proposed highresolution k-space extrapolation enabled (Hi-KEE) CS reconstruction on underand fully-sampled, simulated and experimental MR k-space data. (8 pages)
Development of a Single-nucleotide Polymorphism Genotyping Assay for the Rapid Detection of Vancomycin-intermediate Resistance in Staphylococcus aureus Epidemic Lineage ST5

Background Vancomycin is a treatment option for patients with severe methicillin-resistant Staphylococcus aureus (MRSA) infection. Unfortunately, reduced susceptibility to vancomycin in S. aureus is becoming increasingly common. We developed a method for the rapid and accurate diagnosis of vancomycin-intermediate resistant S. aureus (VISA). Methods We performed a microbial genome-wide association study to discriminate between VISA and vancomycin-susceptible S. aureus (VSSA) using 42 whole-genome sequences. A TaqMan single-nucleotide polymorphism (SNP) genotyping assay was developed to detect target SNPs in VISA strains. Results Four SNPs in the VISA strains resulting in nonsynonymous amino-acid substitutions were associated with reduced susceptibility to vancomycin SA_RS01235 (G203S), SA_RS09725 (V171A), SA_RS12250 (I48F), and SA_RS12550 (G478A). These four SNPs were mainly detected in the typical hospital-associated sequence type (ST)5 clonal lineage. The TaqMan assay successfully detected all four SNPs using as little as 0.2 ng DNA per reaction. Using 10 VSSA and VISA clinical strains each, we validated that the assay accurately discriminates between VISA and VSSA. Conclusions The TaqMan SNP genotyping assay targeting four SNPs may be an alternative to current standard methods for the rapid detection of vancomycin-intermediate resistance in S. aureus epidemic lineage ST5.
Real-world efficacy and safety of vedolizumab in managing ulcerative colitis versus Crohn’s disease: results from an Italian multicenter study

ABSTRACT Background Vedolizumab (VDZ) can be used to treat refractory ulcerative colitis (UC) and Crohn’s disease (CD). We assessed whether there are differences in treating UC vs CD with VDZ. Research design and methods Mayo score in UC and the Harvey-Bradshaw Index (HBI) in CD scored the clinical activity. Achievement and maintenance of clinical remission during the follow-up, and safety were the primary endpoints. Results 729 patients (475 with UC and 254 with CD), median follow-up of 18 (IQR 6-36) months, were enrolled. Clinical remission at the 6th month of treatment was achieved in 488 (66.9%) patients (74.4% in CD vs 62.9% in UC, p<0.002) while, during the follow-up, no difference was found (81.5% in the UC group and 81.5% pts in the CD group; p=0.537). The clinical remission at the 6th month of treatment (p=0.001) and being naïve to biologics (p<0.0001) were significantly associated with prolonged clinical remission. The clinical response was significantly higher in UC (90.1%) vs CD (84.3%) (p=0.023), and surgery occurred more frequently in CD (1.9% in UC vs 5.1% in CD, p=0.016). Conclusion We found differences when using VDZ in UC vs CD in real life. These parameters can help the physician predict this drug’s longterm efficacy.
Testing for Gene–Environment and Gene–Gene Interactions Under Monotonicity Constraints

Recent genome-wide association studies (GWASs) designed to detect the main effects of genetic markers have had considerable success with many findings validated by replication studies. However, relatively few findings of gene–gene or gene–environment interactions have been successfully reproduced. Besides the main issues associated with insufficient sample size in current studies, a complication is that interactions that rank high based on p-values often correspond to extreme forms of joint effects that are biologically less plausible. To reduce false positives and to increase power, we develop various gene–environment/gene–gene tests based on biologically more plausible constraints using bivariate isotonic regressions for case–control data. We extend our method to exploit gene–environment or gene–gene independence information, integrating the approach proposed by Chatterjee and Carroll. We propose appropriate nonparametric and parametric permutation procedures for evaluating the significance of the tests. Simulations show that our method gains power over traditional unconstrained methods by reducing the sizes of alternative parameter spaces. We apply our method to several real-data examples, including an analysis of bladder cancer data to detect interactions between the NAT2 gene and smoking. We also show that the proposed method is computationally feasible for large-scale problems by applying it to the National Cancer Institute (NCI) lung cancer GWAS data.
Identification of Microorganisms that Bind Specifically to Target Materials of Interest Using a Magnetophoretic Microfluidic Platform

Discovery of microorganisms and their relevant surface peptides that specifically bind to target materials of interest can be achieved through iterative biopanning-based screening of cellular libraries having high diversity. Recently, microfluidics-based biopanning methods have been developed and exploited to overcome the limitations of conventional methods where controlling the shear stress applied to remove cells that do not bind or only weakly bind to target surfaces is difficult and the overall experimental procedure is labor-intensive. Despite the advantages of such microfluidic methods and successful demonstration of their utility, these methods still require several rounds of iterative biopanning. In this work, a magnetophoretic microfluidic biopanning platform was developed to isolate microorganisms that bind to target materials of interest, which is gold in this case. To achieve this, gold-coated magnetic nanobeads, which only attached to microorganisms that exhibit high affinity to gold, were used. The platform was first utilized to screen a bacterial peptide display library, where only the cells with surface peptides that specifically bind to gold could be isolated by the high-gradient magnetic field generated within the microchannel, resulting in enrichment and isolation of many isolates with high affinity and high specificity toward gold even after only a single round of separation. The amino acid profile of the resulting isolates was analyzed to provide a better understanding of the distinctive attributes of peptides that contribute to their specific material-binding capabilities. Next, the microfluidic system was utilized to screen soil microbes, a rich source of extremely diverse microorganisms, successfully isolating many naturally occurring microorganisms that show strong and specific binding to gold. The results show that the developed microfluidic platform is a powerful screening tool for identifying microorganisms that specifically bind to a target material surface of interest, which can greatly accelerate the development of new peptide-driven biological materials and hybrid organic–inorganic materials.
Online learning: theory, algorithms and applications (למידה מקוונת.)

Online learning is the process of answering a sequence of questions given knowledge of the correct answers to previous questions and possibly additional available information. Answering questions in an intelligent fashion and being able to make rational decisions as a result is a basic feature of everyday life. Will it rain today (so should I take an umbrella)? Should I fight the wild animal that is after me, or should I run away? Should I open an attachment in an email message or is it a virus? The study of online learning algorithms is thus an important domain in machine learning, and one that has interesting theoretical properties and practical applications. This dissertation describes a novel framework for the design and analysis of online learning algorithms. We show that various online learning algorithms can all be derived as special cases of our algorithmic framework. This unified view explains the properties of existing algorithms and also enables us to derive several new interesting algorithms. Online learning is performed in a sequence of consecutive rounds, where at each round the learner is given a question and is required to provide an answer to this question. After predicting an answer, the correct answer is revealed and the learner suffers a loss if there is a discrepancy between his answer and the correct one. The algorithmic framework for online learning we propose in this dissertation stems from a connection that we make between the notions of regret in online learning and weak duality in convex optimization. Regret bounds are the common thread in the analysis of online learning algorithms. A regret bound measures the performance of an online algorithm relative to the performance of a competing prediction mechanism, called a competing hypothesis. The competing hypothesis can be chosen in hindsight from a class of hypotheses, after observing the entire sequence of question- answer pairs. Over the years, competitive analysis techniques have been refined and extended to numerous prediction problems by employing complex and varied notions of progress toward a good competing hypothesis. We propose a new perspective on regret bounds which is based on the notion of duality in convex optimization. Regret bounds are universal in the sense that they hold for any possible fixed hypothesis in a given hypothesis class. We therefore cast the universal bound as a lower bound
Operationalising multi-sectoral food- and nutrition-related policies to curb the rise in obesity in Ghana

Abstract Objective: To examine the governance of the food and nutrition policy space with particular reference to interests and power among stakeholders. Design: We followed a case study research design to conduct a nutrition policy analysis. We triangulated three sources of data: key-informant interviews, learning journey and relevant policy documents (2010–2020). This study is grounded in a conceptual framework focused on power. Setting: Ghana. Participants: Key informants (n 28) drawn from policy stakeholders from government (Health, Agriculture, Trade and Industry), academia, civil society, development partners, civil society organisation (CSO) and private sector in Accra and Kumasi. Results: Power relations generated tensions, leading to weak multi-sectoral coordination among actors within the nutrition policy space. Governance and funding issues were identified as reasons for the weak multi-sectoral coordination. Formal power rested with government institutions while the private sector and CSO pushed to be invited during policy formulation. Visible stakeholders from industry were trade oriented and held a common interest of profit-making; they sought to receive support from government in order to be more competitive. There were no observed structures at the subnational levels for effective link with the national level. Conclusion: Formal responsibility for decision making within the nutrition and food policy space rested with the health sector and bringing on board nutrition-related sectors remained a challenge due to power tensions. Establishing a National Nutrition Council, with structures at the subnational level, will strengthen policy coordination and implementation. Taxation of sugar-sweetened beverages could provide a fund generation avenue for coordination of programmes to curb obesity.
Small airway disease and asthma control

Abstract Aim Maximum mid-expiratory flow (MMEF) is one of the pulmonary function tests that report small airway disease. Our study aimed to investigate the role of MMEF values in asthma control, the prevalence of small airway disease, and their effect on asthma control in patients with asthma with normal forced expiratory volume in one second (FEV1) values. Material and Method Patients who presented to the Chest Diseases outpatient clinic of our hospital between 2018 and 2019 and were diagnosed as having asthma were included in the study. The characteristics of the patients, pulmonary function tests, their asthma treatment, and asthma control test (ACT) scores were recorded. Patients with FEV1 <80 in the pulmonary function test, those with additional lung disease, those who had an attack in the last 4 weeks, and patients who smoked were excluded from the study. MMEF <65 was defined as small airway disease. Results The MMEF% and MMEF (L/s) values of the group with uncontrolled asthma were found to be statistically significantly lower than those of the controlled asthma group (p = 0.016 and p = 0.003, respectively). MMEF% and MMEF (L/s) values in those with wheezing were found to be significantly lower compared with those without wheezing (p = 0.025 and p = 0.049, respectively). The MMEF% and MMEF (L/s) values of the patients with nocturnal symptoms were found to be statistically significantly lower than in patients without nocturnal symptoms (p = 0.023 and p = 0.041, respectively). ACT values of patients with MMEF <65 were found to be statistically lower than those of patients with MMEF >65 (0.047). Conclusion Considering small airway disease in patients with asthma may be beneficial in clinical practice.