Miracle-dz/UniFAR-FTUs huggingface dataset:
Systemic Lupus Erythematosus

Systemic lupus erythematosus (lupus) is characterized by aberrant activity of the immune system, leading to variable clinical symptoms. Lupus is more prevalent in African American women and women in other ethnic minority groups. Diagnosing, treating, and identifying novel therapies for lupus is challenging because of its genetic and phenotypic heterogeneity. Lupus nephritis is the most common target-organ manifestation and requires individualized care to minimize toxicity. A multidisciplinary approach to caring for pregnant patients with lupus is essential to optimize outcomes.
Current Challenges in Chronic Bronchial Infection in Patients with Chronic Obstructive Pulmonary Disease

Currently, chronic obstructive pulmonary disease (COPD) patients and their physicians face a number of significant clinical challenges, one of which is the high degree of uncertainty related to chronic bronchial infection (CBI). By reviewing the current literature, several challenges can be identified, which should be considered as goals for research. One of these is to establish the bases for identifying the biological and clinical implications of the presence of potentially pathogenic microorganisms in the airways that should be more clearly elucidated according to the COPD phenotype. Another urgent area of research is the role of long-term preventive antibiotics. Clinical trials need to be carried out with inhaled antibiotic therapy to help clarify the profile of those antibiotics. The role of inhaled corticosteroids in patients with COPD and CBI needs to be studied to instruct the clinical management of these patients. Finally, it should be explored and confirmed whether a suitable antimicrobial treatment during exacerbations may contribute to breaking the vicious circle of CBI in COPD. The present review addresses the current state of the art in these areas to provide evidence which will enable us to progressively plan better healthcare for these patients.
Health-related quality of life and symptom burden of epithelioid hemangioendothelioma patients: a global patient-driven Facebook study in a very rare malignancy

Abstract Purpose: Epithelioid hemangioendothelioma (EHE) is an ultra-rare vascular sarcoma with unique clinical features. EHE is characterized by an unpredictable, often protracted, clinical course and highly variable clinical presentation. Due to difficulty recruiting ultra-rare cancer patients, health-related quality of life (HRQoL) of EHE patients has not yet been studied. The aim of this study was to assess EHE symptom burden and its impact on HRQoL and psychological distress. Methods: The study was initiated after EHE patients’ foundations approached our research group to study HRQoL. Patients were recruited from the international EHE Facebook group from May through October 2018. Data were collected using the online PROFILES registry. Latent class cluster analysis was performed to identify groups based on frequently reported symptoms. Differences in HRQoL (EORTC-QLQ-C30) and psychological distress (Hospital Anxiety and Depression Scale) between symptom-based clusters were examined. Results: Among 115 EHE patients from 20 countries, three clusters were identified, with low-, intermediate- and high-symptom burden, respectively. Highly symptomatic patients (33%) had clinically relevantly lower scores on HRQoL compared to the other two groups (p < 0.001). These patients suffered mostly from pain, insomnia and fatigue. Symptom burden significantly correlated with reduced daily functioning and high levels of psychological distress. Only for highly symptomatic patients, HRQoL and symptom levels were worse compared to healthy individuals. Conclusion: For the first time, we studied HRQoL in a large international cohort of ultra-rare cancer patients with distinct clinical characteristics, enabled by collaboration with patients and use of social media. We showed a considerable number of EHE patients were highly symptomatic, with a significant impact on HRQoL and psychological distress.
Solar geoengineering may lead to excessive cooling and high strategic uncertainty

Significance Governing climate change and other global commons is challenging. Climate engineering has recently gained attention as a way to manage climate risks. Solar geoengineering is a technology that allows countries to unilaterally influence the world temperature. Solar geoengineering could trigger conflicting interventions by countries who prefer different temperatures; economic theory suggests that countries wanting a cooler climate impose it on others. Other countries may react through countergeoengineering interventions. We study the governance of solar geoengineering using a laboratory experiment in which participants engage in a public good-or-bad game. Results confirm that too much geoengineering can occur, leading to considerable economic losses and increased inequality. The experiment also highlights unforeseen governance risks associated with such technologies. Climate engineering—the deliberate large-scale manipulation of the Earth’s climate system—is a set of technologies for reducing climate-change impacts and risks. It is controversial and raises novel governance challenges [T. C. Schelling, Climatic Change, 33, 303–307 (1996); J. Virgoe, Climatic Change, 95, 103–119 (2008)]. We focus on the strategic implications of solar geoengineering. When countries engineer the climate, conflict can arise because different countries might prefer different temperatures. This would result in too much geoengineering: the country with the highest preference for geoengineering cools the planet beyond what is socially optimal at the expense of the others—a theoretical possibility termed “free-driving” [M. L. Weitzman, Scand. J. Econ., 117, 1049–1068 (2015)]. This study is an empirical test of this hypothesis. We carry out an economic laboratory experiment based on a public “good or bad” game. We find compelling evidence of free-driving: global geoengineering exceeds the socially efficient level and leads to welfare losses. We also evaluate the possibility of counteracting the geoengineering efforts of others. Results show that countergeoengineering generates high payoff inequality as well as heavy welfare losses, resulting from both strategic and behavioral factors. Finally, we compare strategic behavior in bilateral and multilateral settings. We find that welfare deteriorates even more under multilateralism when countergeoengineering is a possibility. These results have general implications for governing global good or bad commons.
Whole-body amino acid composition of the growing pig

Abstract The whole-body amino acid composition of 20 Landrace × Large White entire male pigs was determined with equal numbers of pigs at 20 and 45 kg liveweight. Except for aspartic acid and alanine, amino acid levels (g/16 g N) were not statistically significantly different at the two liveweights. Overall mean whole-body essential amino acid levels were: lysine = 5.94; methionine = 1.85; cystine = 1.28; tryptophan = 0.68; histidine = 3.49; phenylalanine = 3.86; tyrosine = 2.79; threonine = 3.83; leucine = 7.54; isoleucine = 2.84; and valine = 4.06 g/16 g N. There was general agreement between a pattern of essential amino acids based on these and other published results for pig whole-body composition and recently published empirical estimates of the ideal amino acid balance for growth in the pig.
A FIELD TEST OF THE ACCURACY OF A PASSIVE ACOUSTIC LOCATION SYSTEM

ABSTRACT In this study, we tested the ability of a computer-based passive acoustic location system (ALS) to determine the two-dimensional locations of vocalizing animals. The ALS uses multi-track tape recordings to estimate locations based on arrival time delays between widely-spaced microphones. We tested the accuracy of ALS location estimates using tape recordings of wild free-ranging birds made with 4 microphones placed at the corners of a 40m square. We compared ALS location estimates for these birds with locations determined by surveying the locations of the perches birds vocalized from. ALS location estimates were typically less than lm away from surveyed locations when birds vocalized within the square microphone array, rising to just over 2m for birds vocalizing from within 25m beyond the array boundary. Beyond 25m, accuracy diminished rapidly with increasing distance. ALS accuracy did not depend on the bird species located, but location estimates based on frequency-modulated tonal notes were more than twice as accurate than those made using relatively unmodulated notes from the same songs. Two examples are given to demonstrate the usefulness of the ALS in field studies.
Epigenetic Factors that Control Pericentric Heterochromatin Organization in Mammals

Pericentric heterochromatin (PCH) is a particular form of constitutive heterochromatin that is localized to both sides of centromeres and that forms silent compartments enriched in repressive marks. These genomic regions contain species-specific repetitive satellite DNA that differs in terms of nucleotide sequences and repeat lengths. In spite of this sequence diversity, PCH is involved in many biological phenomena that are conserved among species, including centromere function, the preservation of genome integrity, the suppression of spurious recombination during meiosis, and the organization of genomic silent compartments in the nucleus. PCH organization and maintenance of its repressive state is tightly regulated by a plethora of factors, including enzymes (e.g., DNA methyltransferases, histone deacetylases, and histone methyltransferases), DNA and histone methylation binding factors (e.g., MECP2 and HP1), chromatin remodeling proteins (e.g., ATRX and DAXX), and non-coding RNAs. This evidence helps us to understand how PCH organization is crucial for genome integrity. It then follows that alterations to the molecular signature of PCH might contribute to the onset of many genetic pathologies and to cancer progression. Here, we describe the most recent updates on the molecular mechanisms known to underlie PCH organization and function.
Adherence to prophylaxis and bleeding in children: Significant drop during puberty but no correlation with bleeding

People with severe haemophilia or von Willebrand disease type III lack clotting factor and are at risk of experiencing spontaneous bleeds in the joints, muscles or soft tissue.1 To prevent bleeding, patients must inject themselves with prophylactic clotting factor concentrates, which is a demanding treatment consisting of intravenous infusions 3 to 3.5 times each week, starting before the age of three years.2 In Dutch children with haemophilia or von Willebrand disease, parents generally perform these injections at home until children learn to self-administer injections, which generally occurs during early adolescence, at the average age of 12 years.2 Around the age of 14 years, children begin to slowly take responsibility for their treatments,2 which coincides with the normal physical, cognitive and psychosocial changes that occur at this age. In addition to normal developmental changes, children with haemophilia or von Willebrand disease must manage the additional burden: to adhere to treatment and self-manage their disease.3 In haemophilia and other chronic conditions, reduced adherence is often reported during adolescence. Previous studies have reported adherence differences between children (younger than 18 years) and adults (older than 18 years). 3 Low adherence to prophylaxis could result in more frequent bleeding events and subsequently negative effects on joint status.4 The adherence age cut-off of 18 years used in previous studies is too crude to identify the optimal age for adherence interventions. This study aimed to explore the relationships between adherence to prophylactic treatment, age and the frequency of bleeding events in children and adolescents with severe haemophilia. This study was performed as a cross-sectional study. Patients were included if they were diagnosed with severe haemophilia or von Willebrand disease type III and were prescribed prophylactic treatment. All patients visiting the outpatient's clinic were asked to complete the Validated Haemophilia Regimen Treatment Adherence Scale-Prophylaxis’ questionnaire (VERITAS-Pro). 5 The VERITAS-Pro was normalized into a 0-100 scale, using the following methods:
Ozone Risk Assessment for European Vegetation

Tropospheric ozone is the most critical air pollutant for plants. In recent years, common research goals have brought together different groups working on plant/ozone interactions, interested in establishing a European network that could efficiently make progress in this important research area. In this context, the international workshop on “Ozone risk assessment for European vegetation” was held on May 10- 11, 2007 in Capri (Naples, Italy).
Usefulness of Goal Attainment Scaling in Intensive Stroke Rehabilitation During the Subacute Stage

Objective To investigate the usefulness of goal attainment scaling (GAS) in intensive stroke rehabilitation during the subacute stage. Methods Medical records of subacute post-stroke patients who had undergone intensive rehabilitation under hospitalization, before and after the application of GAS, were collected. GAS was conducted at the initial evaluation of each patient. Specific goals were suggested by physical and occupational therapists and were determined by the responsible physiatrist. A 5-point scale was used for the GAS score after 4 weeks of rehabilitation according to the preset criteria of each goal. To evaluate the influence of GAS in rehabilitation practice, functional improvements were compared between two patient groups before (n=121) and after (n=141) GAS. To assess progress in GAS practice, the standard GAS score was calculated, and the changes were observed over a 3-year period. The standard GAS score converged to 50 points when the goal was achieved. The therapists who used GAS also completed a survey regarding its usefulness. Results There were no statistical differences in the motor and cognitive outcomes of the patient groups before and after applying GAS scoring. Successive yearly changes in the standard GAS scores showed progressive convergence to 50 points, signaling that the patient’s goal-setting abilities improved. According to the survey, most therapists felt that GAS enhanced the quality of therapies (84.6%). Conclusion GAS improved goal-setting for the rehabilitation of subacute post-stroke patients and might have a positive effect on rehabilitation.
The Evolving Outsourcing Landscape in Pharma R&D - Different Collaborative Models and Factors to Consider when Choosing a Contract Research Organization.

Outsourcing has become an integral part of how research and early development (R&D) is executed in biotech companies and large pharmaceutical organizations. Drug discovery organizations can choose from several operational models when partnering with a service provider, ranging from short term, fee-for-service (FFS)-based arrangements to more strategic full time-equivalent (FTE)-based collaborations and even risk-sharing relationships. Clients should consider a number of criteria when deciding which contract research organization (CRO) is best positioned to help meet its goals. Besides cost, other factors such as intellectual property protection, problem solving skills, value-creation ability, communication, data integrity, safety and personnel policies, ease of communication, geography, duration of engagement, scalability of capacity and contractual details deserve proper consideration. In the end, the success of a drug discovery partnership will depend in large part on the people who execute the science.
A Comparative Quantitative Proteomic Analysis of HCMV-Infected Cells Highlights pUL138 as a Multifunctional Protein

Human cytomegalovirus (HCMV) is a widespread virus that can establish life-long latent infection in large populations. The establishment of latent infection prevents HCMV from being cleared by host cells, and HCMV reactivation from latency can cause severe disease and death in people with immature or compromised immune systems. To establish persistent and latent infection in healthy individuals, HCMV encodes a large array of proteins that can modulate different components and pathways of host cells. It has been reported that pUL138 encoded by the UL133-UL138 polycistronic locus promotes latent infection in primary CD34+ hematopoietic progenitor cells (HPCs) infected in vitro. In this study, recombinant HCMV HanUL138del was constructed by deleting the UL138 locus of Han, a clinical HCMV strain. Then, a comparative quantitative proteomic analysis of Han- and HanUL138del-infected MRC5 cells was performed to study the effect of pUL138 on host cells in the context of HCMV infection. Our results indicated that, during the early phase of HCMV infection, the innate immune response was differentially activated, while during the late phase of HCMV infection, multiple host proteins were differentially expressed between Han- and HanUL138del-infected cells, and these proteins are involved in the oxidation-reduction process, ER to Golgi vesicle-mediated transport, and extracellular matrix organization. Among these proteins, STEAP3, BORCS7, FAM172A, RELL1, and WDR48 were further demonstrated to affect HCMV infection. Our study provides a systematic view of the effect of pUL138 on the host cell proteome and highlights the proposition that multiple biological processes or host factors may be involved in the overall role of the UL133-UL138 polycistronic locus in HCMV persistence.
Bound states in the continuum in anisotropic plasmonic metasurfaces.

The concept of optical bound states in the continuum (BICs) currently drives the field of dielectric resonant nanophotonics, providing an important physical mechanism for engineering high-quality (high-Q) optical resonances in high-index dielectric nanoparticles and structured dielectric metasurfaces. For structured metallic metasurfaces, realization of BICs remains a challenge associated with strong dissipative losses of plasmonic materials. Here, we suggest and realize experimentally anisotropic plasmonic metasurfaces supporting high-Q resonances governed by quasi-BIC collective resonant modes. Our metasurfaces are composed of arrays of vertically oriented double-pillar meta-molecules covered by a thin layer of gold. We engineer quasi-BIC modes and observe experimentally sharp resonances in mid-IR reflectance spectra. Our work suggests a direct route to boost the resonant field enhancement in plasmonic metasurfaces via combining a small effective mode volume of plasmonic systems with engineered high-Q resonances provided by the BIC physics, with multiple applications to enhance light-matter interaction for nano-optics and quantum photonics.
CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing

Next-generation sequencing (NGS) has been a widely-used technology in biomedical research for understanding the role of molecular genetics of cells in health and disease. A variety of computational tools have been developed to analyse the vastly growing NGS data, which often require bioinformatics skills, tedious work and a significant amount of time. To facilitate data processing steps minding the gap between biologists and bioinformaticians, we developed CSI NGS Portal, an online platform which gathers established bioinformatics pipelines to provide fully automated NGS data analysis and sharing in a user-friendly website. The portal currently provides 16 standard pipelines for analysing data from DNA, RNA, smallRNA, ChIP, RIP, 4C, SHAPE, circRNA, eCLIP, Bisulfite and scRNA sequencing, and is flexible to expand with new pipelines. The users can upload raw data in FASTQ format and submit jobs in a few clicks, and the results will be self-accessible via the portal to view/download/share in real-time. The output can be readily used as the final report or as input for other tools depending on the pipeline. Overall, CSI NGS Portal helps researchers rapidly analyse their NGS data and share results with colleagues without the aid of a bioinformatician. The portal is freely available at: https://csibioinfo.nus. edu.sg/csingsportal.
Association between Nutrient-Based Dietary Patterns and Bladder Cancer in Italy

Limited knowledge is available on dietary patterns and bladder cancer risk. We analyzed data from an Italian case-control study carried out between 2003 and 2014, including 690 incident bladder cancer cases and 665 hospital-controls. We derived nutrient-based dietary patterns applying principal component factor analysis on 28 selected nutrients. We categorized factor scores according to quartiles, and estimated the odds ratios (ORs) and the corresponding 95% confidence intervals (CIs) through logistic regression models, adjusted for major confounding factors. We identified four dietary patterns named “Animal products”, “Vitamins and fiber”, “Starch-rich”, and “Animal unsaturated fatty acids”. We found an inverse association between the “Vitamins and fiber” pattern and bladder cancer (OR = 0.70, 95% CI: 0.48–0.99, IV versus I quartile category). Inverse relationships of borderline significance were also found for the “Animal products” and the “Animal unsaturated fatty acids” dietary patterns. No significant association was evident for the “Starch-rich” pattern. The current study allowed us to identify major dietary patterns in this Italian population. Our study confirms available evidence and shows that scoring high on a fruit-and-vegetables pattern provides beneficial effects on bladder cancer risk.
Hydrozoa (Cnidaria) symbiotic with Porifera: a review

Many hydroids are symbiotic with other organisms. Sponges, because of their complex canal system and their filter-feeding activity inducing a continuous water flow, are used by numerous species as either exclusive or facultative substrata. The associated hydroid fauna thriving on or inside sponges shows a wide range of relationships with their hosts. Hydroids may be simply epibiotic on sponges, their stolons running on the host surface. Alternatively, the stolons may grow inside the sponge body, the polyps emerging from the sponge surface, having also the possibility of retraction inside the sponge tissue. Finally, stolons and branches may develop deeply inside the sponge body, producing a skeletal network for sponge growth. This paper reviews the described relationships of hydrozoans symbiotic with sponges and reports new observations.