Miracle-dz/UniFAR-FTUs huggingface dataset:
Incomplete lineage sorting and ancient admixture, and speciation without morphological change in ghost-worm cryptic species

Morphologically similar species, that is cryptic species, may be similar or quasi-similar owing to the deceleration of morphological evolution and stasis. While the factors underlying the deceleration of morphological evolution or stasis in cryptic species remain unknown, decades of research in the field of paleontology on punctuated equilibrium have originated clear hypotheses. Species are expected to remain morphologically identical in scenarios of shared genetic variation, such as hybridization and incomplete lineage sorting, or in scenarios where bottlenecks reduce genetic variation and constrain the evolution of morphology. Here, focusing on three morphologically similar Stygocapitella species, we employ a whole-genome amplification method (WGA) coupled with double-digestion restriction-site associated DNA sequencing (ddRAD) to reconstruct the evolutionary history of the species complex. We explore population structure, use population-level statistics to determine the degree of connectivity between populations and species, and determine the most likely demographic scenarios which generally reject for recent hybridization. We find that the combination of WGA and ddRAD allowed us to obtain genomic-level data from microscopic eukaryotes (∼1 millimetre) opening up opportunities for those working with population genomics and phylogenomics in such taxa. The three species share genetic variance, likely from incomplete lineage sorting and ancient admixture. We speculate that the degree of shared variation might underlie morphological similarity in the Atlantic species complex.
Are Chronic Pain Patients with Dementia Being Undermedicated?

Abstract In dementia, neuropathological changes alter the perception and expression of pain. For clinicians and family members, this knowledge gap leads to difficulties in recognizing and assessing chronic pain, which may consequently result in persons with dementia receiving lower levels of pain medication compared to those without cognitive impairment. Although this situation seems to have improved in recent years, considerable geographical variation persists. Over the last decade, opioid use has received global attention as a result of overuse and the risk of addiction, while the literature on older persons with dementia actually suggests undertreatment. This review stresses the importance of reliable assessment and the regular evaluation and monitoring of symptoms in persons with dementia. Based on current evidence, we concluded that chronic pain is still undertreated in dementia.
Deposition and annealing of lead scandium tantalate thin films for high performance thermal detector arrays

Abstract This paper describes the deposition of thin film lead scandium tantalate (Pb2ScTaO6) for use in ferroelectric microbridge thermal detectors and reports on the effect of post-deposition annealing. Two methods for the sputter deposition of PST are described - one using a single target, the other a new method using two targets. Annealing of the samples is carried out in oxygen using a commercial rapid thermal processor. Materials are characterised by X-ray diffraction and transmission electron microscopy and show that films deposited as PST pyrochlore can be transformed to perovskite by annealing. Some annealed films have shown B-site ordering. Induced pyroelectric coefficients over 1×10−3Cm−2K−1 have been measured in the annealed films.
A model of nurses’ intention to care of patients with COVID‐19: Mediating roles of job satisfaction and organisational commitment

Abstract Aim and Objectives This study aims to test the hypothesis that job satisfaction and organisational commitment might play a mediating roles between workload, quality of supervision, extra‐role behaviour, pay satisfaction and intention to care of patients with COVID‐19. Background Given the high incidence of coronavirus and shortage of nurses in Iranian hospitals, learning about nurses’ intention to care for patients with COVID‐19 is important. Design In this cross‐sectional study, 648 Iranian nurses were surveyed during March 2020. The online questionnaire consisted of two parts. The mediating role was explored for the following: job satisfaction and commitment in the association of workload, quality of supervisor, extra‐role behaviours, and pay satisfaction with the intention to care. The study adhered to STROBE checklist for cross‐sectional studies. Results The results of this study show that job satisfaction and organisational commitment mediated the relationship of nurses’ workload, quality of supervisor, extra‐role behaviours, and pay satisfaction with the intention to care for patients with COVID‐19. Conclusion The results of the study indicate the importance of job satisfaction and organisational commitment as mechanisms that help to understand the association of nurses’ workload, quality of supervisor, extra‐role behaviours and pay satisfaction with the intention to care during the COVID‐19 pandemic. Relevance to clinical practice Hospital managers need to attend to the role of nurses’ job satisfaction and other organisational factors to ensure that they can cope with the challenges of the COVID‐19 pandemic.
Thermodynamic Characterization of the Association of Cyanine Dyes with DNA

The association of three monomeric cyanine dyes with double-stranded DNA was investigated. The oxazole yellow dye (YO-PRO-1) and the two thiazole orange dyes (TO-PRO-1 and TO) are structurally similar, differing only in their charge and in the heteroatom in their benzothiazole and benzoxazole rings. On the basis of changes in the UV−visible absorption spectra of the dyes when bound to DNA, equilibrium constants were measured to investigate the factors that influence their intercalative association with DNA. When these positively charged dyes associate with DNA, the number of condensed Na+ ions that are released from the DNA backbone is correlated with the structural charge of the dye. A comparison of the equilibrium constants demonstrates that the charge and structure of the dye influences the strength of its interaction with DNA. As evident from larger equilibrium constants in buffers containing tetramethylammonium cations as opposed to sodium cations, the identity of the cations also influences the stab.
Factors Influencing Depression and Mental Distress Related to COVID-19 Among University Students in China: Online Cross-sectional Mediation Study

Background The COVID-19 epidemic may elevate mental distress and depressive symptoms in various populations in China. Objective This study investigates the levels of depression and mental distress due to COVID-19, and the associations between cognitive, behavioral, and psychosocial factors, and depression and mental distress due to COVID-19 among university students in China. Methods A large-scale online cross-sectional study (16 cities in 13 provinces) was conducted among university students from February 1 to 10, 2020, in China; 23,863 valid questionnaires were returned. The Patient Health Questionnaire-9 was used to assess depression. Structural equation modeling was performed to test mediation and suppression effects. Results Of the 23,863 participants, 47.1% (n=11,235) reported high or very high levels of one or more types of mental distress due to COVID-19; 39.1% (n=9326) showed mild to severe depression. Mental distress due to COVID-19 was positively associated with depression. All but one factor (perceived infection risks, perceived chance of controlling the epidemic, staying at home, contacted people from Wuhan, and perceived discrimination) were significantly associated with mental distress due to COVID-19 and depression. Mental distress due to COVID-19 partially mediated and suppressed the associations between some of the studied factors and depression (effect size of 6.0%-79.5%). Conclusions Both mental distress due to COVID-19 and depression were prevalent among university students in China; the former may have increased the prevalence of the latter. The studied cognitive, behavioral, and psychosocial factors related to COVID-19 may directly or indirectly (via mental distress due to COVID-19) affect depression. Interventions to modify such factors may reduce mental distress and depressive symptoms during the COVID-19 epidemic.
Perioperative treatment compliance, anxiety and depression of elderly patients with ophthalmic surgery and the influential factors.

BACKGROUND Ophthalmic surgery is invasive, and treatment efficacy is affected by a variety of factors. We aimed to analyze perioperative treatment compliance, anxiety and depression of elderly patients undergoing ophthalmic surgery and the influential factors. METHODS The study group comprised 119 elderly patients undergoing ophthalmic surgery between March 2018 and March 2020. Clinical and treatment compliance data of all patients were collected. The self-rating anxiety scale (SAS) and self-rating depression scale (SDS) were administered to all patients, and logistic regression analysis was used for multivariate analysis. RESULTS During the perioperative period the 119 elderly patients had a mean SAS score of 65.13±14.36, and SDS score of 61.94±17.39. Treatment compliance was as follows: 76 cases of complete compliance, 25 of incomplete compliance, and 18 of complete non-compliance. Economic status, complications, treatment options and levels of TNF-α, IL-6, and IL-8 are independent risk factors that affected the compliance of elderly patients undergoing ophthalmology surgery (P<0.05). Education level, marital status, economic status, complications, treatment options and levels of TNF-α, IL-6, and IL-8 were independent risk factors affecting perioperative anxiety and depression. CONCLUSIONS There are many factors affecting the perioperative treatment compliance, anxiety and depression of elderly patients undergoing ophthalmic surgery. Effective intervention measures should be taken to improve patients' compliance, reduce their negative emotions, and improve the surgical efficacy.
Psychosocial outcome measures for conductive and mixed hearing loss treatment: An overview of the relevant literature

Abstract Objective To identify the psychosocial assessments utilized with individuals with conductive and/or mixed hearing loss as part of a broader effort by the Auditory Rehabilitation Outcomes Network (AURONET) group to develop a core set of patient-centred outcome measures. Design A review of articles published between 2006 and 2016 was completed. Included studies had more than three adult participants, were available in English, and reported a psychosocial outcome from any treatment of mixed and/or conductive hearing loss. Study sample Sixty-six articles from seven databases. Results Sixty-six articles met our inclusion/exclusion criteria. Within this set, 15 unique psychosocial or patient-reported outcome measures (PROs) were identified, with the Abbreviated Profile of Hearing Aid Benefit (APHAB) and Glasgow Benefit Inventory (GBI) being the most frequently dispensed. Five of the fifteen were only administered in one study. In-house questionnaires (IHQs) were reported in 19 articles. Conclusions Only 66 (22%) of the 300 articles with outcomes contained a PRO. Some of the mostly frequently employed PROs (e.g., APHAB) were judged to include only social items and no psychological items. Lack of PRO standardization and the use of IHQs make psychosocial comparisons across treatments in this population difficult for patients, clinicians and stakeholders.
The role of alpha-helix on the structure-targeting drug design of amyloidogenic proteins

The most accredited hypothesis links the toxicity of amyloid proteins to their harmful effects on membrane integrity through the formation of prefibrillar-transient oligomers able to disrupt cell membranes. However, damage mechanisms necessarily assume a first step in which the amyloidogenic protein transfers from the aqueous phase to the membrane hydrophobic core. This determinant step is still poorly understood. However, according to our lipid-chaperon hypothesis, free lipids in solution play a crucial role in facilitating this footfall. Free phospholipid concentration in the aqueous phase acts as a switch between ion channel-like pore and fibril formation, so that high free lipid concentration in solution promotes pore and repress fibril formation. Conversely, low free lipids in the solution favor fibril and repress pore formation. This behavior is due to the formation of stable lipid-protein complexes. Here, we hypothesize that the helix propensity is a fundamental requirement to fulfill the lipid-chaperon model. The alpha-helix region seems to be responsible for the binding with amphiphilic molecules fostering the proposed mechanism. Indeed, our results show the dependency of protein-lipid binding from the helical structure presence. When the helix content is substantially lower than the wild type, the contact probability decreases. Instead, if the helix is broadening, the contact probability increases. Our findings open a new perspective for in silico screening of secondary structure-targeting drugs of amyloidogenic proteins.
Harnessing CD8+ T‐cell exhaustion to treat type 1 diabetes

Although immune interventions have shown great promise in type 1 diabetes mellitus (T1D) clinical trials, none are yet in routine clinical use or able to achieve insulin independence in patients. In addition to this, the principles of T1D treatment remain essentially unchanged since the isolation of insulin, almost a century ago. T1D is characterized by insulin deficiency as a result of destruction of insulin‐producing beta cells mediated by autoreactive T cells. Therapies that target beta‐cell antigen‐specific T cells are needed to prevent T1D. CD8+ T‐cell exhaustion is an emerging area of research in chronic infection, cancer immunotherapy, and more recently, autoimmunity. Recent data suggest that exhausted T‐cell populations are associated with improved markers of T1D. T‐cell exhaustion is both characterized and mediated by inhibitory receptors. This review aims to identify which inhibitory receptors may prove useful to induce T‐cell exhaustion to treat T1D and identify limitations and gaps in the current literature.
Infrared Spectroscopy—Mid-infrared, Near-infrared, and Far-infrared/Terahertz Spectroscopy

This article aims to overview infrared (IR) spectroscopy. Simultaneously, it outlines mid-infrared (MIR), near-infrared (NIR), and far-infrared (FIR) or terahertz (THz) spectroscopy separately, and compares them in terms of principles, characteristics, advantages, and applications. MIR spectroscopy is the central spectroscopic technique in the IR region, and is mainly concerned with the fundamentals of molecular vibrations. NIR spectroscopy incorporates both electronic and vibrational spectroscopy; however, in this review, I have chiefly discussed vibrational NIR spectroscopy, where bands due to overtones and combination modes appear. FIR or THz spectroscopy contains both vibrational and rotational spectroscopy. However, only vibrational FIR or THz spectroscopy has been discussed in this review. These three spectroscopy cover wide areas in their applications, making it rather difficult to describe these various topics simultaneously. Hence, I have selected three key topics: hydrogen bond studies, applications of quantum chemical calculations, and imaging. The perspective of the three spectroscopy has been discussed in the last section.
Seizing and realizing the opportunity: A salutogenic perspective on rehabilitation after burnout

BACKGROUND: Most research on burnout has focused on its antecedents, correlates, and consequences. However, little empirical attention has been paid to what constitutes successful rehabilitation after burnout, especially among young employees. OBJECTIVE: The present study empirically examined resources supporting successful rehabilitation after burnout among young employees (between 18 and 35 years of age) from a salutogenic perspective. METHODS: Interpretative phenomenological analysis was used as a methodological framework to explain the experiences of young employees underlying their rehabilitation after burnout. RESULTS: The analysis showed that the rehabilitation process comprises four phases: 1) facing the crisis; 2) addressing the root causes; 3) seizing and achieving the opportunity; and 4) staying at work. Essential overarching resources facilitating successful recovery after burnout included receiving social support from family, friends, and colleagues, as well as having a feeling of control over the rehabilitation process. Participants learned to be aware of potential pitfalls that could trigger burnout symptoms, while having confidence in their ability to prevent burnout from reoccurring. These continuous learning processes were experienced as a prerequisite to remain at work. CONCLUSIONS: Receiving social support and experiencing a feeling of control over the rehabilitation process appear to be key resources in facilitating a stable, meaningful return to work after burnout.
Impact of gas-to-particle partitioning approaches on the simulated radiative effects of biogenic secondary organic aerosol

The oxidation of biogenic volatile organic compounds (BVOCs) gives a range of products, from semi-volatile to extremely low-volatility compounds. To treat the interaction of these secondary organic vapours with the particle phase, global aerosol microphysics models generally use either a thermodynamic partitioning approach (assuming instant equilibrium between semi-volatile oxidation products and the particle phase) or a kinetic approach (accounting for the size dependence of condensation). We show that model treatment of the partitioning of biogenic organic vapours into the particle phase, and consequent distribution of material across the size distribution, controls the magnitude of the first aerosol indirect effect (AIE) due to biogenic secondary organic aerosol (SOA). With a kinetic partitioning approach, SOA is distributed according to the existing condensation sink, enhancing the growth of the smallest particles, i.e. those in the nucleation mode. This process tends to increase cloud droplet number concentrations in the presence of biogenic SOA. By contrast, an approach that distributes SOA according to pre-existing organic mass restricts the growth of the smallest particles, limiting the number that are able to form cloud droplets. With an organically mediated new particle formation mechanism, applying a mass-based rather than a kinetic approach to partitioning reduces our calculated global mean AIE due to biogenic SOA by 24 %. Our results suggest that the mechanisms driving organic partitioning need to be fully understood in order to accurately describe the climatic effects of SOA.
Plantar hyperhidrosis associated with primary palmar hyperhidrosis: Outcome following video-assisted thoracoscopic sympathectomy

Introduction Primary palmar hyperhidrosis is an abnormal over-sweating of palms. It is usually associated with plantar hyperhidrosis. Video-assisted thoracoscopic sympathectomy is the treatment of choice for palmar hyperhidrosis; however, it may affect plantar hyperhidrosis. Objectives The aim of this study was to evaluate the effect of thoracoscopic sympathectomy on plantar hyperhidrosis. Methods This prospective study included patients who presented to the Cardiothoracic Surgery Department with primary palmo-planter hyperhidrosis and received thoracoscopic sympathectomy between January 2014 and December 2018. Preoperatively, patients scored subjectively the degree of palmar and plantar hyperhidrosis on Visual Analogue Scale. Following surgery, scoring was performed at three intervals: 7, 30, and 180 days. Presence of compensatory sweating and its scoring was obtained at the same intervals. Complications and patient satisfaction were recorded. Results A total of 518 patients were included. Complication rate, excluding compensatory hyperhidrosis, was 2.7%. Preoperative Visual Analogue Scale score for palmar hyperhidrosis was 9.9 ± 3.8 that following thoracoscopic sympathectomy decreased to 0.041 ± 0.2 on the seventh postoperative day. Further decrease to 0.3 ± 0.16 was noted on the 30th day and 180th day postoperatively. Preoperative Visual Analogue Scale score for plantar hyperhidrosis was 9.54 ± 0.66 that following sympathectomy decreased to 2.27 ± 1.67 on the seventh postoperative day. However, slight insignificant increase was noted to become 2.73 ± 1.65 on the 30th day and 6th month postoperatively. Compensatory hyperhidrosis was recorded in 3.9% of patients at 6th month postoperatively. Conclusion Palmar hyperhidrosis is usually associated with plantar hyperhidrosis. Thoracoscopic sympathectomy is an effective and safe treatment for palmar hyperhidrosis. It may completely or partially cure plantar hyperhidrosis.
Learning Atomic Interactions through Solvation Free Energy Prediction Using Graph Neural Networks

Solvation free energy is a fundamental property that influences various chemical and biological processes, such as reaction rates, protein folding, drug binding, and bioavailability of drugs. In this work, we present a deep learning method based on graph networks to accurately predict solvation free energies of small organic molecules. The proposed model, comprising three phases, namely, message passing, interaction, and prediction, is able to predict solvation free energies in any generic organic solvent with a mean absolute error of 0.16 kcal/mol. In terms of accuracy, the current model outperforms all of the proposed machine learning-based models so far. The atomic interactions predicted in an unsupervised manner are able to explain the trends of free energies consistent with chemical wisdom. Further, the robustness of the machine learning-based model has been tested thoroughly, and its capability to interpret the predictions has been verified with several examples.
Polymeric nanoparticles containing rapamycin and autoantigen induce antigen-specific immunological tolerance for preventing vitiligo in mice

ABSTRACT Vitiligo is an autoimmune disease in which pigment is lost in patches of the skin. CD4+ T cells are implicated in vitiligo while regulatory T cells (Tregs) could ameliorate vitiligo. Rapamycin together with autoantigen have been shown to induce immunological tolerance and promote Tregs in multiple autoimmune diseases. In the current study, we synthesized nanoparticles containing rapamycin and autoantigen HEL46-61 (NPHEL46-61/Rapa) and investigated their effects on vitiligo. We treated bone marrow-derived dendritic cells (BMDCs) from TrpHEL mice with NPHEL46-61/Rapa and monitored the phenotype of BMDCs. We investigated the effects of NPHEL46-61/Rapa-treated BMDCs on CD4+ T cell proliferation and differentiation. We administrated NPHEL46-61/Rapa to TCR-TrpHEL mice and investigated the effects on vitiligo. We found that BMDCs can uptake the NPHEL46-61/Rapa, which resulted in decreased expression of costimulation molecules CD80 and CD86 in BMDCs. BMDCs treated with NPHEL46-61/Rapa suppressed antigen-specific CD4+ T cell proliferation while promoted the differentiation of these CD4+ T cell to Tregs in vitro. Administration of NPHEL46-61/Rapa to TCR-TrpHEL mice ameliorated vitiligo, promoted Treg production, and suppressed IFN-γ and IL-6 production, while induced IL-10 production. Therefore, our study provides experimental evidence that nanoparticles containing rapamycin and autoantigen could induce antigen-specific immunological tolerance and prevent vitiligo.