Miracle-dz/UniFAR-FTUs huggingface dataset:
Motilimonas cestriensis sp. nov., isolated from an inland brine spring in Northern England

A novel slightly halophilic Gram-stain-negative bacterial strain (MKS20T) was isolated from a brine sample collected from one of the Anderton brine springs in the Cheshire salt district, located in Northern England. Phylogenetic analysis of the 16S rRNA gene sequence revealed a close proximity to Motilimonas eburnea (98.30 %), followed by Motilimonas pumila (96.62 %), the two currently described species within the genus Motilimonas. Strain MKS20T forms white-beige-pigmented colonies and grows optimally at 28–30 °C, in 1–3 % (w/v) NaCl and at pH 7–7.5. The strain was facultatively anaerobic and showed a broader range of carbohydrate use than other species in the genus Motilimonas. Q-8 was the sole respiratory quinone and the major fatty acids (>10 %) were summed feature 3 (C16 : 1 ω6c and/or C16 : 1 ω7c) and C16 : 0. The polar lipid profile included diphosphatidylglycerol, phosphatidylethanolamine, phosphatidyglycerol and several unidentified lipids. The G+C content of the genomic DNA was 44.2 mol%. Average nucleotide identity and DNA–DNA hybridization data were consistent with assignment to a separate species. Based on the phylogenetic and genomic-based analyses, as well as physiological and biochemical characteristics, we propose that strain MKS20T (=DSM 109936T, MCCC 1K04071T) represents a new species of the genus Motilimonas, with the name Motilimonas cestriensis sp. nov.
The psychological experiences of Lebanese ground zero front-line nurses during the most recent COVID-19 outbreak post Beirut blast: A qualitative study

Background: For the past 2 months the number of COVID-19 cases in Lebanon has been on the rise, while frontline nurses after the Beirut Blast of August 4th have been practicing through limited resources and a challenging context. Aim: This paper aims at exploring the psychological experiences of Lebanese frontline nurses serving at ground zero hospital during the current COVID-19 outbreak. Setting: This study was carried out in three main ground-zero hospitals in Beirut which are receiving COVID-19 cases. Method: This study have employed a phenomenological exploratory qualitative research design, where virtual interviews were conducted with 18 frontline nurses during the second week of January 2021. Results: Thematic analysis of the data expressed by the frontline nurses working in the approached ground-zero hospitals gave rise to five themes, namely ‘helplessness and impending doom’, ‘increased mortality rates and depressive mood’, ‘fear of death and obsessive thinking’, ‘flashbacks, panic, and incompetence’, and ‘public recklessness, governmental responsibility, and anger‘. Conclusion: The frontline nurses working at ground zero hospitals in Beirut are facing significant psychological challenges that should be mediated by the government and health policymakers in order to safeguard the quality of care and avoid higher mortality rates.
Evolution of assay interference concepts in drug discovery

Biological assays for small molecules are vulnerable to experimental limitations and artifacts. False-positive activity readouts represent a recurrent and well-appreciated problem for high-throughput screening. Accordingly, hits from a primary high-throughput screen are usually subjected to secondary assays to reevaluate activity signals and establish dose– response behavior of active compounds. Typically, such confirmatory assays eliminate many but not all false-positive hits. While assay artifacts may frequently be attributable to technical issues, they are also caused by compounds that are not specifically active against a target of interest, but fake positive assay signals by a variety of undesired mechanisms. Such chemical entities are often termed assay interference compounds. For drug discovery, major problems arise when such interference compounds are difficult to identify and camouflaged false-positives enter hit-to-lead and lead optimization stages of the discovery pipeline. Significant time and resources might be wasted until their artificial nature is ultimately uncovered, especially if derivatives of pseudo-hits approach the realm of potential candidate compounds. Furthermore, undetected false-positives plague science and hinder progress. For example, in academic settings, new compounds – including those originating from computational screening – are often only investigated in a single assay system. If subtle artifacts occur under such conditions, they are notoriously difficult to detect. Once published, pseudo-hits tend to propagate through the literature and frequently give rise to follow-up studies that are doomed to fail and misleading at best. Over the past decade, it has increasingly been recognized that assay interference effects often are of unexpectedly large magnitude, continue to compromise drug discovery efforts, and pollute the scientific literature [1]. Most of these problems are caused by assay interference compounds, ‘chemical con artists’ [2], which are often rather difficult to uncover [1,2]. Different concepts have been introduced for recognizing and combating assay interference, which are of critical importance for the practice of biological screening and medicinal chemistry. However, these concepts are also controversially viewed for reasons discussed below. To assess their value, different scientific approaches and viewpoints should be taken into consideration.
Evaluation of the Impact of Skewness, Clustering, and Probe Sampling Plan on Aflatoxin Detection in Corn

Probe sampling plans for aflatoxin in corn attempt to reliably estimate concentrations in bulk corn given complications like skewed contamination distribution and hotspots. To evaluate and improve sampling plans, three sampling strategies (simple random sampling, stratified random sampling, systematic sampling with U.S. GIPSA sampling schemes), three numbers of probes (5, 10, 100, the last a proxy for autosampling), four clustering levels (1, 10, 100, 1,000 kernels/cluster source), and six aflatoxin concentrations (5, 10, 20, 40, 80, 100 ppb) were assessed by Monte‐Carlo simulation. Aflatoxin distribution was approximated by PERT and Gamma distributions of experimental aflatoxin data for uncontaminated and naturally contaminated single kernels. The model was validated against published data repeatedly sampling 18 grain lots contaminated with 5.8–680 ppb aflatoxin. All empirical acceptance probabilities fell within the range of simulated acceptance probabilities. Sensitivity analysis with partial rank correlation coefficients found acceptance probability more sensitive to aflatoxin concentration (−0.87) and clustering level (0.28) than number of probes (−0.09) and sampling strategy (0.04). Comparison of operating characteristic curves indicate all sampling strategies have similar average performance at the 20 ppb threshold (0.8–3.5% absolute marginal change), but systematic sampling has larger variability at clustering levels above 100. Taking extra probes improves detection (1.8% increase in absolute marginal change) when aflatoxin is spatially clustered at 1,000 kernels/cluster, but not when contaminated grains are homogenously distributed. Therefore, taking many small samples, for example, autosampling, may increase sampling plan reliability. The simulation is provided as an R Shiny web app for stakeholder use evaluating grain sampling plans.
Sex differences in functional network dynamics observed using coactivation pattern analysis

ABSTRACT Sex differences in the organization of large-scale resting-state brain networks have been identified using traditional static measures, which average functional connectivity over extended time periods. In contrast, emerging dynamic measures have the potential to define sex differences in network changes over time, providing additional understanding of neurobiological sex differences. To meet this goal, we used a Coactivation Pattern Analysis (CAP) using resting-state functional magnetic resonance imaging data from 181 males and 181 females from the Human Connectome Project. Significant main effects of sex were observed across two independent imaging sessions. Relative to males, females spent more total time in two transient network states (TNSs) spatially overlapping with the dorsal attention network and occipital/sensory-motor network. Greater time spent in these TNSs was related to females making more frequent transitions into these TNSs compared to males. In contrast, males spent more total time in TNSs spatially overlapping with the salience network, which was related to males staying for longer periods once entering these TNSs compared to females. State-to-state transitions also significantly differed between sexes: females transitioned more frequently from default mode network (DMN) states to the dorsal attention network state, whereas males transitioned more frequently from DMN states to salience network states. Results show that males and females spend differing amounts of time at rest in two distinct attention-related networks and show sex-specific transition patterns from DMN states into these attention-related networks. This work lays the groundwork for future investigations into the cognitive and behavioral implications of these sex-specific network dynamics.
Experimentally evoked pain in Alzheimer's disease

Supplemental Digital Content is Available in the Text. ABSTRACT Background: Pain continues to be underrecognized and undertreated in Alzheimer's disease (AD) while existing guidance about pain assessment and management in dementia is not widespread. Brain regions involved in pain processing and modulation are damaged during AD, and the pain experience in AD is not well understood. Experimental pain studies using psychophysics can further our understanding of the pain experience in AD, which may lead to improved assessment and management of pain in people living with AD. Objective: A systematic review was conducted to explicate the current understanding of experimentally evoked pain in AD from primary research using psychophysical methods. Data Sources: Peer-reviewed publications were found via PubMed, CINAHL, and PsycINFO. A total of 18 primary research, peer-reviewed full articles that met inclusion criteria were included, representing 929 total participants. Conclusions: Experimentally evoked pain in people with AD demonstrates that despite cognitive impairment and a reduced ability to effectively communicate, individuals with AD experience pain similar to or more unpleasant than cognitively intact older adults. This may mean amplified pain unpleasantness in people with AD. Implications for practice: Our current best practices need to be widely disseminated and put into clinical practice. Self-report of pain continues to be the gold standard, but it is ineffective for noncommunicative patients and those unable to understand pain scales or instructions because of memory/cognitive impairment. Instead, pain treatment should be ethically initiated based on patient reports and behaviors, caregiver/surrogate reports, review of the medical record for painful conditions, analgesic trials, and regular reassessments.
ASH: an Automatic pipeline to generate realistic and individualized chronic Stroke volume conduction Head models

Objective. Large structural brain changes, such as chronic stroke lesions, alter the current pathways throughout the patients’ head and therefore have to be taken into account when performing transcranial direct current stimulation simulations. Approach. We implement, test and distribute the first MATLAB pipeline that automatically generates realistic and individualized volume conduction head models of chronic stroke patients, by combining the already existing software SimNIBS, for the mesh generation, and lesion identification with neighborhood data analysis, for the lesion identification. To highlight the impact of our pipeline, we investigated the sensitivity of the electric field distribution to the lesion location and lesion conductivity in 16 stroke patients’ datasets. Main results. Our pipeline automatically generates 1 mm-resolution tetrahedral meshes including the lesion compartment in less than three hours. Moreover, for large lesions, we found a high sensitivity of the electric field distribution to the lesion conductivity value and location. Significance. This work facilitates optimizing electrode configurations with the goal to obtain more focal brain stimulations of the target volumes in rehabilitation for chronic stroke patients.
Deprescribing in Older Adults With Cancer and Limited Life Expectancy: An Integrative Review

Polypharmacy is common in older adults with cancer and deprescribing potentially inappropriate medications becomes very relevant when life expectancy decreases due to metastatic disease. Especially preventive medications may no longer be beneficial, because they may decrease quality of life and reduction in morbidity and mortality may be futile. Although deprescribing of preventive medication is common in the last period of life, it is still unusual during active cancer treatment for advanced disease, although life expectancy is often limited to less than 1 to 2 years in that stage. We performed a systematic search of the literature in Pubmed and Embase on the discontinuation of commonly utilized groups of preventive medication and evaluated the evidence of potential benefits and harms in patients aged 65 years or older with cancer and a limited life expectancy (LLE). From 21 included studies, it can be concluded that deprescribing lipid lowering drugs, antihypertensive drugs, osteoporosis drugs and antihyperglycemic drugs is feasible in a considerable part of patients with a LLE. Discontinuation may be performed safely, without the occurrence of serious adverse events or decrease of survival. The only study that addressed quality of life after deprescribing showed that discontinuation of statins improves quality of life in patients with a LLE. Recurrence of symptoms requiring reintroduction occurred in 0-13% of patients on antihyperglycemic treatment and 8-60% of patients using antihypertensive drugs. In order to reduce pill burden and futile treatment clinicians should discuss deprescribing of preventive medication with older patients with advanced cancer and a LLE.
Investigation of Acidic Texturization for Multicrystalline Silicon Solar Cells

A new texturing method especially for multicrystalline silicon solar cells was investigated. This technique is based on a maskless acidic etching of silicon. It can texturize surfaces quite homogeneously in a short time and eliminate a saw damage removal process. The authors showed phosphoric acid (H{sub 3}PO{sub 4}) is preferable as a catalytic agent to moderate etching rates without effecting texturing. A simulation was carried out in an attempt to achieve lower reflectance. It was found that the reflectance is dependent on the quotient of the depth and the width of texture (h/D). The authors found that surface active agents are effective in increasing the h/D value. The reflectance decreases corresponding to h/D, and measured reflectance is in good agreement with the simulation. Comparing the electrical characteristics of an acidic textured multicrystalline solar cell and an alkaline textured one, the short-circuit current density of acidic texturing is higher than the other.
Projected economic burden of pancreatic cancer in Sweden in 2030

Abstract Background Pancreatic cancer is predicted to become the second most common cause of cancer-related death by 2030. The objective of this study was to estimate the economic burden of pancreatic cancer for the years 2018 and 2030 based on changing demographics and incidence rates in Sweden. Method The incidence of pancreatic cancer in Sweden and additional relevant data were obtained from official statistics. A linear regression model and the mean incidence rates 2008–2018 were applied to calculate the incidence in 2030. An economic model based on the human capital method was created to calculate the indirect cost of pancreatic cancer in 2018 and 2030. Costs associated with surgery, radiology, oncology, and palliative care constituted the direct costs. A sensitivity analysis was performed. Results The incidence of pancreatic cancer in Sweden in the year 2018 was 1352 patients and projected to between 1554 (+15%) and 1736 (+28%) in 2030. The total cost was calculated to €125 million in 2018 and between €210 million (+68%) and €225 million (+80%) in 2030. The indirect cost in the ≤65-year-old group was €328,344 in 2018 and between €380,738 and €382,109 per individual in 2030. Conclusions The economic burden of pancreatic cancer is expected to increase in Sweden by 2030 due to the increasing incidence of the disease and changing demographics. Pancreatic cancer is a growing health care problem in urgent need of advancements in prevention, early detection, treatment, and control of the disease.
Bidirectional Association between Psoriasis and Atopic Dermatitis: A Nationwide Population-Based Cohort Study

Background: There have been some reports on the coexistence of psoriasis and atopic dermatitis; however, the longitudinal relationship between these two diseases remains unclear. Objective: This study aimed to investigate the bidirectional association between psoriasis and atopic dermatitis. Methods: This cohort study recruited patients from the National Health Insurance Research Database in Taiwan. We included 8,206 patients with psoriasis and 32,824 matched controls to assess the risk of atopic dermatitis and 25,743 patients with atopic dermatitis and 102,972 matched controls to assess the risk of psoriasis. Cox regression model was used for the analyses. Results: After adjusting for potential confounders, patients with psoriasis had a higher risk of atopic dermatitis (adjusted hazard ratio [aHR] 13.01; 95% CI 10.23–16.56) than the controls. Patients with atopic dermatitis had a higher risk of psoriasis (aHR 10.37; 95% CI 6.85–15.69) than the controls. Stratified analyses revealed similar results in both sexes and all age groups. Conclusion: Our study demonstrated a bidirectional association between psoriasis and atopic dermatitis, suggesting that psoriasis and atopic dermatitis are not mutually exclusive and may share some biological mechanisms.
The BOP‐type co‐transcriptional regulator NODULE ROOT1 promotes stem secondary growth of the tropical Cannabaceae tree Parasponia andersonii

Summary Tree stems undergo a massive secondary growth in which secondary xylem and phloem tissues arise from the vascular cambium. Vascular cambium activity is driven by endogenous developmental signalling cues and environmental stimuli. Current knowledge regarding the genetic regulation of cambium activity and secondary growth is still far from complete. The tropical Cannabaceae tree Parasponia andersonii is a non‐legume research model of nitrogen‐fixing root nodulation. Parasponia andersonii can be transformed efficiently, making it amenable for CRISPR‐Cas9‐mediated reverse genetics. We considered whether P. andersonii also could be used as a complementary research system to investigate tree‐related traits, including secondary growth. We established a developmental map of stem secondary growth in P. andersonii plantlets. Subsequently, we showed that the expression of the co‐transcriptional regulator PanNODULE ROOT1 (PanNOOT1) is essential for controlling this process. PanNOOT1 is orthologous to Arabidopsis thaliana BLADE‐ON‐PETIOLE1 (AtBOP1) and AtBOP2, which are involved in the meristem‐to‐organ‐boundary maintenance. Moreover, in species forming nitrogen‐fixing root nodules, NOOT1 is known to function as a key nodule identity gene. Parasponia andersonii CRISPR‐Cas9 loss‐of‐function Pannoot1 mutants are altered in the development of the xylem and phloem tissues without apparent disturbance of the cambium organization and size. Transcriptomic analysis showed that the expression of key secondary growth‐related genes is significantly down‐regulated in Pannoot1 mutants. This allows us to conclude that PanNOOT1 positively contributes to the regulation of stem secondary growth. Our work also demonstrates that P. andersonii can serve as a tree research system.
Adverse childhood experiences, racial microaggressions, and alcohol misuse in Black and White emerging adults.

OBJECTIVE Research indicates that emerging adults (EAs) are at an increased risk for heavy drinking and its associated alcohol problems, and that both proximal and distal stressors (e.g., adverse childhood experiences [ACEs], and subtle racial discrimination [racial microaggressions]) may contribute to these high-risk outcomes. We investigated the relationship of ACEs with alcohol consumption and alcohol problems in a sample of Black and White EAs, and racial microaggressions with alcohol consumption and alcohol problems in the Black EAs in our sample. METHOD Six hundred two EAs (41.5% Black, 47% White; 57.3% women) completed measures assessing ACEs, alcohol consumption, and alcohol problems. One hundred ninety-six Black EAs in the sample were also asked to complete a measure of racial microaggressions that assessed their level of distress related to these experiences. RESULTS Regression analyses demonstrated a positive association of ACEs with alcohol consumption and alcohol problems. Sex moderated the relation of ACEs with alcohol consumption such that the positive relationship between ACEs and alcohol consumption was minimally stronger for females. College status moderated the relation of ACEs with alcohol consumption such that the relationship between ACEs and alcohol consumption was stronger for college students than non-college students. Racial microaggressions were positively associated with alcohol problems, but not alcohol consumption. CONCLUSION Findings underscore the importance of childhood stressors with alcohol consumption and problems for EAs, and the need for additional research on racial microaggressions and alcohol problems in Black EAs. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
Impact of mobility restriction in COVID-19 superspreading events using agent-based model

COVID-19 pandemic is an immediate major public health concern. The search for the understanding of the disease spreading made scientists around the world turn their attention to epidemiological studies. An interesting approach in epidemiological modeling nowadays is to use agent-based models, which allow to consider a heterogeneous population and to evaluate the role of superspreaders in this population. In this work, we implemented an agent-based model using probabilistic cellular automata to simulate SIR (Susceptible-Infected-Recovered) dynamics using COVID-19 infection parameters. Differently to the usual studies, we did not define the superspreaders individuals a priori, we only left the agents to execute a random walk along the sites. When two or more agents share the same site, there is a probability to spread the infection if one of them is infected. To evaluate the spreading, we built the transmission network and measured the degree distribution, betweenness, and closeness centrality. The results displayed for different levels of mobility restriction show that the degree reduces as the mobility reduces, but there is an increase of betweenness and closeness for some network nodes. We identified the superspreaders at the end of the simulation, showing the emerging behavior of the model since these individuals were not initially defined. Simulations also showed that the superspreaders are responsible for most of the infection propagation and the impact of personal protective equipment in the spreading of the infection. We believe that this study can bring important insights for the analysis of the disease dynamics and the role of superspreaders, contributing to the understanding of how to manage mobility during a highly infectious pandemic as COVID-19.