Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered energy metabolism and metabolic gene expression associated with increased metastatic capacity identified in MDA-MB-231 cell line variants

Aim: Despite current advances in therapies and the gradual decline in breast cancer-related mortality, metastasis remains a major therapeutic challenge for treatment. Energy reprogramming is now recognized to be an important part of tumorigenic processes, but its relevance in metastatic dissemination has yet to be elucidated. Methods: Using the MDA-MB-231HM.LNm5 cell line, a novel, highly metastatic variant line derived from TN human breast adenocarcinoma MDA-MB-231 line, alteration in growth and energy metabolisms associated with enhanced metastatic potential were described. Glycolysis and oxidative phosphorylation (OXPHOS) was characterized using the seahorse XF analyzer. Whole transcriptome sequencing (RNA-seq) and quantitative real-time PCR was used to ascertain expression differences in metabolic genes. Results: We observed reduced proliferation, and an elevation of both glycolytic and OXPHOS metabolism in the highly metastatic daughter line. The elevated metabolic rate is only partially reflected by transcript levels of relevant metabolic regulators. Heightened mitochondrial respiration is potentially underpinned by increased expression mitochondrial electron transport chain components. However, increased glycolysis was not underpinned by up-regulation of metabolic genes encoding enzymes participating in glycolysis. Conclusion: Our results indicate breast tumour cells with elevated metastatic propensity are more metabolic active. We also identified differentially expressed metabolic genes, such as IDH2, that may play a part in the metastatic process beyond energy reprogramming. with Resazurin reagent containing 1.5% (w/v) Resazurin, 0.25 (w/v) methylene blue, 2.9% (w/v) potassium hexacyanoferrate (III) and 4.22% (w/v) potassium hexacyanoferrate (II) trihydrate for 2 h at 37 °C in 5% CO 2 . Resorufin formation was measured fluorometrically (excitation 570 nm; emission 620 nm) using a FlexStationII (Molecular Devices, Sunnyvale, CA, USA). Results are expressed in relative fluorescent units.
Featured Series Introduction: SWAT Applications for Emerging Hydrologic and Water Quality Challenges

Many global to local-scale issues such as changing climate, urbanization, intensification of agricultural activities, deforestation, and geopolitical conflicts pose serious challenges to the availability, accessibility, and management of water resources. Researchers, decision makers, and the general public are interested in understanding the impacts of these emerging issues so that water resources can be managed sustainably in the future. Besides availability, decision makers and the general public are also interested in how water quality will be impacted by pesticides, nutrients, pathogens, and emerging contaminants including pharmaceuticals and hormones, which are a serious concern for water security. Simulation models play a critical role in understanding the hydrologic processes of a system, the system’s behavior, and how it will change in the future due to natural and anthropogenic factors. A plethora of models exist in the field of hydrology to address hydrologic and water quality issues at various spatial and temporal scales. Among these, the Soil and Water Assessment Tool (SWAT) (Arnold et al., 1998) has been used globally to address issues related to hydrology, water quality, and agricultural management (e.g., Gassman et al., 2014; Abbaspour et al., 2015; Cousino et al., 2015; Basheer et al., 2016). SWAT is a semidistributed, conceptual and continuous time catchment-scale hydrologic model supported and used by a global community of researchers, decision makers, and practitioners. The model is open source, has multiple geographic information system interfaces such as ArcSWAT and QSWAT for creating input files, and user-friendly tools for model calibration. SWAT has been continuously improved and expanded since it was created in the early 1990s. Arnold and Fohrer (2005) describe the most significant improvements of the model between releases from its creation until SWAT2000 (e.g., incorporation of multiple hydrologic response units, instream kinetic routines, and Green-Ampt infiltration). Recent improvements include the incorporation of routing capabilities between landscape units or grids (Arnold et al., 2010). SWAT is ideally suited for addressing a wide array of issues related to climate change, land use change, bioenergy crops, blue and green water availability, sediment transport, nutrient cycle and contaminant loads, and best management practices. In addition, the model is
Labour income inequality in Mexico: Puzzles solved and unsolved

We analyse the evolution and proximate determinants of labour income inequality in Mexico between 1989 and 2017. Labour income inequality increased between 1989 and 1994 and declined between 1994 and 2006. What happened after 2006 is subject to uncertainty. The national labour force survey shows a steady decline and the income expenditure survey suggests that inequality increased. We correct for high and rising item (labour income) non-response and underrepresentation of high-wage earners through a ‘hot deck’ imputation method and post-survey weight adjustments. We obtain the new weights for formal workers from tabulations recently released by the Mexican social security administration. For informal workers, we correct using the hot deck imputation method. With corrected data, inequality no longer declines between 2006 and 2017.
Repurposing Known Drugs as Covalent and Non-covalent Inhibitors of the SARS-CoV-2 Papain-Like Protease

In the absence of an approved vaccine, developing effective severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antivirals is essential to tackle the current pandemic health crisis due to the coronavirus disease 2019 (COVID-19) spread. As any traditional drug discovery program is a time-consuming and costly process requiring more than one decade to be completed, in silico repurposing of existing drugs is the preferred way for rapidly selecting promising clinical candidates. We present a virtual screening campaign to identify covalent and non-covalent inhibitors of the SARS-CoV-2 papain-like protease (PLpro) showing potential multitarget activities (i.e., a desirable polypharmacology profile) for the COVID-19 treatment. A dataset including 688 phase III and 1,702 phase IV clinical trial drugs was downloaded from ChEMBL (version 27.1) and docked to the recently released crystal structure of PLpro in complex with a covalently bound peptide inhibitor. The obtained results were analyzed by combining protein–ligand interaction fingerprint similarities, conventional docking scores, and MM-GBSA–binding free energies and allowed the identification of some interesting candidates for further in vitro testing. To the best of our knowledge, this study represents the first attempt to repurpose drugs for a covalent inhibition of PLpro and could pave the way for new therapeutic strategies against COVID-19.
Lockdown During COVID-19 and the Increase of Frailty in People With Neurological Conditions

Governments around the globe have introduced quarantine, lockdown, and mandatory isolation to slow the transmission of COVID-19. These public health and policy measures aim to protect the public and vulnerable people. This perspective paper argues that the impacts of lockdown (such as social disconnection, reduced exercise, and fewer physiotherapy treatments) may be amplified for people with neurological conditions with subsequent increases in frailty. The paper outlines why this may occur, and explores how adverse impacts for these vulnerable populations may be minimized through strategies such as telehealth, exercise programs, and health policies.
Disrupted Rhythmicity and Vegetative Functions Relate to PTSD and Gender in Earthquake Survivors

Background: Increasing evidence indicates that survivors to traumatic events may show disruption of sleep pattern, eating and sexual behaviors, and somatic symptoms suggestive of alterations of biorhythmicity and vegetative functions. Therefore, the aim of this study was to investigate these possible alterations in a sample of survivors in the aftermath of earthquake exposure, with particular attention to gender differences and impact of post-traumatic stress disorder (PTSD). Methods: High school senior students, who had been exposed to the 2009 L'Aquila earthquake, were enrolled 21 months after the traumatic event and evaluated by the Trauma and Loss Spectrum Self-Report to investigate PTSD rates and by a domain of the Mood Spectrum Self-Report–Lifetime Version (MOODS-SR), to explore alterations in circadian/seasonal rhythms and vegetative functions. Results: The rates of endorsement of MOODS-SR rhythmicity and vegetative functions domain and subdomain scores were significantly higher in survivors with PTSD with respect to those without it. Among all earthquake survivors, women reported higher scores than men on the rhythmicity and vegetative functions domain and subdomain scores, except for the rhythmicity and sexual functions ones. Female survivors without PTSD showed significantly higher scores than men in the rhythmicity and vegetative functions total scores and the sleep and weight and appetite subdomains. Potentially traumatic events burden predicted rhythmicity and vegetative functions impairment, with a moderation effect of re-experiencing symptoms. Conclusions: We report impairments in rhythmicity, sleep, eating, and sexual and somatic health in survivors to a massive earthquake, particularly among subjects with PTSD and higher re-experiencing symptoms, with specific gender-related differences. Evaluating symptoms of impaired rhythmicity and vegetative functions seems essential for a more accurate assessment and clinical management of survivors to a mass trauma.
What Really Changed? Environments, Instruction, and 21st Century Tools in Emergency Online English Language Arts Teaching in United States Schools During the First Pandemic Response

In this article, a teacher educator and two veteran teachers of 9–12 English Language Arts (ELA) inquire into the opportunities, challenges, and lessons learned from the abrupt transition to online learning caused by the COVID-19 pandemic. The shared setting was a major metropolitan area. The fundamental question addressed is What really changed? In ELA classes that were already rich in digital resources, and where assignments were regularly submitted using internet-based learning management systems, the Spring 2020 school close-down and move to online instruction nevertheless meant profound changes to the authors’ teaching lives. In this article they investigate the approximately 12 weeks that concluded the first pandemic semester, focusing on the impact on teaching and learning environments, instructional purposes, and 21st century tools. The authors believe these changes will have consequences in future classrooms, in whatever physical or virtual contexts teachers find themselves delivering instruction.
Analgesic Effect Comparison Between Nalbuphine and Sufentanil for Patient-Controlled Intravenous Analgesia After Cesarean Section

Background: Efficient maternal pain relief after cesarean delivery remains challenging, but it is important to improve outcomes for the mother and the newborn during the puerperium. We compared the analgesic effect of nalbuphine (a κ receptor agonist/μ receptor antagonistic) with that of sufentanil (a µ-receptor agonist) in patient-controlled intravenous analgesia (PCIA) after cesarean section. Methods: We enrolled 84 patients scheduled for elective cesarean sections with spinal anesthesia and randomized them into either nalbuphine or sufentanil groups (42 patients each). Pain scores, PCIA drug consumptions, degree of satisfaction, and adverse events were recorded as outcome measures. Results: The pain scores at rest and uterine cramping pain scores in the nalbuphine group were lower than those in the sufentanil group at 6, 12, and 24 h after the operation. Also, the pain scores while switching to a seated position were lower in the nalbuphine group than in the sufentanil group at 6 and 12 h after the operation (p < 0.05). We found no significant differences in the PCIA drug consumption between the two groups. The degree of satisfaction in patients in the nalbuphine group was higher than that of patients in the sufentanil group (p = 0.01). Adverse events did not differ in the two groups. Conclusion: PCIA with nalbuphine provides better analgesia and higher patient satisfaction than sufentanil after cesarean section.
Caudate Functional Connectivity Associated With Weight Change in Adolescents

Background Childhood obesity has become a global epidemic and the etiology of maladaptive ingestive behavior in children warrants further research. Mounting evidence suggests that the caudate is associated with body weight gain and obesity in adults. In adolescents, however, how caudate-related neural networks are associated with body weight gain is unclear because their central nervous systems are still developing. Objectives The current longitudinal resting-state functional magnetic resonance imaging (rs-fMRI) study was conducted to investigate the hypothesis that caudate-related neural networks have a role in weight gain in adolescents. Methods The study included 20 healthy adolescents with a mean age of 17.5 ± 2.0 years and a mean body mass index of 20.6 ± 2.1 who underwent baseline rs-fMRI then follow-up rs-fMRI approximately 1 year later. Body mass index (BMI) was measured at both timepoints. Seed-based functional connectivity analysis was utilized to analyze caudate-related functional connectivity (FC) using the caudate as a seed. Associations between caudate-related FC and BMI at baseline were assessed, as were associations between change in BMI and caudate-related FC between baseline and follow-up. Results At baseline, greater caudate-lateral prefrontal cortex FC was correlated with lower BMI (family wise error-corrected p < 0.05). Compared to the baseline, increased FC in the caudate-lateral prefrontal cortex at follow up were negatively associated with increased BMI (p < 0.05). Conclusion Given that the lateral prefrontal cortex and caudate are associated with inhibitory control, the caudate-lateral prefrontal cortex FC may have a preventive effect on weight gain in adolescents. The results of the current study suggest that developing inhibitory control would lead to the prevention of childhood obesity.
Dietary Supplementation of ε-Polylysine Beneficially Affects Ileal Microbiota Structure and Function in Ningxiang Pigs

Intestinal microbiota plays an important role in the health of animals. However, little is known about the gut microbiota in Ningxiang pigs. Thus, we investigated how dietary supplementation with different ε-polylysine concentrations (0, 20, 40, 80, and 160 ppm) affected the ileal microbiota in Ningxiang pigs using a replicated 5 × 5 Latin square method. Each experimental period included 10 days for diet adaptation, 3 days for feces collection and 2 days for digesta collection. The ileal contents were collected and used for sequencing of the V3–V4 hypervariable region of the 16S rRNA gene. The results revealed that ε-polylysine significantly decreased the digestibility of crude protein and crude fiber, as well as the utilization of metabolizable energy (P < 0.05). The relative abundances of 19 bacterial genera significantly increased, while those of 26 genera significantly decreased (P < 0.05). In addition, ε-polylysine increased the abundance of some bacteria (e.g., Faecalibacterium, Bifidobacterium, and lactic acid bacteria) and inhibited some other bacteria (e.g., Micrococcaceae, Acinetobacter, Anaerococcus, Peptoniphilus, Dehalobacterium, Finegoldia, Treponema, and Brevundimonas). Furthermore, based on the 16S rRNA gene data and data from the precalculated GreenGenes database, bacterial communities in the ileal contents exhibited enhanced functional maturation, including changes in the metabolism of carbohydrates, amino acids (e.g., alanine, lysine, tryptophan, cysteine, and methionine), cofactors, and vitamins (e.g., biotin, thiamine, and folate), as well as in the activity of the insulin signaling pathway. This study suggests that ε-polylysine may influence the utilization of feed nutrients by Ningxiang pigs, including proteins, lipids, metabolizable energy, and fiber, by regulating the gut microbiota.
Whole-Genome Sequencing of Bradyrhizobium diazoefficiens 113-2 and Comparative Genomic Analysis Provide Molecular Insights Into Species Specificity and Host Specificity

In the present study, we sequenced the complete genome of Bradyrhizobium diazoefficiens 113-2. The genomic characteristics of six selected rhizobial strains (two fast-growing rhizobia, two medium-slow-growing rhizobia and two slow-growing rhizobia) with four different legume hosts were analyzed by comparative genomic analysis. Genomes of B. diazoefficiens 113-2 and B. diazoefficiens USDA110 were found to share a large synteny blocks and a high ANI value, supporting 113-2 as a strain of B. diazoefficiens. 5,455 singletons and 11,656 clusters were identified among the six rhizobia genomes, and most of the pair-wise comparisons clusters were shared by the two genomes of strains in the same genus. Similar genus-specific gene numbers in the assigned COG functional terms were present in the two strains of the same genus, while the numbers were decreased with the increase of growth rate in most of the COG terms. KEGG pathway analysis of B. diazoefficiens 113-2 suggested that the rhizobial genes in ABC transporters and Two-Component system were mainly species-specific. Besides, the candidate genes related to secretion system and surface polysaccharides biosynthesis in the genomes of the six strains were explored and compared. 39 nodulation gene families, 12 nif gene families and 10 fix gene families in the genomes of these six strains were identified, and gene classes in most of gene families and the types and total gene numbers of gene families were substantially different among these six genomes. We also performed synteny analyses for above-mentioned nod, nif, and fix gene groupings, and selected NodW, NolK, NoeJ, NifB, FixK, and FixJ gene families to perform phylogeny analyses. Our results provided valuable molecular insights into species specificity and host specificity. The genetic information responsible for host specificity will play important roles in expanding the host range of rhizobia among legumes, which might provide new clues for the understanding of the genetic determinants of non-legume-rhizobium symbiosis.
The Application of Lexical Retrieval Training in Tablet-Based Speech-Language Intervention

In the setting of shortened hospitalization periods, periods of confinement and social isolation, limited resources, and accessibility, technology can be leveraged to enhance opportunities for rehabilitative care (1). In the current manuscript, we focus on the use of tablet-based rehabilitation for individuals with aphasia, a language disorder that frequently arises post-stroke. Aphasia treatment that targets naming through effortful and errorful instances of lexical retrieval, where corrective feedback is generated on every trial, may enhance retention and generalizability of gains (2, 3). This pilot evaluation explored how six individuals with aphasia interacted with a tablet-based therapy application that targeted lexical retrieval. Participants with aphasia either (1) autonomously engaged with the therapy tasks or (2) received systematic encouragement to effortfully retrieve words. Behaviors of response latency and cue use were examined to gain insights into the behavioral patterns of both groups, as well as analyses of task accuracy and outcomes on standardized cognitive–linguistic assessments. Despite some variability, initial observations suggest that participants who received systematic training refrained from using cues to complete tasks and spent longer on each trial, which ultimately co-occurred with increased independent engagement with therapy and improved standardized outcomes. Preliminary results present an alternative means of leveraging technology to implement best-practice recommendations in the context of aphasia telerehabilitation.
A Pilot Investigation of the Social Attention and Communication Surveillance (SACS) Tool for the Early Identification of Autism in Tianjin, China (SACS-C)

Introduction: Autism spectrum disorder (ASD) comprises difficulties in social communication and restrictive and repetitive behaviors. Despite an increased global prevalence, little remains known about early detection and diagnosis of autism in Mainland China. Our aim was to conduct a pilot investigation of the implementation of an Australian tool, Social Attention and Communication Surveillance (SACS), in Tianjin, China (SACS-C) by trained professionals to identify autism early compared to the Checklist for Autism in Toddlers-23 (CHAT-23) completed by parents and professionals. Materials and Methods: A total of 10,514 children were monitored across 61 Community Health Service Centres in six Tianjin districts on the SACS-C at 12, 18, and 24 months of age following a half-day training of 225 child health practitioners. Children deemed at “high likelihood” for autism on either the SACS, CHAT-23, or both, were referred for developmental assessments at the Tianjin Women and Children's Health Centre (TWCHC). Results: A total of 87 children (0.8%) were identified at “high likelihood” on the SACS-C, of whom 57 (66%) were assessed for autism; 24 children were subsequently diagnosed with autism (42.1%), and the remaining 33 (57.9%) were diagnosed with developmental and/or language delays. The SACS-C had a positive predictive value (PPV) of 42.1%, a negative predictive value (NPV) of 99.8%, and sensitivity and specificity of 53.3 and 99.7%, respectively. Only 21 children were identified at “high risk” for autism on the CHAT-23 (0.2%), over four times fewer children than the SACS-C, with 14 children assessed for autism (66%); nine were diagnosed with autism (64.3%) and the remaining five children were diagnosed with developmental and/or language delays. The CHAT-23 had an overall PPV of 64.3%, NPV of 99.6%, sensitivity of 27.3%, and specificity of 99.9%. Conclusion: This was the first large-scale study identifying autism in 12–24-month-old children in China. We ascertained the feasibility of training community health practitioners to monitor infants and toddlers for the early signs of autism, and determined the effectiveness of their use of SACS-C which had a better balance between accuracy and sensitivity in detecting autism in contrast to the CHAT-23 which missed the majority of children with autism (72.7%) vs. the SACS-C (46.7%). Given the emphasis on identifying as many children with autism as possible in Mainland China, SACS-C was identified as the tool of choice by the TWCHC. However, more work is needed to improve the psychometric properties in using the SACS-C in Mainland China so that it is comparable to its use in Australia.