julilili42/papers huggingface dataset:
Environmental Stress Determines The Colonization and Impact of An Endophytic Fungus On Invasive Knotweed
2021-10-28

Abstract There is increasing evidence that microbes play a key role in some plant invasions. A diverse and widespread but little understood group of plant-associated microbes are the fungal root endophytes of the order Sebacinales. They are associated with exotic populations of invasive knotweed ( Reynoutria ssp.) in Europe, but their effects on the invaders are unknown. We used the recently isolated Sebacinales root endophyte S erendipita herbamans to experimentally inoculate invasive knotweed and study root colonisation and effects on knotweed growth under different environmental conditions. We verified the inoculation success and fungal colonisation through immunofluorescence microscopy and qPCR. We found that S. herbamans strongly colonized invasive knotweed in low-nutrient and shade environments, but much less under drought or benign conditions. At low nutrients, the endophyte had a positive effect on plant growth, whereas the opposite was true under shaded conditions. Our study demonstrates that the root endophyte S. herbamans has the potential to colonize invasive knotweed fine roots and impact its growth, and it could thus also play a role in natural populations. Our results also show that effects of fungal endophytes on plants can be strongly environment-dependent, and may only be visible under stressful environmental conditions.
Challenges in Biochemical Diagnosis of Krabbe and Gaucher Disease
2021-10-28

Background/Purpose: Krabbe and Gaucher diseases (KD, GD) are rare, inherited disorders caused by the deficiency of a specific lysosomal enzyme. Biochemical verification through enzyme assays remains crucial to guide downstream diagnostic pathway. Although assays with artificial substrates (AS) are preferred due to their less laborious technique, their sensitivity and specificity, however, might not be equal to assays using natural substrates. Based on case examples, we describe potential pitfalls when using AS.
Autoimmune Encephalitis in an Infant with Biallelic AIRE Variants: Unusual Manifestation of Autoimmune Polyendocrinopathy Syndrome Type 1 (APS-1)?
2021-10-28

Background/Purpose: A previously healthy 4-month-old boy presented with urinary retention and torticollis. Within a few days, left-sided gaze paresis and multiple cranial nerve palsies developed, leading to progressive bulbar dysfunction with dysphagia and respiratory failure despite therapy with methylprednisolone and intravenous immunoglobulins. In parallel, reduced level of consciousness and coma developed. Mucocutaneous candidiasis was also noted.
Raw data repository for the article: "Spatially resolved fluorescence of caesium lead halide perovskite supercrystals reveals quasi-atomic behavior of nanocrystals"
2021-10-28

&lt;p&gt;Raw data depository for the article in Nature Communications journal: &lt;a href="https://doi.org/10.1038/s41467-022-28486-3"&gt;DOI: 10.1038/s41467-022-28486-3&lt;/a&gt;. Details and the file description&nbsp;are given in the file &quot;Lapkin_Dataset_Info.pdf&quot;&lt;/p&gt;
Mitchell Syndrome Imitating an Inflammatory Myelitis
2021-10-28

Introduction: (Sub)acute myelitis is often caused by CNS antibody-triggered autoimmune processes, so that the detection of an elevated specific antibody strongly suggests a causative autoimmune disease. However, re-evaluation of this hypothesis is needed, especially when the disease course is unexpected despite correct treatment. The newly described very rare Mitchell syndrome mimics autoimmune disease and may only be recognized in the course of time.
Gastrointestinal Symptoms in Patients with Pontocerebellar Hypoplasia Type 2A
2021-10-28

Background: Pontocerebellar hypoplasia type 2A (PCH2A) is a very rare autosomal recessive neuropediatric condition with a high disease burden. Affected patients typically show severe developmental retardation, dyskinetic movement disorder and epileptic seizures. Besides, patients with PCH2A suffer from severe gastrointestinal symptoms.
Three water restriction schedules used in rodent behavioral tasks transiently impair growth and differentially evoke a stress hormone response without causing dehydration
2021-10-28

Abstract Water restriction is commonly used to motivate rodents to perform behavioral tasks; however, its on hydration and stress hormone levels are unknown. Here, we report daily body weight and bi-weekly packed red blood cell volume and corticosterone in adult male rats across 80 days for three commonly used water restriction schedules. We also assessed renal adaptation to water restriction using post-mortem histological evaluation of renal medulla. A control group received ad libitum water. After one week of water restriction, rats on all restriction schedules resumed similar levels of growth relative to the control group. Nominal hydration was observed, and water restriction did not drive renal adaptation. An intermittent restriction schedule was associated with an increase in corticosterone relative to the control group. Our results suggest that the water restriction schedules used here will maintain welfare in rats. However, intermittent restriction evokes a stress response which could affect behavioral and neurobiological results. Our results also suggest that stable motivation in behavioral tasks may only be achieved after one week of restriction.
Patient-derived endometrial organoids from MRKH patients: Insight in disease causing pathways
2021-10-28

Abstract The uterus is responsible for the nourishment and mechanical protection of the developing embryo and fetus and is an essential part in mammalian reproduction. The Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome is characterized by agenesis of the uterus and upper part of the vagina in females with normal ovarian function. Although heavily studied, the cause of the disease is still enigmatic. Current research in the field of MRKH mainly focusses on DNA-sequencing efforts and, so far, failed to decipher the nature and heterogeneity of the disease, thereby holding back scientific and clinical progress. Here, we developed long-term expandable organoid cultures from endometrium found in uterine rudiment horns of MRKH patients. Phenotypically, they share great similarity with healthy control organoids and are surprisingly fully hormone responsive. Transcriptome analyses, however, identified an array of dysregulated genes that point at potentially disease-causing pathways altered during the development of the female reproductive tract. We consider the endometrial organoid cultures to be a powerful research tool that promise to enable an array of studies into the pathogenic origins of MRKH syndrome and possible treatment opportunities to improve patient quality of life.
Empagliflozin Improves Insulin Sensitivity of the Hypothalamus in Humans With Prediabetes: A Randomized, Double-Blind, Placebo-Controlled, Phase 2 Trial
2021-10-29

OBJECTIVE Insulin action in the human brain reduces food intake, improves whole-body insulin sensitivity, and modulates body fat mass and its distribution. Obesity and type 2 diabetes are often associated with brain insulin resistance, resulting in impaired brain-derived modulation of peripheral metabolism. So far, no pharmacological treatment for brain insulin resistance has been established. Since sodium–glucose cotransporter 2 (SGLT2) inhibitors lower glucose levels and modulate energy metabolism, we hypothesized that SGLT2 inhibition may be a pharmacological approach to reverse brain insulin resistance. RESEARCH DESIGN AND METHODS In this randomized, double-blind, placebo-controlled clinical trial, 40 patients (mean ± SD; age 60 ± 9 years; BMI 31.5 ± 3.8 kg/m2) with prediabetes were randomized to receive 25 mg empagliflozin every day or placebo. Before and after 8 weeks of treatment, brain insulin sensitivity was assessed by functional MRI combined with intranasal administration of insulin to the brain. RESULTS We identified a significant interaction between time and treatment in the hypothalamic response to insulin. Post hoc analyses revealed that only empagliflozin-treated patients experienced increased hypothalamic insulin responsiveness. Hypothalamic insulin action significantly mediated the empagliflozin-induced decrease in fasting glucose and liver fat. CONCLUSIONS Our results corroborate insulin resistance of the hypothalamus in humans with prediabetes. Treatment with empagliflozin for 8 weeks was able to restore hypothalamic insulin sensitivity, a favorable response that could contribute to the beneficial effects of SGLT2 inhibitors. Our findings position SGLT2 inhibition as the first pharmacological approach to reverse brain insulin resistance, with potential benefits for adiposity and whole-body metabolism.
The Eco-Exposome Concept: Supporting an Integrated Assessment of Mixtures of Environmental Chemicals
2021-10-29

Abstract Organisms are exposed to ever-changing complex mixtures of chemicals over the course of their lifetime. The need to more comprehensively describe this exposure and relate it to adverse health effects has led to formulation of the exposome concept in human toxicology. Whether this concept has utility in the context of environmental hazard and risk assessment has not been discussed in detail. In this Critical Perspective, we propose—by analogy to the human exposome—to define the eco-exposome as the totality of the internal exposure (anthropogenic and natural chemicals, their biotransformation products or adducts, and endogenous signaling molecules that may be sensitive to an anthropogenic chemical exposure) over the lifetime of an ecologically relevant organism. We describe how targeted and nontargeted chemical analyses and bioassays can be employed to characterize this exposure and discuss how the adverse outcome pathway concept could be used to link this exposure to adverse effects. Available methods, their limitations, and/or requirement for improvements for practical application of the eco-exposome concept are discussed. Even though analysis of the eco-exposome can be resource-intensive and challenging, new approaches and technologies make this assessment increasingly feasible. Furthermore, an improved understanding of mechanistic relationships between external chemical exposure(s), internal chemical exposure(s), and biological effects could result in the development of proxies, that is, relatively simple chemical and biological measurements that could be used to complement internal exposure assessment or infer the internal exposure when it is difficult to measure. Environ Toxicol Chem 2022;41:30–45. © 2021 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. Abstract Illustration of the eco-exposome assessment and how chemical analysis and bioassays could be used to estimate internal exposure. MIE = molecular initiation event; KE = key event; AO = adverse outcome.
Mammalian face as an evolutionary novelty
2021-10-29

Significance The anatomical framework of the jaw has traditionally been thought to be highly conserved among vertebrates. However, here we show that the therian-unique face (muzzle) evolved via a drastic alteration of the common pattern of the tetrapod jaw. Through comparative morphological and developmental analyses, we demonstrated that the therian mammal’s premaxilla (rostral-most upper jawbone) is derived from the maxillary prominence of the mandibular arch. The developmental primordium that produces the premaxilla in nonmammalian tetrapods rarely contributes to the upper jaw in therian mammals but rather forms a motile nose. We propose that these previously unrecognized rearrangements allowed key innovations such as the highly sensitive tactile perception and olfactory function in mammalian evolution.
Presence of Fe(II) and nitrate shapes aquifer-originating communities leading to an autotrophic enrichment dominated by an Fe(II)-oxidizing Gallionellaceae sp
2021-10-29

ABSTRACT Autotrophic nitrate reduction coupled to Fe(II) oxidation is an important nitrate removal process in anoxic aquifers. However, it remains unknown how changes of O2 and carbon availability influence the community structure of nitrate-reducing Fe(II)-oxidizing (NRFeOx) microbial assemblages and what the genomic traits of these NRFeOx key players are. We compared three metabolically distinct denitrifying assemblages, supplemented with acetate, acetate/Fe(II) or Fe(II), enriched from an organic-poor, pyrite-rich aquifer. The presence of Fe(II) promoted the growth of denitrifying Burkholderiaceae spp. and an unclassified Gallionellaceae sp. This Gallionellaceae sp. was related to microaerophilic Fe(II) oxidizers; however, it did not grow under microoxic conditions. Furthermore, we explored a metagenome and 15 metagenome-assembled genomes from an aquifer-originating, autotrophic NRFeOx culture. The dominant Gallionellaceae sp. revealed the potential to oxidize Fe(II) (e.g. cyc2), fix CO2 (e.g. rbcL) and perform near-complete denitrification leading to N2O formation (e.g. narGHJI,nirK/S and norBC). In addition, Curvibacter spp.,Methyloversatilis sp. and Thermomonas spp. were identified as novel putative NRFeOx taxa. Our findings provide first insights into the genetic traits of the so far only known autotrophic NRFeOx culture originating from an organic-poor aquifer, providing the genomic basis to study mechanisms of nitrate removal in organic-poor subsurface ecosystems.
Contested science: Individuals with higher metacognitive insight into interpretation of evidence are less likely to polarize
2021-10-29

Abstract Societal polarization over contested science has increased in recent years. To explain this development, political, sociological, and psychological research has identified societal macro-phenomena as well as cognitive micro-level factors that explain how citizens reason about the science. Here we take a radically different perspective, and highlight the effects of metacognition: How citizens reason about their own reasoning. Leveraging methods from Signal Detection Theory, we investigated the importance of metacognitive insight for polarization for the heavily contested topic of climate change, and the less heavily contested topic of nanotechnology. We found that, for climate change (but not for nanotechnology), higher insight into the accuracy of own interpretations of the available scientific evidence related to a lower likelihood of polarization over the science. This finding held irrespective of the direction of the scientific evidence (endorsing or rejecting anthropogenicity of climate change). Furthermore, the polarizing effect of scientific evidence could be traced back to higher metacognitive insight fostering belief-updating in the direction of the evidence at the expense of own, prior beliefs. By demonstrating how metacognition links to polarization, the present research adds to our understanding of the drivers of societal polarization over science.
Modulation of Macrophage Activity by Pulsed Electromagnetic Fields in the Context of Fracture Healing
2021-10-29

Delayed fracture healing and fracture non-unions impose an enormous burden on individuals and society. Successful healing requires tight communication between immune cells and bone cells. Macrophages can be found in all healing phases. Due to their high plasticity and long life span, they represent good target cells for modulation. In the past, extremely low frequency pulsed electromagnet fields (ELF-PEMFs) have been shown to exert cell-specific effects depending on the field conditions. Thus, the aim was to identify the specific ELF-PEMFs able to modulate macrophage activity to indirectly promote mesenchymal stem/stromal cell (SCP-1 cells) function. After a blinded screening of 22 different ELF-PEMF, two fields (termed A and B) were further characterized as they diversely affected macrophage function. These two fields have similar fundamental frequencies (51.8 Hz and 52.3 Hz) but are emitted in different groups of pulses or rather send–pause intervals. Macrophages exposed to field A showed a pro-inflammatory function, represented by increased levels of phospho-Stat1 and CD86, the accumulation of ROS, and increased secretion of pro-inflammatory cytokines. In contrast, macrophages exposed to field B showed anti-inflammatory and pro-healing functions, represented by increased levels of Arginase I, increased secretion of anti-inflammatory cytokines, and growth factors are known to induce healing processes. The conditioned medium from macrophages exposed to both ELF-PEMFs favored the migration of SCP-1 cells, but the effect was stronger for field B. Furthermore, the conditioned medium from macrophages exposed to field B, but not to field A, stimulated the expression of extracellular matrix genes in SCP-1 cells, i.e., COL1A1, FN1, and BGN. In summary, our data show that specific ELF-PEMFs may affect immune cell function. Thus, knowing the specific ELF-PEMFs conditions and the underlying mechanisms bears great potential as an adjuvant treatment to modulate immune responses during pathologies, e.g., fracture healing.
Characterization of Lifestyle in Spinocerebellar Ataxia Type 3 and Association with Disease Severity
2021-10-29

ABSTRACT Background Lifestyle could influence the course of hereditary ataxias, but representative data are missing. Objective The objective of this study was to characterize lifestyle in spinocerebellar ataxia type 3 (SCA3) and investigate possible associations with disease parameters. Methods In a prospective cohort study, data on smoking, alcohol consumption, physical activity, physiotherapy, and body mass index (BMI) were collected from 243 patients with SCA3 and 119 controls and tested for associations with age of onset, disease severity, and progression. Results Compared with controls, patients with SCA3 were less active and consumed less alcohol. Less physical activity and alcohol abstinence were associated with more severe disease, but not with progression rates or age of onset. Smoking, BMI, or physiotherapy did not correlate with disease parameters. Conclusion Differences in lifestyle factors of patients with SCA3 and controls as well as associations of lifestyle factors with disease severity are likely driven by the influence of symptoms on behavior. No association between lifestyle and disease progression was detected. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society
The meaning of respect under varying context conditions
2021-10-29

<p xmlns="http://www.ncbi.nlm.nih.gov/JATS1">The concept of respect figures prominently in several theories on intergroup relations. Previous studies suggested that the experience of being respected is primarily related to the feeling of being recognized as an equal, as opposed to social recognition of needs or achievements. Those studies focused, however, on either minority groups or ad hoc groups, thereby possibly giving equality recognition an advantage. This article extends previous findings by comparing societal groups situated in various contexts. We examined eight groups from four countries. We anticipated and found that the link between respect and equality recognition was stronger for groups that are in the position of minorities compared to groups associated with majorities. Owing to the moral and legal force of the norm of equality, disadvantaged minorities in particular might be able to improve their societal position by founding their claims on the equality principle. Need recognition, in contrast, was less influential for minority groups than for majority groups. While we observed these context-dependent variations, an internal meta-analysis showed that feeling recognized as an equal was, overall, the strongest indicator for feeling respected. This suggests that demands for respect could often be addressed by establishing relationships in society that are based on mutual recognition as equals, while the implications of achievement and need recognition should additionally be considered in specific contexts.
Protein Crystallization from a Preordered Metastable Intermediate Phase Followed by Real-Time Small-Angle Neutron Scattering
2021-10-29

We present a systematic study using real-time small-angle neutron scattering (SANS) and optical microscopy to follow the protein crystallization process in the presence of a metastable intermediate phase (MIP). Using bovine β-lactoglobulin (BLG) in the presence of the divalent salt CdCl2 as a model system, we first determine the experimental phase behavior in D2O. The protein solutions become turbid after crossing the first threshold salt concentration c*, and upon further increasing the salt concentration, the solutions become less turbid but not completely clear again. Thus, the second border is called pseudo-c**. Near pseudo-c**, crystallization follows a nonclassical process with a MIP, which is further explored with a focus on the structural evolution and the growth kinetics of the MIP prior to crystal nucleation. Real-time SANS measurements show that a correlation peak develops inside the MIP, and its peak position shifts to higher q-values with time, finally stabilizing at a characteristic length scale of dMIP ≈ 84 Å. The area of this peak (proportional to the amount of MIP in the sample) increases with time first, reaches a maximum, and then decreases quickly upon crystallization due to consumption by crystal growth. The evolution of the correlation peak indicates a "preordering" nature of the MIP as precursors of crystal nucleation, which lowers the nucleation barrier for subsequent crystallization. These results of structural evolution and the role of MIPs during a nonclassical crystallization process may be relevant for other fields ranging from structural biology to pharmacy.
RNA Biological Characteristics at the Peak of Cell Death in Different Hereditary Retinal Degeneration Mutants
2021-10-29

Purpose: The present work investigated changes in the gene expression, molecular mechanisms, and pathogenesis of inherited retinal degeneration (RD) in three different disease models, to identify predictive biomarkers for their varied phenotypes and to provide a better scientific basis for their diagnosis, treatment, and prevention. Methods: Differentially expressed genes (DEGs) between retinal tissue from RD mouse models obtained during the photoreceptor cell death peak period ( Pde6b rd1 at post-natal (PN) day 13, Pde6b rd10 at PN23, Prph rd2 at PN29) and retinal tissue from C3H wild-type mice were identified using Illumina high-throughput RNA-sequencing. Co-expression gene modules were identified using a combination of GO and KEGG enrichment analyses and gene co-expression network analysis. CircRNA-miRNA-mRNA network interactions were studied by genome-wide circRNA screening. Results: Pde6b rd1 , Pde6b rd10 , and Prph rd2 mice had 1,926, 3,096, and 375 DEGs, respectively. Genes related to ion channels, stress, inflammatory processes, tumor necrosis factor (TNF) production, and microglial cell activation were up-regulated, while genes related to endoplasmic reticulum regulation, metabolism, and homeostasis were down-regulated. Differential expression of transcription factors and non-coding RNAs generally implicated in other human diseases was detected (e.g., glaucoma, diabetic retinopathy, and inherited retinal degeneration). CircRNA-miRNA-mRNA network analysis indicated that these factors may be involved in photoreceptor cell death. Moreover, excessive cGMP accumulation causes photoreceptor cell death, and cGMP-related genes were generally affected by different pathogenic gene mutations. Conclusion: We screened genes and pathways related to photoreceptor cell death. Additionally, up-stream regulatory factors, such as transcription factors and non-coding RNA and their interaction networks were analyzed. Furthermore, RNAs involved in RD were functionally annotated. Overall, this study lays a foundation for future studies on photoreceptor cell death mechanisms.