Miracle-dz/UniFAR-FTUs huggingface dataset:
Discontinuing Hemodialysis with Patient Care and a Successful 9-Year Follow-up in a Patient Presumed to have End-Stage Kidney Disease Scheduled to Lifelong Hemodialysis: A Case Report

End-stage kidney disease patients who require hemodialysis for more than 3 months have a small chance of leaving dialysis unless they have a kidney transplant. Educating the patient about lifestyle changes can play a major role in improving kidney function. Therefore, we created a patient education program according to our nephrology experiences. Herein, we show an end-stage kidney disease patient who underwent hemodialysis for 6 months. Afterwards, dialysis was terminated with patient care, and the patient was then followed up for 9 years without dialysis. To date, there have been no reports regarding the termination of long-term dialysis with a kidney care program and the ensuing 9-year follow-up without renal replacement therapy.
Functional innovation promotes diversification of form in the evolution of an ultrafast trap-jaw mechanism in ants

Evolutionary innovations underlie the rise of diversity and complexity—the 2 long-term trends in the history of life. How does natural selection redesign multiple interacting parts to achieve a new emergent function? We investigated the evolution of a biomechanical innovation, the latch-spring mechanism of trap-jaw ants, to address 2 outstanding evolutionary problems: how form and function change in a system during the evolution of new complex traits, and whether such innovations and the diversity they beget are repeatable in time and space. Using a new phylogenetic reconstruction of 470 species, and X-ray microtomography and high-speed videography of representative taxa, we found the trap-jaw mechanism evolved independently 7 to 10 times in a single ant genus (Strumigenys), resulting in the repeated evolution of diverse forms on different continents. The trap mechanism facilitates a 6 to 7 order of magnitude greater mandible acceleration relative to simpler ancestors, currently the fastest recorded acceleration of a resettable animal movement. We found that most morphological diversification occurred after evolution of latch-spring mechanisms, which evolved via minor realignments of mouthpart structures. This finding, whereby incremental changes in form lead to a change of function, followed by large morphological reorganization around the new function, provides a model for understanding the evolution of complex biomechanical traits, as well as insights into why such innovations often happen repeatedly.
Abnormalities in reparative function of lung-derived mesenchymal stromal cells in emphysema.

Mesenchymal stromal cells (MSCs) may provide crucial support in the regeneration of destructed alveolar tissue (emphysema) in COPD. We hypothesized that lung-derived MSCs (LMSCs) from emphysema patients are hampered in their repair capacity, either intrinsically or due to their interaction with the damaged micro-environment. LMSCs were isolated from lung tissue of controls and severe emphysema patients, and characterized at baseline. Additionally, LMSCs were seeded onto control and emphysematous decellularized lung tissue scaffolds and assessed for deposition of extracellular matrix (ECM). We observed no differences in surface markers, differentiation/proliferation potential and expression of ECM genes between control- and COPD-derived LMSCs. Notably, COPD-derived LMSCs displayed lower expression of FGF10 and HGF mRNA, and HGF and decorin protein. When seeded on control decellularized lung tissue scaffolds, control and COPD-derived LMSCs showed no differences in engraftment, proliferation or survival within 2 weeks, with similar ability to deposit new matrix on the scaffolds. Moreover, LMSC numbers and ability to deposit new matrix was not compromised on emphysematous scaffolds. Collectively, our data show that LMSCs from COPD patients compared to controls show less expression of FGF10 mRNA, HGF mRNA and protein and decorin protein, while other features including the mRNA expression of various ECM molecules are unaffected. Furthermore, COPD-derived LMSCs are capable of engraftment, proliferation and functioning on native lung tissue scaffolds. The damaged, emphysematous micro-environment as such does not hamper the potential of LMSCs. Thus, specific intrinsic deficiencies in growth factor production by diseased LMSCs may contribute to impaired alveolar repair in emphysema.
A Salmonella Typhi RNA thermosensor regulates virulence factors and innate immune evasion in response to host temperature

Sensing and responding to environmental signals is critical for bacterial pathogens to successfully infect and persist within hosts. Many bacterial pathogens sense temperature as an indication they have entered a new host and must alter their virulence factor expression to evade immune detection. Using secondary structure prediction, we identified an RNA thermosensor (RNAT) in the 5’ untranslated region (UTR) of tviA encoded by the typhoid fever-causing bacterium Salmonella enterica serovar Typhi (S. Typhi). Importantly, tviA is a transcriptional regulator of the critical virulence factors Vi capsule, flagellin, and type III secretion system-1 expression. By introducing point mutations to alter the mRNA secondary structure, we demonstrate that the 5’ UTR of tviA contains a functional RNAT using in vitro expression, structure probing, and ribosome binding methods. Mutational inhibition of the RNAT in S. Typhi causes aberrant virulence factor expression, leading to enhanced innate immune responses during infection. In conclusion, we show that S. Typhi regulates virulence factor expression through an RNAT in the 5’ UTR of tviA. Our findings demonstrate that limiting inflammation through RNAT-dependent regulation in response to host body temperature is important for S. Typhi’s “stealthy” pathogenesis.
Four new species of sequestrate Inocybe from Chilean Nothofagaceae forests

ABSTRACT Sequestrate fungi have enclosed hypogeous, subhypogeous, or epigeous basidiomes and have lost the ability to actively discharge their spores. They can be distinguished as gasteroid (basidiome fully enclosed with a loculated hymenophore) or secotioid (basidiome with some agaricoid or pileate-stipitate features, but the lamellae are misshapen and unexposed or mostly unexposed at maturity). There are only four reports of sequestrate taxa within the ectomycorrhizal family Inocybaceae, three from Australia and one from western North America. Recent field work in Nothofagaceae forests in the Chilean coastal range revealed novel sequestrate forms of Inocybe. We examined specimens using a combination of morphological and molecular data from nuc rDNA internal transcribed spacer region ITS1-5.8S-ITS2 (ITS) and portions of nuc 28S rDNA (28S) and the gene encoding the second largest subunit of RNA polymerase II (rpb2). Here, we describe four new sequestrate Inocybe species, I. ranunculiformis, I. anfractuosa, I. illariae, and I. nahuelbutensis. Results of our phylogenetic analysis resolved the four new species as distinct species-level clades with strong support, suggesting that these fungi have convergently evolved sequestrate forms independently. The species described here were all placed along with members of the “smooth-spored temperate austral clade,” which includes almost exclusively Australasian and South American species of Inocybe.
The 2020 Updated KDOQI Clinical Practice Guidelines for Nutrition in Chronic Kidney Disease

Over the last 2 decades, there has been a great accumulation of new evidence regarding the management of nutritional and metabolic aspects of kidney disease. The 2020 update to the KDOQI Clinical Practice Guideline for Nutrition in CKD provides a comprehensive up-to-date information on the understanding and care of patients with CKD. It provides updated information on nutritional aspects of kidney disease for the practicing clinician and allied health-care workers. The current manuscript provides an overview of the updated guideline statements on major subjects including nutritional assessment, dietary protein and energy intake, nutritional supplementation, micronutrients, and electrolytes. The guidelines are focused on dietary management rather than all possible nutritional interventions.
Yokoyama procedure for esotropia associated with high myopia: real‐world data from a large‐scale multicentre analysis

High myopic patients may develop strabismus due to globe dislocation out of the normal extraocular muscle cone. Surgical correction of this strabismus type is possible by joining the superior and lateral rectus muscles without the need for a scleral suture called the Yokoyama procedure. Data from large patient samples and the evaluation of a potential effect of an additional medial rectus recession (MRR) have been lacking so far.
Surface crosslinking effects on contamination resistance of functionalised polymers

We have applied a theoretical modelling approach to aid in the rational design of contamination resistant coatings. Using in silico nano-indentation we have characterised the adhesion between a contaminant particle and engineered polymer surfaces that include functionalised-surface-crosslinked and functionalised non-surface-crosslinked polyesters. The roughness, density and morphology of the surfaces were dynamically monitored as the coatings responded to the approaching particle. Our results suggest that surface crosslinking provides a stable platform for incorporation of functional groups that would otherwise migrate into the bulk substrate upon aging. However surface crosslinking with rigid cyclic curing agents renders the coatings far too stiff, which can result in slip whereby surface crosslinkers shift to the side of the incoming contaminant particle, leading to both the exposure of the flexible substrate and the envelopment of the contaminant. This type of deformation negates steric repulsions of the functional groups, crucial for preventing undesirable adhesion. In contrast, functionalisation combined with flexible acyclic surface crosslinks results in superior contamination resistance.
Causal Effects of Lifetime Smoking on Breast and Colorectal Cancer Risk: Mendelian Randomization Study

Background: Observational evidence has shown that smoking is a risk factor for breast and colorectal cancer. We used Mendelian randomization (MR) to examine causal associations between smoking and risks of breast and colorectal cancer. Methods: Genome-Wide Association Study summary data were used to identify genetic variants associated with lifetime amount of smoking (n = 126 variants) and ever having smoked regularly (n = 112 variants). Using two-sample MR, we examined these variants in relation to incident breast (122,977 cases/105,974 controls) and colorectal cancer (52,775 cases/45,940 controls). Results: In inverse-variance weighted models, a genetic predisposition to higher lifetime amount of smoking was positively associated with breast cancer risk [OR per 1-SD increment: 1.13; 95% confidence interval (CI): 1.00–1.26; P = 0.04]; although heterogeneity was observed. Similar associations were found for estrogen receptor–positive and estrogen receptor–negative tumors. Higher lifetime amount of smoking was positively associated with colorectal cancer (OR per 1-SD increment, 1.21; 95% CI, 1.04–1.40; P = 0.01), colon cancer (OR, 1.31; 95% CI, 1.11–1.55; P < 0.01), and rectal cancer (OR, 1.36; 95% CI, 1.07–1.73; P = 0.01). Ever having smoked regularly was not associated with risks of breast (OR, 1.01; 95% CI, 0.90–1.14; P = 0.85) or colorectal cancer (OR, 0.97; 95% CI, 0.86–1.10; P = 0.68). Conclusions: These findings are consistent with prior observational evidence and support a causal role of higher lifetime smoking amount in the development of breast and colorectal cancer. Impact: The results from this comprehensive MR analysis indicate that lifetime smoking is a causal risk factor for these common malignancies.
Mediators of the longitudinal relationship between childhood adversity and late adolescent psychopathology

Abstract Background Childhood adversity (CA) is commonly associated with an increased risk of subsequent psychopathology. It is important to identify potential mediators of this relationship which can allow for the development of interventions. In a large population-based cohort study we investigated the relationship between CA and late adolescent psychopathology and early adolescent candidate mediators of this relationship. Methods We used data from three waves (n = 6039) of Cohort 98′ of the Growing up in Ireland Study (age 9, 13 and 17). We used doubly robust counterfactual analyses to investigate the relationship between CA (reported at age-9) with psychopathology (internalizing and externalizing problems), measured using the Strengths and Difficulties Questionnaire at age-17. Counterfactual and traditional mediation was used to investigate the mediating effects of the parent-child relationship, peer relations, self-concept, computer usage and physical activity. Results CA was associated with an increased risk of internalizing and externalizing problems at age-17. Parent-child conflict mediated 35 and 42% of the relationship between CA and late adolescent externalizing problems and internalizing problems, respectively. Self-concept and physical activity mediated an additional proportion of the relationship between CA and internalizing problems. These results were robust to unmeasured confounding. Conclusions Parent-child conflict explains more than a third of the relationship between CA and later psychopathology. Self-concept and physical activity explain the additional proportion of the relationship between CA and internalizing problems. This suggests that these factors may be good targets for intervention in young people who have experienced CA to prevent subsequent psychopathology.
Introduction of Two Prolines and Removal of the Polybasic Cleavage Site Lead to Higher Efficacy of a Recombinant Spike-Based SARS-CoV-2 Vaccine in the Mouse Model

A vaccine for SARS-CoV-2 is urgently needed. A better understanding of antigen design and attributes that vaccine candidates need to have to induce protective immunity is of high importance. The data presented here validate the choice of antigens that contain the PP mutations and suggest that deletion of the polybasic cleavage site may lead to a further-optimized design. ABSTRACT The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified as the prime target for vaccine development. The spike protein mediates both binding to host cells and membrane fusion and is also so far the only known viral target of neutralizing antibodies. Coronavirus spike proteins are large trimers that are relatively unstable, a feature that might be enhanced by the presence of a polybasic cleavage site in SARS-CoV-2 spike. Exchange of K986 and V987 for prolines has been shown to stabilize the trimers of SARS-CoV-1 and the Middle East respiratory syndrome coronavirus spike proteins. Here, we test multiple versions of a soluble spike protein for their immunogenicity and protective effect against SARS-CoV-2 challenge in a mouse model that transiently expresses human angiotensin-converting enzyme 2 via adenovirus transduction. Variants tested include spike proteins with a deleted polybasic cleavage site, proline mutations, or a combination thereof, besides the wild-type protein. While all versions of the protein were able to induce neutralizing antibodies, only the antigen with both a deleted cleavage site and the K986P and V987P (PP) mutations completely protected from challenge in this mouse model. IMPORTANCE A vaccine for SARS-CoV-2 is urgently needed. A better understanding of antigen design and attributes that vaccine candidates need to have to induce protective immunity is of high importance. The data presented here validate the choice of antigens that contain the PP mutations and suggest that deletion of the polybasic cleavage site may lead to a further-optimized design.
Community-wide changes reflecting bacterial interspecific interactions in multispecies biofilms

Abstract Existence of most bacterial species, in natural, industrial, and clinical settings in the form of surface-adhered communities or biofilms has been well acknowledged for decades. Research predominantly focusses on single-species biofilms as these are relatively easy to study. However, microbiologists are now interested in studying multispecies biofilms and revealing interspecific interactions in these communities because of the existence of a plethora of different bacterial species together in almost all natural settings. Multispecies biofilms-led emergent properties are triggered by bacterial social interactions which have huge implication for research and practical knowledge useful for the control and manipulation of these microbial communities. Here, we discuss some important bacterial interactions that take place in multispecies biofilm communities and provide insights into community-wide changes that indicate bacterial interactions and elucidate underlying mechanisms.
Impact of Top Electrodes on the Nonvolatile Resistive Switching Properties of Citrus Thin Films

Natural citrus thin films on an indium tin oxide (ITO)/glass substrate were synthesized using the solution method for resistive random access memory (RRAM) applications. The results indicated that the citrus memory device possessed stable resistive switching behavior. For a clear understanding of the role of the interface reaction between the top metal electrode and the citrus film, we investigated the influences of various top electrode (TE) materials on the resistive switching in TE/citrus/ITO devices. In comparison with Au/citrus/ITO and Ti/citrus/ITO devices, the Al/citrus/ITO device can be reproduced with a DC voltage of more than 100 times while only showing a slight decrease in the ON/OFF ratio. In addition, the Al/citrus/ITO device exhibited a high ON/OFF ratio of over 104 and an outstanding uniformity, which was attributed to the fast formation of a native oxide layer (AlOx), as confirmed by the line scan analysis. This indicated that the interface layer, created by the redox reaction between the Al electrode and citrus film, played an important role in the resistive switching properties of TE/citrus/ITO structures. These findings can serve as design guidelines for future bio-based RRAM devices.
Growth responses and accumulation of cadmium in switchgrass (Panicumvirgatum L.) and prairie cordgrass (Spartinapectinata Link)

Phytoextraction could be an efficient technique to remediate heavy metals from contaminated soils. Identifying bioenergy crops that can be produced successfully on marginal lands, such as those polluted by heavy metals, also reduces the pressure to produce energy crops on land that would otherwise be used to produce food crops. The objective of this study was to determine the phytoremediation capability of two warm season perennials, prairie cordgrass (Spartinapectinata Link, ‘Savoy’) and switchgrass (Panicumvirgatum L., ‘Cave-In-Rock’ (CIR)) through their growth response to cadmium (Cd). Growth rate, Cd tolerance, accumulation and translocation were measured at concentrations of 0 (control), 5, 10, 30, and 50 mg L−1 of Cd mixed with Hoagland's solution in an aerated hydroponic system. Although a reduction of plant growth was observed when the Cd concentration was higher than 10 mg L−1 for both species, there were significant differences in Cd tolerance, translocation and accumulation between species. The tolerance index (Ti) was between 72.5 and 107.1 in Savoy and 48.7 and 75.7 in CIR under Cd concentrations of 50 mg L−1 and 5 mg L−1, respectively. The translocation factor (Tf) for both species was increased with increasing Cd concentration in solution, but the Tf of Savoy was higher than CIR. The highest bio-concentration factor (BCF) of the roots reached 325.7 for Savoy and 144.5 for CIR when the Cd concentration was 5 mg L−1 and the BCF of the shoots in both species was consistently low (13.7 to 16.8 and 4.1 to 6.0 for Savoy and CIR, respectively) indicating higher Cd retention in the roots than shoots. It was concluded that both species could be utilized in phytoremediation when the Cd concentration is less than 10 mg L−1, however Savoy has the higher tolerance, translocation and accumulation capabilities which makes it a better candidate for phytoremediation and biomass production on Cd polluted soils.
Degradation of N-nitrosodimethylamine (NDMA) in water by UV/O3

Experiments were carried out under various conditions to study the effects of ozone dosage, solution pH and initial concentration of N -nitrosodimethylamine (NDMA) and humic acid on degradation of NDMA by UV/O 3 . Results indicated that NDMA could be completely decomposed to form intermediates within 20 minutes. The degradation of NDMA by UV/O 3 was found to follow pseudo-first-order kinetics. Reaction rates of NDMA degradation did not fluctuate with pH increasing from acid to neutral but dramatically decreased in basic aqueous solution. NDMA initial concentration did not have an obvious effect on NDMA degradation. However, the presence of humic acid inhibited NDMA degradation. Methylamine (MA), dimethylamine (DMA), NO 2 − and NO 3 − were focused on as NDMA degradation intermediates. Degradation of NDMA by UV/O 3 promoted the conversion from DMA to MA and from NO 2 − to NO 3 − , respectively. With the help of tert-butanol and sodium azide, both 1 O 2 and ∙OH were verified to be reactive species present in the process of NDMA degradation by UV/O 3 . The mechanism of NDMA degradation by UV/O 3 was discussed based on the products detected in the present study and the previous literature. Several possible pathways of NDMA degradation were proposed.
Combined effects of tannate and ageing on structural and surface properties of aluminum precipitates

The influence of organics on the crystallization of Al precipitates has been well documented. However, the effects of organics and ageing on the transformation and structural configuration of Al precipitates in relation to their surface and charge properties are not fully understood. This study investigated the structural, microporous and surface properties of Al precipitates formed under the influence of tannate and ageing. The Al precipitates were synthesized at an initial Al concentration of 7 × 10−3 M, an OH/Al molar ratio (MR) of 3.0, and initial tannate/Al MRs of 0, 0.001, 0.01 and 0.1, and aged for 1, 10 and 40 days. As indicated by a decrease in gibbsite and bayerite and an increase in the oxalate-extractable Al contents, the non-crystalline precipitates increased with the increase of the initial tannate/Al MR. This observation is in accord with the X-ray diffraction and Fourier transform infrared (FTIR) data. The impact of tannic acid on the nature of the Al precipitates is also reflected in the increase of the contents of the pyrophosphate-extractable Al, which is indicative of organically bound Al. This observation is in agreement with the increase in the intensity of characteristic FTIR absorption bands of tannate and the organic C and adsorbed water contents. The decrease in the crystallinity of Al precipitates with increase in the tannate/Al MR resulted in the development of microporosity, increase in BET specific surface area and decrease of the average pore diameter and point of zero salt effect (PZSE). The FTIR absorption bands characteristic of tannate of the Al precipitates became weaker with ageing, in accord with the ageing-induced decrease in the contents of organic C and pyrophosphate-extractable Al. Ageing drastically decreased the BET specific surface area of the Al precipitates formed in the absence of tannate but this effect was less conspicuous for the products formed at the tannate/Al molar ratio of 0.1. The ageing-induced change in the PZSE of the Al precipitates formed both in the absence and presence of tannate was not significant. The results accomplished in this study are of fundamental significance to our understanding of the combined effects of organics and ageing on structural configuration of hydrolytic precipitates of Al in relation to their microporosity, surface and charge properties in the environment.