Miracle-dz/UniFAR-FTUs huggingface dataset:
Fraxinus americana Roots Respond to Subsurface Feeding of Mycorrhizal Inoculum and Nitrogen Fertilizer

Abstract Ball and burlap Fraxinus americana (Autumn purple ash) trees were evaluated for their response to subsurface feeding of mycorrhizal inoculum with root biostimulant (mycorrhiza Roots) and nitrogen fertilizer (Coron 28-0-0) on difficult sites in the Colorado front range. Two root ingrowth cores were installed around each of twelve trees following planting in fall 1998 and excavated in fall 1999. Inoculation with mycorrhiza Roots alone resulted in sigificantly increased dry root weights and mycorrhizal colonization percentage on treated purple ash trees (p ≤ 0.05). Mycorrhiza Roots with Coron also significantly increased dry root weights and mycorrhizal colonization percentage on treated ash (p ≤ 0.05). Increases in root growth were dramatic. Purple ash trees treated with mycorrhiza Roots and Coron had greater than 3.5 times the dry root weights in excavated root ingrowth cores compared controls. Trees treated with mycorrhiza Roots alone had greater than 3 times the dry weights compared to controls. Trees treated with mycorrhiza Roots alone had more than 12 times higher mycorrhi-zal colonization percentage compared to controls. Control trees were poorly colonized by mycorrhizal fungi. This study indicates that subsurface feeding of purple ash ball and burlap trees following outplanting with mycorrhizal inoculum and root biostimulant can greatly improve root growth and mycorrhizal colonization.
Potential Markers of Dietary Glycemic Exposures for Sustained Dietary Interventions in Populations without Diabetes

ABSTRACT There is considerable interest in dietary and other approaches to maintaining blood glucose concentrations within the normal range and minimizing exposure to postprandial hyperglycemic excursions. The accepted marker to evaluate the sustained maintenance of normal blood glucose concentrations is glycated hemoglobin A1c (HbA1c). However, although this is used in clinical practice to monitor glycemic control in patients with diabetes, it has a number of drawbacks as a marker of efficacy of dietary interventions that might beneficially affect glycemic control in people without diabetes. Other markers that reflect shorter-term glycemic exposures have been studied and proposed, but consensus on the use and relevance of these markers is lacking. We have carried out a systematic search for studies that have tested the responsiveness of 6 possible alternatives to HbA1c as markers of sustained variation in glycemic exposures and thus their potential applicability for use in dietary intervention trials in subjects without diabetes: 1,5-anhydroglucitol (1,5-AG), dicarbonyl stress, fructosamine, glycated albumin (GA), advanced glycated end products (AGEs), and metabolomic profiles. The results suggest that GA may be the most promising for this purpose, but values may be confounded by effects of fat mass. 1,5-AG and fructosamine are probably not sensitive enough to the range of variation in glycemic exposures observed in healthy individuals. Use of measures based on dicarbonyls, AGEs, or metabolomic profiles would require further research into possible specific molecular species of interest. At present, none of the markers considered here is sufficiently validated and sensitive for routine use in substantiating the effects of sustained variation in dietary glycemic exposures in people without diabetes.
Long non-coding RNA SLC16A1-AS1: its multiple tumorigenesis features and regulatory role in cell cycle in oral squamous cell carcinoma

ABSTRACT Altered expressions of long non-coding RNAs (lncRNAs) are potential cancer prognostic biomarkers that play a critical role in the development of tumorigenesis and metastasis of cancer. However, the relationship between the expression of lncRNAs in oral squamous cell carcinoma (OSCC) and the diagnosis, progression, and prognosis of OSCC has not been thoroughly elucidated. To identify the differentially expressed lncRNAs between OSCC tissue and normal tissue, RNA-Seq data were used. lncRNA SLC16A1-AS1 was significantly highly expressed in OSCC samples than that in normal samples. Systematic bioinformatics analysis revealed that SLC16A1-AS1 was associated with histological tumor grades and overall survival status, as well as copy number variation, somatic mutation, tumor mutation burden, tumor stemness, tumor microenvironment and infiltrating immune cells. According to three advanced bioinformatic algorithms prediction (WGCNA, GSEA and GSVA), SLC16A1-AS1 played an essential role in OSCC proliferation and its biological function was related to cell-cycle regulation. Loss-of-function experiments were performed to determine the biological functions of SLC16A1-AS in OSCC cells. Silencing SLC16A1-AS1 significantly reduced the cell proliferation rate and colony-forming ability in both CAL27 and SCC25 cell lines. Flow cytometry and western blot analysis revealed that SLC16A1-AS1 silencing induced G0/G1 cell cycle arrest and inhibited the expression of cyclin D1 in both CAL27 and SCC25 cells. In conclusion, our study comprehensively investigated the role of the lncRNA SLC16A1-AS1 in OSCC growth and proved that it may serve as a new diagnostic indicator and a new target for the treatment of OSCC.
Gastroesophageal Reflux Disease-Functional Dyspepsia Overlap: Do Birds of a Feather Flock Together?

INTRODUCTION Gastroesophageal reflux disease (GERD) and functional dyspepsia (FD) are 2 of the most prevalent upper gastrointestinal (GI) disorders in the Western world. Previous Rome definitions excluded patients with predominant heartburn from the definition of FD because they were considered to have GERD. However, more recent studies showed that heartburn and acid regurgitation are also common symptoms in patients with FD. The aim of this study is to provide an overview of the prevalence of overlap between GERD and FD, the underlying pathophysiology and implications for treatment. METHODS A review of the literature was performed using the PubMed database, and a meta-analysis with random effects model was completed. RESULTS This review showed considerable overlap between GERD and FD. A meta-analysis on the data included in this review showed 7.41% (confidence interval [CI]: 4.55%-11.84%) GERD/FD overlap in the general population, 41.15% (CI: 29.46%-53.93%) GERD with FD symptoms, and 31.32% (CI: 19.43%-46.29%) FD with GERD symptoms. Although numerous committees and consensus groups attempted to develop uniform definitions for the diagnosis of GERD and FD, various diagnostic criteria are used across studies and clinical trials (frequency, severity, and location of symptoms). Several studies showed that the overlap between GERD and FD can be explained by a shared pathophysiology, including delayed gastric emptying and disturbed gastric accommodation. DISCUSSION For diagnoses of GERD and FD, uniform definitions that are easy to implement in population studies, easy to interpret for physicians, and that need to be well explained to patients to avoid overestimation or underestimation of true prevalence are needed. Both GERD and FD coexist more frequently than expected, based on coincidence, suggesting a potential pathophysiological link. More research is needed to explore the common GERD/FD overlap population to identify the underlying pathophysiological mechanisms, which may lead to a more effective therapeutic approach.
Protein quality evaluation and in vitro

Plant protein isolates from potato (POPI), soya bean protein isolates (SOPI) and leaf protein concentrate from glyricidia and Manihot esculenta leaves (LPCs) were bio-nutriently evaluated. They were compared with the reference diet casein using some protein quality evaluation (rat bio-assay) indices and in vitro multi-enzyme digestibility. The results showed that all the rats fed the Glyricidia leaf protein concentrates (GLPC) or Manihot leaf protein concentrate (MALPC) lost weight while those fed soya bean protein isolates (SOPI) or potato protein isolate (POPI) gained more weight than those fed with reference diets. Other protein quality indices such as protein efficiency ratio (PER), net protein ratio (NPR), net protein utilization (NPU), biological value (BV), apparent and true protein digestibility (AD & TD) respectively were significantly higher P(<0.05) in both SOPI and POPI than the leaf protein concentrates (LPCs). It was demonstrated that the LPCs were unsuitable as sole source of dietary protein in rat feeding. The in vitro multi-enzyme protein digestibilities of the leaves are 86.29±0.3%; 99.68±0.6% MALPC, GLPC respectively while 79.1±0.3 and 86.5±0.5 were recorded for SOPI and POPI respectively.
The αBβC Integrin Is Expressed on the Surface of the Sea Urchin Egg and Removed at Fertilization

Abstract Integrins are expressed on the surface of some vertebrate eggs where they are thought to have a role in fertilization. The objective of this study is to determine if integrins are expressed on sea urchin eggs. The αB and βC subunits were cloned using the homology polymerase chain reaction. Monoclonal and polyclonal antibodies were developed against bacterially expressed fragments of the extracellular domains of the βC subunit and the αB subunit. As well, a monoclonal antibody was developed against a synthesized peptide corresponding to part of the cytoplasmic domain of βC. Analysis of biotinylated egg cortex extracts immunoprecipitated with either anti-βC or anti-αB yields bands of 130 and 225 kDa. Immunoblots confirm that βC is part of the complex immunoprecipitated with anti-αB. Confocal immunofluorescence and immunogold electron microscopy show that βC is present on the surface of the unfertilized egg at the tips of microvilli and in cortical granules. During the cortical reaction, immunoreactivity with antibodies to the extracellular domains of βC and αB disappears from the egg surface, and microvillar casts on the fertilization envelope become immunoreactive. With antibodies to the cytoplasmic domain of βC, immunoreactivity is lost from the surface of the egg, but the fertilization envelope does not immediately become immunoreactive. In immunoblots of egg cortex there are immunoreactive bands of the predicted sizes for αB and βC. However, in fertilization envelopes, a second band that is slightly lower in molecular weight is also present. Eggs fertilized in the presence of soybean trypsin inhibitor have elongated microvilli that remain bound to the elevating fertilization envelope and immunoreactive to anti-βC antibodies. Eggs fertilized in the presence of an ovoperoxidase inhibitor, 3-amino-1,2,4-triazole, have a patchy distribution of βC immunoreactivity in fertilization envelopes. Together, these data suggest that αBβC integrins are expressed on the surface of unfertilized eggs and, during the cortical reaction, the extracellular domains are cleaved by proteases and cross-linked into the fertilization envelope by ovoperoxidase. The αBβC integrin receptors may have several potential functions prior to their removal at fertilization, including attachment of the vitelline envelope to the egg surface and anchoring the cortical cytoskeleton.
Environmental effects on associations among nitrogen use efficiency traits in wheat

Nitrogen use efficiency parameters of twelve bread wheat cultivars were studied in nine environments comprised of three nitrogen applications tested over three years. An environment-by-trait association biplot and a trait-association by environment biplot were applied to understand environmental effects on these traits and relationships among them. The following trait associations were relatively stable across environments: negative associations of straw nitrogen content vs. nitrogen remobilization efficiency, straw nitrogen content vs. nitrogen harvest index and a positive association of nitrogen remobilization efficiency vs. nitrogen harvest index. The selection of genotypes with a high nitrogen harvest index and nitrogen remobilization efficiency could be used in the development of cultivars with desired nitrogen use efficiency. A low straw nitrogen content can also be used as a reliable and cost-effective indicator in the selection of genotypes with high nitrogen use efficiency.
COVID-19 and digestive health

As the outbreak of coronavirus disease (COVID-19) grows globally, adequate support and continuous treatment must be ensured during this public health emergency also in the area of digestive health. Digestive diseases are amongst the most prevalent health conditions in Europe. COVID-19 has various implications on digestive health, as digestive symptoms such as nausea, diarrhoea and cramps occur in COVID-19 positive patients, in some cases, prior to respiratory symptoms. Moreover, people with chronic digestive conditions, including inflammatory bowel disease (IBD), digestive cancers, liver diseases or immunosuppressed liver transplanted patients, could be particularly vulnerable. This paper outlines the status quo, risks and recommendations related to digestive health during the COVID-19 pandemic for IBD, digestive cancers, liver diseases and endoscopy.
Improving efficiency within a trauma nurse practitioner team.

BACKGROUND Clinicians, including nurse practitioners (NPs), face a number of challenges in delivering high-quality care including frequent interruptions that can potentially compromise patient safety and job satisfaction. LOCAL PROBLEM Trauma NPs voiced frustration with their efforts to provide efficient, high-quality care with frequent interruptions most commonly pager alerts. The purpose of this quality improvement (QI) initiative was to increase trauma NPs' perceptions of patient safety and improve NPs' job satisfaction by reducing workflow interruptions. METHODS The Model for Improvement guided this initiative. INTERVENTIONS The aims of this initiative were to reduce the percentage of nonurgent workflow interruptions via pager alerts by 20% and to increase the utilization of a standardized trauma NP patient rounding process from 0% to 50%. RESULTS Use of the standardized rounding process improved from 0% to 87%. Interruptions via pager alerts decreased by 36.2%. All nine (100%) trauma NP survey responses revealed an improvement in NP perception of patient safety and job satisfaction. CONCLUSION The QI initiative found that increasing communication during rounds by using a standardized rounding process involving the bedside registered nurse can minimize interruptions and improve the efficiency of a trauma NP team. The key to the success of the QI initiative was the implementation of a standardized rounding process.
Note: Thermophilic campylobacters in dairy slurries on Lancashire farms: seasonal effects of storage and land application

Slurry storage tanks on Lancashire farms were sampled in May, June, October and November. There was a seasonal pattern in the number of thermophilic campylobacters. The average log10 MPN per gram fresh weight (log10 MPN gfw−1) in stored samples in May and June was 0·78 (S.D. 0·71) compared to 2·07 (S.D. 0·70) in November and December. Campylobacters were readily detected in samples of mature slurry and composted bedding that farmers were about to put to land. The survival of campylobacters in slurry sprayed on land was studied in two seasons. In June, on farm A, stored slurry was mechanically aerated for 48 h and very low numbers of campylobacters (0·9 log10 MPN gfw−1) remained in the slurry before it was sprayed onto land. They became undetectable within 24 h once sprayed on land. In contrast, campylobacters in matured but unaerated slurry that was sprayed onto land on farm B in February were still detectable in samples taken 5 d after application to land, dropping from 2·11 log10 MPN gfw−1–1·37, a decline of only 0·74 log10 MPN gfw−1 in the first 5 d after application.
Cefepime Versus Cefepime Plus Amikacin as an Initial Antibiotic Choice for Pediatric Cancer Patients With Febrile Neutropenia in an Era of Increasing Cefepime Resistance

Supplemental Digital Content is available in the text. Background: We investigated the treatment outcomes before and after the addition of amikacin to cefepime monotherapy as an initial empirical antibiotic treatment in pediatric cancer patients with febrile neutropenia. Methods: This was a retrospective historical cohort study. The subjects were pediatric cancer patients who visited the emergency room at the Samsung Medical Center, Seoul, Korea, due to chemotherapy-induced febrile neutropenia, between January 2011 and December 2016. Since September 2014, the empirical antimicrobial treatment regimen for febrile neutropenia was changed from high-dose cefepime monotherapy to combination therapy of adding a single dose of amikacin. Results: Two hundred twenty-five bacteremia episodes in 164 patients were reported during the study period. Bacteremia caused by cefepime-resistant Gram-negative bacteria was observed in 16% of patients before September 2014 and in 21% of the patients after September 2014 (P = 0.331). Use of appropriate empirical antibiotic treatments increased from 62% to 83% following addition of amikacin to cefepime treatment (P = 0.003). The duration of fever was shorter in the cefepime plus amikacin group than in the cefepime group (22 vs. 34 hours, P = 0.014); however, rates of septic shock and pediatric intensive care unit hospitalizations were not significantly different between the 2 groups (septic shock, both 7%, P = 0.436; pediatric intensive care unit 3% vs. 1%, P = 0.647). Conclusions: We observed no additional benefit of amikacin addition to high-dose cefepime monotherapy. Therefore, adding amikacin to cefepime monotherapy in conditions where cefepime-resistant Gram-negative bacteremia amounts to 20% or less may not be justified.
Chronic Pain in HIV

The evolution of therapeutics for and management of human immunodeficiency virus-1 (HIV-1) infection has shifted it from predominately manifesting as a severe, acute disease with high mortality to a chronic, controlled infection with a near typical life expectancy. However, despite extensive use of highly active antiretroviral therapy, the prevalence of chronic widespread pain in people with HIV remains high even in those with a low viral load and high CD4 count. Chronic widespread pain is a common comorbidity of HIV infection and is associated with decreased quality of life and a high rate of disability. Chronic pain in people with HIV is multifactorial and influenced by HIV-induced peripheral neuropathy, drug-induced peripheral neuropathy, and chronic inflammation. The specific mechanisms underlying these three broad categories that contribute to chronic widespread pain are not well understood, hindering the development and application of pharmacological and nonpharmacological approaches to mitigate chronic widespread pain. The consequent insufficiencies in clinical approaches to alleviation of chronic pain in people with HIV contribute to an overreliance on opioids and alarming rise in active addiction and overdose. This article reviews the current understanding of the pathogenesis of chronic widespread pain in people with HIV and identifies potential biomarkers and therapeutic targets to mitigate it.
Nanoscale Spatial Resolution in Far-Field Raman Imaging Using Hyperspectral Unmixing in Combination with Positivity Constrained Super-Resolution

This work introduces hyper-resolution (HyRes), a numerical approach for spatial resolution enhancement that combines hyperspectral unmixing and super-resolution image restoration (SRIR). HyRes yields a substantial increase in spatial resolution of Raman spectroscopy while simultaneously preserving the undistorted spectral information. The resolving power of this technique is demonstrated on Raman spectroscopic data from a polymer nanowire sample. Here, we demonstrate an achieved resolution of better than 14 nm, a more than eightfold improvement on single-channel image-based SRIR and 25 × better than regular far-field Raman spectroscopy, and comparable to near-field probing techniques.
Translocation of nutrient transporters to cell membrane via Golgi bypass in Aspergillus nidulans

Nutrient transporters, being polytopic membrane proteins, are believed, but not formally shown, to traffic from their site of synthesis, the ER, to the plasma membrane through Golgi‐dependent vesicular trafficking. Here, we develop a novel genetic system to investigate the trafficking of a neosynthesized model transporter, the well‐studied UapA purine transporter of Aspergillus nidulans. We show that sorting of neosynthesized UapA to the plasma membrane (PM) bypasses the Golgi and does not necessitate key Rab GTPases, AP adaptors, microtubules or endosomes. UapA PM localization is found to be dependent on functional COPII vesicles, actin polymerization, clathrin heavy chain and the PM t‐SNARE SsoA. Actin polymerization proved to primarily affect COPII vesicle formation, whereas the essential role of ClaH seems indirect and less clear. We provide evidence that other evolutionary and functionally distinct transporters of A. nidulans also follow the herein identified Golgi‐independent trafficking route of UapA. Importantly, our findings suggest that specific membrane cargoes drive the formation of distinct COPII subpopulations that bypass the Golgi to be sorted non‐polarly to the PM, and thus serving house‐keeping cell functions.
Relationships amongst length, weight and growth of north-eastern New Zealand reef fishes

This paper examines relationships amongst length, weight and growth parameters of teleost fishes found in shallow north-eastern New Zealand waters. Length–weight equations are presented for 51 species. Fish growth was described using the von Bertalanffy growth parameters L∞ (asymptotic length) and K (growth constant), which were available for 19 species. Literature-derived values for adult body length showed a strong positive correlation with L∞ (r2 = 0.89), which, after conversion to weight, was strongly negatively correlated with K (r 2 = 0.80). Regression equations describing these relationships can be used to predict L∞ and K for fish species lacking such growth data.
The spatial structure of populations

1. Studies of the spatio-temporal dynamics and structure of populations have identified many categories of population type. However, recognized categories intergrade, making it difficult to assign empirical population systems to single categories. 2. We suggest that most population categories can be arranged along two axes that combine per capita birth (B), death (D), emigration (E) and immigration (I) rates. The ‘Compensation Axis’ describes the source-sink component of population structure, with source populations exporting individuals (B > D, E > I) and sinks and pseudosinks consuming individuals (B < D, E < I). The ‘Mobility Axis’ describes the involvement of a local population in regional (I + E) rather than local (B + D) processes, running from separate populations, through metapopulations, to patchy populations. 3. Each sample area within a spatially structured population system can potentially be assigned to a position along each of these axes, with individual sample areas weighted by local population size. The positions of these sample areas and their relative weightings allow the relative importance of different types of process to be judged. A worked exampled is provided, using the butterfly Hesperia comma. This approach shifts the emphasis from pattern (categories that real population systems do not fit) onto process. 4. In many systems, continuous variation in habitat quality and demographic parameters make clear distinctions between ‘habitat’ and ‘non-habitat’ difficult to sustain. In such cases, we advocate the use of a spatial grid system, with effects of patch size and isolation combined into a single, weighted distance function (neighbourhood). 5. The relative importance of different processes depends on the spatial scale at which the system is observed. This again emphasizes the value of a process-based approach.