Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and Characterization of Plant Growth-Promoting Rhizobacteria

Biotechnology has opened up new possibilities concerning the application of beneficial bacteria to the soil for the promotion of plant growth and the biological control of soil-borne pathogens. 1-3 Since the large scale release of genetically engineered bacteria to the environment faces a number of regulatory hurdles, the need to isolate and select superior, naturally occurring rhizosphere bacteria continues to be of interest. Apart from rhizobia symbionts, the rhizosphere-associated beneficial bacteria consist of the following genera: (1) Pseudomonas and Bacillus, which antagonize pathogenic or deleterious microorganisms (biological control) and (2) bacteria that enhance plant growth directly such as Azospirillum, Herbaspirillum, Enterobacter, Acetobacter, Azotobater, and Pseudomonas, as well as many unidentified rhizosphere isolates. The nutritional and environmental requirements of these bacteria are very diverse, and hence there is no general method that can be used to isolate all species of Plant GrowthPromoting Rhizobacteria (PGPR). Accordingly, a variety of methods have been developed, primarily within the last two decades.
Energy demand of furrow openers and corn yield according to the soil disturbance in no till system

The performance of the planter is directly linked to the mechanisms of contact with the soil, more specifically to the furrow openers mechanism. The aim of this study was to evaluate the responses of the soil, machine, and the corn crop, according to furrow openers hoe type and working depths, in an eutroferric Red Latossol and no-tillage system. Soil disturbance, drawbar power and force, speed of operation and corn grains yield was evaluated. The soil disturbance presented difference for the factors; openers and depths. The distinct behavior of the openers, due to their geometry, was a limiting factor for the working depth that determines the area of disturbed soil. Energy demand to the tractor presented difference for openers and depths. The opener with angle of inclination of 17° and width of 21 mm (Opener 1) caused higher soil disturbance and lower force and power. In a Red Latosol with no-tillage system, the working depth of 90 mm âârequired lower draft demand and a soil disturbance suitable to the corn crop development. Key words: Agricultural mechanization, direct seeding, planter.
Relational continuity and patients' perception of GP trust and respect: a qualitative study.

BACKGROUND Despite the benefits of relational continuity of care, particularly for patients with multimorbidity, the traditional model of continuity is changing. Revisiting what patients with ongoing problems want from relational continuity could encourage initiatives to achieve these within a modern healthcare system. AIM To examine the attributes of GPs that patients with long-term conditions value most, and which attributes patients believe are facilitated by relational continuity. DESIGN AND SETTING Qualitative study in UK general practice. METHOD A thematic analysis was carried out, based on secondary analysis of interviews with 25 patients with long-term conditions that were originally conducted to inform a patient-reported outcome measure for primary care. RESULTS Patients with long-term conditions wanted their GPs to be clinically competent, to examine, listen to, care for, and take time with them, irrespective of whether they have seen them before. They believed that relational continuity facilitates a GP knowing their history, giving consistent advice, taking responsibility and action, and trusting and respecting them. Patients acknowledged practical difficulties and safety issues in achieving the first three of these without relational continuity. However, patients felt that GPs should trust and respect them even when continuity was not possible. CONCLUSION Policy initiatives promoting continuity with a GP or healthcare team should continue. Many patients see continuity as a safety issue. When patients experience relationship discontinuity, they often feel that they are not taken seriously or believed by their GP. GPs should therefore consistently seek to visibly demonstrate trust in their patients, particularly when they have not seen them before.
Penetrating Abdominal Aortic Injury: Comparison of ACS-Verified Level-I and II Trauma Centers

Objectives: Penetrating abdominal aortic injury (PAAI) is a highly acute injury requiring prompt surgical management. When compared to surgeons at level-II trauma centers, surgeons at level-I trauma centers are more likely to take in-house call, and may more often be available within 15 minutes of patient arrival. Thus, we hypothesized that level-I trauma centers would have a lower mortality rate than level-II trauma centers in patients with PAAI. Methods: We queried the Trauma Quality Improvement Program database for patients with PAAI, and compared patients treated at American College of Surgeons (ACS)-verified level-I centers to those treated at ACS level-II centers. Results: PAAI was identified in 292 patients treated at level-I centers and 86 patients treated at level-II centers. Patients treated at the 2 center types had similar median age, injury severity scores and prevalence of diabetes, hypertension, and smoking (p > 0.05). There was no difference in the frequency of additional intra-abdominal vascular injuries (p > 0.05). Median time to hemorrhage control (level-I: 40.8 vs level-II: 49.2 minutes, p = 0.21) was similar between hospitals at the 2 trauma center levels. We found no difference in the total hospital length of stay or post-operative complications (p > 0.05). When controlling for covariates, we found no difference in the risk of mortality between ACS verified level-I and level-II trauma centers (OR:1.01, CI:0.28-2.64, p = 0.99). Conclusion: Though the majority of PAAIs are treated at level-I trauma centers, we found no difference in the time to hemorrhage control, or the risk of mortality in those treated at level-I centers when compared to those treated at level-II trauma centers. This finding reinforces the ACS-verification process, which strives to achieve similar outcomes between level-I and level-II centers.
Serum metabonomic study on the antidepressant-like effects of ellagic acid in a chronic unpredictable mild stress-induced (CUMS) mouse model.

As a polyphenol, ellagic acid (EA) has shown potential antidepressant activity. In this study, the effects and serum metabolomics analysis of EA against depression were investigated using a CUMS model. EA (20 or 100 mg/kg body weight) significantly ameliorated the CUMS-induced depression-like behaviors, including reduced body weight, decreased sucrose preference, and increased immobility time in both the tail suspension test and the forced swimming test. Furthermore, EA attenuated the CUMS-induced hippocampal damage and significantly increased the brain-derived neurotrophic factor (BDNF) and the serotonin (5-HT) levels as well as suppressed the inflammatory response. The metabolomics analysis showed that the disturbance of glycerophospholipid (phosphatidylethanolamine and phosphatidylinositol), amino acid (L-arginine and N-stearoyl serine), purine (uric acid) metabolism induced by CUMS were attenuated by the EA treatment. Furthermore, the correlation analysis indicated that the metabolites changes were strongly correlated with behavioral disorders, BDNF, 5-HT, and inflammatory cytokines levels. This study provided new insights for the antidepressant effects of EA and suggests that EA may be a potential nutraceutical for improving the management of depression.
DNA methylation status of imprinted H19 and KvDMR1 genes in human placentas after conception using assisted reproductive technology.

Background Assisted reproductive technologies (ARTs), such as in vitro fertilization (IVF) and intracytoplasmic sperm injection (ICSI), are thought to destabilize genomic imprints. Previous studies examining the association between ART and aberrant DNA methylation have been inconclusive. Method The DNA methylation status of H19 and KvDMR1was compared between newborns conceived through ART and those conceived naturally to evaluate the safety of ART. Placental tissues from 6 full-term, naturally conceived pregnancies (no gestational comorbidities) and six full-term ART pregnancies (no gestational complication) were collected. Genomic DNA (gDNA) and RNA were extracted from both groups. Real-time PCR was used to analyze the mRNA expression levels of H19 and KvDMR1 in the placenta for both groups. A whole-genome DNA methylation microarray was used to examine three placentas from full-term, naturally conceived pregnancies and three placentas from full-term IVF pregnancies. Result The expression level of H19 in the IVF group was significantly higher than that in the natural pregnancy group, whereas the expression level of KvDMR1 was significantly lower in the ART group than in the natural pregnancy group. Also, human ART manipulation resulted in placental gDNA methylation modifications. Conclusion: Abnormal methylation patterns were detected in phenotypically normal phenotype conceived by ART, which may occur due to imprinting errors in sperm/oocyte cells or side effects of in vitro embryo culture procedures. Further investigation is necessary to determine whether imprinted gene expression and DNA methylation can be regulated through other mechanisms. Keywords Assisted reproductive technology (ART); placenta; methylation; H19; KvDMR1.
Treatment Limitation Decisions in Critically Ill Patients With a Malignancy on the Intensive Care Unit

Background: Treatment limitation decisions (TLDs) on the ICU can be challenging, especially in patients with a malignancy. Up-to-date literature regarding TLDs in critically ill patients with a malignancy admitted to the ICU is scarce. The aim was to compare the incidence of written TLDs between patients with an active malignancy, patients with a malignancy in their medical history (complete remission, CR) and patients without a malignancy admitted unplanned to the ICU. Methods: We conducted a retrospective cohort study in a large university hospital in the Netherlands. We identified all unplanned admissions to the ICU in 2017 and categorized the patients in 3 groups: patients with an active malignancy (study population), with CR and without a malignancy. A TLD was defined as a written instruction not to perform life-saving treatments, such as CPR in case of cardiac arrest. A multivariate binary logistic regression analysis was used to identify whether having a malignancy was associated with TLDs. Results: Of the 1046 unplanned admissions, 125 patients (12%) had an active malignancy and 76 (7.3%) patients had CR. The incidence of written TLDs in these subgroups were 37 (29.6%) and 20 (26.3%). Age (OR 1.03; 95% CI 1.01 -1.04), SOFA score at ICU admission (OR 1.11; 95% CI 1.05 -1.18) and having an active malignancy (OR 1.75; 95% CI 1.04-2.96) compared to no malignancy were independently associated with written TLDs. SOFA scores on the day of the TLD were not significantly different in patients with and without a malignancy. Conclusions: This study shows that the presence of an underlying malignancy is independently associated with written TLDs during ICU stay. Patients with CR were not at risk of more written TLDs. Whether this higher incidence of TLDs in patients with a malignancy is justified, is at least questionable and should be evaluated in future research.
Greenhouse and field evaluations of commonly occurring weed species for their host suitability to Meloidogyne species

Since weeds serve as hosts for nematode pests, the host status of 20 weed species (commonly occurring in fields of developing farmers) to Meloidogyne incognita and M. javanica, respectively, were investigated. Greenhouse studies showed that seven weed species had Rf values >1 for both nematode species indicating susceptibility, while 13 had Rf values ≤ 1 indicating resistance. Greenhouse results showed that Hibiscus trionum and Amaranthus tricolor were identified as the most susceptible and Chenopodium carinatum and Datura ferox the poorest hosts for M. incognita and M. javanica. For field experiments at Kuruman, Solanum retroflexum was the most susceptible weed to a M. javanica population, while the same was evident for H. trionum at Nelspruit, where a mixed population of M. incognita and M. javanica occurred and at Potchefstroom, where a population of M. incognita was present. Results from this study indicated that certain weed species are highly susceptible to root-knot nematodes and should be removed timely and effectively to prevent population level increases of root-knot nematode pests in the fields of farmers.
Transcriptomic and epigenomic dynamics associated with development of human iPSC-derived GABAergic interneurons

Abstract GABAergic interneurons (GINs) are a heterogeneous population of inhibitory neurons that collectively contribute to the maintenance of normal neuronal excitability and network activity. Identification of the genetic regulatory elements and transcription factors that contribute toward GIN function may provide new insight into the pathways underlying proper GIN activity while also indicating potential therapeutic targets for GIN-associated disorders, such as schizophrenia and epilepsy. In this study, we examined the temporal changes in gene expression and chromatin accessibility during GIN development by performing transcriptomic and epigenomic analyses on human induced pluripotent stem cell-derived neurons at 22, 50 and 78 days (D) post-differentiation. We observed 13 221 differentially accessible regions (DARs) of chromatin that associate with temporal changes in gene expression at D78 and D50, relative to D22. We also classified families of transcription factors that are increasingly enriched at DARs during differentiation, indicating regulatory networks that likely drive GIN development. Collectively, these data provide a resource for examining the molecular networks regulating GIN functionality.
Media composition and light affect storability and poststorage recovery of micropropagated hosta plantlets

Hosta (Hosta tokudama Makeawa 'Newberry Gold') plantlets were micro- propagated photoautotrophically (without sucrose in medium) or photomixotrophically (with 2% sucrose in medium) for 3 weeks at 23 °C under 80 μmol·m -2 ·s -1 photosynthetic photon flux (PPF) prior to long-term storage. Plantlets were stored for 4, 8, or 12 weeks at 5, 10, or 22 °C in darkness or under white (400-800 nm), blue (400-500 nm), or red (600- 700 nm) light at or near light compensation points. Illumination during storage was necessary to maintain dry weight and regrowth potentials of plantlets in vitro, but light quality had no effect on these parameters. All photoautotrophic plantlets stored in darkness were of poor quality at the time of removal from storage and died when transferred to the greenhouse. Dark-stored photomixotrophic plantlets survived storage for 12 weeks at 5 °C, but declined in appearance (visual quality) as the storage duration increased. Decline in visual quality was greater when plantlets were stored at 10 and 22 °C. Leaf dry weight of illuminated plantlets increased and percentage of leaf yellowing decreased as storage temperature increased. Recovery of illuminated plantlets from photomixotrophic storage was best when plantlets were stored at 22 °C. These plantlets were characterized by increased visual quality (color and form) and increased dry weight compared with those in other treatments. After 60 days in the greenhouse, the dry weight of these plantlets was similar for 4-, 8-, and 12-week storage durations, indicating flexibility in storage time if specific light and temperature provisions are met.
Gcn5p and Ubp8p Affect Protein Ubiquitylation and Cell Proliferation by Altering the Fermentative/Respiratory Flux Balance in Saccharomyces cerevisiae

We propose a study showing a novel role of Gcn5p and Ubp8p in the process of ubiquitylation of the yeast proteome which includes main glycolytic enzymes. Interestingly, in the absence of Gcn5p and Ubp8p glucose consumption and redox balance were altered in yeast. We believe that these results and the role of Gcn5p and Ubp8p in sugar metabolism might open new perspectives of research leading to novel protocols for counteracting the enhanced glycolysis in tumors. ABSTRACT Protein ubiquitylation regulates not only endocellular trafficking and proteasomal degradation but also the catalytic activity of enzymes. In Saccharomyces cerevisiae, we analyzed the composition of the ubiquitylated proteomes in strains lacking acetyltransferase Gcn5p, Ub-protease Ubp8p, or both to understand their involvement in the regulation of protein ubiquitylation. We analyzed His6Ub proteins with a proteomic approach coupling micro-liquid chromatography and tandem mass spectrometry (μLC-MS/MS) in gcn5Δ, ubp8Δ and ubp8Δ gcn5Δ strains. The Ub-proteome altered in the absence of Gcn5p, Ubp8p, or both was characterized, showing that 43% of the proteins was shared in all strains, suggesting their functional relationship. Remarkably, all major glycolytic enzymes showed increased ubiquitylation. Phosphofructokinase 1, the key enzyme of glycolytic flux, showed a higher and altered pattern of ubiquitylation in gcn5Δ and ubp8Δ strains. Severe defects of growth in poor sugar and altered glucose consumption confirmed a direct role of Gcn5p and Ubp8p in affecting the REDOX balance of the cell. IMPORTANCE We propose a study showing a novel role of Gcn5p and Ubp8p in the process of ubiquitylation of the yeast proteome which includes main glycolytic enzymes. Interestingly, in the absence of Gcn5p and Ubp8p glucose consumption and redox balance were altered in yeast. We believe that these results and the role of Gcn5p and Ubp8p in sugar metabolism might open new perspectives of research leading to novel protocols for counteracting the enhanced glycolysis in tumors.
GENETIC VARIATION AMONG EGYPTIAN WHITE LUPIN (LUPINUS ALBUS L.) GENOTYPES

Field Evaluation of eighteen lupin genotypes was carried out during 2012/13 and 2013/14 at Giza Agriculture Research Station, Egypt, to assess the genetic variation on phenological parameters. Simultaneously, molecular diversity assessment was performed using 11 SRAP primer pair combinations. High significant differences among genotypes were observed for field performance during the two seasons and their combined data. The Australian genotype 75 B9.10 and landrace Fayed1 recorded the highest seed yield/plant while the Egyptian landraces Sohag2, Fayed1 and the cultivar Giza1 were superiors in seed yield/hectare (2.8, 2.6 and 2.6t, respectively). Only the first two principle components explained 97 % of variability. Characters, number of pods, seed yield/plant and seed yield/hectare were grouped on the positive PC1 axis of the biplot with genotypes Sohag2, 75B9.10 and Fayed1. The molecular analysis revealed coherent results. The 11 SRAP primers generated 3286 amplified fragments represents 337 genetic loci across the lupin genome. The average detected loci per primer pair was 30.64 with 322 polymorphic loci across the studied genotypes (96.05%). The polymorphism information content (PIC) values were generally high and ranged from 0.883 to 0.981. The high PIC values highlight the power of SRAP markers in detecting the molecular diversity in lupin genotypes. The genotypes tended to cluster based on their origin and genetic background.
Correlations of amide proton transfer-weighted MRI of cerebral infarction with clinico-radiological findings

Objective To clarify the relationship between amide proton transfer-weighted (APTW) signal, which reflects intracellular pH, and clinico-radiological findings in patients with hyperacute to subacute cerebral infarction. Materials and methods Twenty-nine patients (median age, 70 years [IQR, 54 to 74]; 15 men) were retrospectively examined. The 10th, 25th, 50th, 75th, and 90th percentiles of APTW signal (APT10, APT25, APT50, APT75 and APT90, respectively) were measured within the infarction region-of-interest (ROI), and compared between poor prognosis and good prognosis groups (modified Rankin Scale [mRS] score ≥2 and mRS score <2, respectively). Correlations between APTW signal and time after onset, lesion size, National Institutes of Health Stroke Scale (NIHSS) score, mRS score, and mean apparent diffusion coefficient (ADC) were evaluated. Results The poor prognosis group had lower APT50, APT75, and APT90 than the good prognosis group (–0.66 [–1.19 to –0.27] vs. –0.09 [–0.62 to –0.21]; –0.27 [–0.63 to –0.01] vs. 0.31 [–0.15 to 1.06]; 0.06 [–0.21 to 0.34] vs. 0.93 [0.36 to 1.50] %; p <0.05, respectively). APT50 was positively correlated with time after onset (r = 0.37, p = 0.0471) and negatively with lesion size (r = –0.39, p = 0.0388). APT75 and APT90 were negatively correlated with NIHSS (r = –0.41 and –0.43; p <0.05, respectively). APT50, APT75 and APT90 were negatively correlated with mRS (r = –0.37, –0.52 and –0.57; p <0.05, respectively). APT10 and APT25 were positively correlated with mean ADC (r = 0.37 and 0.38; p <0.05, respectively). Conclusion We demonstrated correlations between APTW signals of infarctions and clinico-radiological findings in patients with hyperacute to subacute infarctions. The poor prognosis group had a lower APTW signal than the good prognosis group. APTW signal was reduced in large infarctions, infarctions with low ADC, and in patients with high NIHSS and mRS scores.
SINAT E3 ligases regulate the stability of the ESCRT component FREE1 in response to iron deficiency in plants.

The endosomal sorting complex required for transport (ESCRT) machinery is an ancient, evolutionarily conserved membrane remodeling complex that is essential for multivesicular body (MVB) biogenesis in eukaryotes. FYVE DOMAIN PROTEIN REQUIRED FOR ENDOSOMAL SORTING 1 (FREE1), which was previously identified as a plant-specific ESCRT component, modulates MVB-mediated endosomal sorting and autophagic degradation. Although the basic cellular functions of FREE1 as an ESCRT component have been described, the regulators that control FREE1 turnover remain unknown. Here, we analyzed how FREE1 homeostasis is mediated by the RING-finger E3 ubiquitin ligases, SINA of Arabidopsis thaliana (SINATs), in response to iron deficiency. Under iron-deficient growth conditions, SINAT1-4 were induced and ubiquitinated FREE1, thereby promoting its degradation and relieving the repressive effect of FREE1 on iron absorption. By contrast, SINAT5, another SINAT member that lacks ubiquitin ligase activity due to the absence of the RING domain, functions as a protector protein that stabilizes FREE1. Collectively, our findings uncover a hitherto unknown mechanism of homeostatic regulation of FREE1, and demonstrate a unique regulatory SINAT-FREE1 module that subtly regulates plant response to iron deficiency stress. This article is protected by copyright. All rights reserved.