Miracle-dz/UniFAR-FTUs huggingface dataset:
Relation between light qualities and accumulation of steroidal glycoalkaloids as well as signal molecule in cell in potato tubers.

The potato steroidal glycoalkaloids (SGAs) are secondary metabolites,two major SGA in cultivated potato (Solanum tuberosum) are α-chaconine and α-solanine,and their total content in tubers should not exceed the safety limit of 20 mg 100 g-1 FW,otherwise it can be toxic to humans. Accumulation of SGAs in potato tubers is influenced by many factors including the key environmental factors,temperature and light. In order to reduce the content of SGAs and research the accumulation mechanism of SGAs in potato tubers,in the present study we attempted to compare the contents of SGAs,second messengers—calmodulin and the G protein in potato tubers,treated with the treatments of red light,blue light,white light and darkness under the same tem-perature (15℃ ). The results indicated that red light significantly (P 0.01) increased the average content of SGAs in potato tubers,with 26.02%,55.50%,and 100.79% higher than that treated with blue light,white light and darkness,respectively. It was confirmed that light with different wavelengths has different effects on accumulation of SGAs in potato tubers. Among factors influencing the accumulation of SGAs in potato tubers,the red light took the first place and the blue light took the second place. Meanwhile,the content of second messengers—the G protein in potato tubers treated with red light was 0.95%,2.01%,and 3.86% higher than that treated with blue light,white light and darkness,respectively. And the content of calmodulin in potato tubers treated with red light was 7.94%,37.41%,and 87.24% higher than that treated with blue light,white light and darkness,respectively. It was inferred that the red light is the signal molecule for SGAs accumulation,which stimulates the acceptor (PHYB) of red light and participate in accumulation of SGAs in potato tubers,together with the second messenger G protein,calmodulin,and so on.
Manipulation of hunger levels affects great spotted cuckoo and magpie host nestlings differently

Brood parasitic nestlings usually exhibit an exaggerated begging behaviour, which is mainly attributed to reduced inclusive fitness costs since they typically share the nest with unrelated individuals. However, energetic costs also constrain begging expression and accordingly a relation between food requirements and intensity of begging behaviour could also exist in brood parasites, just as in nesting bird species. Here, we tested this hypothesis in the great spotted cuckoo Clamator glandarius and its main host, the magpie Pica pica, by studying the effect of an appetite enhancer, cyproheptadine hydrochloride, on nestling provisioning and development (size, body mass and cell-mediated immune response). To study nestling provisioning, neck-collars were meticulously placed around nestling necks allowing normal respiration but avoiding the ingestion of food delivered by adult magpies during ca 2.5 h. Loss in body mass during neck-collar trials was used as a proxy for energetic begging costs, while the amount of food received during these trials and growth during the whole nestling period were used as variables reflecting short- and long-term effects of the experimental treatment. During neck-collar trials, we found that experimental nestlings of both species received more food than control nestlings. However, experimental magpies, but not cuckoos, lost more body mass than control nestlings. These results suggest a short-term beneficial effect of an escalated begging behaviour in both species that would be energetically cheaper for cuckoos than for magpies. We found positive long-term effects of the appetite enhancer only in magpies (in terms of tarsus and wing length at fledging, but not in terms of immune response and body mass); suggesting that exaggerated begging would be beneficial for hosts only. We discuss the possible effect of begging behaviour on the risk of predation and on inclusive fitness, but also the possibility that our results may be explained by some kind of limitation in the capability of food assimilation by parasitic species.
Decompressive Craniectomy Is Associated With Good Quality of Life Up to 10 Years After Rehabilitation From Traumatic Brain Injury.

OBJECTIVES Traumatic brain injury is the number one cause of death in children and young adults and has become increasingly prevalent in the elderly. Decompressive craniectomy prevents intracranial hypertension but does not clearly improve physical outcome 6 months after traumatic brain injury. However, it has not been analyzed if decompressive craniectomy affects traumatic brain injury patients' quality of life in the long term. DESIGN Therefore, we conducted a cross-sectional study assessing health-related quality of life in traumatic brain injury patients with or without decompressive craniectomy up to 10 years after injury. SETTING Former critical care patients. PATIENTS Chronic traumatic brain injury patients having not (n = 37) or having received (n = 98) decompressive craniectomy during the acute treatment. MEASUREMENTS AND MAIN RESULTS The Quality of Life after Brain Injury questionnaire was used as outcome measure with a total score from zero to 100, representing lowest and best health-related quality of life, respectively. Health-related quality of life was compared between patients with or without decompressive craniectomy for the entire cohort, for the traumatic brain injury severity (mild, moderate, severe) measured by the initial Glasgow Coma Scale, for age and time variables (age at traumatic brain injury, age at survey, elapsed time since traumatic brain injury) using the Mann-Whitney U test. Differences were considered significant at a p value of less than 0.05. Decompressive craniectomy was necessary in all initial traumatic brain injury severity groups. Eight percent more decompressive craniectomy patients reported good health-related quality of life with a Quality of Life after Brain Injury total score greater than or equal to 60 compared with the no decompressive craniectomy patients up to 10 years after traumatic brain injury (p = 0.004). Initially, mild classified traumatic brain injury patients had a median Quality of Life after Brain Injury total score of 83 (decompressive craniectomy) versus 62 (no decompressive craniectomy) (p = 0.028). Health-related quality of life regarding physical status was better in decompressive craniectomy patients (p = 0.025). Decompressive craniectomy showed a trend toward better health-related quality of life in the 61-85-year-old reflected by median Quality of Life after Brain Injury total scores of 62 (no decompressive craniectomy) versus 79 (decompressive craniectomy) (p = 0.06). CONCLUSIONS Our results suggest that decompressive craniectomy is associated with good health-related quality of life up to 10 years after traumatic brain injury. Thus, decompressive craniectomy may have an underestimated therapeutic potential after traumatic brain injury.
Dissociation between wanting and liking for coffee in heavy drinkers

Background: There is an ongoing discussion about the addictive strength of caffeine. According to the incentive-sensitization theory, the development and the maintenance of drug addiction is the result of a selective sensitization of brain regions that are relevant for wanting without a corresponding increase in liking. Dissociations of wanting and liking have been observed with a wide range of drugs in animals. For human subjects, results are inconclusive, which is possibly due to invalid operationalizations of wanting and liking. Aim: The present study examined dissociations of wanting and liking for coffee in heavy and low/non-consumers with newly developed and validated response time-based assessment procedures for wanting and liking. Methods: For this study 24 heavy and 32 low/non-consumers of coffee completed two versions of the Implicit-Association Test (IAT), one of which has been developed and validated recently to assess wanting for coffee, whereas the other reflects an indicator of liking for coffee. Results: Results revealed a significant interaction between group (heavy vs. low/non-consumers) and IAT type (wanting vs. liking) indicating that heavy coffee drinkers differed from low/non-consumers by displaying increased wanting but not liking for coffee. Interpretation: These data confirm that heavy coffee consumption is associated with strong wanting despite low liking for coffee, indicating that wanting becomes independent from liking through repeated consumption of caffeine. This dissociation provides a possible explanation for the widespread and stable consumption of caffeine-containing beverages.
Neural dysfunction correlates with heat coma and CTmax in Drosophila but does not set the boundaries for heat stress survival

ABSTRACT When heated, insects lose coordinated movement followed by the onset of heat coma (critical thermal maximum, CTmax). These traits are popular measures to quantify interspecific and intraspecific differences in insect heat tolerance, and CTmax correlates well with current species distributions of insects, including Drosophila. Here, we examined the function of the central nervous system (CNS) in five species of Drosophila with different heat tolerances, while they were exposed to either constant high temperature or a gradually increasing temperature (ramp). Tolerant species were able to preserve CNS function at higher temperatures and for longer durations than sensitive species, and similar differences were found for the behavioural indices (loss of coordination and onset of heat coma). Furthermore, the timing and temperature (constant and ramp exposure, respectively) for loss of coordination or complete coma coincided with the occurrence of spreading depolarisation (SD) events in the CNS. These SD events disrupt neurological function and silence the CNS, suggesting that CNS failure is the primary cause of impaired coordination and heat coma. Heat mortality occurs soon after heat coma in insects; to examine whether CNS failure could also be the proximal cause of heat death, we used selective heating of the head (CNS) and abdomen (visceral tissues). When comparing the temperature causing 50% mortality (LT50) of each body part versus that of the whole animal, we found that the head was not particularly heat sensitive compared with the abdomen. Accordingly, it is unlikely that nervous failure is the principal/proximate cause of heat mortality in Drosophila. Summary: Hyperthermic failure of the Drosophila central nervous system causes heat coma, a trait varying in temperature between drosophilids, but neural failure is not the primary cause of heat mortality.
Relationships for estimating N2 fixation in legumes: incidence for N balance of legume‐based cropping systems in Europe

Management of nitrogen (N) inputs into agricultural systems is of increasing interest due to the intensive use of synthetic fertilizers in modern cash crop systems, which has caused considerable environmental damage, including nitrate contamination of surface and groundwater, eutrophication of coastal marine areas and emission of greenhouse gases. The use of legumes grown in rotations or intercropping is nowadays regarded as an alternative and sustainable way of introducing N into low-input cropping systems. In order to develop a simple tool to assess biological nitrogen fixation (BNF) by legume pulse and forages within crop rotations, we conducted a systematic literature survey with a quantitative statistical analysis intended to define a robust relationship between measurable variables and N2 fixation. We found highly significant correlations between total N accumulation in shoot matter and fixed N2 in forage (y = 0.79x − 0.49) and grain (y = 0.70x + 1.01) legumes. Accurately estimating the contribution.
Genetic analysis of resistance genes in an Indica-type rice (Oryza sativa L.), Kasalath, using DNA markers.

We searched for blast resistance genes in an Indica-type rice (Oryza sativa L.) cultivar, Kasalath. The resistance gene was estimated based on the reaction patterns to standard differential blast isolates from Japan and Philippines against the monogenic lines as differential varieties targeting 24 kinds of resistance genes. Kasalath showed complete resistance only to a Japanese isolate, Hoku1, which was avirulent to genotypes containing the Piz allele genes and virulent to genotypes containing Pia and Pish. Kasalath was susceptible, or only moderately resistant, to the Philippine isolates. A QTL analysis for resistance to Hoku1 was performed in backcross inbred lines derived from crosses between Kasalath and a Japonica-type cultivar, Nipponbare (recurrent parent), harboring Pia and Pish. A resistance QTL with the Kasalath genotype was detected in the same region as Pia on chromosome 11. Association analysis in 50 chromosome segment substitution lines detected three associations, on chromosomes 6, 8 and 11; the association located in the same region as the QTL on chromosome 11 had a strong resistance effect. These reaction patterns indicated that Kasalath did not harbor Pia and that the QTL on chromosome 11 was the other allele of Pia or a novel resistance gene.
A NEW APPROACH TO LOCALIZE GLUCOCORTICOID RECEPTOR USING DNA PROBE CONTAINING GLUCOCORTICOID RESPONSIVE ELEMENT DNA CONSENSUS SEQUENCES

A method to localize glucocorticoid receptor (GR) by utilizing the specific interaction between GR and glucocorticoid responsive element (GRE) is described. In this study, pBR 322 DNA was thymine-thymine (T-T) dimerized by UV-irradiation and used as a probe, since pBR 322 DNA harbors GRE DNA consensus sequences and it is known that GR binds to pBR 322 DNA specifically. T-T dimerized pBR 322 DNA was incubated with fresh frozen sections of adrenalectomized rat liver, which were fixed in 4% paraformaldehyde in phosphate buffered saline, and the sites of reaction were visualized by a successive use of rabbit anti-T-T antibody and horseradish-peroxidase labeled goat anti-rabbit IgG antibody. As a result, GR was localized to the nuclei and nuclear membranes as well as cytoplasm of hepatocytes, and most of the staining was lost in the liver sections from rats, which were intraperitoneally injected with hydrocortisone. On the other hand, the staining for T-T dimerized DNA probe with cyclic AMP responsive element consensus sequence was localized solely to the nuclei and the staining pattern was not altered by an injection of the steroid, indicating that the staining for pBR 322 DNA is sequence-specific. Finally, this method should provide useful information on the localization of steroid hormone receptors with DNA-binding activity.
Suppression of PRDX4 inhibits cell proliferation and invasion of ectopic endometrial stromal cells in endometriosis

Abstract Oxidative stress (OS) has been proposed to play a role in the development of EMs. Peroxiredoxins are a family of antioxidant proteins that exhibit peroxidase activity in a thioredoxin-dependent manner, protecting cells against OS. The Western blotting results showed that the relative expression of PRDX4 was significantly increased in ectopic endometria compared with the normal endometria of EMs-free (p < .05). The H2O2 concentration was also significantly higher in the ectopic endometrium. PRDX4 siRNA was transfected into primary ectopic endometrial stromal cells (EESCs). The viability of the transfected EESCs was measured by CCK-8 assay, and the results showed significantly decreased cell viability. Furthermore, the apoptosis rate and ROS generation in flow cytometry assays were significantly increased after the knockdown of PRDX4 expression (p < .05). Scratch assays and transwell assays revealed that decreased expression of PRDX4 mediated by siRNA inhibited EESC migration and invasion. In conclusion, these findings indicate the potential role of PRDX4 in the development of EMs and PRDX4 as a possible therapeutic target for EMs treatment.
Bone Marrow Mesenchymal Stem Cell-Derived Exosomes Attenuate LPS-Induced ARDS by Modulating Macrophage Polarization Through Inhibiting Glycolysis in Macrophages.

Macrophages play a key role in the development of sepsis-induced acute respiratory distress syndrome (ARDS). Recent evidence has proved that glycolysis plays an important role in regulating macrophage polarization through metabolic reprogramming. Bone marrow mesenchymal stem cells (BMSCs) can alleviate sepsis-induced lung injury and possess potent immunomodulatory and immunosuppressive properties via secreting exosomes. However, it is unknown whether BMSCs-derived exosomes exert their therapeutic effect against sepsis-induced lung injury by inhibiting glycolysis in macrophages. Therefore, the present study aimed to evaluate the anti-inflammatory effects of exosomes released from BMSCs on acute lung injury induced by lipopolysaccharide (LPS) in mice and explored the possible underlying mechanisms in vitro and in vivo. We found that BMSCs inhibited M1 polarization and promoted M2 polarization in MH-S cells (a murine alveolar macrophage cell line) by releasing exosomes. Further experiments showed that exosomes secreted by BMSCs modulated LPS-treated MH-S cells polarization by inhibiting cellular glycolysis. Moreover, our results showed that BMSCs-derived exosomes down-regulated the expression of several essential proteins of glycolysis via inhibition of HIF-1α. Finally, a model of LPS-induced ARDS in mice was established, we found that BMSCs-derived exosomes ameliorated the LPS-induced inflammation and lung pathological damage. Meanwhile, we found that intratracheal delivery of BMSCs-derived exosomes effectively down-regulated LPS-induced glycolysis in mice lung tissue. These findings reveal new mechanisms of BMSCs-derived exosomes in regulating macrophage polarization which may provide novel strategies for the prevention and treatment of LPS-induced ARDS.
The effects of dietary L-carnitine and rumen-protected choline on growth performance, carcass characteristics and blood and rumen metabolites of Holstein Young bulls

An experiment was conducted to determine the effects of L-carnitine (LC) and rumen-protected choline (RPC) on growth performance, carcass characteristics and blood and rumen metabolites of finishing bulls. Twenty-eight Holstein young bulls (average initial weigh 310±24 kg) were used in a completely randomized design with four treatments and seven replicates with 2×2 factorial arrangement for 90 days. Basal diets were formulated for 14% crude protein and 1.14 Mcal/kg of net energy for growth and contained 24% of dietary dry matter (DM) as corn silage, 6.8% alfalfa hay, 46.50% barley grain and 9.5% canola meal. Treatments included: (1) without LC and RPC or control; (2) 4g/d LC head−1; (3) 5 g/d RPC head-1; (4) 4 g/d LC head−1 and 5 g/d RPC head−1. Calves were fed ad libitum and had free access to fresh water. There were no differences between diets for DM intake, average daily gain and gain:feed. Plasma concentrations of glucose, insulin, nonesterified fatty acid, β-hydroxybutyrate, cholestrol and aspartate aminotransferase were not affected by treatments, but plasma triglyceride concentration decreased in calves fed RPC (P < 0.05). Longissimus muscle area, pelvic, kidney, heart and rumen and intestine fats were not affected by treatments. Subcutaneous fat and backfat thickness decreased in calves fed RPC (P < 0.05). LC and RPC had no significant effects on chemical composition of meat and liver (protein, fat, ash and dry mater). There was no significant difference between diets for rumen liquor volatile fatty acid and pH. This study showed that LC and RPC supplements cannot affect growth performance in Holstein young bulls, but lipid metabolism may be affected by LC and RPC.
Preclinical assessment of Autologous Tolerogenic Dendritic Cells from End-stage renal disease patients.

BACKGROUND Kidney transplantation is the therapeutic of choice for patients suffering from kidney failure. Whilst immunosuppressive drugs can control graft rejection, their use is associated with increased infections and cancer, and they do not effectively control chronic graft rejection. Cell therapy is an attractive strategy to minimize the use of pharmacological drugs. METHODS We recently developed a protocol to generate human monocyte-derived autologous tolerogenic dendritic cells (ATDCs) from healthy volunteers. Herein, we transferred the ATDC manufacturing protocol to a Good Manufacturing Practice (GMP)-compliant facility. Furthermore, we compared the phenotype and in vitro functions of ATDCs generated from patients with end stage renal disease to those generated from healthy volunteers. RESULTS We describe the critical steps for GMP-compliant production of ATDCs, and define the quality criteria required to allow release of the cell products. Furthermore, we showed that ATDCs generated from healthy volunteers and patients suffering from kidney failure display the same tolerogenic profile based on their phenotype, resistance to maturation, and ability to modulate T cell responses. CONCLUSIONS Together, these results allowed us to define the production process and the quality criteria for the release of ATDCs prior to their administration in patients receiving a kidney transplant.
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features

X-ray crystallography is the major approach for determining atomic-level protein structures. Because not all proteins can be easily crystallized, accurate prediction of protein crystallization propensity provides critical help in guiding experimental design and improving the success rate of X-ray crystallography experiments. This study has developed a new machine-learning-based pipeline that uses a newly developed deep-cascade forest (DCF) model with multiple types of sequence-based features to predict protein crystallization propensity. Based on the developed pipeline, two new protein crystallization propensity predictors, denoted as DCFCrystal and MDCFCrystal, have been implemented. DCFCrystal is a multistage predictor that can estimate the success propensities of the three individual steps (production of protein material, purification and production of crystals) in the protein crystallization process. MDCFCrystal is a single-stage predictor that aims to estimate the probability that a protein will pass through the entire crystallization process. Moreover, DCFCrystal is designed for general proteins, whereas MDCFCrystal is specially designed for membrane proteins, which are notoriously difficult to crystalize. DCFCrystal and MDCFCrystal were separately tested on two benchmark datasets consisting of 12 289 and 950 proteins, respectively, with known crystallization results from various experimental records. The experimental results demonstrated that DCFCrystal and MDCFCrystal increased the value of Matthew's correlation coefficient by 199.7% and 77.8%, respectively, compared to the best of other state-of-the-art protein crystallization propensity predictors. Detailed analyses show that the major advantages of DCFCrystal and MDCFCrystal lie in the efficiency of the DCF model and the sensitivity of the sequence-based features used, especially the newly designed pseudo-predicted hybrid solvent accessibility (PsePHSA) feature, which improves crystallization recognition by incorporating sequence-order information with solvent accessibility of residues. Meanwhile, the new crystal-dataset constructions help to train the models with more comprehensive crystallization knowledge.