Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytokinin-Facilitated Plant Regeneration of Three Brachystelma Species with Different Conservation Status

In Africa and Asia, members of the genus Brachystelma are well-known for their diverse uses, especially their medicinal and nutritional values. However, the use of many Brachystelma species as a valuable resource is generally accompanied by the concern of over-exploitation attributed to their slow growth and general small size. The aim of the current study was to establish efficient micropropagation protocols for three Brachystelma species, namely Brachystelma ngomense (endangered), Brachystelma pulchellum (vulnerable) and Brachystelma pygmaeum (least concern), as a means of ensuring their conservation and survival. This was achieved using nodal segments (~10 mm in length) as the source of explants in the presence of different concentrations of three cytokinins (CK) namely N6-benzyladenine (BA), isopentenyladenine (iP) and meta-topolin riboside (mTR), over a period of 6 weeks. The highest (25 µM) concentration of cytokinin treatments typically resulted in significantly higher shoot proliferation. However, each species differed in its response to specific CK: the optimal concentrations were 25 µM mTR, 25 µM iP and 25 µM BA for Brachystelma ngomense, Brachystelma pulchellum and Brachystelma pygmaeum, respectively. During the in vitro propagation, both Brachystelma ngomense and Brachystelma pygmaeum rooted poorly while regenerated Brachystelma pulchellum generally lacked roots regardless of the CK treatments. Following pulsing (dipping) treatment of in vitro-regenerated shoots with indole-3-butyric acid (IBA), acclimatization of all three Brachystelma species remained extremely limited due to poor rooting ex vitro. To the best of our knowledge, the current protocols provide the first successful report for these Brachystelma species. However, further research remains essential to enhance the efficiency of the devised protocol.
Acetylation-mediated remodeling of the nucleolus regulates cellular acetyl-CoA responses

The metabolite acetyl-coenzyme A (acetyl-CoA) serves as an essential element for a wide range of cellular functions including adenosine triphosphate (ATP) production, lipid synthesis, and protein acetylation. Intracellular acetyl-CoA concentrations are associated with nutrient availability, but the mechanisms by which a cell responds to fluctuations in acetyl-CoA levels remain elusive. Here, we generate a cell system to selectively manipulate the nucleo-cytoplasmic levels of acetyl-CoA using clustered regularly interspaced short palindromic repeat (CRISPR)-mediated gene editing and acetate supplementation of the culture media. Using this system and quantitative omics analyses, we demonstrate that acetyl-CoA depletion alters the integrity of the nucleolus, impairing ribosomal RNA synthesis and evoking the ribosomal protein-dependent activation of p53. This nucleolar remodeling appears to be mediated through the class IIa histone deacetylases (HDACs). Our findings highlight acetylation-mediated control of the nucleolus as an important hub linking acetyl-CoA fluctuations to cellular stress responses.
Avoidance behavior of juvenile common toads (Bufo bufo) in response to surface contamination by different pesticides

Most agricultural soils are expected to be contaminated with agricultural chemicals. As the exposure to pesticides can have adverse effects on non-target organisms, avoiding contaminated areas would be advantageous on an individual level, but could lead to a chemical landscape fragmentation with disadvantages on the metapopulation level. We investigated the avoidance behavior of juvenile common toads (Bufo bufo) in response to seven pesticide formulations commonly used in German vineyards. We used test arenas filled with silica sand and oversprayed half of each with different pesticide formulations. We placed a toad in the middle of an arena, filmed its behavior over 24 hours, calculated the proportion of time a toad spent on the contaminated side and compared it to a random side choice. We found evidence for the avoidance of the folpet formulation Folpan® 500 SC, the metrafenone formulation Vivando® and the glyphosate formulation Taifun® forte at maximum recommended field rates for vine and a trend for avoidance of Wettable Sulphur Stulln (sulphur). No avoidance was observed when testing Folpan® 80 WDG (folpet), Funguran® progress (copper hydroxide), SpinTorTM (spinosad), or 10% of the maximum field rate of any formulation tested. In the choice-tests in which we observed an avoidance, toads also showed higher activity on the contaminated side of the arena. As video analysis with tracking software is not always feasible, we further tested the effect of reducing the sampling interval for manual data analyses. We showed that one data point every 15 or 60 minutes results in a risk of overlooking a weak avoidance behavior, but still allows to verify the absence/presence of an avoidance for six out of seven formulations. Our findings are important for an upcoming pesticide risk assessment for amphibians and could be a template for future standardized tests.
Techno-Cultural Factors Affecting Policy Decision-Making: A Social Network Analysis of South Korea’s Local Spatial Planning Policy

Increasing interest in various local construction forms necessitate examining its link to human life. Construction culture should be adapted and applied to the contemporary context to create a harmonious coexistence with diverse local cultures and to strengthen regional sustainability, avoiding the rigid, one-dimensional local construction development. Thus, this study aims to analyze the factors of influence needed for policy decision-making at the local spatial planning stage, with regional technologies and cultural contents from a convergent perspective taken into consideration. This study derived tangible and intangible policy decision-making factors during the spatial planning stage using text mining analysis. Additionally, social network analysis was also used to seek multi-angle correlations among factors. Through big data analytics, 16 key decision-making contents in the spatial planning stage were derived, with ‘regional development, urban policy’ as most influential. Such a result indicates the need for regional and urban policy engagement with strategic development from a holistic perspective—in view of socio-cultural relations and forms of change—and local perceptions of spatial value and significance affecting decision-making in the local spatial planning stage (LSPS). Understanding the decision-making process in the spatial planning stage requires a holistic approach with both visible technological factors (structure, form, and construction method) and invisible cultural factors (ways of life projected during space formation, zeitgeist, religion, learning, and art) included.
Pre-existing resistance in the latent reservoir can compromise VRC01 therapy during chronic HIV-1 infection

Passive immunization with broadly neutralizing antibodies (bNAbs) of HIV-1 appears a promising strategy for eliciting long-term HIV-1 remission. When administered concomitantly with the cessation of antiretroviral therapy (ART) to patients with established viremic control, bNAb therapy is expected to prolong remission. Surprisingly, in clinical trials on chronic HIV-1 patients, the bNAb VRC01 failed to prolong remission substantially. Identifying the cause of this failure is important for improving VRC01-based therapies and unraveling potential vulnerabilities of other bNAbs. In the trials, viremia resurged rapidly in most patients despite suppressive VRC01 concentrations in circulation, suggesting that VRC01 resistance was the likely cause of failure. ART swiftly halts viral replication, precluding the development of resistance during ART. If resistance were to emerge post ART, virological breakthrough would have taken longer than without VRC01 therapy. We hypothesized therefore that VRC01-resistant strains must have been formed before ART initiation, survived ART in latently infected cells, and been activated during VRC01 therapy, causing treatment failure. Current assays preclude testing this hypothesis experimentally. We developed a mathematical model based on the hypothesis and challenged it with available clinical data. The model integrated within-host HIV-1 evolution, stochastic latency reactivation, and viral dynamics with multiple-dose VRC01 pharmacokinetics. The model predicted that single but not higher VRC01-resistant mutants would pre-exist in the latent reservoir. We constructed a virtual patient population that parsimoniously recapitulated inter-patient variations. Model predictions with this population quantitatively captured data of VRC01 failure from clinical trials, presenting strong evidence supporting the hypothesis. We attributed VRC01 failure to single-mutant VRC01-resistant proviruses in the latent reservoir triggering viral recrudescence, particularly when VRC01 was at trough levels. Pre-existing resistant proviruses in the latent reservoir may similarly compromise other bNAbs. Our study provides a framework for designing bNAb-based therapeutic protocols that would avert such failure and maximize HIV-1 remission.
Antimicrobial Secretions of Toads (Anura, Bufonidae): Bioactive Extracts and Isolated Compounds against Human Pathogens

Species of the family Bufonidae, better known as true toads, are widespread and produce bioactive substances in the secretions obtained from specialized skin macroglands. Some true toads have been employed as a folk remedy to treat infectious diseases caused by microbial pathogens. Recent publications based on in silico analysis highlighted the Bufonidae as promising sources of antimicrobial peptides. A review of the literature reveals that Bufonidae skin secretion extracts show inhibitory activity in vitro against clinical isolates of bacteria, resistant and standard strains of bacterial, and fungal and parasitic human pathogens. Secondary metabolites belonging to the classes of alkaloids, bufadienolides, and peptides with antimicrobial activity have been isolated from species of the genera Bufo, Bufotes, Duttaphrynus, and Rhinella. Additionally, some antimicrobial extracts and purified compounds display low cytotoxicity against mammal cells.
Hemolysis induced by Left Ventricular Assist Device is associated with proximal tubulopathy

Background Chronic subclinical hemolysis is frequent in patients implanted with Left Ventricular Assist Device (LVAD) and is associated with adverse outcomes. Consequences of LVADs-induced subclinical hemolysis on kidney structure and function is currently unknown. Methods Thirty-three patients implanted with a Heartmate II LVAD (Abbott, Inc, Chicago IL) were retrospectively studied. Hemolysis, Acute Kidney Injury (AKI) and the evolution of estimated Glomerular Filtration Rate were analyzed. Proximal Tubulopathy (PT) groups were defined according to proteinuria, normoglycemic glycosuria, and electrolytic disorders. The Receiver Operating Characteristic (ROC) curve was used to analyze threshold of LDH values associated with PT. Results Median LDH between PT groups were statistically different, 688 IU/L [642–703] and 356 IU/L [320–494] in the “PT” and “no PT” groups, respectively p = 0.006. To determine PT group, LDH threshold > 600 IU/L was associated with a sensitivity of 85.7% (95% CI, 42.1–99.6) and a specificity of 84.6% (95% CI, 65.1–95.6). The ROC's Area Under Curve was 0.83 (95% CI, 0.68–0.98). In the “PT” group, patients had 4.2 [2.5–5.0] AKI episodes per year of exposure, versus 1.6 [0.4–3.7] in the “no PT” group, p = 0.03. A higher occurrence of AKI was associated with subsequent development of Chronic Kidney Disease (CKD) (p = 0.02) and death (p = 0.05). Conclusions LVADs-induced subclinical hemolysis is associated with proximal tubular functional alterations, which in turn contribute to the occurrence of AKI and subsequent CKD. Owing to renal toxicity of hemolysis, measures to reduce subclinical hemolysis intensity as canula position or pump parameters should be systematically considered, as well as specific nephroprotective therapies.
The Essential Oil Composition And Antioxidant Activity Of Achillea Spp. Growing In The Southwest Of Iran

The composition of essential oil isolated from Achillea eriophora, Achillea millefolium, Achillea biebersteinii and Achillea tenuifolia growing wild in the south west of Iran, was analyzed. A. eriophora, A. millefolium and A. tenuifolia essential oils were characterized by sabinene, 1, 8-cineole, terpinene-4-ol, ά –bisabolol, p-Cymene, β-pinene and α-pinene. The A. biebersteinii essential oil was characterized by sabinene, borneol, camphor, piperitone and α-pinene. Antioxidant activity was analyzed using the 1,1-diphenyl-2picrylhydrazyl free radical scavenging and Fe 3+ reducing power methods. Results indicated essential oil obtained from A. eriophora, A. millefolium, A. tenuifolia and A. biebersteinii exhibited a dose-dependent increase with a radical scavenging effect of 85.0%, 82.0% , 82.0% and 64.0% at 350 μg/ml, which are close to the 1,1-diphenyl-2picrylhydrazyl inhibition of the positive control Butylated Hydroxytoluene (88.0%) at the same concentration. It was shown that the A. biebersteinii essential oil exhibited the weakest antioxidant effect than Butylated Hydroxytoluene or other Achillea spp. essential oils. In this study chamazulene, ά-bisabolol and ά –bisabolol oxide percentage were higher in A. eriophora, A. millefolium and A. tenuifolia essential oil compared to A. biebersteinii essential oil and these compounds improved antioxidant capacity of Achillea spp.
Electron microscopy of particles collected at Praia, Cape Verde, during the Saharan Mineral Dust Experiment: particle chemistry, shape, mixing state and complex refractive index

A large field experiment of the Saharan Mineral Dust Experiment (SAMUM) was performed in Praia, Cape Verde, in January and February 2008. The aerosol at Praia is a superposition of mineral dust, sea-salt, sulphates and soot. Particles smaller than 500 nm are mainly mineral dust, mineral dust–sulphate mixtures, sulphates and soot–sulphate mixtures. Particles larger then 2. 5μm consist of mineral dust, sea-salt and few mineral dust–sulphate mixtures. A transition range exists in between. The major internal mixtures are mineral dust–sulphate and soot–sulphate. Mineral dust–sea-salt mixtures occur occasionally, mineral dust–soot mixtures were not observed. The aspect ratio was 1.3–1.4 for dry particles smaller than 500 nm and 1.6–1.7 for larger ones. Parameterizations are given for dry and humid state. Although the real part of the refractive index showed low variation (1.55–1.58 at 532 nm), a multi-modal imaginary part was detected as function of particle size, reflecting the complex composition. Soot mainly influences the absorption for wavelengths longer than the haematite absorption edge, whereas for shorter wavelengths dust is dominating. The refractive index of the aerosol depends on the source region of the mineral dust and on the presence/absence of a marine component.
Hepatitis B Core Protein Is Post-Translationally Modified through K29-Linked Ubiquitination

Hepatitis B virus (HBV) core protein (HBc) plays many roles in the HBV life cycle, such as regulation of transcription, RNA encapsidation, reverse transcription, and viral release. To accomplish these functions, HBc interacts with many host proteins and undergoes different post-translational modifications (PTMs). One of the most common PTMs is ubiquitination, which was shown to change the function, stability, and intracellular localization of different viral proteins, but the role of HBc ubiquitination in the HBV life cycle remains unknown. Here, we found that HBc protein is post-translationally modified through K29-linked ubiquitination. We performed a series of co-immunoprecipitation experiments with wild-type HBc, lysine to arginine HBc mutants and wild-type ubiquitin, single lysine to arginine ubiquitin mutants, or single ubiquitin-accepting lysine constructs. We observed that HBc protein could be modified by ubiquitination in transfected as well as infected hepatoma cells. In addition, ubiquitination predominantly occurred on HBc lysine 7 and the preferred ubiquitin chain linkage was through ubiquitin-K29. Mass spectrometry (MS) analyses detected ubiquitin protein ligase E3 component N-recognin 5 (UBR5) as a potential E3 ubiquitin ligase involved in K29-linked ubiquitination. These findings emphasize that ubiquitination of HBc may play an important role in HBV life cycle.
The Influence of Response Inhibition Training on Food Consumption and Implicit Attitudes toward Food among Female Restrained Eaters

Restrained eaters display difficulties engaging in self-control in the presence of food. Undergoing cognitive training to form associations between palatable food and response inhibition was found to improve self-control and influence eating behaviors. The present study assessed the impact of two such response inhibition trainings on food consumption, food-related anxiety, and implicit attitudes toward food among female restrained eaters (Dutch Eating Behavior Questionnaire-restrained eating subscale ≥ 2.5). In Experiment 1, 64 restrained eaters completed either one of two training procedures in which they were asked to classify food vs. non-food images: a food-response training, in which stop cues were always associated with non-food images, or a balanced food-response/inhibition training, in which participants inhibited motor actions to food and non-food stimuli equally. The results revealed reduced snack consumption following the food-response/inhibition training compared to the food-response training. The food-response training was associated with increased levels of food-related anxiety. In Experiment 2, the same training procedures were administered to 47 restrained eaters, and implicit attitudes toward palatable foods were assessed. The results revealed an increase in positive implicit attitudes toward palatable foods in the food-response/inhibition group but not in the food-response training group. The results suggest that balancing response inhibition and execution across food and non-food stimuli may reduce overeating while retaining positive attitudes toward food among female restrained eaters.
Genome-Wide Association Studies for the Concentration of Albumin in Colostrum and Serum in Chinese Holstein

Simple Summary The early death and illness of newborn calves result in enormous economic losses in the dairy industry. As the immune system has not been fully developed in neonates, the adequate intake of nutrients and immune substances in colostrum is essential for protecting neonates from infections in their early life. The term albumin refers to a group of multifunctional proteins that are important in anti-inflammatory and anti-oxidative reactions and can help calves against various infections. Albumin of bovine whey is derived from the serum; hence, the concentration of albumin in colostrum and serum could be important traits for the breeding of potential natural disease resistance in dairy cattle. Herein, genome-wide association studies (GWASs) were performed to identify the candidate genes associated with albumin concentrations in colostrum and serum to provide useful molecular information for the genetic improvement of disease resistance traits in dairy cattle. Abstract Albumin can be of particular benefit in fighting infections for newborn calves due to its anti-inflammatory and anti-oxidative stress properties. To identify the candidate genes related to the concentration of albumin in colostrum and serum, we collected the colostrum and blood samples from 572 Chinese Holstein cows within 24 h after calving and measured the concentration of albumin in the colostrum and serum using the ELISA methods. The cows were genotyped with GeneSeek 150 K chips (containing 140,668 single nucleotide polymorphisms; SNPs). After quality control, we performed GWASs via GCTA software with 91,620 SNPs and 563 cows. Consequently, 9 and 7 genome-wide significant SNPs (false discovery rate (FDR) at 1%) were identified. Correspondingly, 42 and 206 functional genes that contained or were approximate to (±1 Mbp) the significant SNPs were acquired. Integrating the biological process of these genes and the reported QTLs for immune and inflammation traits in cattle, 3 and 12 genes were identified as candidates for the concentration of colostrum and serum albumin, respectively; these are RUNX1, CBR1, OTULIN, CDK6, SHARPIN, CYC1, EXOSC4, PARP10, NRBP2, GFUS, PYCR3, EEF1D, GSDMD, PYCR2 and CXCL12. Our findings provide important information for revealing the genetic mechanism behind albumin concentration and for molecular breeding of disease-resistance traits in dairy cattle.
Diabetes-Specific Nutrition Formulas in the Management of Patients with Diabetes and Cardiometabolic Risk

Food-based dietary management, enhanced with evidence-based commercial products, such as diabetes-specific nutrition formulas (DSNFs), can help control the development, progression, and severity of certain chronic diseases. In this review, evidence is detailed on the use of DSNFs in patients with or at risk for diabetes and cardiometabolic-based chronic disease. Many DSNF strategies target glycemic excursions and cardiovascular physiology, taking into account various elements of healthy eating patterns. Nevertheless, significant research, knowledge, and practice gaps remain. These gaps are actionable in terms of formulating and testing relevant and pragmatic research questions, developing an educational program for the uniform distribution of information, and collaboratively writing clinical practice guidelines that incorporate the evidence base for DSNF. In sum, the benefits of DNSF as part of validated clinical practice algorithms include mitigation of chronic disease progression, cost-savings for the healthcare system, and applicability on a global scale
REV-ERBα mediates complement expression and diurnal regulation of microglial synaptic phagocytosis

The circadian clock regulates various aspects of brain health including microglial and astrocyte activation. Here, we report that deletion of the master clock protein BMAL1 in mice robustly increases expression of complement genes, including C4b and C3, in the hippocampus. BMAL1 regulates expression of the transcriptional repressor REV-ERBα, and deletion of REV-ERBα causes increased expression of C4b transcript in neurons and astrocytes as well as C3 protein primarily in astrocytes. REV-ERBα deletion increased microglial phagocytosis of synapses and synapse loss in the CA3 region of the hippocampus. Finally, we observed diurnal variation in the degree of microglial synaptic phagocytosis which was antiphase to REV-ERBα expression. This daily variation in microglial synaptic phagocytosis was abrogated by global REV-ERBα deletion, which caused persistently elevated synaptic phagocytosis. This work uncovers the BMAL1-REV-ERBα axis as a regulator of complement expression and synaptic phagocytosis in the brain, linking circadian proteins to synaptic regulation.