Miracle-dz/UniFAR-FTUs huggingface dataset:
Ethylene-Related Gene Expression Networks in Wood Formation

Thickening of tree stems is the result of secondary growth, accomplished by the meristematic activity of the vascular cambium. Secondary growth of the stem entails developmental cascades resulting in the formation of secondary phloem outwards and secondary xylem (i.e., wood) inwards of the stem. Signaling and transcriptional reprogramming by the phytohormone ethylene modifies cambial growth and cell differentiation, but the molecular link between ethylene and secondary growth remains unknown. We addressed this shortcoming by analyzing expression profiles and co-expression networks of ethylene pathway genes using the AspWood transcriptome database which covers all stages of secondary growth in aspen (Populus tremula) stems. ACC synthase expression suggests that the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) is synthesized during xylem expansion and xylem cell maturation. Ethylene-mediated transcriptional reprogramming occurs during all stages of secondary growth, as deduced from AspWood expression profiles of ethylene-responsive genes. A network centrality analysis of the AspWood dataset identified EIN3D and 11 ERFs as hubs. No overlap was found between the co-expressed genes of the EIN3 and ERF hubs, suggesting target diversification and hence independent roles for these transcription factor families during normal wood formation. The EIN3D hub was part of a large co-expression gene module, which contained 16 transcription factors, among them several new candidates that have not been earlier connected to wood formation and a VND-INTERACTING 2 (VNI2) homolog. We experimentally demonstrated Populus EIN3D function in ethylene signaling in Arabidopsis thaliana. The ERF hubs ERF118 and ERF119 were connected on the basis of their expression pattern and gene co-expression module composition to xylem cell expansion and secondary cell wall formation, respectively. We hereby establish data resources for ethylene-responsive genes and potential targets for EIN3D and ERF transcription factors in Populus stem tissues, which can help to understand the range of ethylene targeted biological processes during secondary growth.
The efficacy of intra-alveolar 0.2% chlorhexidine gel on alveolar osteitis: a meta-analysis.

OBJECTIVES The objective of this meta-analysis was to assess the effect of 0.2% chlorhexidine gel in preventing alveolar osteitis following mandibular third molar extraction(s). METHODS PubMed, Cochrane Library, Embase, Web of Science, Science Direct and the references of identified articles were searched for relevant studies that met our eligibility criteria. Treatment effects were combined by meta-analysis using RevMan 5.3 and Stata 12.0 software. RESULTS We included 11 trials in this meta-analysis. Compared to the control, 0.2% chlorhexidine gel reduced the risk of alveolar osteitis by 62% (RR = 0.38, 95% CI = 0.28-0.53, P < 0.00001) following mandibular third molar extraction(s). The subgroup analysis results indicated that 0.2% chlorhexidine gel reduced the risk of alveolar osteitis after mandibular third molar extraction(s) by 75% (RR = 0.25, 95% CI = 0.11-0.58) and 56% (RR = 0.44, 95% CI = 0.30-0.63) compared to no treatment and placebo, respectively. However, the occurrence of alveolar osteitis following mandibular third molar extraction(s) was not significantly different between 0.2% chlorhexidine gel and 0.12% chlorhexidine mouthwash (RR = 0.24, 95% CI = 0.06-1.00). CONCLUSION The results showed that 0.2% chlorhexidine gel was effective in preventing alveolar osteitis after lower third molar extraction(s).
Protein quality of conventional and high protein rice and digestibility of glutinous and non-glutinous rice by preschool children.

The bulkiness of cooked rice imposes limits on the quanti ties that can be consumed, especially by infants and small children. Rices of higher protein content should offer a nutritional advantage if protein quality does not suffer. Protein quality of a high protein rice (IR480-5-9, 11.4% protein) was compared isonitrogenously with that of a rice of lower protein content (IR32, 7.1% protein) and with casein by nitrogen balance studies in eight children 12 to 18 months of age. Diets provided 100 to 125 kcal and 240 to 300 mg N/kg body weight/day constant for each child. Non-protein energy was supplied by sucrose and a blend (80:20) of soy bean :cottonseed oil. Two 7-day rice dietary periods (alternating IR32 and IR480-5-9) were preceded and followed by 9-day casein control periods. Apparent N absorption from rice ( 65.7 Â± 6.7% ) was significantly less than from casein ( 84.9 Â± 4.27Â? ) â€¢ Apparent N retention from IR480-5-9 was 23.0 Â± 2.5%, that from IR32 28.6 Â± 9.4% (initial casein period: 35.2 Â± 5.9%). Digestibility of these two non-glutinous rices was compared with that of a glutinous variety, IR29, in further studies in which equal quanti ties of rice (13.2 or 16.5 g/kg body weight/day) were consumed. Fecal wet weight tended to be lower during rice consumption than during con sumption of the control diet, significantly so only for IR29. Fecal dry weight, fecal energy and calculated fecal carbohydrate did not differ between rice and control periods. There were significant linear correlations of fecal wet and dry weight with fecal energy for both the rice and control diets. Al though several factors suggested that the protein quality of IR480-5-9 was inferior to that of IR32, this would more than be offset by the increased protein content of the former when equal quantities of rice were consumed. Overall digestibility of rice by children appeared to be excellent and should not limit consumption by this age group. J. Nutr. IOS: 1740-1747, 1978.
From intraperitoneal onlay mesh repair to preperitoneal onlay mesh repair

Laparoscopic repair for ventral and incisional hernias was first reported in the early 1990s. It uses intraperitoneal only mesh placement to achieve a tension‐free repair of the hernia. However, in recent years, there has been greater concern about long‐term complication involving intraperitoneal mesh placement. Many case reports and case series have found evidence of mesh adhesion, mesh fistulation, and mesh migration into hollow organs including the esophagus, small bowel, and large bowel, resulting in various major acute abdominal events. Subsequent management of these complications may require major surgery that is technically demanding and difficult; in such cases, laparotomy and bowel resection have often been performed. Because of these significant, but not common, adverse events, many surgeons favor open sublay repair for ventral and incisional hernias. Investigators are therefore searching for a laparoscopic approach for ventral and incisional hernias that might overcome the mesh‐induced visceral complications seen after intraperitoneal only mesh placement repair. Laparoscopic preperitoneal onlay mesh is one such approach. This article will explore the fundamental of intraperitoneal only mesh placement and its problems, the currently available peritoneal visceral‐compatible meshes, and upcoming developments in laparoscopic ventral and incisional hernia repair. The technical details of preperitoneal onlay mesh, as well as its potential advantages and disadvantages, will also be discussed.
A defined, plant‐based diet utilized in an outpatient cardiovascular clinic effectively treats hypercholesterolemia and hypertension and reduces medications

Cardiovascular disease (CVD) is a major economic burden in the United States. CVD risk factors, particularly hypertension and hypercholesterolemia, are typically treated with drug therapy. Five‐year efficacy of such drugs to prevent CVD is estimated to be 5%. Plant‐based diets have emerged as effective mitigators of these risk factors.
Vitamin E bioavailability from fortified breakfast cereal is greater than that from encapsulated supplements.

BACKGROUND Conflicting results from vitamin E intervention studies suggest supplemental vitamin E malabsorption. OBJECTIVE We compared vitamin E bioavailability from a supplement with that from a fortified breakfast cereal. DESIGN Vitamin E bioavailability was evaluated by using deuterium-labeled all-rac-alpha-tocopherol in three 4-d trials (2 wk apart). Five fasting subjects sequentially consumed the following (with 236 mL fat-free milk): 400 IU d(9)-alpha-tocopheryl acetate (400-IU capsule), 41 g ready-to-eat wheat cereal containing 30 IU d(9)-alpha-tocopheryl acetate (30-IU cereal), and 45 g cereal containing 400 IU d(9)-alpha-tocopheryl acetate (400-IU cereal). Five months later (trial 4), they consumed a 400-IU capsule with 41 g vitamin E-free cereal. Blood was obtained up to 72 h after the start of each trial. RESULTS The mean (+/-SD) vitamin E bioavailabilities of the 30-IU cereal and the 400-IU cereal were 6 +/- 2 and 26 +/- 8 times, respectively, the vitamin E bioavailability of the 400-IU capsule. The areas under the 0-72-h d(9)-alpha-tocopherol curves for the 400-IU capsule, the 30-IU cereal, and the 400-IU cereal were 30 +/- 7, 153 +/- 43, and 765 +/- 164 micro mol. h/L (all trial comparisons, P < 0.0001). In trial 4, 3 subjects barely responded and 2 subjects had areas under the curve that were similar to their 400-IU cereal responses. CONCLUSION The low bioavailability of vitamin E from the 400-IU capsule and the variability observed when the capsule was consumed with cereal suggest that encapsulated vitamin E is poorly absorbed when consumed with a low-fat meal and that bioavailability can be enhanced by food fortification with vitamin E.
“Crowdsourcing” ten years in: A review

Background First coined by Howe in 2006, the field of crowdsourcing has grown exponentially. Despite its growth and its transcendence across many fields, the definition of crowdsourcing has still not been agreed upon, and examples are poorly indexed in peer–reviewed literature. Many examples of crowdsourcing have not been scaled–up past the pilot phase. In spite of this, crowdsourcing has great potential, especially in global health where resources are lacking. This narrative review seeks to review both indexed and grey crowdsourcing literature broadly in order to explore the current state of the field. Methods This is a review of reviews of crowdsourcing. Semantic searches were conducted using Google Scholar rather than indexed databases due to poor indexing of the topic. 996 articles were retrieved, of which 69 were initially identified as being reviews or theoretically–based. 21 of these were found to be irrelevant and 48 articles were reviewed. Results This narrative review focuses on defining crowdsourcing, taxonomies of crowdsourcing, who constitutes the crowd, research that is amenable to crowdsourcing, regulatory and ethical aspects of crowdsourcing and some notable examples of crowdsourcing. Conclusions Crowdsourcing has the potential to be hugely promising, especially in global health, due to its ability to collect information rapidly, inexpensively and accurately. Rigorous ethical and regulatory controls are needed to ensure data are collected and analysed appropriately and crowdsourcing should be considered complementary to traditional research methods.
SLC2A3 single‐nucleotide polymorphism and duplication influence cognitive processing and population‐specific risk for attention‐deficit/hyperactivity disorder

BACKGROUND Attention-deficit/hyperactivity disorder (ADHD) is a common, highly heritable neurodevelopmental disorder with profound cognitive, behavioral, and psychosocial impairments with persistence across the life cycle. Our initial genome-wide screening approach for copy number variants (CNVs) in ADHD implicated a duplication of SLC2A3, encoding glucose transporter-3 (GLUT3). GLUT3 plays a critical role in cerebral glucose metabolism, providing energy for the activity of neurons, which, in turn, moderates the excitatory-inhibitory balance impacting both brain development and activity-dependent neural plasticity. We therefore aimed to provide additional genetic and functional evidence for GLUT3 dysfunction in ADHD. METHODS Case-control association analyses of SLC2A3 single-nucleotide polymorphisms (SNPs) and CNVs were conducted in several European cohorts of patients with childhood and adult ADHD (SNP, n = 1,886 vs. 1,988; CNV, n = 1,692 vs. 1,721). These studies were complemented by SLC2A3 expression analyses in peripheral cells, functional EEG recordings during neurocognitive tasks, and ratings of food energy content. RESULTS Meta-analysis of all cohorts detected an association of SNP rs12842 with ADHD. While CNV analysis detected a population-specific enrichment of SLC2A3 duplications only in German ADHD patients, the CNV + rs12842 haplotype influenced ADHD risk in both the German and Spanish cohorts. Duplication carriers displayed elevated SLC2A3 mRNA expression in peripheral blood cells and altered event-related potentials reflecting deficits in working memory and cognitive response control, both endophenotypic traits of ADHD, and an underestimation of energy units of high-caloric food. CONCLUSIONS Taken together, our results indicate that both common and rare SLC2A3 variation impacting regulation of neuronal glucose utilization and energy homeostasis may result in neurocognitive deficits known to contribute to ADHD risk.
Nutrient Interactions and Toxicity Research Communication Total Fumonisins Are Reduced in Tortillas Using the Traditional Nixtamalization Method of Mayan Communities

Fumonisin B1 (FB1) is a maize mycotoxin. In tortilla preparation, maize is treated with lime (nixtamalization), producing hydrolyzed FB1 (HFB1) due to loss of the tricarballylic acid side chains. This study determined the following: 1) whether nixtamalization by Mayan communities reduces total fumonisins, and 2) the steps in the process at which reduction occurs. Tortillas prepared by the traditional process contained FB1, FB2 and FB3 and their hydrolyzed counterparts. There were equimolar amounts of FB1 and HFB1 in the tortillas, but the total fumonisins were reduced 50%. The total FB1 plus HFB1 in the residual lime water and water washes of the nixtamal accounted for 50% of the total FB1 in the uncooked maize. HFB1 and FB1 were present in a 1:1 mol/L ratio in the water washes of the nixtamal, the masa dough and the cooked tortillas, whereas the ratio of HFB1:FB1 in lime water after steeping was 21. Water washes contained 11% of the FB1 that was in the uncooked maize. The results show that the traditional method reduced the total fumonisins in tortillas and reduced the sphinganine elevation (a biomarker closely correlated with fumonisin toxicity) in cells treated with extracts of tortillas compared with cells treated with extracts of contaminated maize. J. Nutr. 133: 3200–3203,
Mutational Analysis of the QRRQ Motif in the Yeast Hig1 Type 2 Protein Rcf1 Reveals a Regulatory Role for the Cytochrome c Oxidase Complex*

The yeast Rcf1 protein is a member of the conserved family of proteins termed the hypoxia-induced gene (domain) 1 (Hig1 or HIGD1) family. Rcf1 interacts with components of the mitochondrial oxidative phosphorylation system, in particular the cytochrome bc1 (complex III)-cytochrome c oxidase (complex IV) supercomplex (termed III-IV) and the ADP/ATP carrier proteins. Rcf1 plays a role in the assembly and modulation of the activity of complex IV; however, the molecular basis for how Rcf1 influences the activity of complex IV is currently unknown. Hig1 type 2 isoforms, which include the Rcf1 protein, are characterized in part by the presence of a conserved motif, (Q/I)X3(R/H)XRX3Q, termed here the QRRQ motif. We show that mutation of conserved residues within the Rcf1 QRRQ motif alters the interactions between Rcf1 and partner proteins and results in the destabilization of complex IV and alteration of its enzymatic properties. Our findings indicate that Rcf1 does not serve as a stoichiometric component, i.e. as a subunit of complex IV, to support its activity. Rather, we propose that Rcf1 serves to dynamically interact with complex IV during its assembly process and, in doing so, regulates a late maturation step of complex IV. We speculate that the Rcf1/Hig1 proteins play a role in the incorporation and/or remodeling of lipids, in particular cardiolipin, into complex IV and. possibly, other mitochondrial proteins such as ADP/ATP carrier proteins.
Methotrexate Aspasomes Against Rheumatoid Arthritis: Optimized Hydrogel Loaded Liposomal Formulation with In Vivo Evaluation in Wistar Rats

Aspasomes of methotrexate with antioxidant, ascorbyl palmitate, were developed and optimized using factorial design by varying parameters such as lipid molar ratio, drug to lipid molar ratio, and type of hydration buffer for transdermal delivery for disease modifying activity in rheumatoid arthritis (RA). Aspasomes were characterized by drug-excipients interaction, particle size analysis, determination of zeta potential, entrapment efficiency, and surface properties. The best formulation was loaded into hydrogel for evaluation of in vitro drug release and tested in vivo against adjuvant induced arthritis model in wistar rats, by assessing various physiological, biochemical, hematological, and histopathological parameters. Optimized aspasome formulation exhibited smooth surface with particle size 386.8 nm, high drug loading (19.41%), negative surface potential, and controlled drug release in vitro over 24 h with a steady permeation rate. Transdermal application of methotrexate-loaded aspasome hydrogel for 12 days reduced rat paw diameter (21.25%), SGOT (40.43%), SGPT (54.75%), TNFα (33.99%), IL β (34.79%), cartilage damage (84.41%), inflammation (82.37%), panus formation (84.38%), and bone resorption (80.52%) as compared to arthritic control rats. Free methotrexate-treated group showed intermediate effects. However, drug-free aspasome treatment did not show any effect. The experimental results indicate a positive outcome in development of drug-loaded therapeutically active carrier system which presents a non-invasive controlled release transdermal formulation with good drug loading, drug permeation rate, and having better disease modifications against RA than the free drug, thereby providing a more attractive therapeutic strategy for rheumatoid disease management.
Evidence for verbal memory enhancement with electrical brain stimulation in the lateral temporal cortex

Direct electrical stimulation of the human brain can elicit sensory and motor perceptions as well as recall of memories. Stimulating higher order association areas of the lateral temporal cortex in particular was reported to activate visual and auditory memory representations of past experiences (Penfield and Perot, 1963). We hypothesized that this effect could be used to modulate memory processing. Recent attempts at memory enhancement in the human brain have been focused on the hippocampus and other mesial temporal lobe structures, with a few reports of memory improvement in small studies of individual brain regions. Here, we investigated the effect of stimulation in four brain regions known to support declarative memory: hippocampus, parahippocampal neocortex, prefrontal cortex and temporal cortex. Intracranial electrode recordings with stimulation were used to assess verbal memory performance in a group of 22 patients (nine males). We show enhanced performance with electrical stimulation in the lateral temporal cortex (paired t-test, P = 0.0067), but not in the other brain regions tested. This selective enhancement was observed both on the group level, and for two of the four individual subjects stimulated in the temporal cortex. This study shows that electrical stimulation in specific brain areas can enhance verbal memory performance in humans.awx373media15704855796001.
Dietary Chlorella vulgaris Ameliorates Altered Immunomodulatory Functions in Cyclophosphamide-Induced Immunosuppressive Mice

Based on the well-known toxicity of cyclophosphamide (CYP) on the immune system, this research investigated the modulating effects of the long-term dietary Chlorella vulgaris (CV) supplementation on the immunosuppression induced by CYP in mice, in order to provide a novel dietary design to mitigate the side effects of CYP therapy. Control, CYP-treated, CYP + CV (6%), CYP + CV (12%) and CYP + CV (24%) were used for 6 weeks, CV supplement in diet recovered the significantly reduced immunological function in CYP treated mice. As CV may have a modulating function through the inducible expression of cytokines, we assayed the expressions of interleukin-2 (IL-2), interleukin-12 (IL-12), tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ). Our results suggested that CYP significantly reduced the lymphocytes proliferation and phagocytic activities of macrophages, and stimulated the production of IL-2, IL-12, TNF-α and IFN-γ and that this impairment has been successfully adjusted by CV supplementation. Treatment with the algae also enhanced the natural killer (NK) cells cytotoxicity, and ameliorate histological changes of the spleen in CYP-treated mice. Therefore, as we found in this study, a diet supplemented with whole CV has beneficial effects on CVP-induced immunosuppression, through its immunomodulatory potential.
Engineering a light-activated caspase-3 for precise ablation of neurons in vivo

Significance We have engineered a light-activated caspase (Caspase-LOV) to better understand the roles of caspases in cells and to create a tool that would kill cells with temporal and spatial selectivity. This modified caspase is created based on the endogenous mechanism of caspase activation by adding a light-sensitive protein domain (LOV2) from oats into the intersubunit linker of the caspase. We tested variations of the Caspase-LOV construct in vitro and in Drosophila and found that it will kill many types of cells with light specificity. We were also able to use the Caspase-LOV to determine the time course of degeneration in two different neuronal cell types after caspase activation. The circuitry of the brain is characterized by cell heterogeneity, sprawling cellular anatomy, and astonishingly complex patterns of connectivity. Determining how complex neural circuits control behavior is a major challenge that is often approached using surgical, chemical, or transgenic approaches to ablate neurons. However, all these approaches suffer from a lack of precise spatial and temporal control. This drawback would be overcome if cellular ablation could be controlled with light. Cells are naturally and cleanly ablated through apoptosis due to the terminal activation of caspases. Here, we describe the engineering of a light-activated human caspase-3 (Caspase-LOV) by exploiting its natural spring-loaded activation mechanism through rational insertion of the light-sensitive LOV2 domain that expands upon illumination. We apply the light-activated caspase (Caspase-LOV) to study neurodegeneration in larval and adult Drosophila. Using the tissue-specific expression system (UAS)-GAL4, we express Caspase-LOV specifically in three neuronal cell types: retinal, sensory, and motor neurons. Illumination of whole flies or specific tissues containing Caspase-LOV–induced cell death and allowed us to follow the time course and sequence of neurodegenerative events. For example, we find that global synchronous activation of caspase-3 drives degeneration with a different time-course and extent in sensory versus motor neurons. We believe the Caspase-LOV tool we engineered will have many other uses for neurobiologists and others for specific temporal and spatial ablation of cells in complex organisms.