Miracle-dz/UniFAR-FTUs huggingface dataset:
In vivo diagnosis and characterization of gastric Crohn’s disease using endomicroscopy and virtual chromoendoscopy

Crohn’s disease using endomicroscopy and virtual chromoendoscopy Confocal laser endomicroscopy (CLE) and virtual (dyeless) chromoendoscopy are sophisticated, so-called advanced imaging techniques within contemporary endoscopy. I-Scan (Pentax, Tokyo, Japan) is a computer-based color program that enhances the contrast of mucosal details, especially the superficial vascularization [1]. In contrast, CLE provides a deeper view, meaning that a real-time and in vivo visualization of a plethora of cellular and subcellular details can be achieved, which correlates with conventional histology [2,3]. Both techniques have an immense impact on modern endoscopic diagnosis and surveillance. Several studies have described the utility of CLE for in vivo diagnosis of gastric disorders, such as Helicobacter gastritis [4], gastric intestinal metaplasia, and cancer [5]. However, no data are available regarding the utility of CLE and/or virtual chromoendoscopy for the in vivo description and diagnosis of gastric Crohn’s disease. This brief article reports the first in vivo description and diagnosis of gastric Crohn’s disease by two modern imaging techniques, i-Scan and CLE. A 33-year-old man with a 1-year history of ileocolic Crohn’s disease, currently being treated with topical budesonide therapy, was admitted to our department with progressively worsening nausea, vomiting, abdominal pain, and diarrhea over the preceding few weeks. High definition white-light esophagogastroduodenoscopy (Pentax; EG-2990i) showed an edematous mucosa and scattered, typical aphthous lesions throughout the entire gastric mucosa (●" Fig.1) and duodenal mucosa (not shown). After switching to the i-Scan mode, we were able to observe spots scattered throughout the erythematous mucosa especially in the gastric antrum (●" Fig.1a), which had not been evident in the white-light imaging (see insert in●" Fig.1a). The endoscopes were then changed to perform CLE (Pentax; EC-3870 CIK). After the intravenous administration of 5mL of fluorescein (10%; Alcon Pharma, Freiburg, Germany) as a contrast agent, we examined one of the spotted areas of the antral mucosa that had been highlighted by the i-Scan (marked between two biopsies). Endomicroscopy revealed an altered gastric epithelial architecture. In the mucosa of the lamina propria between the dilated and distorted gastric glands, we were able to identify leaking dilated vessels (fluorescein extravasation) and an inflammatory infiltrate (●" Fig.2a). Subsequent histoFig.1 Endoscopic appearances of the stomach in a 33-year-old man with a history of ileocolic Crohn’s disease. a Virtual chromoendoscopy (i-Scan) revealing an erythematous and edematous inflamed mucosa in the gastric antrum, along with scattered typical Crohn’s disease aphthous lesions (black arrowhead). b High definition white-light endoscopy showing less severe inflammation in the corpus, along with scattered typical Crohn’s disease aphthous lesions (black arrowheads).
Ascorbate degradation in tomato leads to accumulation of oxalate, threonate and oxalyl threonate

Ascorbate content in plants is controlled by its synthesis from carbohydrates, recycling of the oxidized forms and degradation. Of these pathways, ascorbate degradation is the least studied and represents a lack of knowledge that could impair improvement of ascorbate content in fruits and vegetables as degradation is non-reversible and leads to a depletion of the ascorbate pool. The present study revealed the nature of degradation products using [14 C]ascorbate labelling in tomato, a model plant for fleshy fruits; oxalate and threonate are accumulated in leaves, as is oxalyl threonate. Carboxypentonates coming from diketogulonate degradation were detected in relatively insoluble (cell wall-rich) leaf material. No [14 C]tartaric acid was found in tomato leaves. Ascorbate degradation was stimulated by darkness, and the degradation rate was evaluated at 63% of the ascorbate pool per day, a percentage that was constant and independent of the initial ascorbate or dehydroascorbic acid concentration over periods of 24 h or more. Furthermore, degradation could be partially affected by the ascorbate recycling pathway, as lines under-expressing monodehydroascorbate reductase showed a slight decrease in degradation product accumulation.
Identification and characterization of a stable intermediate in photosystem I assembly in tobacco

Photosystem I (PSI) is the most efficient bioenergetic nanomachine in nature and one of the largest membrane protein complexes known. It is composed of 18 protein subunits that bind more than 200 co-factors and prosthetic groups. While the structure and function of PSI have been studied in great detail, very little is known about the PSI assembly process. In this work, we have characterized a PSI assembly intermediate in tobacco plants, which we named PSI*. We found PSI* to contain only a specific subset of the core subunits of PSI. PSI* is particularly abundant in young leaves where active thylakoid biogenesis takes place. Moreover, PSI* was found to overaccumulate in PsaF-deficient mutant plants, and we show that re-initiation of PsaF synthesis promotes the maturation of PSI* into PSI. The attachment of antenna proteins to PSI also requires the transition from PSI* to mature PSI. Our data could provide a biochemical entry point into the challenging investigation of PSI biogenesis and allow us to improve the model for the assembly pathway of PSI in thylakoid membranes of vascular plants.
Factors influencing older adults to complete advance directives

Abstract Objective: The purpose of this study was to determine the factors which influence advance directive (AD) completion among older adults. Method: Direct interviews of hospitalized and community-dwelling cognitively intact patients >65 years of age were conducted in three tertiary teaching settings in New York. Analysis of AD completion focused on its correlation with demographics, personal beliefs, knowledge, attitudes, and exposure to educational media initiatives. We identified five variables with loadings of at least 0.30 in absolute value, along with five demographic variables (significant in the univariate analyses) for multiple logistic regression. The backward elimination method was used to select the final set of jointly significant predictor variables. Results: Of the 200 subjects consenting to an interview, 125 subjects (63%) had completed ADs. In comparing groups with and without ADs, gender (p < 0.0002), age (p < 0.0161), race (p < 0.0001), education (p < 0.0039), and religion (p < 0.0104) were significantly associated with having an AD. Factors predicting AD completion are: thinking an AD will help in the relief of suffering at the end of life, (OR 76.3, p < 0.0001), being asked to complete ADs/ or receiving explanation about ADs (OR 55.2, p < 0.0001), having undergone major surgery (OR 6.3, p < 0.0017), female gender (OR 11.1, p < 0.0001) and increasing age (76–85 vs. 59–75: OR 3.4, p < 0.0543; <85 vs. 59–75: OR 6.3, p < 0.0263). Significance of results: This study suggests that among older adults, the probability of completing ADs is related to personal requests by health care providers, educational level, and exposure to advance care planning media campaigns.
Analysis of transcriptional and epigenetic changes in hybrid vigor of allopolyploid Brassica napus uncovers key roles for small RNAs

Heterosis is a fundamental biological phenomenon characterized by the superior performance of a hybrid compared with its parents. The underlying molecular basis for heterosis, particularly for allopolyploids, remains elusive. In this study we analyzed the transcriptomes of Brassica napus parental lines and their F1 hybrids at three stages of early flower development. Phenotypically, the F1 hybrids show remarkable heterosis in silique number and grain yield. Transcriptome analysis revealed that various phytohormone (auxin and salicylic acid) response genes are significantly altered in the F1 hybrids relative to the parental lines. We also found evidence for decreased expression divergence of the homoeologous gene pairs in the allopolyploid F1 hybrids and suggest that high-parental expression-level dominance plays an important role in heterosis. Small RNA and methylation studies aimed at examining the epigenetic effect of the changes in gene expression level in the F1 hybrids showed that the majority of the small interfering RNA (siRNA) clusters had a higher expression level in the F1 hybrids than in the parents, and that there was an increase in genome-wide DNA methylation in the F1 hybrid. Transposable elements associated with siRNA clusters had a higher level of methylation and a lower expression level in the F1 hybrid, implying that the non-additively expressed siRNA clusters resulted in lower activity of the transposable elements through DNA methylation in the hybrid. Our data provide insights into the role that changes in gene expression pattern and epigenetic mechanisms contribute to heterosis during early flower development in allopolyploid B. napus.
An Intron Sense Suppression Construct Targeting Soybean FAD2-1 Requires a Double-Stranded RNA-Producing Inverted Repeat T-DNA Insert[OA]

We demonstrate that the transformation of soybean (Glycine max) with sense suppression constructs using intron sequences from the fatty acid oleyl Δ12 desaturase gene FAD2-1A leads to efficient and specific reduction of FAD2-1 transcripts in developing seeds, increased oleic acid, and decreased polyunsaturated fatty acids. The related FAD2-2 transcripts are only marginally affected. Despite screening a large number of independent transformants, no single-copy efficacious transformants could be found. Invariably, all the least complex transgenic loci have two T-DNA copies in an inverted repeat configuration, centered at the right borders. We show that this T-DNA configuration produces an inverted repeat transcript and that small interfering RNAs accumulate against the target sequence.
Stress Fracture Risk Factors in Basic Combat Training

Abstract This study examined demographic and physical risk factors for stress fractures in a large cohort of basic trainees. New recruits participating in US Army BCT from 1997 through 2007 were identified, and birth year, race/ethnicity, physical characteristics, body mass index, and injuries were obtained from electronic databases. Injury cases were recruits medically diagnosed with inpatient or outpatient stress fractures. There were 475 745 men and 107 906 women. Stress fractures incidences were 19.3 and 79.9 cases/1 000 recruits for men and women, respectively. Factors that increased stress fracture risk for both men and women included older age, lower body weight, lower BMI, and race/ethnicity other than black. Compared to Asians, those of white race/ethnicity were at higher stress fractures risk. In addition, men, but not women, who were taller or heavier were at increased stress fracture risk. Stress fracture risk generally increased with age (17–35 year range) at a rate of 2.2 and 3.9 cases/1 000 recruits per year for men and women, respectively. This was the largest sample of military recruits ever examined for stress fractures and found that stress fracture risk was elevated among recruits who were female, older, had lower body weight, had lower BMI, and/or were not of black race/ethnicity.
Successful Reproduction Requires the Function of Arabidopsis YELLOW STRIPE-LIKE1 and YELLOW STRIPE-LIKE3 Metal-Nicotianamine Transporters in Both Vegetative and Reproductive Structures1[W][OA]

Several members of the Yellow Stripe-Like (YSL) family of proteins are transporters of metals that are bound to the metal chelator nicotianamine or the related set of mugineic acid family chelators known as phytosiderophores. Here, we examine the physiological functions of three closely related Arabidopsis (Arabidopsis thaliana) YSL family members, AtYSL1, AtYSL2, and AtYSL3, to elucidate their role(s) in the allocation of metals into various organs of Arabidopsis. We show that AtYSL3 and AtYSL1 are localized to the plasma membrane and function as iron transporters in yeast functional complementation assays. By using inflorescence grafting, we show that AtYSL1 and AtYSL3 have dual roles in reproduction: their activity in the leaves is required for normal fertility and normal seed development, while activity in the inflorescences themselves is required for proper loading of metals into the seeds. We further demonstrate that the AtYSL1 and AtYSL2 proteins, when expressed from the AtYSL3 promoter, can only partially rescue the phenotypes of a ysl1ysl3 double mutant, suggesting that although these three YSL transporters are closely related and have similar patterns of expression, they have distinct activities in planta. In particular, neither AtYSL1 nor AtYSL2 is able to functionally complement the reproductive defects exhibited by ysl1ysl3 double mutant plants.
Evaluation of Diabetes Mellitus as a Risk Factor for Major Complications in Patients Undergoing Aesthetic Surgery.

BACKGROUND Diabetes mellitus has been linked with a variety of perioperative adverse events across surgical disciplines. There is a paucity of studies systematically examining risk factors, including diabetes, and complications of aesthetic surgical procedures. OBJECTIVES The purpose of this study was to compare incidence and type of complications between diabetic and non-diabetic patients undergoing various aesthetic surgical procedures, to identify specific procedures where diabetes significantly increases risk of complications, and to study diabetes as an independent risk factor for major complications following aesthetic surgery. METHODS A prospective cohort of 129,007 patients who enrolled into the CosmetAssure insurance program and underwent cosmetic surgical procedures between May 2008 and May 2013 were reviewed. Diabetes was evaluated as risk factor for major complications, requiring hospital admission, emergency room visit, or a reoperation within 30 days after surgery. Multivariate regression analysis was performed controlling for the effects of age, smoking, obesity, gender, type of procedures, and surgical facility. RESULTS Overall, 2506 patients (1.9%) had a major complication. Diabetics had significantly more complications compared to non-diabetics (3.1% vs 1.9%, P < 0.01). In univariate analysis, infectious (1.1% vs 0.5%, P < 0.01) and pulmonary (0.3% vs 0.1%, P < 0.01) complications were significantly higher among diabetics. Notably, diabetics had higher risks of complication in body cases (4.3% vs 2.6%, P < 0.01) and specifically abdominoplasty (6.1% vs 3.0%, P < 0.01). In multivariate analysis, diabetes was found to be an independent risk factor of any complication (relative risk 1.31, P = 0.03) and infection (relative risk 1.70, P < 0.01). CONCLUSIONS Diabetes is an independent risk factor of major complications, particularly infection, after aesthetic surgical procedures.
Abscisic Acid Receptors

Abscisic acid (ABA), a sesquiterpenoid phytohormone, was first discovered in the 1960s, and has since been found to be a key regulator of such diverse processes as dormancy, germination, seed development, and responses to biotic and abiotic stress (Cutler et al., 2010). Since the discovery of its structure, advances have been made in understanding ABA metabolism, synthesis, and hormone-responsive genes; however, the understanding of the early stage of ABA perception by the plant cell remained a mystery. During the past decade receptor proteins for the other traditional plant hormones (auxin, gibberellins, cytokinin, and ethylene) were discovered, while the identity of the ABA receptor remained elusive, creating controversy. Finally, in 2009, two research groups converged upon the PYR/PYL/RCAR family of soluble proteins in Arabidopsis (Arabidopsis thaliana), which evidence indicates are one type of ABA-binding receptor-like proteins (Ma et al., 2009; Park et al., 2009). This protein family has 14 members, almost all of which appear capable of forming an ABA-receptor complex that is able to activate the transcription of ABA-responsive genes. The use of multiple biochemical, chemical genetics, and proteomic approaches has provided the evidence to paint a remarkable picture of ABA binding, receptor complex formation, and initial downstream signaling. While the receptors and some important signal mediators have been elucidated, the molecular mechanisms by which they regulate the ABA signaling pathway continue to intrigue researchers and drive the field forward.
The genetics underlying natural variation of plant-plant interactions, a beloved but forgotten member of the family of biotic interactions.

Despite the importance of plant-plant interactions on crop yield and plant community dynamics, our understanding of the genetic and molecular bases underlying natural variation of plant-plant interactions is largely limited in comparison with other types of biotic interactions. By listing 63 quantitative trait loci (QTL) mapping and global gene expression studies based on plants directly challenged by other plants, we explored whether the genetic architecture and the function of the candidate genes underlying natural plant-plant interactions depend on the type of interactions between two plants (competition versus commensalism versus reciprocal helping versus asymmetry). The 16 transcriptomic studies are unevenly distributed between competitive interactions (n = 12) and asymmetric interactions (n = 4, all focusing on response to parasitic plants). By contrast, 17 and 30 QTL studies were identified for competitive interactions and asymmetric interactions (either weed suppressive ability or response to parasitic plants), respectively. Surprisingly, no studies have been carried out on the identification of genetic and molecular bases underlying natural variation in positive interactions. The candidate genes underlying natural plant-plant interactions can be classified into seven categories of plant function that have been identified in artificial environments simulating plant-plant interactions either frequently (photosynthesis, hormones), only recently (cell wall modification and degradation, defense pathways against pathogens) or rarely (ABC transporters, histone modification and meristem identity/life history traits). Finally, we introduce several avenues that need to be explored in the future to obtain a thorough understanding of the genetic and molecular bases underlying plant-plant interactions within the context of realistic community complexity.
Lignin and Biomass: A Negative Correlation for Wood Formation and Lignin Content in Trees1

Studies in populations of forest tree hybrids have shown a negative correlation of biomass growth (usually measured as wood volume) and lignin content ([Kirst et al., 2004][1]; [Novaes et al., 2009][2]). The control of growth and lignin appears to be highly regulated, implying that selection for
The glabra1 Mutation Affects Cuticle Formation and Plant Responses to Microbes1[C][W][OA]

Systemic acquired resistance (SAR) is a form of defense that provides resistance against a broad spectrum of pathogens in plants. Previous work indicates a role for plastidial glycerolipid biosynthesis in SAR. Specifically, mutations in FATTY ACID DESATURASE7 (FAD7), which lead to reduced trienoic fatty acid levels and compromised plastidial lipid biosynthesis, have been associated with defective SAR. We show that the defective SAR in Arabidopsis (Arabidopsis thaliana) fad7-1 plants is not associated with a mutation in FAD7 but rather with a second-site mutation in GLABRA1 (GL1), a gene well known for its role in trichome formation. The compromised SAR in gl1 plants is associated with impairment in their cuticles. Furthermore, mutations in two other components of trichome development, GL3 and TRANSPARENT TESTA GLABRA1, also impaired cuticle development and SAR. This suggests an overlap in the biochemical pathways leading to cuticle and trichome development. Interestingly, exogenous application of gibberellic acid (GA) not only enhanced SAR in wild-type plants but also restored SAR in gl1 plants. In contrast to GA, the defense phytohoromes salicylic acid and jasmonic acid were unable to restore SAR in gl1 plants. GA application increased levels of cuticular components but not trichome formation on gl1 plants, thus implicating cuticle, but not trichomes, as an important component of SAR. Our findings question the prudence of using mutant backgrounds for genetic screens and underscore a need to reevaluate phenotypes previously studied in the gl1 background.
An Arabidopsis Pentatricopeptide Repeat Protein, SUPPRESSOR OF VARIEGATION7, Is Required for FtsH-Mediated Chloroplast Biogenesis1[W][OA]

The Arabidopsis (Arabidopsis thaliana) yellow variegated2 (var2) mutant has green- and white-sectored leaves due to loss of VAR2, a subunit of the chloroplast FtsH protease/chaperone complex. Suppressor screens are a valuable tool to gain insight into VAR2 function and the mechanism of var2 variegation. Here, we report the molecular characterization of 004-003, a line in which var2 variegation is suppressed. We found that the suppression phenotype in this line is caused by lack of a chloroplast pentatricopeptide repeat (PPR) protein that we named SUPPRESSOR OF VARIEGATION7 (SVR7). PPR proteins contain tandemly repeated PPR motifs that bind specific RNAs, and they are thought to be central regulators of chloroplast and mitochondrial nucleic acid metabolism in plants. The svr7 mutant has defects in chloroplast ribosomal RNA (rRNA) processing that are different from those in other svr mutants, and these defects are correlated with reductions in the accumulation of some chloroplast proteins, directly or indirectly. We also found that whereas var2 displays a leaf variegation phenotype at 22°C, it has a pronounced chlorosis phenotype at 8°C that is correlated with defects in chloroplast rRNA processing and a drastic reduction in chloroplast protein accumulation. Surprisingly, the cold-induced phenotype of var2 cannot be suppressed by svr7. Our results strengthen the previously established linkage between var2 variegation and chloroplast rRNA processing/chloroplast translation, and they also point toward the possibility that VAR2 mediates different activities in chloroplast biogenesis at normal and chilling temperatures.
AtMYB2 Regulates Whole Plant Senescence by Inhibiting Cytokinin-Mediated Branching at Late Stages of Development in Arabidopsis1[C][W][OA]

Whole plant senescence of monocarpic plants consists of three major processes: arrest of shoot apical meristem, organ senescence, and permanent suppression of axillary buds. At early stages of development, axillary buds are inhibited by shoot apex-produced auxin, a mechanism known as apical dominance. How the buds are suppressed as an essential part of whole plant senescence, especially when the shoot apexes are senescent, is not clear. Here, we report an AtMYB2-regulated post apical dominance mechanism by which Arabidopsis (Arabidopsis thaliana) inhibits the outgrowth of axillary buds as part of the whole plant senescence program. AtMYB2 is expressed in the compressed basal internode region of Arabidopsis at late stages of development to suppress the production of cytokinins, the group of hormones that are required for axillary bud outgrowth. atmyb2 T-DNA insertion lines have enhanced expression of cytokinin-synthesizing isopentenyltransferases genes, contain higher levels of cytokinins, and display a bushy phenotype at late stages of development. As a result of the continuous generation of new shoots, atmyb2 plants have a prolonged life span. The AtMYB2 promoter-directed cytokinin oxidase 1 gene in the T-DNA insertion lines reduces the endogenous cytokinin levels and restores the bushy phenotype to the wild type.