Miracle-dz/UniFAR-FTUs huggingface dataset:
Differences in Effective Ploidy Drive Genome-Wide Endosperm Expression Polarization and Seed Failure in Wild Tomato Hybrids

Parental imbalances in the endosperm leading to impaired development and eventual hybrid seed failure are common causes of postzygotic isolation in flowering plants. Endosperm sensitivity to parental dosage is reflected by canonical phenotypes of “parental excess” in reciprocal interploid crosses. Moreover, parental-excess traits are also evident in many homoploid interspecific crosses, potentially reflecting among-lineage variation in “effective ploidy” driven by endosperm properties. However, the genetic basis of effective ploidy is unknown and genome-wide expression perturbations in parental-excess endosperms from homoploid crosses have yet to be reported. The tomato clade (Solanum section Lycopersicon), encompassing closely related diploids with partial-to-complete hybrid seed failure, provides outstanding opportunities to study these issues. Here, we compared replicated endosperm transcriptomes from six crosses within and among three wild tomato lineages. Strikingly, strongly inviable hybrid crosses displayed conspicuous, asymmetric expression perturbations that mirror previously characterized parental-excess phenotypes. Solanum peruvianum, the species inferred to have evolved higher effective ploidy than the other two, drove expression landscape polarization between maternal and paternal roles. This global expression divergence was mirrored in functionally important gene families such as MADS-box transcription factors and E3 ubiquitin ligases, and revealed differences in cell cycle tuning that match phenotypic differences in developing endosperm and mature seed size between reciprocal crosses. Our work starts to uncover the complex interactions between expression divergence, parental conflict, and hybrid seed failure that likely contributed to plant diversity.
Determinants of diagnostic delay in axial spondyloarthritis: an analysis based on linked claims and patient-reported survey data.

OBJECTIVES The objective of this study was to assess the current diagnostic delay in axial SpA (axSpA) and to analyse factors associated with it. METHODS A stratified sample of subjects with a diagnosis of axSpA (International Classification of Diseases, 10th Revision code M45) was drawn from health insurance data in Germany and was questioned on disease-related, lifestyle and socio-economic characteristics. The diagnostic delay was calculated as the time from back pain onset until a diagnosis of axSpA. A multivariable linear regression analysis was performed to explore factors associated with the diagnostic delay. RESULTS Among 1677 patients with axSpA included in the analysis, the mean diagnostic delay was 5.7 years (median 2.3). Of those, 407 patients were diagnosed in 1996-2005 and 484 patients in 2006-2015. The mean diagnostic delay was not substantially different in both periods: 6.3 years (median 2.6) and 7.4 (2.7), respectively. Multivariable linear regression revealed that female sex [β = 1.85 (95% CI 1.06, 2.65)], negative HLA-B27 status [β = 3.61 (95% CI 2.07, 5.14)], presence of psoriasis [β = 1.40 (95% CI 0.08, 2.73)] and younger age at symptom onset [β = 1.91 (95% CI 1.53, 2.29)] were factors associated with a longer diagnostic delay. CONCLUSION The diagnostic delay in axSpA is still unacceptably long. Patients who are female, young at symptom onset, HLA-B27 negative or have psoriasis have a longer diagnostic delay. Specific referral strategies might be necessary in order to decrease the diagnostic delay in patients presenting with these characteristics.
CyaC, a redox‐regulated adenylate cyclase of Sinorhizobium meliloti with a quinone responsive diheme‐B membrane anchor domain

The nucleotide cyclase CyaC of Sinorhizobium meliloti is a member of class III adenylate cyclases (AC), a diverse group present in all forms of life. CyaC is membrane‐integral by a hexahelical membrane domain (6TM) with the basic topology of mammalian ACs. The 6TM domain of CyaC contains a tetra‐histidine signature that is universally present in the membrane anchors of bacterial diheme‐B succinate‐quinone oxidoreductases. Heterologous expression of cyaC imparted activity for cAMP formation from ATP to Escherichia coli, whereas guanylate cyclase activity was not detectable. Detergent solubilized and purified CyaC was a diheme‐B protein and carried a binuclear iron‐sulfur cluster. Single point mutations in the signature histidine residues caused loss of heme‐B in the membrane and loss of AC activity. Heme‐B of purified CyaC could be oxidized or reduced by ubiquinone analogs (Q0 or Q0H2). The activity of CyaC in bacterial membranes responded to oxidation or reduction by Q0 and O2, or NADH and Q0H2 respectively. We conclude that CyaC‐like membrane anchors of bacterial ACs can serve as the input site for chemical stimuli which are translated by the AC into an intracellular second messenger response.
Diallel Analysis of some Quantitative Traits in Eight Inbred Lines of Maize and Gge Biplot Analysis for Elite Hybrids

An 8x8 half diallel analysis were performed at two planting dates to study the importance of types of combining ability (GCA and SCA) and its interaction with environment in F1 of maize. Planting dates (D), crosses (Cr), GCA, SCA, CrxD, GCAxD, SCAxD were significant for all traits. GCA/SCA exceeded the unity for most traits. Non-additive seemed to be more prevalent for plant, ear heights and grain yield plant. P8 gave significant positive ( i ĝ ) effects for all studied traits. High SCA effects were exhibited by the crosses P1xP7, P1xP8, P2xP5, P3xP4, P3xP8, P4xP7, P4xP8 and P5xP6 for grain yield plant across planting dates. Superiority of P2xP5 and P3xP8 over SC Hytech 2031 reached 13.84 and 6.16%, respectively. However, useful heterotic effects relative to SC 128 mean value were 21.14 and 10.22%, for the aforementioned crosses, respectively. P1xP8, P4xP8 and P5xP6 gave positive insignificant out-yielded than check hybrids. The five superior hybrids P2xP5 (G1), P3xP8 (G2), P5xP6 (G3), P1xP8 (G4) and P4xP8 (G5) along with SC10 (G6), SC 128 (G7) and SC Hytech 2031(G8) were evaluated in 2019 season at various environments using RCBD with 3 replicates to identify environments and suitable adapted maize hybrids. Stable genotypes are ranked descending for means of grain yield as follows: G1 > G8> G2> G7. G1, G8, and G2 were above average stability while genotypes G7 showed below average stability. Thus, G1 (P2xP5) and G2 (P3xP8) are promising crosses, and it's recommended to register as new varieties with high productivity and stability across environments.
Comparison of Periodontal Status Between Male Exclusive Narghile Smokers and Male Exclusive Cigarette Smokers

Studies evaluating the effects of narghile use on the periodontium present conflicting conclusions. This study aimed to compare the periodontal status of exclusive narghile smokers (ENSs, n = 74) to that of exclusive cigarette smokers (ECSs, n = 74). Males aged 20–40 years were recruited to participate in this comparative study. Information concerning oral health habits (number of yearly visits to the dentist, daily toothbrushing frequency) and tobacco exposure were obtained. Clinical measurements were performed on all the existing teeth, except the third molars. The number of remaining teeth and decayed/missing/filled teeth (DMFT) were noted. The plaque levels were recorded using the plaque index of Löe and Silness. The gingival index modified by Löe was used to evaluate gingival inflammation. Teeth mobility was measured using bidigital mobility. The probing pocket depth was measured using a periodontal probe. Periodontal disease was defined as the presence of at least 10 sites with a probing depth ≥5 mm. Student’s t and chi-square tests were used to compare, respectively, the two groups’ quantitative and qualitative data. The two groups were matched for quantities of used tobacco, age, daily toothbrushing frequency, teeth mobility, number of remaining teeth, plaque index, and DMFT. Compared to the ECS group, the ENS group had a significantly lower number of yearly visits to the dentist (mean ± SD: 0.2 ± 0.5 vs. 0.1 ± 0.2), lower probing pocket depth (mean ± SD: 2.33 ± 0.63 vs. 2.02 ± 0.80 mm), and gingival index (median [interquartile]: 0.46 [0.10–0.89] vs. 0.00 [0.00–0.50]), and it included significantly lower percentages of smokers with periodontal disease (24.3% vs. 9.5%). In conclusion, chronic exclusive narghile smoking has fewer adverse effects on the periodontium than chronic exclusive cigarette smoking.
Efficacy of different fungicides and weedicides against Macrophomina phaseolina (Tassi) Goid causing groundnut root rot

In this study, different systemic, non-systemic, combination fungicides and weedicides at four different concentration were evaluated in vitro against groundnut root rot pathogen Macrophomina phaseolina. Among the non-systemic fungicides, Mancozeb 75% WP and Propineb 70% WP were found most effective and showed (99.98 and 99.96 per cent) mycelia growth inhibition at all concentrations. Whereas in systemic fungicides, Carbendazim 50% WP were found most effective with (94.24 per cent) mean mycelial growth inhibition. Among different combination fungicides tested, Carboxin 37.5% + Thiram 37.5% WP were found most effective with mean mycelial growth inhibition of (97.16 per cent). In case of weedicides tested, Quizalofo-p-pethyle 5% EC found as most effective inhibiting the mycelial growth of M. phaseolina at all concentrations with (90.92 per cent) mean mycelial growth inhibition. Sclerotial formation was also absent in all this treatments.
Liraglutide exerts an anti-inflammatory action in obese patients with type 2 diabetes

Abstract Introduction. Liraglutide (L) is the analogue of human glucagon-like peptide 1 which stimulates glucose-dependent insulin secretion and can modify the level of inflammatory biomarkers. L can influence NF-kB inflammatory cascade, but the mechanisms of anti-inflammatory activities of L remain to be determined. In animal models L influenced an activity of Sirtuin 1(SIRT1). Moreover, recent evidences strongly suggest that SIRT1 up-regulation may serve as a potent therapeutic approach against development and progression of diabetic complications. The aim of this study was to investigate L effects directed on the pro-inflammatory NF-kB pathway and expression of SIRT1 in obese patients with type 2 diabetes mellitus (DM). Materials and Methods. 15 obese patients with type 2 diabetes were studied, all using metformin (1-2 g/day) and sulfonylurea (glimiperide). All patients received L 1.2 mg daily add-on to stable therapy for 6 weeks. Blood samples were collected before, 6 weeks after start of treatment and after an overnight fast 6 weeks after stopping L, mononuclear cells (MNC) were isolated. The mRNA expressions of TNF-α, TLR2, TLR4, NOD1, IL-2 and SIRT1 were measured in MNC by RT-PCR. Ceruloplasmin concentration was measured in plasma by photometric method. Results. In this add-on pilot clinical investigation we received new data that L can inhibit proinflammatory NF-kB pathway by increased SIRT1 expression in obese patients with type 2 DM improving metabolic profile. The mRNA expression in MNC of TNF-α, IkB, TLR2, TLR4, and plasma ceruloplasmin fell after 6 weeks of L. Expressions of IL-2 and NOD-1 were stable. There was a significant increase of SIRT1 mRNA expression. The mRNA expression in MNC of TNF-α, IkB, TLR2, TLR4, NOD1, SIRT1 and ceruloplasmin concentrations did not reverse to baseline levels after 6 weeks stopping of L treatment. IL-2 expression decreased in comparison with basic level. Conclusions. L has a potent anti-inflammatory effect as do GLP-1 agonists due to inhibition of NF-kB pathways and up-regulate SIRT1 expression, down-regulating pro-inflammatory factors including cytokines (TNF-α), extra- and intracellular receptors (TLR2, TLR4), and inflammation markers such as ceruloplasmin. Long lasting effects of L can be mediated by epigenetic regulation of NF-kB pathway by SIRT-1.
Inadvertent Paralog Inclusion Drives Artifactual Topologies and Timetree Estimates in Phylogenomics

Abstract Increasingly, large phylogenomic data sets include transcriptomic data from nonmodel organisms. This not only has allowed controversial and unexplored evolutionary relationships in the tree of life to be addressed but also increases the risk of inadvertent inclusion of paralogs in the analysis. Although this may be expected to result in decreased phylogenetic support, it is not clear if it could also drive highly supported artifactual relationships. Many groups, including the hyperdiverse Lissamphibia, are especially susceptible to these issues due to ancient gene duplication events and small numbers of sequenced genomes and because transcriptomes are increasingly applied to resolve historically conflicting taxonomic hypotheses. We tested the potential impact of paralog inclusion on the topologies and timetree estimates of the Lissamphibia using published and de novo sequencing data including 18 amphibian species, from which 2,656 single-copy gene families were identified. A novel paralog filtering approach resulted in four differently curated data sets, which were used for phylogenetic reconstructions using Bayesian inference, maximum likelihood, and quartet-based supertrees. We found that paralogs drive strongly supported conflicting hypotheses within the Lissamphibia (Batrachia and Procera) and older divergence time estimates even within groups where no variation in topology was observed. All investigated methods, except Bayesian inference with the CAT-GTR model, were found to be sensitive to paralogs, but with filtering convergence to the same answer (Batrachia) was observed. This is the first large-scale study to address the impact of orthology selection using transcriptomic data and emphasizes the importance of quality over quantity particularly for understanding relationships of poorly sampled taxa.
Aspiration of rural youth towards different agricultural activities

The present study was conducted purposively in Majhgawan block of Satna district to know the aspiration level of rural youth towards different agricultural activities. The Ex-Post Facto research design was used for the study. Multi stage sampling technique was employed to select the respondents. A sample of 80 rural youth was selected from 5 villages of Majhgawan block. The primary data were collected through personal interview method with the help of interview schedule which was prepared on the basis of objectives of investigation and variables. The data were analyzed with the help of statistical tools like- frequency, mean, percentage, mean score and statistical test viz. x2 test and coefficient of association etc. The present study revealed that, majority of the rural youth had medium (35.00%) level of aspiration towards different agricultural activities. In case of association education, caste, annual income, size of land holding, social participation, farming experience, innovativeness, extension participation, material possession, scientific orientation and risk orientation had significantly associated with the aspiration level of rural youth towards different agricultural activities.
Prominent Injury Types in Vehicle Underbody Blast.

BACKGROUND To fully understand the injury mechanisms during an underbody blast (UBB) event with military vehicles and develop new testing standards specific to military vehicles, one must understand the injuries sustained by the occupants. METHODS Injury data from Service Members (SM) involved in UBB theater events that occurred from 2010 to 2014 were analyzed. Analysis included the investigation of prominent skeletal and visceral torso injuries. Results were categorized by killed-in-action (n = 132 SM) and wounded-in-action (n = 1,887 SM). RESULTS Over 90% (553/606 SM) of casualties in UBB events with Abbreviated Injury Scale (AIS) 2+ injury sustained at least one skeletal fracture, when excluding concussion. The most frequent skeletal injuries from UBB were foot fractures (13% of injuries) for wounded-in-action and tibia/fibula fractures (10% of injuries) for killed-in-action. Only 1% (11/1037 SM) of all casualties with AIS 2+ injuries had visceral torso injuries without also sustaining skeletal fractures. In these few casualties, the coded injuries were likely due to trauma from a loading path other than direct UBB loading. CONCLUSION Skeletal fractures are the most frequent AIS 2+ injury resulting from UBB events. Visceral torso injuries are infrequent in individuals that survive and they generally occur in conjunction with skeletal injuries.
Drug Transport across Porcine Intestine Using an Ussing Chamber System: Regional Differences and the Effect of P-Glycoprotein and CYP3A4 Activity on Drug Absorption

Drug absorption across viable porcine intestines was investigated using an Ussing chamber system. The apparent permeability coefficients, Papp,pig, were compared to the permeability coefficients determined in humans in vivo, Peff,human. Eleven drugs from the different Biopharmaceutical Classification System (BCS) categories absorbed by passive diffusion with published Peff,human values were used to test the system. The initial experiments measured Papp,pig for each drug after application in a Krebs–Bicarbonate Ringer (KBR) buffer and in biorelevant media FaSSIF V2 and FeSSIF V2, mimicking fasted and fed states. Strong sigmoidal correlations were observed between Peff,human and Papp,pig. Differences in the segmental Papp,pig of antipyrine, cimetidine and metoprolol confirmed the discrimination between drug uptake in the duodenum, jejunum and ileum (and colon); the results were in good agreement with human data in vivo. The presence of the P-gp inhibitor verapamil significantly increased Papp,pig across the ileum of the P-gp substrates cimetidine and ranitidine (p < 0.05). Clotrimazole, a potent CYP3A4 inhibitor, significantly increased Papp,pig of the CYP3A4 substrates midazolam, verapamil and tamoxifen and significantly decreased the formation of their main metabolites. In conclusion, the results showed that this is a robust technique to predict passive drug permeability under fasted and fed states, to identify regional differences in drug permeability and to demonstrate the activity of P-gp and CYP3A4.
Bone Marrow Absorbed Doses and Correlations with Hematologic Response During 177Lu-DOTATATE Treatments Are Influenced by Image-Based Dosimetry Method and Presence of Skeletal Metastases

This study aimed to compare different image-based methods for bone marrow dosimetry and study the dose–response relationship during treatment with 177Lu-DOTATATE in patients with and without skeletal metastases. Methods: This study included 46 patients with advanced neuroendocrine tumors treated with at least 2 fractions of 177Lu-DOTATATE at Sahlgrenska University Hospital. High- and low-uptake compartments were automatically outlined in planar images collected at 2, 24, 48, and 168 h after injection. The bone marrow absorbed doses were calculated from the cross doses of the high- and low-uptake compartments and the self-dose, using the time–activity concentration curve for the low-uptake compartment. This time–activity concentration curve was adjusted using a fixed constant of 1.8 for the planar dosimetry method and using the activity concentrations in vertebral bodies in SPECT images at 24 h after injection of 177Lu-DOTATATE in 4 hybrid methods: L4-SPECT used the activity concentration in the L4 vertebra, whereas V-SPECT, L-SPECT, and T-SPECT used the median activity concentration in all visible vertebrae, lumbar vertebrae, and thoracic vertebrae, respectively. Results: Using the planar method, L4-SPECT, V-SPECT, L-SPECT, and T-SPECT, the estimated median bone marrow absorbed doses were 0.19, 0.36, 0.40, 0.39, and 0.46 Gy/7.4 GBq, respectively, with respective ranges of 0.12–0.33, 0.15–1.44, 0.19–1.71, 0.21–1.60, and 0.18–2.12 Gy/7.4 GBq. For all methods, the bone marrow absorbed dose significantly correlated with decreased platelet counts. This correlation increased after treatment fraction 2: the Spearman correlation (rs) were −0.49 for the planar method, −0.61 for L4-SPECT, −0.63 for V-SPECT, −0.63 for L-SPECT, and −0.57 for T-SPECT. A separate analysis revealed an increased correlation for patients without skeletal metastases using the planar method (rs = −0.67). In contrast, hybrid methods had poor correlations for patients without metastases and stronger correlations for patients with skeletal metastases (rs = −0.61 to −0.74). The mean bone marrow absorbed doses were 3%–69% higher for patients with skeletal metastases than for patients without. Conclusion: The estimated bone marrow absorbed doses by image-based techniques and the correlation with platelets are influenced by the choice of measured vertebrae and the presence of skeletal metastases.
A Novel Gradient Echo Plural Contrast Imaging Method Detects Brain Tissue Abnormalities in Patients With TBI Without Evident Anatomical Changes on Clinical MRI: A Pilot Study.

RESEARCH OBJECTIVES It is widely accepted that mild traumatic brain injury (mTBI) causes injury to the white matter, but the extent of gray matter (GM) damage in mTBI is less clear. METHODS We tested 26 civilian healthy controls and 14 civilian adult subacute-chronic mTBI patients using quantitative features of MRI-based Gradient Echo Plural Contrast Imaging (GEPCI) technique. GEPCI data were reconstructed using previously developed algorithms allowing the separation of R2t*, a cellular-specific part of gradient echo MRI relaxation rate constant, from global R2* affected by BOLD effect and background gradients. RESULTS Single-subject voxel-wise analysis (comparing each mTBI patient to the sample of 26 control subjects) revealed GM abnormalities that were not visible on standard MRI images (T1w and T2w). Analysis of spatial overlap for voxels with low R2t* revealed tissue abnormalities in multiple GM regions, especially in the frontal and temporal regions, that are frequently damaged after mTBI. The left posterior insula was the region with abnormalities found in the highest proportion (50%) of mTBI patients. CONCLUSIONS Our data suggest that GEPCI quantitative R2t* metric has potential to detect abnormalities in GM cellular integrity in individual TBI patients, including abnormalities that are not detectable by a standard clinical MRI.