Miracle-dz/UniFAR-FTUs huggingface dataset:
Lingering Effects of Prenatal Alcohol Exposure on Basal and Ethanol-Evoked Expression of Inflammatory-Related Genes in the CNS of Adolescent and Adult Rats

Emerging data suggest that alcohol’s effects on central inflammatory factors are not uniform across the lifespan. In particular, prenatal alcohol exposure (PAE) significantly alters steady-state levels of neuroimmune factors, as well as subsequent reactivity to later immune challenge. Thus, the current experiment investigated developmental sensitivities to, and long-lasting consequences of, PAE on ethanol-evoked cytokine expression in male and female adolescent and adult rats. Pregnant dams received either an ad libitum ethanol liquid diet (2.2% GD 6–8; 4.5% GD 9–10; 6.7% GD11–20; 35% daily calories from ethanol) or free-choice access to a control liquid diet and water. At birth, offspring were fostered to dams given free-choice access to the control liquid diet. Pups then matured until mid-adolescence [postnatal day (PD) 35] or adulthood (PD90), at which time they were challenged with either a binge-like dose of ethanol (4 g/kg; intragastrically) or tap water. During intoxication (3 h post-ethanol challenge), brains and blood were collected for assessment of neuroimmune gene expression (reverse transcription-polymerase chain reaction; RT-PCR) in the hippocampus, amygdala, and PVN, as well as for blood ethanol concentrations (BEC) and plasma corticosterone levels. Results revealed that rats challenged with ethanol at either PD35 or PD90 generally exhibited a characteristic cytokine signature of acute intoxication that we have previously reported: increased Il-6 and IkBα expression, with decreased Il-1β and Tnfα gene expression. With a few exceptions, this pattern of gene changes was observed in all three structures examined, at both ages of postnatal ethanol challenge, and in both sexes. While few significant effects of PAE were observed for ethanol-induced alterations in cytokine expression, there was a consistent (but nonsignificant) trend for PAE to potentiate the expression of Il-6 and IkBα in all groups except adult females. Although these data suggest that later-life ethanol challenge was a far greater driver of inflammatory signaling than PAE, the current results demonstrate PAE resulted in subtle long-term alterations in the expression of many key neuroinflammatory factors associated with NF-κB signaling. Such long-lasting impacts of PAE that may engender vulnerability to later environmental events triggering neuroinflammatory processes, such as chronic ethanol exposure or stress, could contribute to heightened vulnerability for PAE-related alterations and deficits.
ON THE USE OF THE ROBUST DESIGN WITH TRANSIENT CAPTURE-RECAPTURE MODELS

Abstract Capture-mark-recapture studies provide a useful mechanism for estimating the components of the population dynamics of birds, especially survival. In such studies, it is important that the population being captured matches the population of interest. In many studies, transients are captured along with the population of interest (e.g. resident breeders). Ignoring that phenomenon produces negatively biased survival estimates, because transients do not return. Although transients cannot be distinguished from residents in the hand, previous methods have adjusted for transience by relying on those captured in more than one year to provide direct estimates of survival rate for residents. Here, we extend that approach by supplementing that cohort of known residents with those previously unmarked birds captured twice or more, at least d days apart, within a season. We provide an ad hoc approach to that extension in detail and outline two more formal approaches. That extension increases the precision of survival estimates.
Antibacterial and Antivirulence Properties of Phenolic-Rich Drip Brewed Coffees

Over the years, much research had been performed on coffee beans due to their vast potential health benefits. Nevertheless, there is yet any study conducted on the bioactivities of drip brewed coffee commonly prepared in cafes. Hence, this work aimed to compare the antibacterial activities of drip coffee from different bean varieties; Coffea arabica, Coffea robusta, and Coffea liberica. The coffee phytocompounds were then tested for their in silico inhibitory potential against bacterial virulence factor, MrkD adhesion protein, responsible for binding to human kidney. Growth inhibition of four urinary tract infection bacteria (Proteus mirabilis, Escherichia coli, Pseudomonas aeruginosa and Klebsiella pneumoniae) using the coffee extracts were evaluated using Kirby-Bauer disk diffusion and broth microdilution assays. Molecular docking experiment was further conducted to determine the interaction of coffee phytocompounds with MrkD adhesion protein. Among the tested bacteria, K. pneumoniae showed significantly higher susceptibility towards the coffee extracts. C. robusta charted the lowest minimum inhibition concentration (MIC) value of 2000μg/mL followed by C. arabica (4000μg/mL) and C. liberica (>4000μg/mL) against this bacterium. High performance liquid chromatography (HPLC) analysis revealed presence of chlorogenic acid and caffeine in all drip coffees but caffeic acid was found to be absent. Interestingly, chlorogenic acid demonstrated strong binding to an active pocket of MrkD receptor binding domain. This compound interacted with Arg105 residue which was vital in the binding of MrkD to collagen V of the host. In view of that, further investigation should be performed focusing on the inhibition machinery of coffee extracts towards the virulency of K. pneumoniae.
Production of cuticle - degrading proteases by Beauveria bassiana and their induction in different media

The concern for the development of hyphomycete fungi as suitable biocontrol agents of insect pests leads to the isolation of various insect pathogenic fungi. Amongst them, one of the most studied entomopathogenic fungus is Beauveria bassiana. The conidia of mitosporic fungi adhere to the host cuticle and germinate to produce an infectious propagule, and produce a sequential release of extra cellular enzymes to breach the insect cuticle. Protease is one of the most important and earliest enzymes involved in the host invasion. Extracellular protease production by seventeen B. bassiana isolates was investigated in the present study. High protease activity was observed during four to six days of culture incubation. Induction mechanism of subtillisin type Pr1 and trypsin type Pr2 activity were investigated utilizing different media. Minimal medium supplemented with casein (1%) showed high protease production and minimal medium supplemented with colloidal chitin (2%) was also able to induce Pr1 activity. The pH, ammonia and oxalic acid production in in vitro conditions was also investigated and the alteration in pH for protease production was not significant irrespective of the medium used. The protease activity gel was also studied and a common 66 kDa protease was observed in all the seven isolates studied. Key words: Ammonia, B. bassiana, oxalic acid, subtillisin type Pr1, trypsin type Pr2, protease, pH.
Mesenchymal Stem Cell Mechanobiology and Tendon Regeneration

Tendon function is essential for quality of life, yet the pathogenesis and healing of tendinopathy remains poorly understood compared to other musculoskeletal disorders. The aim of regenerative medicine is to replace traditional tissue and organ transplantation by harnessing the developmental potential of stem cells to restore structure and function to damaged tissues. The recently discovered interdependency of cell phenotype and biophysical environment has created a paradigm shift in cell biology. This dissertation introduces a dynamic in vitro model for tendon function, dysfunction and development, engineered to characterize the mechanobiological relationships dictating stem cell fate decisions so that they may be therapeutically exploited for tendon healing. Cells respond to mechanical deformation via a complex set of behaviors involving force-sensitive membrane receptor activity, changes in cytoskeletal contractility and transcriptional regulation. Effective ex vivo model systems are needed to emulate the native environment of a tissue and to translate cell-matrix forces with high fidelity. A naturally-derived decellularized tendon scaffold (DTS) was invented to serve as a biomimetic tissue culture platform, preserving the structure and function of native extracellular matrix. DTS in concert with a newly designed dynamic mechanical strain system comprises a tendon bioreactor that is able to emulate the three-dimensional topography, extracellular matrix proteins, and mechanical
On Perceived Stress and Social Support: Depressive, Anxiety and Trauma-Related Symptoms in Arabic-Speaking Refugees in Jordan and Germany

Current literature points toward several challenges in the access to sufficient and effective psychosocial care for Syrian refugees in host settings. This study is a comparative investigation into the relationship between “perceived social stress” and “perceived social support” on three of the most prevalent symptom dimensions in Syrian refugees across two host capitals, Berlin and Amman. Eighty nine Syrians refugees were recruited between January 2017 and March 2018. Participants were contacted through local institutions and organizations collaborating with the Charité—Universitätsmedizin Berlin. Assessments include the PHQ-9, GAD-7, HTQ, MSPSS, and PSS. Primary analyses consist of non- or parametric tests and multiple linear regression analyses. Subsample analyses showed relevant depressive, anxiety and trauma-related symptoms. Significant differences in PTSD symptoms (p < 0.04) were found. Participants reported high perceived stress and moderate to high social support. Linear regressions revealed that perceived stress had a significant negative effect (p < 0.01) on clinical outcomes in both subsamples. Perceived social support had a positive influence on depressive (p = 0.02) and PTSD symptoms (p = 0.04) for participants in Berlin. Analyses revealed significant positive effects of “significant others” (p = 0.05) on depressive- in Berlin and “family” (p = 0.03) support for PTSD symptoms in Amman. Study results show that levels of “perceived stress” appear to be the same across different host countries, whereas types of social support and their effect on mental health differ significantly depending on the host setting. Outcomes may guide future comparative study designs and investigations to promote well-being, integration, and the development of effective social support structures for the diverse needs of Arabic-speaking refugees.
TFEB/Mitf links impaired nuclear import to autophagolysosomal dysfunction in C9-ALS

Disrupted nucleocytoplasmic transport (NCT) has been implicated in neurodegenerative disease pathogenesis; however, the mechanisms by which impaired NCT causes neurodegeneration remain unclear. In a Drosophila screen, we identified Ref(2)p/p62, a key regulator of autophagy, as a potent suppressor of neurodegeneration caused by the GGGGCC hexanucleotide repeat expansion (G4C2 HRE) in C9orf72 that causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We found that p62 is increased and forms ubiquitinated aggregates due to decreased autophagic cargo degradation. Immunofluorescence and electron microscopy of Drosophila tissues demonstrate an accumulation of lysosome-like organelles that precedes neurodegeneration. These phenotypes are partially caused by cytoplasmic mislocalization of Mitf/TFEB, a key transcriptional regulator of autophagolysosomal function. Additionally, TFEB is mislocalized and downregulated in human cells expressing GGGGCC repeats and in C9-ALS patient motor cortex. Our data suggest that the C9orf72-HRE impairs Mitf/TFEB nuclear import, thereby disrupting autophagy and exacerbating proteostasis defects in C9-ALS/FTD.
The infection cushion: a fungal “weapon” of plant-biomass destruction

Grey mold disease affects fruits, vegetables and ornamental plants around the world, causing considerable losses every year. Its causing agent, the necrotrophic fungus Botrytis cinerea, produces infection cushions (IC) that are compound appressorial structures dedicated to the penetration of the plant tissues. A microarray analysis was performed to identify genes up-regulated in mature IC. The expression data were supported by RT-qPCR analysis performed in vitro and in planta, proteomic analysis of the IC secretome and mutagenesis of two candidate genes. 1,231 up-regulated genes and 79 up-accumulated proteins were identified. They highlight a secretion of ROS, secondary metabolites including phytotoxins, and proteins involved in virulence: proteases, plant cell wall degrading enzymes and necrosis inducers. The role in pathogenesis was confirmed for two up-regulated fasciclin genes. DHN-melanin pathway and chitin deacetylases genes are up-regulated and the conversion of chitin into chitosan was confirmed by differential staining of the IC cell wall. In addition, up-regulation of sugar transport and sugar catabolism encoding genes was found. These results support a role for the B. cinerea IC in plant penetration and suggest other unexpected roles for this fungal organ, in camouflage, necrotrophy or nutrition of the pathogen.
A novel method, using ubiquitin-trapping with a UIM peptide and immunoprecipitation, for identification in non-denaturing conditions of molecules associated with ubiquitinated proteins

Objective: To demonstrate a novel method, using ubiquitin (Ub)-trapping with a ubiquitin-interacting motif (UIM) peptide and immunoprecipitation, for purification of Ub-proteins and isolation of proteins that associate with epidermal growth factor (EGF) receptors. Methods: HeLa cells were cultured with or without EGF. Cell lysates were subjected to Ub-trapping, immunoprecipitation with an anti-EGFR antibody, and then liquid chromatography (LC)-tandem mass spectrometry (MS/MS) (LC-MS/MS) or immunoblotting with antibodies to proteins identified by LC-MS/MS. Results: Ub-trapping isolated Ub-proteins, including Ub-EGFR, but not non-Ub-EGFR. The combination of Ub-trapping and immunoprecipitation with an anti-EGFR antibody isolated pure UbEGFR. Cbl-c and c-Cbl were detected by LC-MS/MS in EGF-stimulated cell lysates. Some Cbl-b was shown to be associated with Ub-EGFR, unlike c-Cbl. Although HUWE1 was also detected by LC-MS/MS, HUWE1 was shown to interact with Ub-proteins other than Ub-EGFR. Conclusions: The method described, a combination of Ub-trapping, immunoprecipitation and immunoblotting, is effective to obtain information regarding specific interactions of various proteins with a target Ub-protein. It should prove useful in future investigations involving ubiquitination mechanisms.
Does more maternal investment mean a larger brain? Evolutionary relationships between reproductive mode and brain size in chondrichthyans

Chondrichthyans have the most diverse array of reproductive strategies of any vertebrate group, ranging from egg-laying to live-bearing with placental matrotrophy. Matrotrophy is defined as additional maternal provisioning beyond the yolk to the developing neonate; in chondrichthyans, this occurs through a range of mechanisms including uterine milk, oophagy, uterine cannibalism and placentotrophy. Chondrichthyans also exhibit a wide range of relative brain sizes and highly diverse patterns of brain organisation. Brains are energetically expensive to produce and maintain, and represent a major energetic constraint during early life in vertebrates. In mammals, more direct maternal–fetal placental connections have been associated with larger brains (steeper brain–body allometric scaling relationships). We test for a relationship between reproductive mode and relative brain size across 85 species from six major orders of chondrichthyans by using several phylogenetic comparative analyses. Ordinary least-squares (OLS) and reduced major axis (RMA) regression of body mass versus brain mass suggest that increased maternal investment results in a larger relative brain size. Our findings were supported by phylogenetic generalised least-squares models (pGLS), which also highlighted that these results vary with evolutionary tempo, as described by different branch-length assumptions. Across all analyses, maximum body size had a significant influence on the relative brain size, with large-bodied species (body mass >100 kg) having relatively smaller brains. The present study suggests that there may be a link between reproductive investment and relative brain size in chondrichthyans; however, a more definitive test requires a better-resolved phylogeny and a more nuanced categorisation of the level of maternal investment in chondrichthyans.
Studies on effect of media composition and biofertilizer inoculants on seedling growth and seedling vigour of tamarind (Tamarindus indica L.).

dicotyledonous family Fabaceae and belongs to the sub family Caesalpinoideae. It is a diploid species with chromosome number 2n= 24 (Purseglove, 1987). The name of tamarind is derived from an Arabic word “TamarindEHind” meaning “Date of India” popularly known as “Indian date”. Tamarind is a short trunked, multistemmed, large, evergreen or semi-evergreen tree growing up to 30 m with a trunk of about 8 m circumference and a crown diameter of up to 12m. Tamarind trees starts bearing the fruits at the age of 13 to 14 years and continue to produce fruits even after 60 years and some up to 200 years. Tamarind half the pod weight is contributed by pulp. Pulp contains both sugars (30-40%) and organic acids (8-18%), predominantly tartaric acid. The pulp is also a rich source of vitamins, minerals and calcium. Members of the Research Forum
Biomimetic synthesis of 6-substituted dihydrobenzophenanthridine alkaloids based on visible-light promoted radical addition reaction

Abstract Oxidative C–H functionalization of dihydrobenzophenanthridines catalyzed by dihydrobenzophenanthridine oxidase (DBOX) is believed to be the key step involved in the biosynthetic pathway of some novel 6-substituted benzophenanthridine alkaloids. In this study, a visible-light promoted biomimetic synthesis of 6-substituted benzophenanthridines was reported under photoredox-neutral conditions. α-Amino radical that derived from dihydrobenzophenanthridines was supposed to be the key intermediate in this visible-light promoted radical-type Michael addition reaction. Graphical Abstract
Impact of Flooding on the Species Richness, Density and Composition of Amazonian Litter‐Nesting Ants

Litter‐nesting ants are diverse and abundant in tropical forests, but the factors structuring their communities are poorly known. Here we present results of the first study to examine the impact of natural variation in flooding on a highly diverse (21 genera, 77 species) litter‐nesting ant community in a primary Amazonian forest. Fifty‐six 3 × 3 m plots experiencing strong variation in flooding and twenty‐eight 3 × 3 m terra firme plots were exhaustively searched for litter‐nesting ants to determine patterns of density, species richness and species composition. In each plot, flooding, litter depth, twig availability, canopy cover, plant density, percent soil nitrogen, carbon, and phosphorus were measured. Degree of flooding, measured as flood frequency and flood interval, had the strongest impact on ant density in flooded forest. Flooding caused a linear decrease in ant abundance, potentially due to a reduction of suitable nesting sites. However, its influence on species richness varied: low‐disturbance habitat had species richness equal to terra firme forest after adjusting for differences in density. The composition of ant genera and species varied among flood categories; some groups known to contain specialist predators were particularly intolerant to flooding. Hypoponera STD10 appeared to be well‐adapted to highly flooded habitat. Although flooding did not appear to increase species richness or abundance at the habitat scale, low‐flooding habitat contained a mixture of species found in the significantly distinct ant communities of terra firme and highly flooded habitat.
The impact of preoperative pain-related psychological factors on pain intensity post-surgery in Jordan

This study aimed to investigate the impact of preoperative psychological factors on postoperative pain. We included 300 postoperative patients who underwent open reduction and internal fixation surgery. Pain Scale, Pain Catastrophizing Scale, and Depression, Anxiety, and Stress Scale were completed by patients preoperatively and at 24 hours after surgery. Clinical characteristics were obtained from medical records. Data were analyzed using multiple linear regression. Postoperative pain was predicted by pain catastrophizing and anxiety symptoms. High preoperative catastrophizing and anxiety levels were associated with increased pain postoperatively. However, the relationships between preoperative depressive and stress symptoms and postoperative pain were not significant.
Perceived Barriers to Type 2 Diabetes Prevention for Low-Income Women With a History of Gestational Diabetes: A Qualitative Secondary Data Analysis

Purpose The purpose of this qualitative study was to examine perceived barriers to adoption of lifestyle changes for type 2 diabetes prevention among a diverse group of low-income women with a history of gestational diabetes mellitus (GDM). Methods A secondary data analysis of 10 semistructured focus group discussions was conducted. Participants were low-income African American, Hispanic, and Appalachian women ages 18 to 45 years who were diagnosed with GDM in the past 10 years. A qualitative content analysis was conducted to identify key themes that emerged within and between groups. Results Four key themes emerged on the role of knowledge, affordability, accessibility, and social support in type 2 diabetes prevention. Women discussed a lack of awareness of the benefits of breastfeeding and type 2 diabetes prevention, inaccessibility of resources in their local communities to help them engage in lifestyle change, and the desire for more culturally relevant education on healthful food options and proper portion sizes. Discussion Study findings suggests that to improve effectiveness of type 2 diabetes prevention efforts among low-income women with GDM history, health care providers and public health practitioners should avoid using “one-size-fits-all” approaches to lifestyle change and instead use tailored interventions that address the cultural and environmental factors that impact women’s ability to engage in recommended behavior change.