Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico identification, phylogeny and expression analysis of expansin superfamily in Medicago truncatula

ABSTRACT Expansins are important components of plant cell walls, which are involved in the process of cell wall loosening under low extracellular pH. By using a combinational method for homology search and protein domain analysis, a total of 42 expansin genes were identified from Medicago truncatula genome in this study. They were divided into four families, based on sequence alignment and phylogenetic analysis. Gene duplication events were identified in the expansins superfamily, especially in the extension of α-expansin family. By analysis of RNA-sequencing data from National Center for Biotechnology Information, the expansin (EXP) genes expressed during tissues development were characterized. Meanwhile, lots of cis-acting regulatory DNA elements in the EXP superfamily were identified, which were mainly related to plant growth and development processes. The results presented in this study are expected to facilitate further research works on this gene superfamily and provide new insights about the molecular mechanisms of expansins in M. truncatula.
Molecular characterization of the vernalization response in Lolium Perenne

Control of flowering time in a wide variety of plant species is one of the most important developmental switches during plant development and depends on various environmental factors. In the past, the isolations of many flowering mutants in the model system Arabidopsis thaliana contributed to a better understanding of the regulation of flowering time. In this species four main promoting pathways were identified and among those, the vernalization pathway allows an acceleration of flowering induction in climatic areas with long periods of cold. The main objective of this thesis was to study and identify the genes involved in vernalization requirement in Lolium perenne, and compare the genetic control of prolonged cold exposure in Arabidopsis and this cereal species. Chapter 1 describes the process of promotion of flowering induced by the vernalization pathway in Arabidopsis and winter cereals. The current view on the molecular function of genes controlling the vernalization response in Arabidopsis and in winter cereals is presented. In Chapter 2 a comprehensive expression analysis of 1500 unique cDNA clones from Lolium perenne is described, in order to identify genes up- or down-regulated during the vernalization response.Chapter 3 reports the regulation of flowering time in vernalization- sensitive andinsensitive Lolium perenne accessions. In Chapter 5 a differential subtractive approach aiming at the isolation of a sub-set of genes that are responsive to vernalization in perennial ryegrass was followed. One of the identified genes, named LpLIR1 was initially a good candidate for a vernalization-related gene. Chapter 6 introduces the results obtained by the characterization of two MADS box genes involved in the regulation of flowering time in Arabidopsis by a new approach. In Chapter 7 a final discussion is presented in which once more the genetic control of vernalization in Arabidopsis and cereal species is compared.
Article on and Transplantation of Spermatogonia and Testicular Tissue for Preservation of Male Fertility

The existence of spermatogonial stem cells in the testis offers clinically relevant options for preservation and restoration of male fertility. New approaches based on male germ cell transplantation and testicular tissue grafting can be applied to generate a limited number of sperm cells and could therefore be considered important new avenues for restoration of fertility in oncological patients. We have developed approaches to infuse germ cells into rodent and primate testes and shown that germ cell transplantation is a procedure for restoration of spermatogenesis in the testis that might be adaptable to primates. As a promising alternative, grafting of testicular tissue has been used to produce fertile sperm. The rapid progress in the development of novel experimental strategies to generate sperm by transplantation of spermatogonial stem cells or by grafting of testicular tissue should stimulate oncologists to consider the cryopreservation of testicular tissue. This review introduces the reader to the physiology of spermatogonial stem cells and summarizes the current and potential future options for fertility preservation in male oncological patients. [J Natl Cancer Inst Monogr 2005;34:51–6]
Are Bacteria The Main Producers of Hydrolytic Enzymes in Aquatic Environment

Bacteria play an important role in the decomposition of organic matter, which is a key process in aquatic microbial food webs as well as its application in water bioremediation processes. DOM (Dissolved Organic Matter) is the major fraction of organic matter in most aquatic environments. Most of DOM is present as high molecular weight compounds that cannot be taken up by bacteria directly. Therefore, they must be hydrolysed enzymatically to be transported across microbial cell membranes. Molecular fluorosensors have been used as artificial substrates to study hydrolytic enzymes in situ. The present study wants to investigate the following hypothesis i.e. bacteria are the main producers of hydrolytic enzyme in aquatic systems. There were not any significant correlations between bacteria and the investigated hydrolases (esterase, peptidase, and β-glucosidase) in the meso- to eutrophic aquatic systems near Rostock city – North East Germany, although a wide range of bacterial abundances were covered. Enzyme saturations were not detected in all samples which may be explained by a high KM indicating a low affinity of enzymes (1) and or the contribution of many enzymes with different kinetics to the respective substrate degradation (2). There is also increasing evidence that bacteria may not be the sole or dominant source of esterases, peptidases and β-glucosidases in aquatic ecosystems. Invertebrate, fungi and other eukaryotes (diatoms, protozoa etc.) must be considered as possible and even important producers of hydrolytic enzymes. Several other factors may influence the correlations of bacteria to hydrolytic enzyme activities, i.e. variations in the species composition (1), a wide ranged variability of hydrolytic activities influenced directly by other substrates (low enzyme affinity), element availability (N and P), temperature and other abiotic factors (2), the existence and persistence of enzymes caused by other (passive) processes (e.g. cell lysis) (3).
Antisecretory (Antidiarrhoeal) Activity of Indian Medicinal Plants Against Escherichia Coli Enterotoxin-Induced Secretion in Rabbit and Guinea Pig Ileal Loop Models

AbstractAlcohol, Hexane, Chloroform, Butanol and Aqueous Extracts Of Different Parts Of 31 Indigenous Medicinal Plants Of India Were Screened For Their Antisecretory Activity Against Escherichia Coli Enterotoxin (Lt, St and Lt/St)-Induced Secretory Responses In Rabbit and Guinea Pig Ileal Loop Models. The Extracts Of 5 Plants, Andrographis Panic Ulata, Cassiafistula, Coleusforskohlii, Tridex Procumbens and Papaver Somniferum, Showed Highly Significant Antisecretory Activity.
Pharmacotherapeutic considerations in solid organ transplant patients with COVID-19

ABSTRACT Introduction Coronavirus disease 2019 (COVID-19) has spread rapidly worldwide. While there are presently a few case reports/series on COVID-19 amongst solid organ transplant (SOT) patients, there is no official guideline for the management of SOT patients. Areas covered The authors discuss the pharmacotherapeutic management of SOT patients during the COVID-19 outbreak and provide their expert perspectives. Expert opinion Prophylactic reduction of immunosuppression because of fear of COVID-19 is not suggested in SOT patients. With maintenance immunosuppressive regimens, corticosteroids can be continued during COVID-19. Continuing other immunosuppressive drugs with lowest effective dose/blood concentration is suggested for patients with mild to moderate COVID-19. Discontinuation of antimetabolites and perhaps inhibitors of mammalian target of rapamycin (mTOR) is suggested in moderate to severe COVID-19. Calcineurin inhibitors (CNIs) may be continued or substituted for mTOR inhibitors with lowest therapeutic concentrations in moderate to severe COVID-19. If continued in patients with COVID-19, therapeutic drug monitoring of CNIs/mTOR inhibitors and appropriate dose reduction is recommended in co-administration with protease inhibitors, hydroxychloroquine/chloroquine, or interleukin (IL)-1/IL-6 receptor antagonists. Complete blood count monitoring is recommended in patients who continue taking antimetabolites or mTOR inhibitors. Dose modification/avoidance should be considered for chloroquine, atazanavir, oseltamivir, ribavirin, anakinra, and Janus associated kinase inhibitors in patients with organ function impairment.
Identification and characterization of a Bacillus subtilis strain TS06 as bio-control agent of strawberry replant disease ( Fusarium and Verticilium wilts)

Replant disease is a major limitation for strawberry production in greenhouse. Bio-control may be a good way to cope with the replant diseases. Here, we report identification and characterization of a bacterial strain TS06 that may be used as a bio-control agent against the replant diseases in strawberry. TS06 was identified as a new strain of Bacillus subtilis based on the homology of its 16S rRNA and gyrA sequences to the reference strains in Genbank. It has a 7 bp difference from the most homologous strain B. subtilis NRRL B-23978. TS06 formed a monophyletic group with species of the B. subtilis complex group in the 16S rDNA sequence analysis, and shared similarity values of 99.9% with the B. subtilis type strains in the sequence analysis of the gyrA genes. TS06 was demonstrated to be a potent inhibitor to Fusarium oxysporum and Verticillium dahliae . There were 89.6 and 84.5% growth inhibition of TS06 on F. oxysporum and V.dahliae respectively in the antagonism test of TS06 strain in vitro . The mycelia growth inhibition rate of TS06 for F. oxysporum and V.dahliae reached 65.96 and 68.45% respectively, in the 40% TS06 culture filtrate treatments. Strain TS06 reduced the average percentage of strawberry diseases ( Fusarium and Verticillium Wilts) by 88.94 and 79.94% respectively in greenhouse. In summary, B. subtilis strain TS06 has a broad antifungal spectrum and synchronously bio-control the two severe replant diseases (Fusarium and Verticilium Wilts), and TS06 can be developed as a biocontrol agent to be applied in strawberry production. Key words : Bacillus subtilis , strain TS06, biological control, strawberry Fusarium wilt , strawberry Verticillium wilt.
Genome-wide analyses of the prognosis-related mRNA alternative splicing landscape and novel splicing factors based on large-scale low grade glioma cohort

Alternative splicing (AS) changes are considered to be critical in predicting treatment response. Our study aimed to investigate differential splicing patterns and to elucidate the role of splicing factor (SF) as prognostic markers of low-grade glioma (LGG). We downloaded RNA-seq data from a cohort of 516 LGG tumors in The Cancer Genome Atlas and analyzed independent prognostic factors using LASSO regression and Cox proportional regression to build a network based on the correlation between SF-related survival AS events. We collected 100 patients from our center for immunohistochemistry and analyzed survival using χ2 test and Cox and Kaplan-Meier analyses. A total of 9,616 AS events related to LGG were screened and identified as well as established related models. Through analyzing specific splicing patterns in LGG, we screened 16 genes to construct a prognostic model to stratify the risk of LGG patients. Validation revealed that the expression level of the prognostic model in LGG tissue was increased, and patients with high expression showed worse prognosis. In summary, we demonstrated the role of SFs and AS events in the progression of LGG, which may provide insights into the clinical significance and aid the future exploration of LGG-associated AS.
Transmembrane TNF drives osteoproliferative joint inflammation reminiscent of human spondyloarthritis

The authors show that SpA synovitis comprises less sTNF and more tmTNF expression compared to RA synovitis associated with less active ADAM17. Moreover, tmTNF overexpression induces SpA-like pathophysiology in mice. tmTNF signaling through TNF-RI induced inflammation, but not osteoproliferation.
Highly active antibacterial ferrocenoylated or ruthenocenoylated Arg-Trp peptides can be discovered by an L-to-D substitution scan

The rapid increase in resistance against common antibiotics calls for the development of novel antibiotics, particularly against multi-resistant bacteria such as the methicillin-resistant Staphylococcus aureus (MRSA). In this work, the two group 8 metallocenoyl derivatives ferrocenoyl (FcC(O)-) or ruthenocenoyl (RcC(O)-) were attached to the N-terminus of two libraries of short antimicrobial peptides (AMPs), resulting in organometallic-AMP derivatives with as yet unparalleled antibacterial activities. In addition, these organometallic AMPs only cause limited lysis of human red blood cells (hRBCs). Our structure–activity relationship (SAR) study on these metallocenoylated peptides showed that specific combinations of L- and D-amino acid residues result in peptides with significantly improved antibacterial activity. Whereas the all-L FcC(O)-containing lead peptide had a MIC of 12 μM against MRSA, several peptides were found with MIC-values as low as 1.5–3 μM, a 4–8-fold increase in activity. For the RcC(O)-derivatized peptides a similar result was obtained: against MRSA a MIC value of 5.8 μM for the all-L peptide could be lowered to 0.7 μM, an 8-fold improvement. In addition, exposure of human red blood cells with 121 μM of the most active peptides led to a maximum hemolysis of 6%, indicating prominent selectivity that can be used to realize antibiotics based on organometallic-AMPs. We have hereby performed a systematic and highly successful SAR optimization against the two crucial parameters, i.e. antibacterial activity and hemolysis. Importantly, some of the RcC(O)-derivatized peptides presented here are among the most active antibacterial peptides; they approach or even exceed the activity of vancomycin.
Posttraumatic Stress Symptoms and Associated Comorbidity During the COVID‐19 Pandemic in Ireland: A Population‐Based Study

Abstract The prevalence of posttraumatic stress disorder (PTSD) as it relates to individuals’ experiences of the COVID‐19 pandemic has yet to be determined. This study was conducted to determine rates of COVID‐19–related PTSD in the Irish general population, the level of comorbidity with depression and anxiety, and the sociodemographic risk factors associated with COVID‐19–related PTSD. A nationally representative sample of adults from the general population of the Republic of Ireland (N = 1,041) completed self‐report measures of all study variables. The rate of COVID‐19–related PTSD was 17.7% (n = 184), 95% CI [15.35%, 19.99%], and there was a high level of comorbidity with generalized anxiety (49.5%) and depression (53.8%). Meeting the diagnostic requirement for COVID‐19–related PTSD was associated with younger age, male sex, living in a city, living with children, moderate and high perceived risk of COVID‐19 infection, and screening positive for anxiety or depression. Posttraumatic stress symptoms related to the COVID‐19 pandemic are common in the general population. Our results show that health professionals responsible for responding to the COVID‐19 pandemic should expect to routinely encounter symptoms and concerns related to posttraumatic stress.
Circulating exosomal long non-coding RNA H19 as a potential novel diagnostic and prognostic biomarker for gastric cancer

Objective Long non-coding RNAs (lncRNAs) are involved in carcinogenesis and could be used as diagnostic biomarkers. Our study aimed to elucidate the clinical role of serum exosomal lncRNA H19 in gastric cancer (GC). Methods In this prospective clinical study, we determined serum exosomal lncRNA H19 levels in 81 patients with GC and analysed the correlations between serum lncRNA H19 levels and clinical characteristics. Receiver operating characteristics (ROC) curves were constructed to determine the diagnostic performance of exosomal lncRNA H19 in GC. Results Serum exosomal lncRNA H19 levels were significantly upregulated in patients with GC both before and after surgery compared with healthy controls. Furthermore, serum exosomal lncRNA H19 levels were significantly decreased after compared with before surgery in patients with GC. Preoperative lncRNA H19 levels were significantly correlated with TNM stage. The area under the ROC curve (AUC) value for exosomal lncRNA H19 was 0.849, which was significantly higher than the AUC values for cancer antigens 19-9 and 72-4 and carcinoembryonic antigen, either alone or combined. Conclusions These results suggest that circulating exosomal lncRNA H19 may be a potential biomarker with diagnostic and prognostic value in GC.
Aspergillus flavus Blast2GO Gene Ontology Database: Elevated Growth Temperature Alters Amino Acid Metabolism

The availability of a representative Gene Ontology (GO) database is a prerequisite for a successful functional genomics study. Using the online Blast2GO tool we constructed a GO database of Aspergillus flavus, a plant and human pathogen. Of the predicted total 13,485 A. flavus genes 8,987 were annotated with GO terms. The mean GO level was 5.64. Using a low stringency setting of a sequence cut-off number of 10 and a node score of 20, we obtained 1,177 GO terms associated with biological process, 388 GO terms associated with molecular function and 200 GO terms associated with cellular component. Of the 8,987 annotated genes 4,232 were mapped to 129 reference pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The utility of the GO database was evaluated with published transcriptomic data by assessing physiological states in relation to the metabolic capacity of A. flavus growing at 30°C and 37°C. Results showed that growth at 30°C favored degradation of amino acids with nonpolar side chains, such as valine, leucine, isoleucine, phenylalanine and tryptophan. In contrast, growth at 37°C favored the degradation of arginine and histidine (basic), aspartate and glutamate (acidic), and serine and threonine (uncharged but polar) but biosynthesis of the aforementioned nonpolar-side-chain amino acids. KEGG pathways of amino acid degradation contributing to acetyl-CoA production, (saturated) fatty acid biosynthesis and degradation as well as biosynthesis of unsaturated fatty acids were active at 30°C, which suggests a requirement that A. flavus maintain a high content of unsaturated fatty acids at the optimal growth temperature. The proposition was supported by the finding that the GO cellular component involved at 30°C growth was mainly a fatty acid synthase complex. The constructed A. flavus GO database was proven to be useful in our functional genomics study. We also outlined the procedures for future update and refinement of the current A. flavus GO database, which can be achieved by concerted efforts of the Aspergillus research community.
Factors associated with time to defecate and outcomes in critically ill patients: a prospective, multicentre, observational study

Delayed defecation is common in patients on intensive care. We aimed to determine factors associated with time to defecation after admission to intensive care and in turn its association with length of stay and mortality. We studied 396 adults admitted to one of five intensive care units in whom at least 2 days’ invasive ventilation was anticipated during an expected stay of at least 3 days. The median (IQR [range]) time to defecate by the 336 out of 396 (84%) patients who did so before intensive care discharge was 6 (4‐8 [1–18]) days. Defecation was independently associated with five factors, hazard ratio (95%CI), higher values indicating more rapid defecation: alcoholism, 1.32 (1.05–1.66), p = 0.02; laxatives before admission, 2.35 (1.79–3.07), p < 0.001; non‐invasive ventilation, 0.54 (0.36–0.82), p = 0.004; duration of ventilation, 0.78 (0.74–0.82), p < 0.001; laxatives after admission, 1.67 (1.23–2.26), p < 0.001; and enteral nutrition within 48 h of admission, 1.43 (1.07–1.90), p = 0.01. Delayed defecation was associated with prolonged intensive care stay but not mortality.
Culture of fertilized cattle eggs

SUMMARY Culture studies were conducted with eggs recovered from cattle following super-ovulation treatment. Transfer of eggs to pseudo-pregnant rabbits led to continued cleavage in 71 of 138 attempts. Culture of eggs in vitro met with limited success in 58 of 189 attempts. The maximum cleavage stage reached in the in vivo studies was 64 cells; in the in vitro work it was 24 cells.
The Role of Camel's Milk against Some Oxidant-Antioxidant Markers of Male Rats Treated With CCl4

Carbon tetrachloride (CCl4) is a highly toxic chemical agent. Therefore, the present study was carried out to investigate the protective effects of camel's milk against CCL4 induced oxidative stress in male white albino rats. White albino male rats (150-200 g) were divided into four groups of 6 rats: a control group fed only with diet and tap water for two weeks, the second group fed with standard diet and camel milk, the third group intoxicated with CCl4 on first two days of the experimental 14 days and fed with tap water and diet, and the fourth group intoxicated with CCl4 on first two days of the experimental 14 days and then treated with camel milk . Intrapretoneal injection of male rats with CCl4 induced lipid peroxidation in the liver, which was indicated by a significant increase in lipid peroxidation biomarkers (TBARS). Also the data showed that the treated of male rats with CCl4 caused a significant increases in the serum levels of iron and ceruloplasmin, while the levels of transferrin and albumin were decreased significantly in male rats treated with CCl4. In all rats treated with camel’s milk after given CCl4, oxidant-antioxidant markers were altered compared with male rats treated with CCl4 only.
Association Between Blue Whale (Balaenoptera musculus) Mortality and Ship Strikes Along the California Coast

Blue whales (Balaenoptera musculus) are distributed worldwide, and although severely depleted by commercial whaling, their abundance off the California coast now appears to be increasing. Little is known about natural causes of mortality of blue whales, but human-related mortality continues despite legal protection. Ship strikes are a significant mortality factor for other species of baleen whale, and changes in shipping traffic have been advocated to minimize further deaths. Between 1988 and 2007, 21 blue whale deaths were reported along the California coast, typically one or two cases annually. Three pulses in strandings were observed, with three carcasses observed in fall 1988, three in 2002, and four in fall 2007. Two of the four animals in 2007 were first observed dead in the Santa Barbara Channel and had wounds typical of a ship strike. Blue whale strandings were spatially associated with locations of shipping lanes, especially those associated with the Ports of Los Angeles and Long Beach, and were most common in the fall months.