Miracle-dz/UniFAR-FTUs huggingface dataset:
Host preferences of arbuscular mycorrhizae along the soil nutrient and hydrological gradient

78 Arbuscular mycorrhizal fungi (AMF) (Phylum Glomeromycota) [1] form mutualistic symbiotic associations with the roots of rough ly 80% of all terrestrial plant species [2] ac ting as an extension of the plant root system to support plant development under nutrient limiting and stress conditions. AMF alleviate water stress via the direct uptake and transfer of water and nutrients through the fungal hyphae to the host plants resulting in a signi ficant increase in plant height, stem diameter, and fresh weight of the plant, which in turn provides carbohydrates to the fungus. Plant growth is greatly affected by environmental stresses such as drought, nutrient limitation and salt loading; nutrient exchange by AMF may be critically important when soil fertility and water availability are low. A number of studies reported benefits of AMF associations to plants under environmental stress [3–6]. Several studies show that the presence of AMF alters plant communities by affecting the rela tive abundance of plant species and plant species diversity [7–9]. The plants and soil in turn also influence the species composition of the AMF community. Eom et al. [10] suggest that AMF do not show host specificity and are randomly distributed in natural ecosystems. However, others suggest some preference may exist between host plant and AMF since the effect of symbiosis on individual plants can differ by AMF species and small scale varia tion in soil factors such as pH, nutrient con centration, moisture, temperature or organic matters may influence AMF communities [11–15]. In this study we use PCR with Glome romycota specific primers and denaturing gradient gel electrophoresis (DGGE) to inves tigate the effect of local environmental varia tion (a hydrological and soil nutrient gradient along a hillslope) as well as the effect of plant host on natural AMF populations colonizing two widespread, native eastern Texas USA plants. Previously we sequenced the PCR products from root samples from these two plants and confirmed glomalean origin of the amplicons [16].
Molecular characterization of iron-oxidizing Leptospirillum strains from around the world

More than sixteen isolates of iron-oxidizing bacteria belonging to the genus Leptospirillum were included in this study, with the finding that they were clearly divisible into two major groups. Group I leptospirilla had mol% G+C ratios within the range 49-52%, three copies of rrn genes and based on 16S rRNA sequence data, clustered together with the Leptospirillum ferrooxidans type strain (DSM2705or LI5). Group II leptospirilla had mol% G+C ratios of 55-58%, two copies of rrn genes and based on 16S rRNA sequence form a separate cluster. Genome DNA-DNA hybridization experiments indicated that three similarity subgroups were present amongst the leptospirilla tested with two DNA-DNA hybridization similarity subgroups being found within group I. The two groups could also be distinguished based on the sizesof their 16S-23SrRNA gene spacer regions. We propose that the group II leptospirilla should be recognized as a new species with the name Leptospirillum ferriphilum sp. nov. Members of the two species can be rapidly distinguished from each other by amplification of their 16S rRNA genes and carrying out restriction enzyme digests of the products. Several but not all isolates of the group II leptospirilla, but none from group I (L. ferrooxidans) were capable of growth at 45°C. Plasmid DNA was isolated from strain ATCC49879 (L. ferrooxidans). Restriction endonuclease mapping of what appeared to be about 60 kb of plasmid DNA, established that two plasmids of approximately 30.0 kb and 27.0 kb were present. These were named p49879.1 and p49879.2 respectively. Attempts to isolate the plasmids separately were not successful. Partial sequencing of the two plasmids was carried out and sequence analysis of p49879.1 and p49879.2 indicated that the plasmids shared regions of homology. Total plasmid DNA was DIG-labelled and used as a probe in Southern hybridization experiments with genomic DNA from all sixteen original leptospirilla isolates as the target DNA. All leptospirilla belonging to Group I gave a positive signal, little or no homology to Group II leptospirilla was obtained. The region of homology present in all L. ferrooxidans strains was localized to an area on plasmid p49879.2 showing high amino acid identity to a Stellenbosch University http://scholar.sun.ac.za
Draft Genomes of Gammaproteobacterial Methanotrophs Isolated from Terrestrial Ecosystems

ABSTRACT Genome sequences of Methylobacter luteus, Methylobacter whittenburyi, Methylosarcina fibrata, Methylomicrobium agile, and Methylovulum miyakonense were generated. The strains represent aerobic methanotrophs typically isolated from various terrestrial ecosystems.
Mechanisms Of MicroRNA evolution, regulation and function: computational insight, biological evaluation and practical application

Transposable Elements (TEs) account for nearly one-half of the sequence content in the human genome. De novo germline transposition into regulatory or coding sequences of protein-coding genes causes several heritable disorders. However, TEs are prevalent in and around protein-coding genes, sparking inquiry into possible regulatory function. Computational studies revealed miRNA genes and miRNA Recognition Elements (MREs) residing within TE sequences, but little evidence exists to support a role for these sequences. In this work, I functionally validate miRNAs and MREs derived from the most prevalent TE families, including evolutionarily ancient LINE2 and MIR retrotransposons as well as primate-specific Alu elements. Introduction Transposable Elements (TEs or transposons) mobilize and reintegrate within a host organism’s genome and different TE classes have diverse structural features, transposition mechanisms and evolutionary origins. Some elements mobilize via "copy and paste" mechanisms and others through "cut and paste. ” Retrotransposons (Type I) replicate by transcribing an RNA copy that subsequently reintegrates into the host genome and serves as a template for RNA-dependent DNA polymerase (a.k.a. reverse transcriptase) activity. Analogous mechanisms are essential in the life cycle of infectious retroviruses like Human Immunodeficiency Virus (HIV) and Human T-Cell Leukemia Virus (HTLV). Non-infectious Endogenous Retroviruses (ERVs) are predominant members of the Long Terminal Repeat (LTR)-containing subclass of retrotransposons. Non-LTR-containing retrotransposons, including Long and Short Interspersed Nuclear Elements (LINEs and SINEs, respectively), are the most abundant TE class in the human
Physiological Responses of the Fathead Minnow ( Pimephales promelas ) to Anthropogenic Sources of Endocrine Disruptors

Title of Dissertation: PHYSIOLOGICAL RESPONSES OF THE FATHEAD MINNOW (PIMEPHALES PROMELAS) TO ANTHROPOGENIC SOURCES OF ENDOCRINE DISRUPTORS Sara Jane Pollack, Doctor of Philosophy, 2008 Dissertation Directed By: Dr. William O. Lamp Department of Entomology Anthropogenic sources of endocrine disrupting compounds (EDCs) are prevalent in aquatic ecosystems. As a result, these compounds target the most vulnerable physiological mechanisms of reproductive development in fish. The main focus of this study was to assess the impact of two sources of EDCs; a single potent EDC, 17αethinylestradiol (EE2), as well as an agricultural source of an EDC mixture, poultry litter leachate, on the reproductive processes of the fathead minnow, Pimephales promelas. The experimental paradigms included a 21-day laboratory reproductive assay, a larval exposure including a depuration step until 8 months of age to determine the response in the adult animal, and a whole-organism, partial life-cycle assessment of reproductively active adult fish and development of their offspring.
Chemical signals inducing attraction and alarm in European Reticulitermes termites (Isoptera, Rhinotermitidae)

Chemical signals causing attraction and alarm in four European subterranean termite species of the genus Reticulitermes (R. santonensis, R. lucifugus, R. grassei, R. banyulensis) were investigated. Natural extracts and isolated compounds from workers and soldiers were offered as odor source in a petri dish to groups of termites, and their behavioral reaction was registered. Pentane extracts of whole workers were attractive, and in three of the species induced a slight alarm reaction. The extracts contained 3-octanone, 3-octanol, and six fatty acids (C14-C18), presumably originating from the cuticle. Species-specific differences were quantitative. When tested individually or as synthetic mixture the worker compounds were significantly less effective than the natural extract. Only the ketone, the alcohol, and one of the fatty acids had any effect, functioning predominantly as attractants. Reticulitermes soldiers possess a frontal gland, which is employed for chemical defense of the colony, and contains species-specific mixtures of terpenes: monoterpenes, sesquiterpenes, diterpene alcohols, and a sesterterpene. All compounds of the frontal gland secretions proved to be highly attractive to the respective species, acting significantly stronger than worker compounds. The minor volatile compounds, the mono- and sesquiterpenes, function as alarm pheromone in Reticulitermes: they were the most attractive components, and also the ones inducing an intense alarm reaction in both workers and soldiers.
Hypertension and risk of cholangiocarcinoma: a systematic review and meta-analysis

Background: Hypertension has been demonstrated to enhance the risk of cholangiocarcinoma (CCC) by several researches, which, however, still remains controversial. To this end, a systematic review and meta-analysis was performed to further investigate the association between hypertension and CCC risk. Methods: We searched PubMed, EMBASE, ISI Web of Science to collect relevant researches published before November 2017. Afterwards, random effects model proposed by DerSimonian and Laird was employed to determine the correlation between hypertension and CCC risk. Results: Nine articles, comprising 2,016 patients with CCC and 199,812 healthy controls, were finally enrolled in our study. Our findings failed to support the correlation between hypertension and elevated risk of CCC among these heterogeneous studies [summary odds ratio (OR), 0.87; 95% confidence interval (CI), 0.57–1.17; I 2 =79.5%]. In subgroup analysis following separation of intrahepatic cholangiocarcinoma (ICC) and extrahepatic cholangiocarcinoma (ECC), hypertension also failed to harbor a correlation with elevated risk of ECC (OR, 0.74; 95% CI, 0.42–1.37) and ICC (OR, 1.07; 95% CI, 0.43–1.71). Conclusions: Hypertension did not harbor any correlation with elevated risk of CCC.
Modification of age-related changes in cardiovascular structure and function using exercise training

Increasing age is associated with substantial changes in cardiovascular structure and function, the cause and permanence ofwhich are unknown. Diastolic function in particular alters appreciably in older adults but non-invasive measurement of cardiac function during diastole has significant limitations. Magnetic resonance imaging with tagging was used to identify changes in three dimensional myocardial strain in older compared to young normal volunteers. This technique identified significantly delayed myocardial relaxation with more myocardial strain persisting in early diastole in older compared to younger individuals. These findings were thought to be attributable to the aging process. Epidemiological studies and small, non-randomised trials suggest that physical activity might slow cardiovascular aging and improve diastolic function in older adults. A randomised controlled trial was therefore performed to assess whether exercise training could modify age-related changes in older, normal volunteers who had been screened to exclude significant cardiovascular disease. The intervention group underwent six months of supervised exercise training whilst participants in the control group were asked to maintain their pre-trial levels of activity. Measurements made at baseline and after six months included transthoracic echocardiography, cardiac MRI, body composition, blood lipid concentrations, applanation tonometry, quality of life and maximal exercise capacity. Despite significant increases in exercise capacity in the intervention group, no other significant changes in cardiovascular structure or function, body composition, cholesterol concentration or quality of life were observed when compared to changes seen in the control group. Six months of exercise training in previously sedentary older adults are insufficient to modify cardiovascular function and structure despite causing marked improvements in exercise capacity. These findings contrast with previously reported non-randomised trials of exercise training in older people. However, they add important, robust information regarding the likely effects of short periods of exercise training on cardiovascular function and structure in older normal adults.
High-Output Cardiac Failure

High-output cardiac failure is a less common form of heart failure, and although it may sound contradictory at first, in the simplest form, it is still the heart's inability to provide sufficient blood for the body’s demand. Most patients with heart failure are either classified as a systolic or diastolic dysfunction with increased systemic vascular resistance, however, patients with high output cardiac failure have normal cardiac function and decreased systemic vascular resistance, either secondary to diffuse arteriolar dilation or possible bypass of the arterioles and capillary beds, leading to activation of neurohormones. The problem lies with an increase in the body’s demand for perfusion that the heart is not able to provide, even with a normal cardiac function. In terms of cardiac output, a high cardiac output state is defined as a resting cardiac output greater than 8 L/min or a cardiac index of greater than 4.0/min/m2 , and heart failure occurs when that cardiac output is insufficient to supply the demand. High-output cardiac failure is more of a consequence of an underlying disease process. The underlying etiology of this type of cardiac failure largely dictates the presenting symptoms and signs, evaluation, and treatment.
Translation

well worth reproducing in English. Edts. , I. M. Gazette. ] On the loss of the epithelium of the intestinal canal, consequent on the excessive secretion of fluid from its surface. We are all well acquainted with the fact, that in certain diseases the outer layers of the epithelial cells protecting the skin are thrown off in flakes ; and I believe that it is the same in Asiatic cholera as regards epithelial cells lining the surface of the jntestinal mucous membrane? a matter of greater pathological significance than that concerning the skin, because the intestinal epithelium is intended to guard more delicate and important structures than the cells that cover the cutis. The symptoms of cholera, however, are very much dependent on this desquamation of the epithelia? a fact which may be demonstrated by the aid of the microscope; but we are not to suppose that all parts of the intestinal canal are equally affected in cholera. The epithelium of the stomach suffers less than that of the intestines, and the upper part of the small intestines is not so deeply involved in the disease as the lower part of the ileum. In the duodenum, where the peristaltic action of the canal is not very strong, you often find the epithelial cells lining the mucous membrane ; the cells are loosened, but riot detached, because this part of the canal has less mechanical work to do than the lower portion of the gut. The valvulae conniventes (kerkring), which are large and closely approximated in the second part of the duodenum, protect by covering in the epithelial celh that lie between them, but on the surface of these folds wo shall observe the commencement of the desquamative process which is so marked in the ileum. We shall see with the naked eye that the epithelium, which should cover the valvulae conniventes, has disappeared in places, leaving small isolated patches of the denuded mucous membrane. In their early stages, these spots are distinguishable by their whiter colour, and by a soft velvet-like texture, which may be well demonstrated if a spot of this kind is isolates1, and fixed on a plate under the object glass of the microscope, little water being allowed to trickle over it. You may also in this way examine the villi, which are clearly denuded of epithelial cells in the patches of the valvulae conniventes above referred to. In some parts wo notice that a space evidently extends through the length of the villi, and externally the villi are covered
Phase I of the Detecting and Evaluating Childhood Anxiety and Depression Effectively in Subspecialties (DECADES) Study: Development of an Integrated Mental Health Care Model for Pediatric Gastroenterology

Background Children with gastrointestinal symptoms have a very high rate of anxiety and depression. Rapid identification of comorbid anxiety and depression is essential for effective treatment of a wide variety of functional gastrointestinal disorders. Objective The objective of our study was to determine patient and parent attitudes toward depression, anxiety, and mental health screening during gastroenterology (GI) visits and to determine patient and parent preferences for communication of results and referral to mental health providers after a positive screen. Methods We augmented standard qualitative group session methods with patient-centered design methods to assess patient and parent preferences. We used a variety of specific design methods in these sessions, including card sorting, projective methods, experience mapping, and constructive methods. Results Overall, 11 families (11 patients and 14 parents) participated in 2 group sessions. Overall, patients and their parents found integrated mental health care to be acceptable in the subspecialty setting. Patients’ primary concerns were for the privacy and confidentiality of their screening results. Patients and their parents emphasized the importance of mental health services not interfering with the GI visit and collaboration between the GI physician, psychologist, and primary care provider. Conclusions Patients and their families are open to integrated mental health care in the pediatric subspecialty clinic. The next phase of the DECADES study will translate patient and parent preferences into an integrated mental health care system and test its efficacy in the pediatric GI office.
Acute transverse myelitis and intramedullary spinal cord tumors in children– clinical presentation, differential diagnosis and prognostic factors

1 Department of Pediatrics and Developmental Age Neurology, Chair of Pediatrics, School of Medicine in Katowice, Medical University of Silesia, Poland 2 Department of Pediatric Neurosurgery, School of Public Health in Bytom, Medical University of Silesia, Poland 3 Department of Pediatrics and Pediatric Endocrinology, School of Medicine in Katowice, Medical University of Silesia, Poland 4 Department of Neurosurgery1, School of Medicine in Katowice, Medical University of Silesia, Poland; Department of Neurosurgery2, School of Medicine in Katowice, Medical University of Silesia, Poland 5 Department of Drug Technology, School of Pharmacy with the Division of Laboratory Medicine in Sosnowiec, Medical University of Silesia, Poland 6 Department of Biostatistics, School of Public Health in Bytom, Medical University of Silesia, Poland
Managing a side effect: Cyclosporine-Induced nephrotoxicity

intrODuCtiOn Cyclosporine (CsA), an immunosuppressant, is a calcineurin inhibitor (CNI) which is specific for T-cells. It was discovered in Sandoz Laboratories in Basel, Switzerland by isolating it from the soil fungus Tolypocladium inflatum gams. [1] Initially used for rheumatoid and psoriatic arthritis, it was later approved for prophylaxis of organ rejection. Dermatologists often prescribe CsA in the dose of 3–5 mg/ kg/day for management of papulosquamous disorders, mainly psoriasis and autoimmune connective tissue disorders. It is also used off-label in atopic dermatitis. Nowadays, CsA is increasingly being used for the treatment of toxic epidermal necrolysis with good effects. Calne et al. used CsA following transplantation in a dose of 25 mg/kg and found unexpected nephrotoxicity that had previously not been seen in animal experiments. [2] Most of the persistent renal dysfunction is seen when the drug is used for a long duration of time and when dose of CsA is >5 mg/kg/day, especially in patients of psoriasis. This is an important side effect that needs to be recognized at early stages to avoid chronic kidney damage or irreversible nephrotoxicity.
A Pilot Study of the Acute Ingestion of No. 1 Rosemary Water: Evidence of Cognitive, Physiological and Subjective Effects in Healthy Adults

This study investigated the potential impact of the acute ingestion of No. 1 Rosemary water—a commercially available carbonated water containing an extract of Rosemary (Rosmarinus officinalis). Twenty healthy adults were randomly allocated to consume either 330 ml of No. 1 Rosemary water or plain carbonated water. They then completed a series of subjective measures and cognitive tasks including a fifteen-minute session on a stress inducing multi-tasking framework, followed by a second completion of the subjective measures. Heart rate and blood pressure were monitored throughout the procedure. Given the pilot nature of the study, analysis of the data eschewed significance testing for the calculation of Cohen’s d measure of effect sizes. These revealed a number of small enhancement effects on cognition, consistent with those found previously for the inhalation of the aroma of Rosemary essential oil, and oral administration of dried herb. Of particular interest here are the reduced subjective evaluations of stress, and the blunted physiological reactivity noted for heart rate and blood pressure, which represent novel findings in this area. Taken together the data suggest further investigation of this product is warranted with regard to its potential beneficial properties.
Going through laparoscopic liver resection in patients with colorectal liver metastases—A qualitative study

Colorectal cancer is one of the most common cancers worldwide. Surgery is seen as the only curative treatment. There are two approaches to liver resection: open or laparoscopic surgery. Knowledge from the patient perspective can illuminate how it is experienced going through laparoscopic surgery. We aimed to study patient perspectives of the experience of undergoing laparoscopic liver resection surgery in patients with colorectal liver metastases.