Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of pH and Antibiotics on Microbial Overgrowth in the Stomachs and Duodena of Patients Undergoing Percutaneous Endoscopic Gastrostomy Feeding

ABSTRACT Enteral nutrition via a percutaneous endoscopic gastrostomy (PEG) tube is often part of management in patients with dysphagia due to neurological or oropharyngeal disease. Gastrostomy placement can affect normal innate defense mechanisms in the upper gut, resulting in bacterial overgrowth. In this study microbiological investigations were done with gastric and duodenal aspirates from 20 patients undergoing PEG tube placement and PEG tubes from 10 patients undergoing tube replacement. Aspirate and PEG tube microbiotas were assessed by using viable counts and selective solid media followed by aerobic and anaerobic incubation to assess cell viabilities. The antibiotic susceptibility profiles of the isolates were determined by the disk diffusion method, and gas chromatography was used to study the bacterial metabolic products in the aspirates. The aspirates and PEG tubes contained mainly streptococci, staphylococci, lactobacilli, yeasts, and enterobacteria. Enterococci were detected only in PEG tube biofilms and not in aspirates. Gastric pH affected the composition of the aspirate microbiotas but not the total microbial counts. Staphylococci, Escherichia coli, and Candida spp. were isolated only from antibiotic-treated patients, despite the sensitivities of the bacteria to the agents used. Antibiotic treatment had no effect on the incidence of infection or the length of hospital stay in these patients.
Compressed Sensing Maximum Likelihood Channel Estimation for Ultra-Wideband Impulse Radio

One of the most attractive features of ultra-wideband impulse radio is the collection of rich multipath with the transmission of ultra-short pulses. Exploiting the rich multi-path diversity with channel estimating Rake receivers enables significant energy capture, higher performance and flexibility than suboptimal receivers. Although data-aided (DA) maximum likelihood (ML) channel estimator shows a promising performance, its implementation is restricted by the Nyquist sampling criterion. The emerging theory of compressed sensing (CS) describes a novel framework to jointly compress and detect a sparse signal with fewer samples than the traditional Nyquist criterion. In this paper, we propose a CS-ML channel estimator which combines the compression framework of CS for sampling rate reduction while retaining the noise statistics formulation of ML to achieve a reliable performance. Simulation assessment indicates that, with far fewer measurements, the performance of our proposed scheme supersedes that of the l1-norm minimization estimator of CS and can be as close as the ML, but with a reduction in complexity.
CD36 Mediates the In Vitro Inhibitory Effects of Thrombospondin-1 on Endothelial Cells

Thrombospondin-1 (TSP-1) is a naturally occurring inhibitor of angiogenesis that is able to make normal endothelial cells unresponsive to a wide variety of inducers. Here we use both native TSP-1 and small antiangiogenic peptides derived from it to show that this inhibition is mediated by CD36, a transmembrane glycoprotein found on microvascular endothelial cells. Both IgG antibodies against CD36 and glutathione-S-transferase–CD36 fusion proteins that contain the TSP-1 binding site blocked the ability of intact TSP-1 and its active peptides to inhibit the migration of cultured microvascular endothelial cells. In addition, antiangiogenic TSP-1 peptides inhibited the binding of native TSP-1 to solid phase CD36 and its fusion proteins, as well as to CD36-expressing cells. Additional molecules known to bind CD36, including the IgM anti-CD36 antibody SM∅, oxidized (but not unoxidized) low density lipoprotein, and human collagen 1, mimicked TSP-1 by inhibiting the migration of human microvascular endothelial cells. Transfection of CD36-deficient human umbilical vein endothelial cells with a CD36 expression plasmid caused them to become sensitive to TSP-1 inhibition of their migration and tube formation. This work demonstrates that endothelial CD36, previously thought to be involved only in adhesion and scavenging activities, may be essential for the inhibition of angiogenesis by thrombospondin-1.
Harmine Hydrochloride Triggers G2 Phase Arrest and Apoptosis in MGC‐803 Cells and SMMC‐7721 Cells by Upregulating p21, Activating Caspase‐8/Bid, and Downregulating ERK/Bad Pathway

This study aimed to investigate the effects of harmine hydrochloride (HMH) on digestive tumor cells in vitro and its molecular mechanism. MTT assays showed that HMH inhibited the proliferation of some human cancer cell lines and had no obvious inhibitory effects on human LO2 cells. Flow cytometry assays showed that HMH trigged G2 phase arrest in MGC‐803 cells and SMMC‐7721 cells, while the expression of cyclin A, cyclin B, p21, Myt1, and p‐cdc2 (Tyr15) was upregulated. Flow cytometry assays also showed that the percentages of apoptotic cells were increased, the mitochondrial transmembrane potential (ΔΨm) decreased, and the cleavage of caspase‐9, caspase‐3, and poly (Adenosine diphosphate ribose) polymerase (PARP) were observed, the expression of Bad increased, phospho‐Bad (S112) decreased, pro‐caspase‐8 was cleaved, and Bid (22 kDa) was cleaved. The expression of p‐ERK decreased in both cells. In conclusion, these results demonstrated that HMH upregulates the expression of p21, activates Myt1 and inhibits cdc2 by phospho‐cdc2 (Y15), and triggers G2 phase arrest in both MGC‐803 cells and SMMC‐7721 cells. It can also activate the mitochondria‐related cell apoptosis pathway through the caspase‐8/Bid pathway, inhibiting the ERK/Bad pathway and promoting apoptosis in both of these two cell types. Copyright © 2015 John Wiley & Sons, Ltd.
Inflammation as a Risk of Developing Chronic Kidney Disease in Rheumatoid Arthritis

Objective The relationship between chronic inflammation and the incidence of chronic kidney disease (CKD) remained not-clear in patients with rheumatoid arthritis (RA). This study aims to examine the relationship between persistently high C-reactive protein (CRP), a marker of inflammation, and the incidence of CKD in RA. Methods We retrospectively examined the relationship between the levels of CRP and incidence of CKD in 345 RA patients. The outcome of interest was incidence of CKD, defined as an estimated glomerular filtration rate (eGFR) <60 mL/min/1.73 m2 and/or positive dipstick testing for proteinuria for ≥3 months. We defined high CRP, as >3.0 mg/L. On the basis of three measurements of CRP for 6-months period, patients were divided into three groups: group 1, including patients with no high CRP values; group 2, patients with transient high CRP values (once or twice) and group 3, patients with persistently high CRP values. Results During a median follow-up period of 89 months, 14% of all patients developed CKD. The cumulative incidence of CKD was 7% in group 1, 14% in group 2 and 22% in group 3 (P = 0.008, log-rank test). In a multivariate analysis, including classical risk factors for CKD, persistently high CRP was an independent predictor of the incidence of CKD (hazard ratio, 3.00; 95% confidence interval, 1.23–8.53; P = 0.01). Conclusions Persistently high CRP was a significant risk factor for the incidence of CKD. Results suggest that persistent inflammation is a marker for the high risk of CKD in RA.
Motor enrichment sustains hindlimb movement recovered after spinal cord injury and glial transplantation.

PURPOSE This study investigated whether enrichment improves hindlimb movement following complete spinal cord transection and transplantation of olfactory ensheathing glia (OEG), with or without a Schwann cell (SC) bridge. METHODS Motor activity was encouraged through provision of motor enrichment housing (MEH); a multi-level cage containing ramps, textured surfaces and rewards. Hindlimb joint movement was assessed weekly for 22 weeks starting one week post-surgery, comparing rats housed in MEH to those in basic housing (BH). Transganglionic tracer was injected into the crushed right sciatic nerve three days prior to sacrifice, allowing sensory axons in the dorsal columns to be visualized by immunolabeling. Serotonergic axons and glial cells expressing low affinity nerve growth factor receptor were identified by immunolabeling. RESULTS All rats, having received transplants, recovered some hindlimb movement. Rats housed in BH progressively lost recovered hindlimb function whereas recovered hindlimb movements were sustained in most rats in MEH. In rats transplanted with SCs and OEG, effects of MEH were first significant 14 weeks after injury. In rats transplanted with OEG, a trend was seen from 14 weeks after injury, but this did not reach significance. In all rats, traced sensory axons died back from sites of transplantation and did not regenerate rostrally. Further, in no rat were serotonergic axons observed regenerating into, around or beyond transplants. CONCLUSIONS Transection and transplantation of SC/OEG or OEG induced recovery of hindlimb function. This recovered hindlimb movement was sustained in rats housed in MEH but was progressively lost in rats housed in BH. Because benefits of MEH were not observed until 14 weeks after injury, long-term assessment of behavior is recommended. BH conditions are not conducive to maintenance of recovered hindlimb function, and MEH should be used in studies of recovery of function following spinal cord injury.
The Bacteriological Quality, Safety, and Antibiogram of Salmonella Isolates from Fresh Meat in Retail Shops of Bahir Dar City, Ethiopia

The habit of raw meat consumption in addition to the poor hygienic standards and lack of knowledge contribute to food-borne diseases outbreaks. The objective of this research was to assess the bacterial quality and safety of fresh meat from retail Bahir Dar City, Ethiopia. A total of 30 fresh meat samples were collected from butcher shops. Standard bacteriological methods were used to isolate and enumerate bacteria. Kirby-Bauer disk diffusion method was used for antimicrobial susceptibility testing of Salmonella isolates. The mean counts of AMB, TC, and S. aureus were log104.53, 3.97, and 3.88 log10cfu/g, respectively. Salmonella was isolated from 21 (70%) of the samples. Salmonella isolates in this study were highly susceptible to ciprofloxacin, gentamycin, and norfloxacin while they were resistant to erythromycin and tetracycline. High rate of multiple drug resistance was also noticed in Salmonella isolates. The microbial loads of meat were above the recommended microbial safety limits. Besides this, the isolation rate of Salmonella was high and high levels of drug resistance were documented for Salmonella isolates. Measures on handling and appropriate personal hygiene practices of workers in the retail shops are recommended to reduce the change of forborne disease outbreaks.
Swedish Spring Wheat Varieties with the Rare High Grain Protein Allele of NAM-B1 Differ in Leaf Senescence and Grain Mineral Content

Some Swedish spring wheat varieties have recently been shown to carry a rare wildtype (wt) allele of the gene NAM-B1, known to affect leaf senescence and nutrient retranslocation to the grain. The wt allele is believed to increase grain protein concentration and has attracted interest from breeders since it could contribute to higher grain quality and more nitrogen-efficient varieties. This study investigated whether Swedish varieties with the wt allele differ from varieties with one of the more common, non-functional alleles in order to examine the effect of the gene in a wide genetic background, and possibly explain why the allele has been retained in Swedish varieties. Forty varieties of spring wheat differing in NAM-B1 allele type were cultivated under controlled conditions. Senescence was monitored and grains were harvested and analyzed for mineral nutrient concentration. Varieties with the wt allele reached anthesis earlier and completed senescence faster than varieties with the non-functional allele. The wt varieties also had more ears, lighter grains and higher yields of P and K. Contrary to previous information on effects of the wt allele, our wt varieties did not have increased grain N concentration or grain N yield. In addition, temporal studies showed that straw length has decreased but grain N yield has remained unaffected over a century of Swedish spring wheat breeding. The faster development of wt varieties supports the hypothesis of NAM-B1 being preserved in Fennoscandia, with its short growing season, because of accelerated development conferred by the NAM-B1 wt allele. Although the possible effects of other gene actions were impossible to distinguish, the genetic resource of Fennoscandian spring wheats with the wt NAM-B1 allele is interesting to investigate further for breeding purposes.
A Dish-based Semi-quantitative Food Frequency Questionnaire for Assessment of Dietary Intakes in Epidemiologic Studies in Iran: Design and Development

Background: Earlier forms of food frequency questionnaire (FFQ) used in Iran have extensive lists of foods, traditional categories and food-based design, mostly with the interviewer-administered approach. The aim of the current paper is to describe the development of a dish-based, machine-readable, semi-quantitative food frequency questionnaire (DFQ). Methods: Within the framework of the Study on the Epidemiology of Psychological, Alimentary Health and Nutrition project, we created a novel FFQ using Harvard FFQ as a model. Results: The following steps were taken to develop the questionnaire: Construction of a list of commonly consumed Iranian foods, definition of portion sizes, design of response options for consumption frequency of each food item and finally a pilot test of the preliminary DFQ. From a comprehensive list of foods and mixed dishes, we included those that were nutrient-rich, consumed reasonably often or contributed to between-person variations. We focused on mixed dishes, rather than their ingredients, along with foods. To shorten the list, the related food items or mixed dishes were categorized together in one food group. These exclusions resulted in a list of 106 foods or dishes in the questionnaire. The portion sizes used in the FFQ were obtained from our earlier studies that used dietary recalls and food records. The frequency response options for the food list varied from 6-9 choices from “never or less than once a month” to “12 or more times per day”. Conclusions: The DFQ could be a reasonable dietary assessment tool for future epidemiological studies in the country. Validation studies are required to assess the validity and reliability of this newly developed questionnaire.
Chemokine stimulation of monocyte matrix metalloproteinase‐9 requires endogenous TNF‐α 

Leukocyte extravasation into tissues is a multi‐step process culminating in the migration of cells through the basement membrane. This requires the production of matrix‐degrading enzymes, in particular matrix metalloproteinases (MMP). We investigated the role of chemokines in regulating MMP production in the monocytic cell line THP‐1 and in peripheral blood monocytes (PBM). The CC chemokines CCL2 (MCP‐1), CCL3 (MIP‐1α), and CCL5 (RANTES) stimulated the release of monocyte MMP‐9 protein in a bell‐shaped dose‐dependent manner. The increase in MMP‐9 protein detected at 24 h was due to de novo synthesis, confirmed by Northern blotting, with MMP‐9 mRNA detectable at 6–8 h. Autocrine TNF‐α was necessary for chemokine stimulation of MMP‐9. Chemokines increased TNF‐α mRNA levels and protein release in monocytes and THP‐1 cells, and neutralizing anti‐TNF‐α antibodies inhibited CCL2‐induced MMP‐9 release. Furthermore, the broad spectrum MMP inhibitor BB 2516, which inhibits TNF‐α release, abrogated CCL2‐ and CCL5‐induced MMP‐9 release in both THP‐1 cells and freshly isolated monocytes. Monocyte production of MMP is of major importance in the pathology of cancer, asthma, and rheumatoid arthritis. An understanding of the mechanisms by which these MMP are produced may lead to novel therapies to modulate extravasation of leukocytes in disease.
Pregnancy and multiple sclerosis

At any one time, there are around 20 000 women of childbearing age with multiple sclerosis (MS) in the UK who may be considering having children. Neurologists can be asked for information from both patients and obstetric colleagues on a range of topics related to pregnancy and MS that extend beyond the well-known implications for relapse risk. This article aims to provide a brief overview for the general neurologist of the most commonly encountered issues and questions including those occasionally related to pregnancy management. The take-home message is that pregnancy does not hold adverse risks for the majority of patients with MS, or vice versa.
Evaluation of Antibiogram, Genotype and Phylogenetic Analysis of Biofield Treated Nocardia otitidis

Nocardiosis is a soil-borne aerobic infection caused by Nocardia species commonly affects the respiratory tract. Nocardia otitidis (N. otitidis) is the key organism for non-mycobacterial tuberculosis. The current study was attempted to investigate the effect of Mr. Trivedi’s biofield energy treatment on N. otitidis and analyzed for antimicrobial susceptibility pattern, minimum inhibitory concentration (MIC), DNA polymorphism by Random Amplified Polymorphic DNA (RAPD) and 16S rDNA sequencing. The strain of N. otitidis (ATCC 14630) was divided into two parts, control and treated. Antimicrobial susceptibility was studied using the broth microdilution technique. Overall, the MIC values of 16.67% antimicrobials were changed in the treated group of N. otitidis as compared to the control. Moreover, MIC value of trimethoprim/sulfamethoxazole was reduced by two-fold (0.5/9.5 to 0.25/4.75 μg/mL) in the biofield energy treated sample as compared to the control without alteration in the sensitivity spectrum. The 16S rDNA analysis showed that the treated sample was detected as Enterobacter aerogenes strain NCTC10006T (GenBank Accession No: AJ251468) with 98% identity of gene sequencing data. However, the nearest homolog genus-species was found as Kluyvera cryocrescens (GenBank Accession No: AM184245). Using RAPD biomarkers, the sample showed an average range of 34 to 53% of polymorphism among treated samples as compared to the control. The 16S rDNA sequencing of treated sample was carried out to correlate the phylogenetic relationship of N. otitidis with other bacterial species. These results suggested that Mr. Trivedi’s biofield energy treatment has a significant impact on N. otitidis.
Functional significance of M-type potassium channels in nociceptive cutaneous sensory endings

M-channels carry slowly activating potassium currents that regulate excitability in a variety of central and peripheral neurons. Functional M-channels and their Kv7 channel correlates are expressed throughout the somatosensory nervous system where they may play an important role in controlling sensory nerve activity. Here we show that Kv7.2 immunoreactivity is expressed in the peripheral terminals of nociceptive primary afferents. Electrophysiological recordings from single afferents in vitro showed that block of M-channels by 3 μM XE991 sensitized Aδ- but not C-fibers to noxious heat stimulation and induced spontaneous, ongoing activity at 32°C in many Aδ-fibers. These observations were extended in vivo: intraplantar injection of XE991 selectively enhanced the response of deep dorsal horn (DH) neurons to peripheral mid-range mechanical and higher range thermal stimuli, consistent with a selective effect on Aδ-fiber peripheral terminals. These results demonstrate an important physiological role of M-channels in controlling nociceptive Aδ-fiber responses and provide a rationale for the nocifensive behaviors that arise following intraplantar injection of the M-channel blocker XE991.
Validation of EuroSCORE II in a modern cohort of patients undergoing cardiac surgery.

OBJECTIVE We aimed to validate the new EuroSCORE II risk model in a contemporary cardiac surgery practice in the United Kingdom (UK). METHODS The original logistic EuroSCORE was compared to EuroSCORE II with regard to accuracy of predicting in-hospital mortality. Analysis was performed on isolated coronary artery bypass grafts (CABG; n = 2913), aortic valve replacement (AVR; n = 814), mitral valve surgery (MVR; n = 340), combined AVR and CABG (n = 517), aortic (n = 350) and miscellaneous procedures (n = 642), and the above cases combined (n = 5576). RESULTS In a single-institution experience, EuroSCORE II is a reasonable risk model for in-hospital mortality from isolated CABG (C-statistic 0.79, Hosmer-Lemeshow P = 0.052) and aortic procedures (C-statistic 0.81, Hosmer-Lemeshow P = 0.43), and excellent for mitral valve surgery (C-statistic 0.87, Hosmer-Lemeshow P = 0.6). EuroSCORE II is better than the original EuroSCORE, using contemporaneous data for combined AVR and CABG operations (C-statistic 0.74, Hosmer-Lemeshow P = 0.38). However, EuroSCORE II failed to improve on the original EuroSCORE model for isolated AVR (C-statistic 0.69, Hosmer-Lemeshow P = 0.07) and miscellaneous procedures (C-statistic 0.70, Hosmer-Lemeshow P = 0.99). EuroSCORE II has better calibration than the original EuroSCORE or the Society of Cardiothoracic Surgeons of Great Britain and Ireland (SCTS) modified EuroSCORE for cumulative sum survival (CUSUM) curves. CONCLUSIONS EuroSCORE II improves on the original logistic EuroSCORE, though mainly for combined AVR and CABG cases. Concerns still exist, however, over its use for isolated AVR procedures, aortic surgery and miscellaneous procedures. There is still room for improvement in risk modelling.
A Passive Available Bandwidth Estimation Methodology 1

The Available Bandwidth (AB) of an end-to-end path is its remaining capacity and it is an important metric for several applications such as overlay routing and P2P networking. That is why many AB estimation tools have been published recently. Most of these tools use the Probe Rate Model, which requires sending packet trains at a rate matching the AB. Its main issue is that it congests the path under measurement. We present a different approach: a novel passive methodology to estimate the AB that does not introduce probe traffic. Our methodology, intended to be applied between two separate nodes, estimates the path’s AB by analyzing specific parameters of the traffic exchanged. The main challenge is that we cannot rely on any given rate of this traffic. Therefore we rely on a different model, the Utilization Model. In this paper we present our passive methodology and a tool (PKBest) based on it. We evaluate its applicability and accuracy using public NLANR data traces. Our results -more than 300Gbshow that our tool is more accurate than pathChirp, a state-of-the-art active PRM-based tool. At the best of the authors’ knowledge this is the first passive AB estimation methodology.
Peptide hydrolases of Lactobacillus casei: isolation and general properties of various peptidase activities

Summary Discovery of an endopeptidase by gel chromatography and separation of 3 exopeptidases (a dipeptidase, an aminopeptidase and a specific carboxypeptidase) from Lactobacillus casei NCDO 151 by affinity chromatography is described. The 3 exopeptidases were strongly inhibited by the metal chelators EDTA and 1,10-phenanthroline but were reactivated with Co2+ and Mn2+. The pH optima for aminopeptidase, dipeptidase and carboxypeptidase activities were 6·5, 7·6 and 7·2, respectively. Maximum activity was obtained at 45 °C for the aminopeptidase, at 30 °C for the dipeptidase and at 40 °C for the carboxypeptidase. The substrate specificities of the 3 enzymes were also studied. The properties of these 3 enzymes are compared with those of other bacteria.