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https://www.readbyqxmd.com/read/28108446/chaincleaner-improves-genome-alignment-specificity-and-sensitivity
#1
Hernando G Suarez, Bjoern E Langer, Pradnya Ladde, Michael Hiller
MOTIVATION: Accurate alignments between entire genomes are crucial for comparative genomics. However, computing sensitive and accurate genome alignments is a challenging problem, complicated by genomic rearrangements. RESULTS: Here we present a fast approach, called chainCleaner, that improves the specificity in genome alignments by accurately detecting and removing local alignments that obscure the evolutionary history of genomic rearrangements. Systematic tests on alignments between the human and other vertebrate genomes show that chainCleaner (i) improves the alignment of numerous orthologous genes, (ii) exposes alignments between exons of orthologous genes that were masked before by alignments to pseudogenes, and (iii) recovers hundreds of kilobases in local alignments that otherwise would fall below a minimum score threshold...
January 19, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28108378/the-pressure-induced-deformation-response-of-the-human-lamina-cribrosa-analysis-of-regional-variations
#2
Dan E Midgett, Mary E Pease, Joan L Jefferys, Mohak Patel, Christian Franck, Harry A Quigley, Thao D Nguyen
: The objective of this study was to measure the pressure-induced deformation response of the human lamina cribrosa (LC) and analyze for variations with age and anatomical region. The posterior scleral cup of 8 eyes from 6 human donors was mounted onto a custom inflation chamber. A laser-scanning microscope was used for second harmonic generation (SHG), imaging the collagen structure in the posterior volume of the LC at pressures from 5 mmHg to 45 mmHg. The SHG volumes were analyzed by the Fast-Fourier Iterative Digital Volume Correlation (DVC) algorithm for the three dimensional (3D) displacement field...
January 17, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28107984/development-and-validation-of-a-fast-micro-extraction-by-packed-sorbent-uhplc-pda-method-for-the-simultaneous-determination-of-linezolid-and-ciprofloxacin-in-human-plasma-from-patients-with-hospital-acquired-pneumonia
#3
Vincenzo Ferrone, Maura Carlucci, Roberto Cotellese, Paolo Raimondi, Annadomenica Cichella, Lorenzo Di Marco, Giuseppe Carlucci
An ultra high-performance liquid chromatographic (UHPLC) method with PDA detection was developed and validated for the simultaneous quantification of linezolid and ciprofloxacin in human plasma and applied in hospital acquired pneumonia patients (HAP). The method uses a semi-automated microextraction by packed sorbent for sample preparation. All parameters in the extraction step (pH, sample volume, sample dilution and number of aspiration - ejection cycles) and in the desorption step (percentage of acetonitrile in the solvent of elution and number of aspirations of elution solvent through the device) were statistically significant when the recovery was used as response...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107959/use-of-quantum-dot-beads-labeled-monoclonal-antibody-to-improve-the-sensitivity-of-a-quantitative-and-simultaneous-immunochromatographic-assay-for-neuron-specific-enolase-and-carcinoembryonic-antigen
#4
Kun Xiao, Kan Wang, Weijian Qin, Yafei Hou, Wenting Lu, Hao Xu, Yan Wo, Daxiang Cui
Detection of multiplex tumor markers was of great importance for cancer diagnosis. Immunochromatographic test strip (ICTS) was the most frequently-used point-of-care detection means. Herein, a convenient and fast method for simultaneous quantitative detection of neuron specific enolase (NSE) and carcinoembryonic antigen (CEA) was developed based on ICTS using quantum dot beads (QBs) as marking material. Good monodispersity, high colloidal stability and carboxyl-modified (COOH-) QBs were used. For this method, two test lines were applied to the NC membrane for simultaneous analysis of CEA and NSE respectively...
March 1, 2017: Talanta
https://www.readbyqxmd.com/read/28107506/association-between-increased-gastric-juice-acidity-and-sliding-hiatal-hernia-development-in-humans
#5
Hiroshi Kishikawa, Kayoko Kimura, Asako Ito, Kyoko Arahata, Sakiko Takarabe, Shogo Kaida, Takanori Kanai, Soichiro Miura, Jiro Nishida
OBJECTIVES: Several clinical factors; overweight, male gender and increasing age, have been implicated as the etiology of hiatal hernia. Esophageal shortening due to acid perfusion in the lower esophagus has been suggested as the etiological mechanism. However, little is known about the correlation between gastric acidity and sliding hiatus hernia formation. This study examined whether increased gastric acid secretion is associated with an endoscopic diagnosis of hiatal hernia. METHODS: A total of 286 consecutive asymptomatic patients (64 were diagnosed as having a hiatal hernia) who underwent upper gastrointestinal endoscopy were studied...
2017: PloS One
https://www.readbyqxmd.com/read/28106818/potential-benefits-and-harms-of-intermittent-energy-restriction-and-intermittent-fasting-amongst-obese-overweight-and-normal-weight-subjects-a-narrative-review-of-human-and-animal-evidence
#6
REVIEW
Michelle Harvie, Anthony Howell
Intermittent energy restriction (IER) has become popular as a means of weight control amongst people who are overweight and obese, and is also undertaken by normal weight people hoping spells of marked energy restriction will optimise their health. This review summarises randomised comparisons of intermittent and isoenergetic continuous energy restriction for weight loss to manage overweight and obesity. It also summarises the potential beneficial or adverse effects of IER on body composition, adipose stores and metabolic effects from human studies, including studies amongst normal weight subjects and relevant animal experimentation...
January 19, 2017: Behavioral Sciences
https://www.readbyqxmd.com/read/28106271/mapping-the-intermediate-digestion-phases-of-human-healthy-intestinal-contents-from-distal-ileum-and-caecum-at-fasted-and-fed-state-conditions
#7
Thuy Tran, Dimitrios G Fatouros, Maria Vertzoni, Christos Reppas, Anette Müllertz
OBJECTIVES: To investigate at the ultrastructural level, the colloidal phases formed in the lumen of the distal ileum and caecum of healthy adults. METHODS: Cryogenic transmission electron microscopy (Cryo-TEM) was employed to image the intermediate colloidal phases of human intestinal contents collected from distal ileum and caecum of two healthy volunteers under fasted and fed state conditions. KEY FINDINGS: In samples collected both in the fasted and fed states, Cryo-TEM study revealed the presence of large spherical unilamellar and occasionally bi-lamellar and oligolamellar vesicles with diameters ranging from 50 to 200 nm for both volunteers in distal ileum and caecum...
January 20, 2017: Journal of Pharmacy and Pharmacology
https://www.readbyqxmd.com/read/28105832/sensitive-and-fast-humidity-sensor-based-on-a-redox-conducting-supramolecular-ionic-material-for-respiration-monitoring
#8
Hailong Yan, Li Zhang, Ping Yu, Lanqun Mao
Real-time monitoring of respiratory rate (RR) is highly important for human health, clinical diagnosis, and fundamental scientific research. Exhaled humidity-based RR monitoring has recently attracted increased attention because of its accuracy and portability. Here, we report a new design of an exhaled humidity sensor for the real-time monitoring of the RR based on a synthetic redox conducting supramolecular ionic material (SIM). The humidity-dependent conducting SIM is prepared by ionic self-assembly in aqueous solutions of electroactive 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) and 1,10-bis(3-methylimidazolium-1-yl) decane (C10(mim)2)...
January 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28104434/effects-of-human-opiorphin-on-food-intake-and-water-intake-in-mice-following-central-administration
#9
Yong Chen, Xiao-Zhu Tian, Lu Bai, Ze-Qi Liu, Xing-Peng Xiao, Pu Liu, Xiang-Kai Li
Human opiorphin, plays important pharmacological functions in rats or mice. The present study was performed to investigate effects and underlying mechanism of central injected opiorphin on food intake and water intake in mice. Intracerebroventricularly (i.c.v.) administered opiorphin (5-20μg/kg) dose-dependently suppressed food intake in fasted mice, but had no influence on food intake in freely feeding mice. The cumulative food intake was significantly decreased at 60min after injection of 10 and 20μg/kg opiorphin and the food intake was significantly reduced during the 20-60min period after treatment...
January 16, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28103963/sex-differences-in-early-life-programming-of-the-hypothalamic-pituitary-adrenal-axis-in-humans-suggest-increased-vulnerability-in-females-a-systematic-review
#10
T Carpenter, S M Grecian, R M Reynolds
Fetal glucocorticoid overexposure is a key mechanism linking early development with later-life disease. In humans, low birth weight associates with increased fasting cortisol, hypothalamic-pituitary-adrenal (HPA) axis reactivity, and with cardiovascular risk and cognitive decline. As there are sex differences in these adult diseases, we hypothesized that there may be sex differences in programming of the HPA axis in response to prenatal stressors. We conducted a systematic review following Meta-Analysis of Observational Studies in Epidemiology and Preferred Reporting Items for Systematic Reviews and Meta-Analysis...
January 20, 2017: Journal of Developmental Origins of Health and Disease
https://www.readbyqxmd.com/read/28102671/structural-analysis-of-glycosylated-intact-hiv-1-gp120-b12-antibody-complex-using-hydroxyl-radical-protein-footprinting
#11
Xiaoyan Li, Oliver C Grant, Keigo Ito, Aaron Wallace, Shixia Wang, Peng Zhao, Lance Wells, Shan Lu, Robert J Woods, Joshua S Sharp
Glycoprotein gp120 is a surface antigen and virulence factor of the human immunodeficiency virus-1 (HIV-1). Broadly neutralizing antibodies (bNAbs) that are reactive to gp120 from a variety of HIV isolates offer hope for the development of broadly effective immunogens for vaccination purposes, if the interactions between gp120 and bNAbs can be understood. From a structural perspective, gp120 is a particularly difficult system due to its size, the presence of multiple flexible regions, and the large amount of glycosylation, all of which are important in gp120-bNAb interactions...
January 19, 2017: Biochemistry
https://www.readbyqxmd.com/read/28102570/simultaneous-determination-of-free-and-total-prostate-specific-antigen-by-a-magnetic-particle-based-time-resolved-fluoroimmunoassay
#12
Bin Zhou, Jue Zhang, Zhongwei Lv, Jun Fan, Yi Zhang, Biao Huang
OBJECTIVES: In this paper, a novel, sensitive and rapid method to simultaneously determine the free and total prostate-specific antigen (fPSA and tPSA) in serum by combining a time-resolved fluoroimmunoassay (TRFIA) and immunomagnetic separation was described. METHODS: The new approach uses magnetic particles as an immobilization matrix and means of separation, whereas the luminescent europium (Eu) and samarium (Sm) chelates are used as probes. The proposed method was evaluated via a single-step, sandwich-type TRFIA immunoassay of tPSA and fPSA as model analytes in serum...
January 19, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28102513/incidence-of-cryptosporidium-andersoni-in-diarrheal-patients-from-southern-assam-india-a-molecular-approach
#13
G Hussain, S Roychoudhury, B Singha, J Paul
The distribution and public health significance of Cryptosporidium species and genotypes in humans and bovine differ across geographical areas. Cryptosporidium species causes a disease known as cryptosporidiosis in humans and animals. To characterize the prevalence of cryptosporidiosis in humans in southern Assam, India, stool samples (n = 1119) of diarrhea patients were collected from different hospitals and from the community during the period January 2014 to July 2016. Fecal smears were examined microscopically for Cryptosporidium species using modified acid fast staining and were screened to ascertain the presence of Cryptosporidium antigen by enzyme-linked immunosorbent assay (ELISA)...
January 19, 2017: European Journal of Clinical Microbiology & Infectious Diseases
https://www.readbyqxmd.com/read/28101528/discriminating-valid-from-spurious-indices-of-phase-amplitude-coupling
#14
Ole Jensen, Eelke Spaak, Hyojin Park
Recently there has been a strong interest in cross-frequency coupling, the interaction between neuronal oscillations in different frequency bands. In particular, measures quantifying the coupling between the phase of slow oscillations and the amplitude of fast oscillations have been applied to a wide range of data recorded from animals and humans. Some of the measures applied to detect phase-amplitude coupling have been criticized for being sensitive to nonsinusoidal properties of the oscillations and thus spuriously indicate the presence of coupling...
November 2016: ENeuro
https://www.readbyqxmd.com/read/28101405/deep-tissue-photoacoustic-computed-tomography-with-a-fast-and-compact-laser-system
#15
Depeng Wang, Yuehang Wang, Weiran Wang, Dandan Luo, Upendra Chitgupi, Jumin Geng, Yang Zhou, Lidai Wang, Jonathan F Lovell, Jun Xia
Photoacoustic computed tomography (PACT) holds great promise for biomedical imaging, but wide-spread implementation is impeded by the bulkiness of flash-lamp-pumped laser systems, which typically weigh between 50 - 200 kg, require continuous water cooling, and operate at a low repetition rate. Here, we demonstrate that compact lasers based on emerging diode technologies are well-suited for preclinical and clinical PACT. The diode-pumped laser used in this study had a miniature footprint (13 × 14 × 7 cm(3)), weighed only 1...
January 1, 2017: Biomedical Optics Express
https://www.readbyqxmd.com/read/28101401/human-heart-failure-biomarker-immunosensor-based-on-excessively-tilted-fiber-gratings
#16
Binbin Luo, Shengxi Wu, Zhonghao Zhang, Wengen Zou, Shenghui Shi, Mingfu Zhao, Nianbing Zhong, Yong Liu, Xue Zou, Lingling Wang, Weina Chai, Chuanmin Hu, Lin Zhang
A label-free immunosensor platform based on excessively tilted fiber gratings (Ex-TFGs) was developed for highly specific and fast detection of human N-terminal pro-B-type natriuretic peptide (NT-proBNP), which is considered a powerful biomarker for prognosis and risk stratification of heart failure (HF). High-purity anti-NT-proBNP monoclonal antibodies (MAbs) prepared in our laboratory were immobilized on fiber surface through the staphylococcal protein A (SPA) method for subsequent specific binding of the targeted NT-proBNP...
January 1, 2017: Biomedical Optics Express
https://www.readbyqxmd.com/read/28100310/growth-inhibition-of-fungus-phycomyces-blakesleeanus-by-anion-channel-inhibitors-anthracene-9-carboxylic-and-niflumic-acid-attained-through-decrease-in-cellular-respiration-and-energy-metabolites
#17
Marina Stanić, Strahinja Križak, Mirna Jovanović, Tanja Pajić, Ana Ćirić, Milan Žižić, Joanna Zakrzewska, Tijana Cvetić Antić, Nataša Todorović, Miroslav Živić
Increasing resistance of fungal strains to known fungicides has prompted identification of new candidates for fungicides among substances previously used for other purposes. We have tested the effects of known anion channel inhibitors anthracene-9-carboxylic (A9C) and niflumic acid (NFA) on growth, energy metabolism and anionic current of mycelium of fungus Phycomyces blakesleeanus. Both inhibitors significantly decreased growth and respiration of mycelium, but complete inhibition was only achieved by 100 or 500 µM NFA, for growth and respiration, respectively...
January 18, 2017: Microbiology
https://www.readbyqxmd.com/read/28100205/a-fast-and-effective-determination-of-the-biodistribution-and-subcellular-localization-of-fluorescent-immunoliposomes-in-freshly-excised-animal-organs
#18
Felista L Tansi, Ronny Rüger, Ansgar M Kollmeier, Claudia Böhm, Roland E Kontermann, Ulf K Teichgraeber, Alfred Fahr, Ingrid Hilger
BACKGROUND: Preclinical research implementing fluorescence-based approaches is inevitable for drug discovery and technology. For example, a variety of contrast agents developed for biomedical imaging are usually evaluated in cell systems and animal models based on their conjugation to fluorescent dyes. Biodistribution studies of excised organs are often performed by macroscopic imaging, whereas the subcellular localization though vital, is often neglected or further validated by histological procedures...
January 18, 2017: BMC Biotechnology
https://www.readbyqxmd.com/read/28100104/theoretical-predication-of-temperature-effects-on-accommodative-processes-in-simulated-amyotrophic-lateral-sclerosis-during-hypothermia-and-hyperthermia
#19
D I Stephanova, A Kossev
Electrotonic potentials allow the accommodative processes to long-lasting subthreshold polarizing stimuli to be assessed. The present study investigates such potentials in previously simulated cases of amyotrophic lateral sclerosis, termed as ALS1, ALS2 and ALS3, respectively, when the temperature is changed during hypothermia ([Formula: see text]C) and hyperthermia ([Formula: see text]C). The ALS cases are modeled as three progressively severe uniform axonal dysfunctions along the human motor nerve fiber which is simulated by our temperature-dependent multi-layered numerical model...
January 18, 2017: Journal of Integrative Neuroscience
https://www.readbyqxmd.com/read/28099755/comparing-effects-of-insulin-analogues-and-human-insulin-on-nocturnal-glycaemia-in-hypoglycaemia-prone-people-with-type-1-diabetes
#20
P L Kristensen, L Tarnow, C Bay, K Nørgaard, T Jensen, H-H Parving, H Perrild, H Beck-Nielsen, J S Christiansen, B Thorsteinsson, U Pedersen-Bjergaard
AIMS: To assess the difference between analogue and human insulin with regard to nocturnal glucose profiles and risk of hypoglycaemia in people with recurrent severe hypoglycaemia. METHODS: A total of 72 people [46 men, mean ± sd age 54 ± 12 years, mean ± sd HbA1c 65 ± 12 mmol/mol (8.1 ± 1.1%), mean ± sd duration of diabetes 30 ± 14 years], who participated in a 2-year randomized, crossover trial of basal-bolus therapy with insulin detemir/insulin aspart or human NPH insulin/human regular insulin (the HypoAna trial) were studied for 2 nights during each treatment...
January 18, 2017: Diabetic Medicine: a Journal of the British Diabetic Association
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