Miracle-dz/UniFAR-FTUs huggingface dataset:
Major human milk oligosaccharides are absorbed into the systemic circulation after oral administration in rats

Abstract Human milk oligosaccharides (HMO) are involved in many biological functions influencing infant health. Although HMO act locally at the intestine, recent evidence has demonstrated that HMO are partially incorporated into the systemic circulation of breast-fed infants. In the last few years, a large amount of research has been conducted using preclinical models to uncover new biological functions of HMO. The aim of this study was to evaluate the absorption and urine excretion of HMO in rats. We administered a single oral dose of the following HMO: 2'-fucosyllactose (2'-FL), 6'-sialyllactose and lacto-N-neotetraose at different concentrations to adult rats. The time course of absorption of HMO into the bloodstream and their appearance in urine was studied. Our results showed that rats, similar to human infants, are able to effectively absorb a portion of HMO from the intestine into plasma and to excrete them in urine. On the basis of this, we also conducted a specific kinetic absorption study with 2'-FL, the most predominant HMO in human milk, in 9–11-d-old rat pups. Our results confirmed that a significant amount of 2'-FL was absorbed into the systemic circulation and subsequently excreted in urine during lactation in rats in a dose-depended manner. We also found basal levels of these HMO in plasma and urine of adult rats as well as rat pups as a natural result of nursing. Our data suggest that the rat may be a useful preclinical model that provides new insights into the metabolism and functions of HMO.
Assessment of in vitro antiovulatory activities of nonsteroidal anti‐inflammatory drugs and comparison with in vivo reproductive toxicities of medaka (Oryzias latipes)

Nonsteroidal anti‐inflammatory drugs (NSAIDs) are widely used therapeutic agents; however, their pharmacological actions raise concerns about potential risks to the reproductive health of aquatic vertebrates. In the present study, a medaka ovulation assay was applied as an in vitro model to evaluate NSAID‐induced antiovulatory activity. We first tested five NSAIDs, including diclofenac sodium (DCF), ketoprofen (KP), salicylic acid (SA), mefenamic acid (MA), and acetylsalicylic acid (ASA) for their antiovulatory activities toward the follicles isolated from the ovaries of spawning females. Of all the chemicals tested, DCF had the highest antiovulatory activity, with the concentration that caused 50% inhibition (IC50) (101 µM). MA was the second most potent inhibitor following DCF, but KP, SA, or ASA had little inhibitory effect on the ovulation of the follicles. The in vitro antiovulatory activity of five NSAIDs showed good correlation with data published on the inhibitory activity on human COX‐2. Second, we selected DCF and SA as the most and least potent NSAIDs, respectively, and examined the effects on reproduction of intact fish in order to evaluate whether the ovulation assay was a reasonable predictor of potential reproductive effects in fish. Females exposed to DCF showed a concentration‐dependent decrease in the number of spawned eggs and an increment in the gonadosomatic index (GSI), possibly due to an anovulation in the females. In contrast, neither fecundity nor the GSI of females decreased at up to 20 mg/L of SA, at which acute lethality to medaka was induced. In conclusion, the medaka ovulation assay reflected the potency of NSAID‐induced antiovulatory activity and may thus serve as an in vitro model for the prediction of NSAID‐induced reproductive toxicity. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1710–1719, 2016.
Title Near-infrared spectroscopy ( NIRS ) in functional research ofprefrontal cortex

Right © 2015 Masataka, Perlovsky and Hiraki. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Type Journal Article
An evaluation of the ability of chemical measurements to predict polycyclic aromatic hydrocarbon‐contaminated sediment toxicity to Hyalella azteca

The present study examined the ability of three chemical estimation methods to predict toxicity and nontoxicity of polycyclic aromatic hydrocarbon (PAH) ‐contaminated sediment to the freshwater benthic amphipod Hyalella azteca for 192 sediment samples from 12 field sites. The first method used bulk sediment concentrations of 34 PAH compounds (PAH34), and fraction of total organic carbon, coupled with equilibrium partitioning theory to predict pore‐water concentrations (KOC method). The second method used bulk sediment PAH34 concentrations and the fraction of anthropogenic (black carbon) and natural organic carbon coupled with literature‐based black carbon–water and organic carbon–water partition coefficients to estimate pore‐water concentrations (KOCKBC method). The final method directly measured pore‐water concentrations (pore‐water method). The U.S. Environmental Protection Agency's hydrocarbon narcosis model was used to predict sediment toxicity for all three methods using the modeled or measured pore‐water concentration as input. The KOC method was unable to predict nontoxicity (83% of nontoxic samples were predicted to be toxic). The KOCKBC method was not able to predict toxicity (57% of toxic samples were predicted to be nontoxic) and, therefore, was not protective of the environment. The pore‐water method was able to predict toxicity (correctly predicted 100% of the toxic samples were toxic) and nontoxicity (correctly predicted 71% of the nontoxic samples were nontoxic). This analysis clearly shows that direct pore‐water measurement is the most accurate chemical method currently available to estimate PAH‐contaminated sediment toxicity to H. azteca. Environ. Toxicol. Chem. 2010;29:1545–1550. © 2010 SETAC
Technique: Imaging Earliest Tooth Development in 3D Using a Silver‐Based Tissue Contrast Agent

Looking in microscopic detail at the 3D organization of initiating teeth within the embryonic jaw has long‐proved technologically challenging because of the radio‐translucency of these tiny un‐mineralized oral tissues. Yet 3D image data showing changes in the physical relationships among developing tooth and jaw tissues are vital to understand the coordinated morphogenesis of vertebrate teeth and jaws as an animal grows and as species evolve. Here, we present a new synchrotron‐based scanning solution to image odontogenesis in 3D and in histological detail using a silver‐based contrast agent. We stained fixed, intact wild‐type mice aged embryonic (E) day 10 to birth with 1% Protargol‐S at 37°C for 12–32 hr. Specimens were scanned at 4–10 µm pixel size at 28 keV, just above the silver K‐edge, using micro‐computed tomography (µCT) at the Canadian Light Source synchrotron. Synchrotron µCT scans of silver‐stained embryos showed even the earliest visible stages of tooth initiation, as well as many other tissue types and structures, in histological detail. Silver stain penetration was optimal for imaging structures in intact embryos E15 and younger. This silver stain method offers a powerful yet straightforward approach to visualize at high‐resolution and in 3D the earliest stages of odontogenesis in situ, and demonstrates the important of studying the tooth organ in all three planes of view. Anat Rec, 297:222–233, 2014. © 2013 Wiley Periodicals, Inc.
Role of an Internal and Two 3′-Terminal RNA Elements in Assembly of Tombusvirus Replicase

ABSTRACT Plus-strand RNA virus replication requires the assembly of the viral replicase complexes on intracellular membranes in the host cells. The replicase of Cucumber necrosis virus (CNV), a tombusvirus, contains the viral p33 and p92 replication proteins and possible host factors. In addition, the assembly of CNV replicase is stimulated in the presence of plus-stranded viral RNA (Z. Panaviene et al., J. Virol. 78:8254-8263, 2004). To define cis-acting viral RNA sequences that stimulate replicase assembly, we performed a systematic deletion approach with a model tombusvirus replicon RNA in Saccharomyces cerevisiae, which also coexpressed p33 and p92 replication proteins. In vitro replicase assays performed with purified CNV replicase preparations from yeast revealed critical roles for three RNA elements in CNV replicase assembly: the internal p33 recognition element (p33RE), the replication silencer element (RSE), and the 3′-terminal minus-strand initiation promoter (gPR). Deletion or mutagenesis of these elements reduced the activity of the CNV replicase to a minimal level. In addition to the primary sequences of gPR, RSE, and p33RE, formation of two alternative structures among these elements may also play a role in replicase assembly. Altogether, the role of multiple RNA elements in tombusvirus replicase assembly could be an important factor to ensure fidelity of template selection during replication.
Efficacy of a Potential Trivalent Vaccine Based on Hc Fragments of Botulinum Toxins A, B, and E Produced in a Cell-Free Expression System

ABSTRACT Botulinum toxins produced by the anaerobic bacterium Clostridium botulinum are the most potent biological toxins in nature. Traditionally, people at risk are immunized with a formaldehyde-inactivated toxin complex. Second generation vaccines are based on the recombinant carboxy-terminal heavy-chain (Hc) fragment of the neurotoxin. However, the materialization of this approach is challenging, mainly due to the high AT content of clostridial genes. Herein, we present an alternative strategy in which the native genes encoding Hc proteins of botulinum toxins A, B, and E were used to express the recombinant Hc fragments in a cell-free expression system. We used the unique property of this open system to introduce different combinations of chaperone systems, protein disulfide isomerase (PDI), and reducing/oxidizing environments directly to the expression reaction. Optimized expression conditions led to increased production of soluble Hc protein, which was successfully scaled up using a continuous exchange (CE) cell-free system. Hc proteins were produced at a concentration of more than 1 mg/ml and purified by one-step Ni+ affinity chromatography. Mice immunized with three injections containing 5 μg of any of the in vitro-expressed, alum-absorbed, Hc vaccines generated a serum enzyme-linked immunosorbent assay (ELISA) titer of 105 against the native toxin complex, which enabled protection against a high-dose toxin challenge (103 to 106 mouse 50% lethal dose [MsLD50]). Finally, immunization with a trivalent HcA, HcB, and HcE vaccine protected mice against the corresponding trivalent 105 MsLD50 toxin challenge. Our results together with the latest developments in scalability of the in vitro protein expression systems offer alternative routes for the preparation of botulinum vaccine.
Efficient Summarization with Read-Again and Copy Mechanism

Encoder-decoder models have been widely used to solve sequence to sequence prediction tasks. However current approaches suffer from two shortcomings. First, the encoders compute a representation of each word taking into account only the history of the words it has read so far, yielding suboptimal representations. Second, current models utilize large vocabularies in order to minimize the problem of unknown words, resulting in slow decoding times and large storage costs. In this paper we address both shortcomings. Towards this goal, we first introduce a simple mechanism that first reads the input sequence before committing to a representation of each word. Furthermore, we propose a simple copy mechanism that is able to exploit very small vocabularies and handle out-of-vocabulary words. We demonstrate the effectiveness of our approach on the Gigaword dataset and DUC competition outperforming the state-of-the-art.
Prevalence of extra-articular manifestations in patients with ankylosing spondylitis: a systematic review and meta-analysis.

OBJECTIVES Uveitis, psoriasis and inflammatory bowel disease (IBD) are common extra-articular manifestations (EAM) in patients with ankylosing spondylitis (AS); however, summary data of reported prevalence are lacking. The aim of the present study was to summarise the prevalence of EAMs among patients with AS and to identify underlying factors to explain potential heterogeneity of prevalence. METHODS A systematic literature search was performed (Medline, Embase and Cochrane Library) to identify relevant articles. Risk of bias was assessed and data were extracted. Pooled prevalences were calculated. Potential sources of any observed clinical or methodological heterogeneity in the estimates were explored by subgroup and metaregression analysis. RESULTS In the 156 selected articles, 143 reported the prevalence of uveitis (44 372 patients), 56 of psoriasis (27 626 patients) and 69 of IBD (30 410 patients). Substantial heterogeneity was observed in prevalence estimates among all EAMs (I(2)=84-95%). The pooled prevalence of uveitis was 25.8% (95% CI 24.1% to 27.6%), and was positively associated in multivariable metaregression with disease duration (β 0.05, 95% CI 0.03 to 0.08) and random selection of patients (β -0.24, 95% CI -0.43 to -0.04). The pooled prevalence of psoriasis was 9.3% (95% CI 8.1% to 10.6%). The pooled prevalence of IBD was 6.8% (95% CI 6.1% to 7.7%) and was positively associated with the percentage of women in the studies (β 0.02, 95% CI 0.00 to 0.03). Geographical area was associated in multivariable metaregressions with prevalence of all EAMs. CONCLUSIONS EAMs are common in patients with AS. The large heterogeneity between studies can be partly explained by differences in clinical as well as methodological characteristics.
Earnings Supplements and Job Quality among Former Welfare Recipients : Evidence from the Self-Sufficiency Project

The Self-Sufficiency Project (SSP) offered a generous but time-limited earnings supplement to a randomly assigned group of lone parents—who were also long-term social assistance recipients—if they found full-time work and left social assistance. Employment data was collected for this group over a three-year period following the offer, and for a randomly-assigned control group. This article analyzes the characteristics of the first job that SSP participants found after they left social assistance. The occupations and industries of the first job held are analyzed as is SSP’s impact on hourly wages, weekly hours and job stability. The article finds that SSP increased employment in jobs that were no worse (and no better) than the jobs that participants might have taken in the absence of the program.
Shift-Reduce Word Reordering for Machine Translation

This paper presents a novel word reordering model that employs a shift-reduce parser for inversion transduction grammars. Our model uses rich syntax parsing features for word reordering and runs in linear time. We apply it to postordering of phrase-based machine translation (PBMT) for Japanese-to-English patent tasks. Our experimental results show that our method achieves a significant improvement of +3.1 BLEU scores against 30.15 BLEU scores of the baseline PBMT system.
Turbulent mixing of particles under tidal bores: an experimental analysis

A tidal bore develops in an estuary when the tidal range exceeds 4.5–6 m and the estuarine bathymetry amplifies the tidal wave. The bore is an abrupt rise in water depth associated with a discontinuity in velocity and pressure fields at the front. Herein the free-surface properties and the turbulent mixing of light-weight particles were investigated during the passage of tidal bores. The free-surface properties were recorded using a non-intrusive technique, while particle tracking was performed under undular and breaking bores. A basic result was the identification of a broad spectrum of particle trajectories, linked with the existence of large-scale vortical structures. These turbulent structures were responsible for the vertical water mixing as a tidal bore propagates upstream in an estuary. The large-scale eddies were also responsible for the rapid longitudinal dispersion of particulates, such as fish eggs, with some form of preferential motion, depending upon the particle's vertical elevation.
Assessment of left ventricle function in patients with symptomatic and asymptomatic aortic stenosis by 2-dimensional speckle-tracking imaging

Summary Background Global longitudinal peak strain (GLPS) quantifies left ventricle (LV) long-axis contractility. Early detection of LV systolic dysfunction is pivotal in diagnosis and treatment of patients with aortic stenosis (AS). This study was performed to assess LV longitudinal systolic function by GLPS derived from 2-dimensional speckle tracking imaging (2D-STI) in AS patients in comparison to standard echocardiographic parameters. Material/Methods Laboratory tests, standard echocardiography, tissue Doppler imaging (TDI) and 2D-STI examinations with GLPS calculation were performed in 49 consecutive patients with moderate to severe AS with LV ejection fraction ≥50% and 18 controls. Results While LVEF do not differentiate AS patients from controls, GLPS was significantly decreased in the AS group (−15.30±3.25% vs. −19.60±2.46% in controls, p<0.001). GLPS was significantly reduced in symptomatic AS patients as compared to the asymptomatic AS group [−15.5 (11.8–16.8) vs. −17.5 (14.7–18.9)%, p=0.02]. Conclusions In aortic stenosis patients, despite normal left ventricle ejection fraction, long-axis left ventricular function is impaired, which manifests in global longitudinal peak strain reduction. GLPS reveals that LV function impairment is more pronounced in symptomatic as compared to asymptomatic AS patients. Further studies are needed to determine the prognostic significance of early LV function impairment in aortic stenosis patients showed by GLPS.
How does plate size affect estimated satiation and intake for individuals in normal‐weight and overweight groups?

Manipulating plate sizes could possibly introduce perceptual biases for judging food satiation and intake, which is thought to be related to the Delbeouf illusion – a visual illusion based on the perceived size of one object related to another. This study was to investigate whether an association exists between an individual's susceptibility to the plate‐size‐effect and their weight status (i.e. normal‐weight versus overweight).
Simulation of unmanned aerial vehicles in the determination of accident locations

As part of the aviation regulations in the Netherlands, third party risk models have been developed and are applied in the determination of risks to the people on ground (third parties) due to aircraft departures and arrivals. In the derivation of these models, accident data are required. Such risk model has yet to be developed for unmanned aerial vehicles (UAVs). As foreseen in the future, accidents with increasing UAV use can pose a growing safety risk for the environment. So the challenge is how to safely manage future increase of UAV use. Because data about UAV accidents are scarce, this study explores the use of flight simulation as an alternative for gathering accident data for UAVs. Simulation models for unmanned aerial vehicle in both a fixed wing and a multi-rotorcraft (quadcopter) configuration are adapted. Through modelling and computer simulation of flights by these UAV configurations, insight is collected regarding ground impact locations for various UAV failure situations, including motor failure with full, partially or loss of controllable surfaces, and for various UAV flight conditions.
Cross-Reactive Polyclonal Antibodies to the Inner Core of Lipopolysaccharide from Neisseria meningitidis

ABSTRACT Sera from mice immunized with native or detergent-extracted outer membrane vesicles derived from lipopolysaccharide (LPS) mutant 44/76Mu-4 of Neisseria meningitidis were analyzed for antibodies to LPS. The carbohydrate portion of 44/76Mu-4 LPS consists of the complete inner core, Glcβ1→4[GlcNAc α1→2Hep α1→3]Hep α1→5KDO[4→2αKDO]. Immunoblot analysis revealed that some sera contained antibodies to wild-type LPS which has a fully extended carbohydrate chain of immunotype L3,7, as well as to the homologous LPS. Sera reacted only weakly to LPS from 44/76Mu-3, which lacks the terminal glucose of the inner core. No binding to more truncated LPS was observed. Consequently, the cross-reactive epitopes are expressed mainly by the complete inner core. Dephosphorylation of wild-type LPS abolished antibody binding to LPS in all but one serum. Thus, at least two specificities of cross-reactive antibodies exist: one is dependent on phosphoethanolamine groups in LPS, and one is not. Detection of these cross-reactive antibodies strongly supports the notion that epitopes expressed by meningococcal LPS inner core are also accessible to antibodies when the carbohydrate chain is fully extended. Also, these inner core epitopes are sufficiently immunogenic to induce antibody levels detectable in polyclonal antibody responses. Meningococci can escape being killed by antibodies to LPS that bind only to a specific LPS variant, by altering the carbohydrate chain length. Cross-reactive antibodies may prevent such escape. Therefore, inner core LPS structures may be important antigens in future vaccines against meningococcal disease.
Nanofibrous web quality in dependence on the preparation of poly(ethylene oxide) aqueous solutions

Abstract The method of preparation of polymer solutions significantly influences the quality of the corresponding electrospun nanofibrous webs. However, this factor is often ignored, and in a majority of presentations concerning the electrospinning process, the applied method is not mentioned. This paper compares the influence of magnetic stirring, vibrational shaking and ultrasonication on a solution of poly(ethylene oxide) in distilled water. Along with the methods of preparation, other parameters were altered such as concentration, intensity of mixing and molecular weight. The best results from the viewpoint of electrospinning were achieved with moderate magnetic stirring.
Neuropathic pain: diagnosis and treatment

Neuropathic pain (NP) develops as a consequence of a lesion or disease affecting the somatosensory pathways in the peripheral or central nervous system, and occurs in many neurological diseases (eg, peripheral neuropathy, radiculopathy, spinal cord injury, stroke and multiple sclerosis). It affects 6%–8% of the general population and its impact on quality of life, mood and sleep exceeds the burden of its causative pathology. A peculiar feature of NP is the coexistence of negative and positive symptoms and signs, reflecting loss-of-function and gain-of-function of the somatosensory system, respectively. NP has long been considered a difficult clinical issue because of the lack of a diagnostic gold standard and the unsatisfactory response to treatment. In recent years, a redefinition, diagnostic algorithm, and some guidelines on diagnosis and treatment of NP have been published. This review offers an updated overview on the definition, pathophysiology, clinical evaluation, diagnosis and treatment of NP and focuses on some of the most frequent NP conditions. We intend to help overcome uncertainties on NP and bridge the gap between evidence based medicine and the real clinical world.