Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating the Association Between the Caecal Microbiomes of Broilers and Campylobacter Burden

One of the major transmission routes for the foodborne bacterial pathogen Campylobacter is undercooked poultry meat, contaminated from intestinal contents during processing. In broilers, Campylobacter can grow to very high densities in the caeca, and is often considered to be a commensal or an opportunistic pathogen in poultry. Reduction of caecal loads of Campylobacter may assist in lowering incidence rates of Campylobacter food poisoning. To achieve this, there needs to be a better understanding of the dynamics of Campylobacter colonization in its natural niche, and the effect of the local microbiome on colonization. Previous studies have shown that the microbiome differed between Campylobacter colonized and non-colonized chicken intestinal samples. To characterize the microbiome of Campylobacter-colonized broilers, caecal samples of 100 randomly selected birds from four farms were analyzed using amplified 16S rRNA gene sequences. Bacterial taxonomic analysis indicated that inter-farm variation was greater than intra-farm variation. The two most common bacterial groups were Bacteroidetes and Firmicutes which were present in all samples and constituted 29.7–63.5 and 30.2–59.8% of the bacteria present, respectively. Campylobacter was cultured from all samples, ranging from 2 to 9 log10 CFU g-1. There was no clear link between Campylobacter counts and Firmicutes, Bacteroidetes, or Tenericutes levels in the 16S rRNA operational taxonomic unit (OTU)-based analysis of the caecal microbiome, but samples with high Campylobacter counts (>9 log CFU g-1) contained increased levels of Enterobacteriaceae. A decrease in Lactobacillus abundance in chicken caeca was also associated with high Campylobacter loads. The reported associations with Lactobacillus and Enterobacteriaceae match changes in the intestinal microbiome of chickens and mice previously reported for Campylobacter infection, and raises the question about temporality and causation; as to whether increases in Campylobacter loads create conditions adverse to Lactobacilli and/or beneficial to Enterobacteriaceae, or that changes in Lactobacilli and Enterobacteriaceae levels created conditions beneficial for Campylobacter colonization. If these changes can be controlled, this may open opportunities for modulation of chicken microbiota to reduce Campylobacter levels for improved food safety.
Effects of Single-Dose Dietary Nitrate on Oxygen Consumption During and After Maximal and Submaximal Exercise in Healthy Humans: A Pilot Study

Dietary nitrate (NO3−) has been shown to reduce oxygen consumption (VO2) during moderate to high-intensity (e.g. time to fatigue, time trials) exercise and often in trained athletes. However, less is known regarding prolonged exercise and the potential impact of NO3− on post-exercise excess oxygen consumption (EPOC), particularly in untrained individuals, who may have different metabolic goals during exercise than trained individuals. We tested the hypothesis that acute nitrate supplementation in the form of beet root juice will significantly decrease both VO2 during maximal exercise and EPOC in both maximal and submaximal exercise trials. Eight young, moderately active, healthy males (age: 24.8±1.4 years, body mass index: 23.7±0.4 kg/m2; VO2max: 34.2±3.9 ml/kg/min) performed step-wise maximal cycle exercise (n=4) and prolonged submaximal cycle exercise (n=6) (45 min; 38±2% of max work rate) in control (anti-bacterial mouthwash) and acute NO3− supplemented conditions [70ml concentrated beet root juice (0.4g NO3−), 2 hrs prior to exercise] on separate occasions. Measurements of VO2 (indirect calorimetry), arterial blood pressure (MAP; sphygmomanometry), and heart rate (HR; ECG) were made before, during, and following exercise bouts. NO3− reduced MAP at rest ~1–3mmHg. However, NO3− had no impact on VO2 during maximal (VO2max, Ctrl: 34.2±3.9 ml/kg/min vs NO3−: 31.7±4.4 ml/kg/min), submaximal exercise (average of min 25–45, Ctrl: 24.6±2.4 ml/kg/min vs NO3−: 26.8±3.3 ml/kg/min) or EPOC (area under the curve, Ctrl: 0.57±0.24 L vs NO3−: 0.66±0.16 L). Thus, while NO3− supplementation may have performance benefits in elite athletes exercising at high intensities, in recreationally active males, there appears to be little impact on changes in VO2 due to maximal or submaximal prolonged exercise.
Population Pharmacokinetics and Pharmacodynamics of Dexmedetomidine in Children Undergoing Ambulatory Surgery

BACKGROUND: Dexmedetomidine (DEX) is an &agr;-2 adrenergic agonist with sedative and analgesic properties. Although not approved for pediatric use by the Food and Drug Administration, DEX is increasingly used in pediatric anesthesia and critical care. However, very limited information is available regarding the pharmacokinetics of DEX in children. The aim of this study was to investigate DEX pharmacokinetics and pharmacodynamics (PK–PD) in Mexican children 2–18 years of age who were undergoing outpatient surgical procedures. METHODS: Thirty children 2–18 years of age with American Society of Anesthesiologists physical status score of I/II were enrolled in this study. DEX (0.7 &mgr;g/kg) was administered as a single-dose intravenous infusion. Venous blood samples were collected, and plasma DEX concentrations were analyzed with a combination of high-performance liquid chromatography and electrospray ionization-tandem mass spectrometry. Population PK–PD models were constructed using the Monolix program. RESULTS: A 2-compartment model adequately described the concentration–time relationship. The parameters were standardized for a body weight of 70 kg by using an allometric model. Population parameters estimates were as follows: mean (between-subject variability): clearance (Cl) (L/h × 70 kg) = 20.8 (27%); central volume of distribution (V1) (L × 70 kg) = 21.9 (20%); peripheral volume of distribution (V2) (L × 70 kg) = 81.2 (21%); and intercompartmental clearance (Q) (L/h × 70 kg) = 75.8 (25%). The PK–PD model predicted a maximum mean arterial blood pressure reduction of 45% with an IC50 of 0.501 ng/ml, and a maximum heart rate reduction of 28.9% with an IC50 of 0.552 ng/ml. CONCLUSIONS: Our results suggest that in Mexican children 2–18 years of age with American Society of Anesthesiologists score of I/II, the DEX dose should be adjusted in accordance with lower DEX clearance.
Sphingosine-1-phosphate receptor-2 facilitates pulmonary fibrosis through potentiating IL-13 pathway in macrophages

Idiopathic pulmonary fibrosis is a devastating disease with poor prognosis. The pathogenic role of the lysophospholipid mediator sphingosine-1-phosphate and its receptor S1PR2 in lung fibrosis is unknown. We show here that genetic deletion of S1pr2 strikingly attenuated lung fibrosis induced by repeated injections of bleomycin in mice. We observed by using S1pr2LacZ/+ mice that S1PR2 was expressed in alveolar macrophages, vascular endothelial cells and alveolar epithelial cells in the lung and that S1PR2-expressing cells accumulated in the fibrotic legions. Bone marrow chimera experiments suggested that S1PR2 in bone marrow–derived cells contributes to the development of lung fibrosis. Depletion of macrophages greatly attenuated lung fibrosis. Bleomycin administration stimulated the mRNA expression of the profibrotic cytokines IL-13 and IL-4 and the M2 markers including arginase 1, Fizz1/Retnla, Ccl17 and Ccl24 in cells collected from broncho-alveolar lavage fluids (BALF), and S1pr2 deletion markedly diminished the stimulated expression of these genes. BALF cells from bleomycin–administered wild-type mice showed a marked increase in phosphorylation of STAT6, a transcription factor which is activated downstream of IL-13, compared with saline–administered wild-type mice. Interestingly, in bleomycin–administered S1pr2-/- mice, STAT6 phosphorylation in BALF cells was substantially diminished compared with wild-type mice. Finally, pharmacological S1PR2 blockade in S1pr2+/+ mice alleviated bleomycin–induced lung fibrosis. Thus, S1PR2 facilitates lung fibrosis through the mechanisms involving augmentation of IL-13 expression and its signaling in BALF cells, and represents a novel target for treating lung fibrosis.
Pre-pregnancy dietary carbohydrate quantity and quality, and risk of developing gestational diabetes: the Australian Longitudinal Study on Women’s Health

Abstract Carbohydrate quantity and quality affect postprandial glucose response, glucose metabolism and risk of type 2 diabetes. The aim of this study was to examine the association of pre-pregnancy dietary carbohydrate quantity and quality with the risk of developing gestational diabetes mellitus (GDM). We used data from the Australian Longitudinal Study on Women’s Health that included 3607 women aged 25–30 years without diabetes who were followed up between 2003 and 2015. We examined carbohydrate quantity (total carbohydrate intake and a low-carbohydrate diet (LCD) score) and carbohydrate subtypes indicating quality (fibre, total sugar intake, glycaemic index, glycaemic load and intake of carbohydrate-rich food groups). Relative risks (RR) for development of GDM were estimated using multivariable regression models with generalised estimating equations. During 12 years of follow-up, 285 cases of GDM were documented in 6263 pregnancies (4·6 %). The LCD score, reflecting relatively high fat and protein intake and low carbohydrate intake, was positively associated with GDM risk (RR 1·54; 95 % CI 1·10, 2·15), highest quartile v. lowest quartile). Women in the quartile with highest fibre intake had a 33 % lower risk of GDM (RR 0·67; 95 % CI 0·45, 0·96)). Higher intakes of fruit (0·95 per 50 g/d; 95 % CI 0·90, 0·99) and fruit juice (0·89 per 100 g/d; 95 % CI 0·80, 1·00)) were inversely associated with GDM, whereas cereal intake was associated with a higher risk of GDM (RR 1·05 per 20 g/d; 95 % CI 1·01, 1·07)). Thus, a relatively low carbohydrate and high fat and protein intake may increase the risk of GDM, whereas higher fibre intake could decrease the risk of GDM. It is especially important to take the source of carbohydrates into account.
Learning Attributes from the Crowdsourced Relative Labels

Finding semantic attributes to describe related concepts is typically a hard problem. The commonly used attributes in most fields are designed by domain experts, which is expensive and time-consuming. In this paper we propose an efficient method to learn human comprehensible attributes with crowdsourcing. We first design an analogical interface to collect relative labels from the crowds. Then we propose a hierarchical Bayesian model, as well as an efficient initialization strategy, to aggregate labels and extract concise attributes. Our experimental results demonstrate promise on discovering diverse and convincing attributes, which significantly improve the performance of the challenging zero-shot learning tasks.
Higher Plasma Methylglyoxal Levels Are Associated With Incident Cardiovascular Disease and Mortality in Individuals With Type 2 Diabetes

OBJECTIVE Methylglyoxal (MGO) is a reactive dicarbonyl compound and a potential key player in diabetic cardiovascular disease (CVD). Whether plasma MGO levels are associated with CVD in type 2 diabetes is unknown. RESEARCH DESIGN AND METHODS We included 1,003 individuals (mean ± SD age 59.1 ± 10.5 years, 69.3% male, and 61.6% with prior CVD) with type 2 diabetes from the Second Manifestations of ARTerial disease cohort (SMART). We measured plasma MGO levels and two other dicarbonyls (glyoxal [GO] and 3-deoxyglucosone [3-DG]) at baseline with mass spectrometry. Median follow-up of CVD events was 8.6 years. Data were analyzed with Cox regression with adjustment for sex, age, smoking, systolic blood pressure, total cholesterol, HbA1c, BMI, prior CVD, and medication use. Hazard ratios are expressed per SD Ln-transformed dicarbonyl. RESULTS A total of 287 individuals suffered from at least one CVD event (n = 194 fatal events, n = 146 myocardial infarctions, and n = 72 strokes); 346 individuals died, and 60 individuals underwent an amputation. Higher MGO levels were associated with total (hazard ratio 1.26 [95% CI 1.11–1.42]) and fatal (1.49 [1.30–1.71]) CVD and with all-cause mortality (1.25 [1.11–1.40]), myocardial infarction (1.22 [1.02–1.45]), and amputations (1.36 [1.05–1.76]). MGO levels were not apparently associated with stroke (1.03 [0.79–1.35]). Higher GO levels were significantly associated with fatal CVD (1.17 [1.00–1.37]) but not with other outcomes. 3-DG was not significantly associated with any of the outcomes. CONCLUSIONS Plasma MGO and GO levels are associated with cardiovascular mortality in individuals with type 2 diabetes. Influencing dicaronyl levels may therefore be a target to reduce CVD in type 2 diabetes.
Acute ammonia toxicity to the larvae (glochidia) of the tropical Australian freshwater mussel Velesunio spp. Using a modified toxicity test protocol

Ammonia is recognized as a major pollutant worldwide, originating from natural and anthropogenic sources. Studies have reported that freshwater mussels are among the most sensitive taxa to ammonia, but few data are available on ammonia toxicity for the early life stages of freshwater mussels from tropical regions. We report on the modification of a 24‐h acute toxicity test protocol for tropical freshwater mussels and application of the test using ammonia. Velesunio spp. from 3 different sites were used to assess the toxicity of ammonia at a targeted pH of 6.0 and a water temperature of 27.5 °C, which were the average annual values for some slightly to moderately acidic, soft water (3–6 mg/L as CaCO3) creeks of tropical northern Australia. The valve closure responses of mussel glochidia (larvae) to a sodium chloride solution were used to measure the survival endpoint. Acute toxicity estimates indicate that tropical Velesunio spp. were highly sensitive to ammonia, with 24‐h exposures to ammonium sulfate generating median lethal concentration estimates ranging from 6.8 to 14.2 mg/L total ammonia nitrogen, which, when adjusted to pH 7 and 20 °C, were among the highest sensitivities yet reported for any freshwater mussel species, and among the highest in sensitivity for any tropical taxon. These toxicity estimates can contribute to the derivation or refinement of ammonia guideline values for freshwater ecosystems globally. Environ Toxicol Chem 2018;37:2175–2187. © 2018 SETAC
Image Cosegmentation via Saliency-Guided Constrained Clustering with Cosine Similarity

Cosegmentation jointly segments the common objects from multiple images. In this paper, a novel clustering algorithm, called Saliency-Guided Constrained Clustering approach with Cosine similarity (SGC3), is proposed for the image cosegmentation task, where the common foregrounds are extracted via a one-step clustering process. In our method, the unsupervised saliency prior is utilized as a partition-level side information to guide the clustering process. To guarantee the robustness to noise and outlier in the given prior, the similarities of instance-level and partition-level are jointly computed for cosegmentation. Specifically, we employ cosine distance to calculate the feature similarity between data point and its cluster centroid, and introduce a cosine utility function to measure the similarity between clustering result and the side information. These two parts are both based on the cosine similarity, which is able to capture the intrinsic structure of data, especially for the non-spherical cluster structure. Finally, a K-means-like optimization is designed to solve our objective function in an efficient way. Experimental results on two widely-used datasets demonstrate our approach achieves competitive performance over the state-of-the-art cosegmentation methods.
Expansion microscopy

Super‐resolution optical microscopy techniques have revolutionized how we see and understand biology. In recent past, a new super‐resolution optical microscopy technique called expansion microscopy (ExM) was developed. Unlike other pre‐existing super‐resolution imaging techniques, this technique achieves super‐resolution by physically expanding biological specimens via a swellable hydrogel. After the development of ExM, various techniques based on ExM but with improved performance in various aspects, have been developed. In this review, we introduce the basic principles of ExM and its variants. and compare the advantages and disadvantages of these techniques. In addition, we present the applications of ExM techniques in various fields.
IMPLICATION OF THE OBSERVED SPECTRAL CUTOFF ENERGY EVOLUTION IN XTE J1550−564

The physical mechanisms responsible for the production of non-thermal emission in accreting black holes (BHs) should be imprinted in the observational appearances of the power-law tails in the X-ray spectra from these objects. Phenomenology of different spectral states exhibited by galactic BH binaries allows us to establish the physics of the photon upscattering under different accretion regimes. We revisit the data collected by the Rossi X-ray Timing Explorer from the BH X-ray binary XTE J1550−564 during two periods of X-ray activity in 1998 and 2000 focusing on the behavior of the high-energy cutoff of the power-law part of the spectrum. For the 1998 outburst, the transition from the low-hard state to the intermediate state was accompanied by a gradual decrease in the cutoff energy. This was followed by an extended minimum which then showed an abrupt reversal to a clear increasing trend as the source evolved to the very high and high-soft states. The 2000 outburst showed only the decreasing and extended minimum portions of this pattern. We attribute this difference in the cutoff energy behavior to the different partial contributions of the thermal and non-thermal (bulk motion) Comptonization. Namely, during the 1998 event the higher accretion rate presumably provided more cooling to the Comptonizing media and thus reducing the effectiveness of the thermal upscattering process. Under these conditions, the bulk motion takes a leading role in boosting the input soft photons. Recent Monte Carlo simulations by Laurent & Titarchuk strongly support this scenario.
Greenland shark (Somniosus microcephalus) feeding behavior on static fishing gear, effect of SMART (Selective Magnetic and Repellent-Treated) hook deterrent technology, and factors influencing entanglement in bottom longlines

The Greenland Shark (Somniosus microcephalus) is the most common bycatch in the Greenland halibut (Reinhardtius hippoglossoides) bottom longline fishery in Cumberland Sound, Canada. Historically, this inshore fishery has been prosecuted through the ice during winter but winter storms and unpredictable landfast ice conditions since the mid-1990s have led to interest in developing a summer fishery during the ice-free season. However, bycatch of Greenland shark was found to increase substantially with 570 sharks captured during an experimental Greenland halibut summer fishery (i.e., mean of 6.3 sharks per 1,000 hooks set) and mortality was reported to be about 50% due in part to fishers killing sharks that were severely entangled in longline gear. This study investigated whether the SMART (Selective Magnetic and Repellent-Treated) hook technology is a practical deterrent to Greenland shark predation and subsequent bycatch on bottom longlines. Greenland shark feeding behavior, feeding kinematics, and variables affecting entanglement/disentanglement and release are also described. The SMART hook failed to deter Greenland shark predation, i.e., all sharks were captured on SMART hooks, some with more than one SMART hook in their jaw. Moreover, recently captured Greenland sharks did not exhibit a behavioral response to SMART hooks. In situ observations of Greenland shark feeding show that this species uses a powerful inertial suction mode of feeding and was able to draw bait into the mouth from a distance of 25–35 cm. This method of feeding is suggested to negate the potential deterrent effects of electropositive metal and magnetic alloy substitutions to the SMART hook technology. The number of hooks entangled by a Greenland shark and time to disentangle and live-release a shark was found to increase with body length.
Combined external beam radiotherapy and vaginal brachytherapy versus vaginal brachytherapy in stage I, intermediate- and high-risk cases of endometrium carcinoma

Purpose Randomized trials on the effect of external beam radiotherapy (EBRT) with or without vaginal brachytherapy (VBT) for endometrial carcinoma are very few. In view of this, the current study was conducted with the hypothesizes: whether the escalated dose of 26 Gy (VBT alone) in comparison with various major international trials (PORTEC-2) has any difference in rates of disease-free and overall survival with fewer adverse effects in low resource setting like India. Material and methods An open-labeled, non-inferiority, randomized control trial was undertaken at a regional cancer center among patients with stage IA or IB high-intermediate risk endometrial carcinoma. A total of 50 patients were divided equally among two arms of combined EBRT with VBT (arm I) and VBT alone (arm II). A dose of 50-50.4 Gy in 25-28 fractions of EBRT with 2 fractions of VBT 6.5 Gy each were delivered to patients in arm I and 4 fractions of VBT 6.5 Gy each to patients in arm II, and were followed up for 60 months. Results During the median follow-up of 36.5 months, two patients developed loco-regional recurrence in arm II, three (arm II), and one (arm I) developed distant metastasis. The 5-year survival rates for arms I and II were 96.0% vs. 92.0% overall, and 88.0% vs. 84.0% disease-free, respectively, and were not found to be statistically significantly different. Dermatological, gastro-intestinal toxicities, and cystitis were lower in the VBT group compared to combined group. Conclusions VBT alone is as effective as EBRT+VBT in ensuring loco-regional control and achieving comparable survival rates, with fewer toxic effects for patients with stage I intermediate- and high-risk endometrial carcinoma. The dose escalation did not make a difference in the survival rates and was like in the other major trials (PORTEC-2).
A Nonconvex Projection Method for Robust PCA

Robust principal component analysis (RPCA) is a well-studied problem whose goal is to decompose a matrix into the sum of low-rank and sparse components. In this paper, we propose a nonconvex feasibility reformulation of RPCA problem and apply an alternating projection method to solve it. To the best of our knowledge, this is the first paper proposing a method that solves RPCA problem without considering any objective function, convex relaxation, or surrogate convex constraints. We demonstrate through extensive numerical experiments on a variety of applications, including shadow removal, background estimation, face detection, and galaxy evolution, that our approach matches and often significantly outperforms current state-of-the-art in various ways.