Miracle-dz/UniFAR-FTUs huggingface dataset:
Transposon Mutagenesis Identifies Genes Critical for Growth of Pseudomonas nitroreducens TX1 on Octylphenol Polyethoxylates

ABSTRACT Pseudomonas nitroreducens TX1 is of special interest because of its ability to utilize 0.05% to 20% octylphenol polyethoxylates (OPEO n ) as a sole source of carbon. In this study, a library containing 30,000 Tn5-insertion mutants of the wild-type strain TX1 was constructed and screened for OPEO n utilization, and 93 mutants were found to be unable to grow on OPEO n . In total, 42 separate disrupted genes were identified, and the proteins encoded by the genes were then classified into various categories, namely, information storage and processing (14.3%), cellular processes and signaling (28.6%), metabolism (35.7%), and unknown proteins (21.4%). The individual deletion of genes encoding isocitrate lyase (aceA), malate synthase (aceB), and glycolate dehydrogenase (glcE) was carried out, and the requirement for aceA and aceB but not glcE confirmed the role of the glyoxylate cycle in OPEO n degradation. Furthermore, acetaldehyde dehydrogenase and acetyl-coenzyme A (acetyl-CoA) synthetase activity levels were 13.2- and 2.1-fold higher in TX1 cells grown on OPEO n than in TX1 cells grown on succinate, respectively. Growth of the various mutants on different carbon sources was tested, and based on these findings, a mechanism involving exoscission to liberate acetaldehyde from the end of the OPEO n chain during degradation is proposed for the breakdown of OPEO n . IMPORTANCE Octylphenol polyethoxylates belong to the alkylphenol polyethoxylate (APEO n ) nonionic surfactant family. Evidence based on the analysis of intermediate metabolites suggested that the primary biodegradation of APEO n can be achieved by two possible pathways for the stepwise removal of the C2 ethoxylate units from the end of the chain. However, direct evidence for these hypotheses is still lacking. In this study, we described the use of transposon mutagenesis to identify genes critical to the catabolism of OPEO n by P. nitroreducens TX1. The exoscission of the ethoxylate chain leading to the liberation of acetaldehyde is proposed. Isocitrate lyase and malate synthase in glyoxylate cycle are required in the catabolism of ethoxylated surfactants. Our findings also provide many gene candidates that may help elucidate the mechanisms in stress responses to ethoxylated surfactants by bacteria.
Recognizing Disjoint Clinical Concepts in Clinical Text Using Machine Learning-based Methods

Clinical concept recognition (CCR) is a fundamental task in clinical natural language processing (NLP) field. Almost all current machine learning-based CCR systems can only recognize clinical concepts of consecutive words (called consecutive clinical concepts, CCCs), but can do nothing about clinical concepts of disjoint words (called disjoint clinical concepts, DCCs), which widely exist in clinical text. In this paper, we proposed two novel types of representations for disjoint clinical concepts, and applied two state-of-the-art machine learning methods to recognizing consecutive and disjoint concepts. Experiments conducted on the 2013 ShARe/CLEF challenge corpus showed that our best system achieved a "strict" F-measure of 0.803 for CCCs, a "strict" F-measure of 0.477 for DCCs, and a "strict" F-measure of 0.783 for all clinical concepts, significantly higher than the baseline systems by 4.2% and 4.1% respectively.
Effects of ghrelin in energy balance and body weight homeostasis

Ghrelin is a gut peptide composed of 28 amino acids mostly secreted in the gastric fundus mucosa. It was isolated and described in 1999 by Kojima et al. and only three years later its specific receptor, GHSR1a, was also identified. Ghrelin, the endogenous ligand for the GH secretagogue receptor, is the only peripheral orexigenic hormone that activates the receptors to be found especially in the appetite center (hypothalamus and pituitary gland). Ghrelin is present in human plasma in two forms: an inactive form known as deacylated ghrelin, and an active form called acylated ghrelin synthesized under the action of ghrelin O-acyltransferase enzyme (GOAT). The literature even mentions an extremely complex ghrelin/GOAT/GHSR system involved in the regulation of human energy, metabolism and adaptation of energy homeostasis to environmental changes. In humans, there is a preprandial rise and a postprandial fall in plasma ghrelin levels, which strongly suggest that the peptide plays a physiological role in meal initiation and may be employed in determining the amount and quality of ingested food. Besides the stimulation of food intake, ghrelin determines a decrease in energy expenditure and promotes the storage of fatty acids in adipocytes. Thus, in the human body ghrelin induces a positive energy balance, an increased adiposity gain, as well as an increase in caloric storage, seen as an adaptive mechanism to caloric restriction conditions. In the current world context, when we are witnessing an increasing availability of food and a reduction of energy expenditure to a minimum level, these mechanisms have become pathogenic. As a consequence, the hypothesis that ghrelin is involved in the current obesity epidemic has been embraced by many scholars and researchers
An Accurate System for Fashion Hand-Drawn Sketches Vectorization

Automatic vectorization of fashion hand-drawn sketches is a crucial task performed by fashion industries to speed up their workflows. Performing vectorization on hand-drawn sketches is not an easy task, and it requires a first crucial step that consists in extracting precise and thin lines from sketches that are potentially very diverse (depending on the tool used and on the designer capabilities and preferences). This paper proposes a system for automatic vectorization of fashion hand-drawn sketches based on Pearson's Correlation Coefficient with multiple Gaussian kernels in order to enhance and extract curvilinear structures in a sketch. The use of correlation grants invariance to image contrast and lighting, making the extracted lines more reliable for vectorization. Moreover, the proposed algorithm has been designed to equally extract both thin and wide lines with changing stroke hardness, which are common in fashion hand-drawn sketches. It also works for crossing lines, adjacent parallel lines and needs very few parameters (if any) to run. The efficacy of the proposal has been demonstrated on both hand-drawn sketches and images with added artificial noise, showing in both cases excellent performance w.r. t. the state of the art.
Aphid Infestation Increases Fusarium langsethiae and T-2 and HT-2 Mycotoxins in Wheat

ABSTRACT Fusarium langsethiae is a fungal pathogen of cereal crops that is an increasing problem in northern Europe, but much of its epidemiology is poorly understood. The species produces the mycotoxins T-2 and HT-2, which are highly toxic. It was hypothesized that grain aphids, Sitobion avenae, may transmit F. langsethiae inoculum between wheat plants, and a series of transmission experiments and volatile chemical analyses was performed to test this. Manual translocation of aphids from inoculated to uninfected hosts resulted in pathogen DNA accumulation in hosts. However, the free movement of wingless aphids from infected to healthy plants did not. The addition of winged aphids reared on F. langsethiae-inoculated wheat seedlings to wheat plants also did not achieve successful pathogen transfer. While our data suggested that aphid transmission of the pathogen was not very efficient, we observed an increase in disease when aphids were present. After seedling inoculation, an increase in pathogen DNA accumulation in seedling leaves was observed upon treatment with aphids. Furthermore, the presence of aphids on wheat plants with F. langsethiae-inoculated ears not only led to a rise in the amount of F. langsethiae DNA in infected grain but also to an increase in the concentrations of T-2 and HT-2 toxins, with more than 3-fold higher toxin levels than diseased plants without aphids. This work highlights that aphids increase the susceptibility of wheat host plants to F. langsethiae and that aphid infestation is a risk factor for accumulating increased levels of T-2 and HT-2 in wheat products. IMPORTANCE Fusarium langsethiae is shown here to cause increased contamination levels of grain with toxins produced by fungus when aphids share the host plant. This effect has also recently been demonstrated with Fusarium graminearum, yet the two fungal species show stark differences in their effect on aphid populations. In both cases, aphids improve the ability of the pathogens to cause and initiate Fusarium head blight (FHB) disease in wheat, but F. langsethiae may be able to act as a dispersal agent. F. langsethiae contributes harmful toxins to wheat grain that need to be controlled, but as yet, its epidemiology is unresolved. This work reveals insights into the role aphids play in promoting the successful colonization of this species in wheat and the benefit of controlling aphid populations on crops that are at high risk of FHB.
Everyone Is a Protagonist: Residue Conformational Preferences in High-Resolution Protein Structures

In many structural bioinformatics problems, there is a broad range of unanswered questions about protein dynamics and amino acid properties. Proteins are not strictly static objects, but rather populate ensembles of conformations. One way to understand these particularities is to analyze the information available in experimental databases. The Ramachandran plot, despite being more than half a century old, remains an utterly useful tool in the study of protein conformation. Based on its assumptions, we inspected a large data set (11,130 protein structures, amounting to 5,255,768 residues) and discriminated the conformational preferences of each residue type regarding their secondary structure participation. These data were studied for phi [Formula: see text], psi [Formula: see text], and side chain chi [Formula: see text] angles, being presented in non-Ramachandranian plots. In the largest analysis of protein conformation made so far, we propose an original plot to depict conformational preferences in relation to different secondary structure elements. Despite confirming previous observations, our results strongly support a unique character for each residue type, whereas also reinforcing the observation that side chains have a major contribution to secondary structure and, by consequence, on protein conformation. This information can be further used in the development of more robust methods and computational strategies for structural bioinformatics problems.
Excess Opioid Medication and Variation in Prescribing Patterns Following Common Orthopaedic Procedures

Background: Postoperative pain management in orthopaedic surgery accounts for a substantial portion of opioid medications prescribed in the United States. Understanding prescribing habits and patient utilization of these medications following a surgical procedure is critical to establishing appropriate prescribing protocols that effectively control pain while minimizing unused opioid distribution. We evaluated prescribing habits and patient utilization following elective orthopaedic surgical procedures to identify ways of improving postoperative opioid-prescribing practices. Methods: We performed a review of prescribing data of 1,199 procedures and gathered telephone survey results from 557 patients to determine the number of opioid pills prescribed postoperatively and the number of unused pills. The data were collected from adult patients who underwent 1 of the 5 most common elective orthopaedic procedures at our institution in fiscal year 2015: total hip arthroplasty, total knee arthroplasty, endoscopic carpal tunnel release, arthroscopic rotator cuff repair, or lumbar decompression. We converted all dosages to opioid equivalents of oxycodone 5 mg and performed analyses of prescribing patterns, patient utilization, and patient disposal of unused opioids. Results: Prescribing patterns following the 5 orthopaedic procedures showed wide variation. The median numbers of oxycodone 5-mg equivalent opioid pills prescribed upon discharge were 90 pills (range, 20 to 330 pills) for total hip arthroplasty, 90 pills (range, 10 to 200 pills) for total knee arthroplasty, 20 pills (range, 0 to 168 pills) for endoscopic carpal tunnel release, 80 pills (range, 18 to 100 pills) for arthroscopic rotator cuff repair, and 80 pills (range, 10 to 270 pills) for lumbar decompression. Thirty-seven percent of patients overall requested and received at least 1 refill. The mean number of total pills prescribed (and standard deviation) including refills was 113.6 ± 75.7 for total hip arthroplasty, 176.4 ± 108.0 for total knee arthroplasty, 24.3 ± 29.0 for carpal tunnel release, 98.2 ± 59.6 for rotator cuff repair, and 107.4 ± 64.4 for lumbar decompression. Participants reported unused opioid medication in 61% of cases. During the study year, >43,000 unused opioid pills were prescribed. Forty-one percent of patients reported appropriate disposal of unused opioid pills. Conclusions: Prescribing patterns vary widely, and a large amount of opioid medications remains unused following elective orthopaedic surgical procedures. Effective prescribing protocols are needed to limit this source of potential abuse and opioid diversion within the community.
Early class III protraction facemask treatment reduces the need for orthognathic surgery: a multi-centre, two-arm parallel randomized, controlled trial

Objective To evaluate whether patients who had received early class III protraction facemask treatment were less likely to need orthognathic surgery compared with untreated controls. This paper is a 6-year follow-up of a previous clinical trial. Design Multi-centre 2-arm parallel randomized controlled trial. Setting Eight United Kingdom hospital orthodontic departments. Participants Seventy three 7- to 9–year-old children. Method Patients were randomly allocated, stratified for gender, into an early class III protraction facemask group (PFG) (n = 35) and a control/no treatment group (CG) (n = 38). The primary outcome, need for orthognathic surgery was assessed by panel consensus. Secondary outcomes were changed in skeletal pattern, overjet, Peer Assessment Rating (PAR), self-esteem and the oral aesthetic impact of malocclusion. The data were compared between baseline (DC1) and 6-year follow-up (DC4). A per-protocol analysis was carried out with n = 32 in the CG and n = 33 in the PFG. Result Thirty six percent of the PFG needed orthognathic surgery, compared with 66% of the CG (P = 0.027). The odds of needing surgery was 3.5 times more likely when protraction facemask treatment was not used (odds ratio = 3.34 95% CI 1.21–9.24). The PFG exhibited a clockwise rotation and the CG an anti-clockwise rotation in the maxilla (regression coefficient 8.24 (SE 0.75); 95% CI 6.73–9.75; P < 0.001) and the mandible (regression coefficient 6.72 (SE 0.73); 95% CI 5.27–8.18; P < 0.001). Sixty eight per cent of the PFG maintained a positive overjet at 6-year follow-up. There were no statistically significant differences between the PFG and CG for skeletal/occlusal improvement, self-esteem or oral aesthetic impact. Conclusions Early class III protraction facemask treatment reduces the need for orthognathic surgery. However, this effect cannot be explained by the maintenance of skeletal cephalometric change.
Numerical simulation of breast reduction with a new knitting condition

Breast reduction is one of the most common procedures in breast surgery. The aim of this work is to develop a computational model allowing one to forecast the final breast geometry according to the incision marking parameters. This model can be used in surgery simulators that provide preoperative planning and training, allowing the study of the origin of the errors in breast reduction. From the mathematical point of view, this is a problem of calculus of variations with unusual boundary conditions, known as knitting conditions. The breast tissue is considered as a hyperelastic material, discretized with three‐dimensional finite elements for the body, whereas the skin is modelled with two‐dimensional finite elements on the curved surface. Although the model is of low precision, we show that it is sufficient for a satisfactory prediction of breast reduction surgery results, allowing an analysis of errors frequently performed during the surgery and giving an understanding of how to avoid or correct them. Copyright © 2016 John Wiley & Sons, Ltd.
Tongue-Palate Contact Timing during /s/ and /z/ in English

Abstract Although numerous studies have investigated supraglottal strategies for signalling voicing in fricatives, there is still no agreement about the precise characteristics of tongue-to-palate contact timing during voiced as opposed to voiceless fricatives. In this study we use electropalatography (EPG) to investigate articulatory and coarticulatory characteristics of tongue-to-palate contact timing during /s/ and /z/ in English. Five typically speaking participants, speakers of Southern British English, produced 500 trochaic words containing the intervocalic alveolar fricatives /s/ or /z/. The time between the start of the frication and the maximum contact at the place of articulation was expressed as a percentage of each fricative's total duration (time to target, TT). This measure was used to analyse articulatory and coarticulatory timing during /s/ and /z/. Data for absolute timing were also presented. The results showed that the time between the start of the frication and the maximum contact point was longer for /s/ than for /z/. This difference was consistent across speakers but was not significant for all of them. The results of the coarticulatory effects showed that the influence of vowel context on TT values for /s/ and /z/ did not differ significantly, but there was a tendency for /z/ to be more resistant to coarticulation effects than /s/.
A Novel Intestine Model Apparatus for Drug Dissolution Capable of Simulating the Peristaltic Action

A novel dissolution apparatus has been proposed as an alternative apparatus for dissolution testing. In this study, we evaluated the performance of the new intestine model for simulating the peristaltic action (IMSPA), generating the movement that closely mimics peristaltic contractions of the small intestine. Two polyethylene oxide matrix tablet formulations, containing a model drug belonging to class III of the Biopharmaceutics Classification System, were tested. Dissolution was also performed in the USP2 apparatus. The release profiles were further compared to the in vivo data to evaluate the in vivo relevance of the new apparatus. The results demonstrated that the novel apparatus showed good discriminatory power between different polyethylene oxide formulations. Moreover, a better relation to the in vivo data was established by the IMSPA as compared to the USP2 apparatus. In conclusion, the model parameters were efficiently controlled to ensure the dissolution conditions crucial for evaluating the in vivo release performance of the tested formulations.
A prospective study on the variation in falling and fall risk among community-dwelling older citizens in 12 European countries

Objectives The rate of falling among older citizens appears to vary across different countries, but the underlying aspects causing this variation are unexplained. We aim to describe between-country variation in falling and explore whether intrinsic fall risk factors can explain possible variation. Design Prospective study on data from the cross-national Survey of Health, Ageing and Retirement in Europe (SHARE). Setting Twelve European countries (Austria, Belgium, Czech Republic, Denmark, Estonia, France, Germany, Italy, The Netherlands, Spain, Sweden, Switzerland). Participants Community-dwelling persons aged ≥65 years (n=18 596). Measurements Socio-demographic factors (age, gender, education level and living situation) and intrinsic fall risk factors (less than good self-rated health (SRH), mobility limitations, limitations with activities of daily living (ADL), dizziness, impaired vision, depression and impaired cognition) were assessed in a baseline interview. Falling was assessed 2 years later by asking whether the participant had fallen within the 6 months prior to the follow-up interview. Results There was significant between-country variation in the rate of falling (varying from 7.9% in Switzerland to 16.2% in the Czech Republic). The prevalence of intrinsic fall risk factors varied twofold to fourfold between countries. Associations between factors age ≥80 years, less than good SRH, mobility limitations, ADL limitations, dizziness and depression, and falling were different between countries (p<0.05). Between-country differences in falling largely persisted after adjusting for socio-demographic differences but strongly attenuated after adjusting for differences in intrinsic fall risk factors. Conclusion There is considerable variation in the rate of falling between European countries, which can largely be explained by between-country variation in the prevalence of intrinsic fall risk factors. There are also country-specific variations in the association between these intrinsic risk factors and falling. These findings emphasise the importance of addressing intrinsic fall risk in (inter)national fall-prevention strategies, while highlighting country-specific priorities.
Role of color Doppler ultrasonography in the preoperative management of cold thyroid nodules.

OBJECTIVE To evaluate the application of color flow Doppler (CFD) sonography in the preoperative management of benign and malignant cold thyroid nodules. DESIGN Eighty-five patients with a cold thyroid nodule larger than 1cm were examined with CFD sonography prior to thyroidectomy. The histological examination revealed that 18 (21%) patients had malignant nodules and 67 (79%) had benign ones. The sonographic characteristics of the nodules used for evaluation were: a) absence of vascularization, b) presence of peripheral vascularization, c) presence of central vascularization and d) size of the nodule. The correlations between the pre-operative sonographic characteristics, as defined above, and the histological findings of the nodules were determined. results: The results showed that the vascular signals were absent in 4/18 (22%) of malignant nodules and 16/67 (23%) of benign ones. The smaller nodules (<2.5 cm.) were more frequently avascular (15/37=40%) compared to the larger ones (5/48=10%) (p<0.05). Moreover, for the nodules with vascularization, the peripheral distribution of vascularization was more frequently encountered in benign nodules (p<0.01 specificity=0.77, sensitivity=0.46), while central vascularization was more frequent in malignant ones (p<0.01, specificity=0.70, sensitivity=0.66). Thus, absence of vascularization in a nodule does not exclude the probability of malignancy, since vascularization depends on the size rather than the histological features of the nodule. Furthermore, for the vascularized nodules, peripheral distribution of vascularization is a characteristic of benignancy with high specificity, while central distribution is a characteristic of malignancy with medium specificity. CONCLUSIONS CFD sonography contributes to the differential diagnosis of the large vascularized nodules, but it is less helpful in the smaller non-vascularized ones.