Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural outlier detection for automatic landmark extraction

The aim of this paper is to introduce a structural dissimilarity measure which allows to detect outliers in automatically extracted landmark pairs in two images. In previous work, to extract landmarks automatically, candidate points have been defined using invariance criteria coming from differential geometry such as maximum curvature; or they are statistical entities such as gravity centers of confiners, where the confiners are defined as the connected components of the level sets. After a first estimation of the semi-rigid transformation (representing translation, rotation, and scaling) relating the candidate point sets, outliers are detected applying the euclidian distance between corresponding points. However, this approach does not allow to distinguish between real deformations and outliers coming from noise or additional features in one of the images. In this paper, we define a structural dissimilarity measure which we use to decide if two associated candidate points come from two corresponding confiners. We select landmarks pairs with a dissimilarity value smaller than a given threshold and we calculate the affine transformation relating best all selected landmark pairs. We evaluated our technique on successive slices of a MRI image of the human brain and show that we obtain a significantly sharper error diminution using the new dissimilarity measure instead of the euclidian distance for outlier rejection.
New approach to evaluate rotation of cervical vertebrae

Functional deficits after whiplash injury can be analyzed with a quite novel radiologic method by examination of joint-blocks in C0/1 and C1/2. Thereto the movability of C0, C1 and C2 is determined with three spiral CT-scans of the patient's cervical spine. One series in neutral and one in maximal active lateral right and left rotation each. Previous methods were slice based and time consuming when manually evaluated. We propose a new approach to a computation of these angles in 3D. After a threshold segmentation of bone tissue, a rough 2D classification takes place for C0, C1 and C2 in each rotation series. The center of an axial rotation for each vertebra is gained from the approximation of its center of gravity. The rotation itself is estimated by a cross-correlation of the radial distance functions. From the previous rotation the results are taken to initialize a 3D matching algorithm based on the sum of squared differences in intensity. The optimal match of the vertebrae is computed by means of the multidimensional Powell minimization algorithm. The three translational and three rotational components build a six-dimensional search-space. The vertebrae detection and rotation computation is done fully automatic.
Silent Neoplastic Cardiac Invasion in Small Cell Lung Cancer: A Case Report and Review of the Literature

Patient: Female, 66 Final Diagnosis: Small cell lung cancer Symptoms: Impaired memory Medication: — Clinical Procedure: Chest X-ray • computed tomography • magnetic resonance imaging • electrocardiogram Specialty: Oncology Objective: Rare co-existance of disease or pathology Background: Secondary malignant tumor of the heart is one of the most life-threatening complications of lung cancer. Several published case reports have documented non-small cell lung cancer (NSCLC) patients with neoplastic cardiac invasion. However, the number of reported cases of small cell lung cancer (SCLC) with neoplastic cardiac invasion is limited. Case Report: We present a rare case of advanced SCLC in a patient with asymptomatic neoplastic cardiac invasion. We also discuss radiation therapy modalities that should be considered in SCLC patients with cardiac invasion. Conclusions: Clinicians should be vigilant about cases of SCLC with asymptomatic intra-cardiac invasion and practice caution when diagnosing, as well as treating with radiation as a monotherapy.
Korean Journal for Food Science of Animal Resources

We evaluated the physicochemical and storage characteristics of Hanwoo Tteokgalbi treated with onion skin powder (OSP) and blackcurrant fruit powder (BFP). The experimental design included seven treatments: a control (ascorbic acid 0.1%), T1: OSP 0.3%, T2: OSP 0.6%, T3: BFP 0.3%, T4: BFP 0.6%, T5: OSP 0.15%+BFP 0.15%, and T6: OSP 0.3%+BFP 0.3%. The OSP was higher in both polyphenol and flavonoid contents compared to BFP (p<0.05). The moisture and ash contents of all Tteokgalbi samples with a large amount of added natural antioxidant powder (0.6%) were higher than those with small amounts of added antioxidant (0.3%). The cooking loss and water holding capacity were outstanding in the T2 treatment compared to the others (p<0.05). The lightness, redness, and yellowness values were reduced on the addition of 0.6% antioxidant powder (p<0.05). The springiness and cohesiveness values of the Tteokgalbi samples were higher for the 0.3% addition than the control and 0.6% addition (p<0.05). The Tteokgalbi samples with natural antioxidants showed similar sensory attribute scores compared to the control. The pH values reduced as the BFP increased (p<0.05), and the total microbial count increased after OSP addition. The 2-thiobarbituric acid reactive substance values of the samples treated with OSP were significantly lower than the control after day 10 (p<0.05). As a result, the addition of OSP or BFP did not have a significant negative influence on the quality characteristics of Hanwoo Tteokgalbi. In particular, the addition of 0.6% OSP was effective in increasing water retentivity and inhibiting lipid oxidation.
The relative importance of climate and vegetation properties on patterns of North American breeding bird species richness

Recent advances in remote sensing and ecological modeling warrant a timely and robust investigation of the ecological variables that underlie large-scale patterns of breeding bird species richness, particularly in the context of intensifying land use and climate change. Our objective was to address this need using an array of bioclimatic and remotely sensed data sets representing vegetation properties and structure, and other aspects of the physical environment. We first build models of bird species richness across breeding bird survey (BBS) routes, and then spatially predict richness across the coterminous US at moderately high spatial resolution (1 km). Predictor variables were derived from various sources and maps of species richness were generated for four groups (guilds) of birds with different breeding habitat affiliation (forest, grassland, open woodland, scrub/shrub), as well as all guilds combined. Predictions of forest bird distributions were strong (R2 = 0.85), followed by grassland (0.76), scrub/shrub (0.63) and open woodland (0.60) species. Vegetation properties were generally the strongest determinants of species richness, whereas bioclimatic and lidar-derived vertical structure metrics were of variable importance and dependent upon the guild type. Environmental variables (climate and the physical environment) were also frequently selected predictors, but canopy structure variables were not as important as expected based on more local to regional scale studies. Relatively sparse sampling of canopy structure metrics from the satellite lidar sensor may have reduced their importance relative to other predictor variables across the study domain. We discuss these results in the context of the ecological drivers of species richness patterns, the spatial scale of bird diversity analyses, and the potential of next generation space-borne lidar systems relevant to vegetation and ecosystem studies. This study strengthens current understanding of bird species–climate–vegetation relationships, which could be further advanced with improved canopy structure information across spatial scales.
Elementary Teachers' Commitment Declines: Antecedents, Processes, and Outcomes

This qualitative study examines the organizational, social, and personal factors that may influence elementary teachers' declining commitments. Our findings suggest that when the teachers under study felt unsuccessful, that is, when they experienced low feelings of efficacy and low feelings of community, teachers' commitments' shifted or declined. However, the impact of negative teaching experiences on commitments is far from uniform. Rather the teachers' commitments declined as a function of the teachers' understandings of their perceived failures. This article is available in The Qualitative Report: http://nsuworks.nova. edu/tqr/vol6/iss1/3 Elementary Teachers' Commitment Declines: Antecedents, Processes, and Outcomes by Christine Joffres & Margaret Haughey + The Qualitative Report, Volume 6, Number 1 March, 2001 (http://www.nova.edu/ssss/QR/QR6-1/joffres.html)
fficient in vitro synthesis of cis-polyisoprenes using a thermostable is-prenyltransferase from a hyperthermophilic archaeon Thermococcus odakaraensis

The Tk-idsB encoding cis-prenyltransferase which catalyzes consecutive cis-condensation of isopentenyl diphosphate to allylic diphosphate was isolated from a hyperthermophilic archaeon Thermococcus kodakaraensis, and enzymatic characteristics of the recombinant Tk-IdsB were examined. Tk-IdsB was not fully denatured even at 90 ◦C and preferably utilizes both C10 and C15 allylic diphosphates to yield mainly the C60–C65 products. Based on structural models, single alanine-substitution mutants at Glu68, Lys109, or Leu113 were constructed, showing that all the three produced longer chains (C65–C70) than the wild-type and the substitution at 109 (K109A) was the most effective. Tk-IdsB was applied to an organic-aqueous sopentenyl diphosphate rganic-aqueous dual-phase system hermococcus kodakaraensis dual-phase system and more than 90% of the products were recovered from the organic phase when 1-butanol or 1-pentanol was overlaid. When 1-octanol was overlaid, 70% of the products were obtained from the upper organic phase. The product distributions were changed depending on the hydrophobicity of organic solvents used. Tk-IdsB was then immobilized onto silica beads to make Tk-IdsB more tolerant, showing that half-life of enzyme at 80 ◦C was prolonged by immobilization. When the immobilized TkIdsB was applied in the organic-aqueous dual-phase system, immobilized Tk-IdsB catalyzed consecutive ently condensation more effici
Identification of Landscape Preferences by Using Social Media Analysis

People attribute different values to landscapes. These values are due to people's preferences, which are shaped by aesthetics, recreational benefits, safety, and other features of landscapes. Classic methods for studying landscape preferences include surveys and questionnaires, where study participants score or evaluate photos. Since almost 70% of US adults use social media to connect with friends and families, or to follow news and topics of interest (Pew research, 2015), research is needed to identify whether social media postings provide useful information about preferences for landscape settings. In this paper, we label text comments from Flickr, Instagram, and Twitter to train a lexicon-based sentiment classification model for predicting people's sentiments about green infrastructures, which are a specific landscape element. The results show a 77% correlation between text based sentiments from social media and image based landscape preferences.
Determination of Soil Water Stress Coefficient by different Methods for Computing Crop Transpiration Under Bed Planted Pigeon Pea

To achieve the potential crop yield, time and amount of irrigation required for a particular crop under field condition should be quantified. Since soil water stress occurs after few days of irrigation, it affects root water uptake and hence transpiration rate. This stress effect can be quantified by soil water stress coefficient (Ks). Whenever, total available water (TAW) and readily available water (RAW) data are available, a simple Ks calculation can be done. To present a more realistic scenario, Ks can also be computed from simulated root water uptake (RWU) using HYDRUS-2D model. To check the reliability of model, our study was conducted under permanent raised bed with residue (PBB+R) and conventional tillage (CT) system in a pigeonpea (Cajanus cajan (L.) Millsp. )-wheat (Triticum aestivum) cropping system with the objective to compare actual measured transpiration rate with those simulated from model and calculated from FAO method. Soil water balance simulated (100-125 DAS) from HYDRUS-2D model showed higher cumulative root water uptake (CRWU) (1.72 cm), lower cumulative evaporation (CE) (0.34 cm) and higher soil water retention in PBB+R than in CT. Ks calculated from both the methods showed that under low soil moisture condition in root zone, Ks significantly reduced RWU whereas when root zone is sufficiently wet, Ks have very negligible effect. Model simulated actual transpiration rates were comparable with observed values whereas values computed from FAO method showed substantial deviation. Thus Ks obtained from model output showed the better soil moisture stress condition of the profile as it takes into account root growth parameters, radiation interception and crop canopy conditions. So, this model may be adopted for evaluating different management practices in terms of improvement in soil water use.
Deformation of Red Blood Cells, Air Bubbles, and Droplets in Microfluidic Devices: Flow Visualizations and Measurements

Techniques, such as micropipette aspiration and optical tweezers, are widely used to measure cell mechanical properties, but are generally labor-intensive and time-consuming, typically involving a difficult process of manipulation. In the past two decades, a large number of microfluidic devices have been developed due to the advantages they offer over other techniques, including transparency for direct optical access, lower cost, reduced space and labor, precise control, and easy manipulation of a small volume of blood samples. This review presents recent advances in the development of microfluidic devices to evaluate the mechanical response of individual red blood cells (RBCs) and microbubbles flowing in constriction microchannels. Visualizations and measurements of the deformation of RBCs flowing through hyperbolic, smooth, and sudden-contraction microchannels were evaluated and compared. In particular, we show the potential of using hyperbolic-shaped microchannels to precisely control and assess small changes in RBC deformability in both physiological and pathological situations. Moreover, deformations of air microbubbles and droplets flowing through a microfluidic constriction were also compared with RBCs deformability.
Opioid Use Disorders: Perioperative Management of a Special Population

Opioid-related overdose deaths have reached epidemic levels within the last decade. The efforts to prevent, identify, and treat opioid use disorders (OUDs) mostly focus on the outpatient setting. Despite their frequent overrepresentation, less is known about the inpatient management of patients with OUDs. Specifically, the perioperative phase is a very vulnerable time for patients with OUDs, and little has been studied on the optimal management of acute pain in these patients. The preoperative evaluation should aim to identify those with OUDs and assess factors that may interfere with OUD treatment and pain management. Efforts should be made to provide education and assistance to patients and their support systems. For those who are actively struggling with opioid use, the perioperative phase can be an opportunity for engagement and to initiate treatment. Buprenorphine, methadone, and naltrexone medication treatment for OUD and opioid tolerance complicate perioperative pain management. A multidisciplinary team approach is crucial to provide clinically balanced pain relief without jeopardizing the patient’s recovery. This article reviews the existing literature on the perioperative management of patients with OUDs and provides clinical suggestions for the optimal care of this patient population.
A survey of transcriptome complexity in Sus scrofa using single-molecule long-read sequencing

Abstract Alternative splicing (AS) and fusion transcripts produce a vast expansion of transcriptomes and proteomes diversity. However, the reliability of these events and the extend of epigenetic mechanisms have not been adequately addressed due to its limitation of uncertainties about the complete structure of mRNA. Here we combined single-molecule real-time sequencing, Illumina RNA-seq and DNA methylation data to characterize the landscapes of DNA methylation on AS, fusion isoforms formation and lncRNA feature and further to unveil the transcriptome complexity of pig. Our analysis identified an unprecedented scale of high-quality full-length isoforms with over 28,127 novel isoforms from 26,881 novel genes. More than 92,000 novel AS events were detected and intron retention predominated in AS model, followed by exon skipping. Interestingly, we found that DNA methylation played an important role in generating various AS isoforms by regulating splicing sites, promoter regions and first exons. Furthermore, we identified a large of fusion transcripts and novel lncRNAs, and found that DNA methylation of the promoter and gene body could regulate lncRNA expression. Our results significantly improved existed gene models of pig and unveiled that pig AS and epigenetic modify were more complex than previously thought.
ClusterEnG: an interactive educational web resource for clustering and visualizing high-dimensional data

Background Clustering is one of the most common techniques in data analysis and seeks to group together data points that are similar in some measure. Although there are many computer programs available for performing clustering, a single web resource that provides several state-of-the-art clustering methods, interactive visualizations and evaluation of clustering results is lacking. Methods ClusterEnG (acronym for Clustering Engine for Genomics) provides a web interface for clustering data and interactive visualizations including 3D views, data selection and zoom features. Eighteen clustering validation measures are also presented to aid the user in selecting a suitable algorithm for their dataset. ClusterEnG also aims at educating the user about the similarities and differences between various clustering algorithms and provides tutorials that demonstrate potential pitfalls of each algorithm. Conclusions The web resource will be particularly useful to scientists who are not conversant with computing but want to understand the structure of their data in an intuitive manner. The validation measures facilitate the process of choosing a suitable clustering algorithm among the available options. ClusterEnG is part of a bigger project called KnowEnG (Knowledge Engine for Genomics) and is available at http://education.knoweng. org/clustereng.
One-at-a-time: A Meta-Learning Recommender-System for Recommendation-Algorithm Selection on Micro Level

The effectiveness of recommendation algorithms is typically assessed with evaluation metrics such as root mean square error, F1, or click through rates, calculated over entire datasets. The best algorithm is typically chosen based on these overall metrics. However, there is no single-best algorithm for all users, items, and contexts. Choosing a single algorithm based on overall evaluation results is not optimal. In this paper, we propose a meta-learning-based approach to recommendation, which aims to select the best algorithm for each user-item pair. We evaluate our approach using the MovieLens 100K and 1M datasets. Our approach (RMSE, 100K: 0.973; 1M: 0.908) did not outperform the single-best algorithm, SVD++ (RMSE, 100K: 0.942; 1M: 0.887). We also develop a distinction between meta-learners that operate per-instance (micro-level), per-data subset (mid-level), and per-dataset (global level). Our evaluation shows that a hypothetically perfect micro-level meta-learner would improve RMSE by 25.5% for the MovieLens 100K and 1M datasets, compared to the overall-best algorithms used.
A Case of Right-Sided Ulcerative Colitis with Mesalamine-Induced Hypersensitivity Reactions

Patient: Female, 56 Final Diagnosis: Right-sided ulcerative colitis • mesalamine-induced hypersensitivity Symptoms: High fever • vague discomfort of the upper abdomen Medication: Mesalamine Clinical Procedure: — Specialty: Gastroenterology and Hepatology Objective: Unusual clinical course Background: Ulcerative colitis (UC) is a chronic inflammatory bowel disease, affecting the colon continuously from the rectum proximally. However, a clinical type with right-sided colitis sparing the anal side of the colon is also known. Mesalamine, which is generally used to treat UC, can rarely aggravate the disease. Case Report: A 56-year-old woman with no history of colonic diseases visited our hospital because of a positive fecal occult blood test. The first colonoscopy showed inflamed and edematous mucosa extending from the ascending colon to the right-half of the transverse colon. Colonic biopsy specimens demonstrated infiltrations of chronic inflammatory cells in the mucosa and crypt abscesses, but no epithelioid granulomas, compatible with UC. She was highly positive for PR3-ANCA, confirming the diagnosis of UC. After starting mesalamine, she had hypersensitivity reactions and aggravations of UC, which were confirmed endoscopically. Conclusions: Right-sided colitis may be a subgroup of UC, and this is the first report of this type of disease complicated by aggravation due to mesalamine hypersensitivity.
Spud DB: A Resource for Mining Sequences, Genotypes, and Phenotypes to Accelerate Potato Breeding

Potato is the world's third most important crop, and is becoming increasingly important in developing countries. Cultivated potato is a highly heterozygous tetraploid (2n = 4x = 48) and suffers from significant inbreeding depression when selfed. As potato can be vegetatively propagated, breeding has been based primarily on phenotypic selection in F1 populations. However, recent advances in genome sequencing and genotyping methods have resulted in the development of large genomic, genetic, and phenotypic datasets that will enable more efficient and rapid breeding approaches. We have developed Spud DB (http://potato.plantbiology.msu.edu/) for the community to access the potato genome sequence and associated annotation datasets, along with phenotypic and genotypic data from a diversity panel of 250 potato clones. The Breeder's Assistant is a web tool to retrieve pertinent phenotypic and genotypic data in a user‐guided manner, and query polymorphic markers such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) to identify custom sets of markers for a gene or region of interest. To browse and query the potato genome, a genome browser with 94 tracks of genome annotation, sequence variants, and expression abundance has been deployed. Spud DB also provides a comprehensive search page to data mine the potato genome through tools that query sequence identifiers, functional annotation, gene ontology (GO), InterPro domains, and basic local alignment search tool (BLAST) databases. Collectively, this resource links potato genomic data with phenotypic and genotypic data from a large collection of potato lines for use by the potato community, especially breeders and geneticists.