Miracle-dz/UniFAR-FTUs huggingface dataset:
Phenotypes of Severe Cutaneous Adverse Reactions Caused by Nonsteroidal Anti-inflammatory Drugs

Purpose Nonsteroidal anti-inflammatory drugs (NSAIDs) are common cause of severe cutaneous adverse reactions (SCARs). The present study aimed to investigate the characteristics of SCARs induced by NSAIDs in the Korean SCAR registry. Methods A retrospective survey of NSAID-induced SCARs recorded between 2010 and 2015 at 27 university hospitals in Korea was conducted. Clinical phenotypes of SCARs were classified into Stevens-Johnson syndrome (SJS), toxic epidermal necrolysis (TEN), SJS-TEN overlap syndrome and drug reaction with eosinophilia and systemic symptoms (DRESS). Causative NSAIDs were classified into 7 groups according to their chemical properties: acetaminophen, and propionic, acetic, salicylic, fenamic and enolic acids. Results A total of 170 SCARs, consisting of 85 SJS, 32 TEN, 17 SJS-TEN overlap syndrome and 36 DRESS reactions, were induced by NSAIDs: propionic acids (n=68), acetaminophen (n=38), acetic acids (n=23), salicylic acids (n=16), coxibs (n=8), fenamic acids (n=7), enolic acids (n=5) and unclassified (n=5). Acetic acids (22%) and coxibs (14%) accounted for higher portions of DRESS than other SCARs. The phenotypes of SCARs induced by both propionic and salicylic acids were similar (SJS, TEN and DRESS, in order). Acetaminophen was primarily associated with SJS (27%) and was less involved in TEN (10%). DRESS occurred more readily among subjects experiencing coxib-induced SCARs than other NSAID-induced SCARs (62.5% vs. 19.7%, P = 0.013). The mean time to symptom onset was longer in DRESS than in SJS or TEN (19.1 ± 4.1 vs. 6.8 ±1.5 vs. 12.1 ± 3.8 days). SCARs caused by propionic salicylic acids showed longer latency, whereas acetaminophen- and acetic acid-induced SCARs appeared within shorter intervals. Conclusions The present study indicates that the phenotypes of SCARs may differ according to the chemical classifications of NSAIDs. To establish the mechanisms and incidences of NSAID-induced SCARs, further prospective studies are needed.
Assessment of a Watch-and-Wait Strategy for Rectal Cancer in Patients With a Complete Response After Neoadjuvant Therapy

Importance The watch-and-wait (WW) strategy aims to spare patients with rectal cancer unnecessary resection. Objective To analyze the outcomes of WW among patients with rectal cancer who had a clinical complete response to neoadjuvant therapy. Design, Setting, and Participants This retrospective case series analysis conducted at a comprehensive cancer center in New York included patients who received a diagnosis of rectal adenocarcinoma between January 1, 2006, and January 31, 2015. The median follow-up was 43 months. Data analyses were conducted from June 1, 2016, to October 1, 2018. Exposures Patients had a clinical complete response after completing neoadjuvant therapy and agreed to a WW strategy of active surveillance and possible salvage surgery (n = 113), or patients underwent total mesorectal excision and were found to have a pathologic complete response (pCR) at resection (n = 136). Main Outcomes and Measures Kaplan-Meier estimates were used for analyses of local regrowth and 5-year rates of overall survival, disease-free survival, and disease-specific survival. Results Compared with the 136 patients in the pCR group, the 113 patients in the WW group were older (median [range], 67.2 [32.1-90.9] vs 57.3 [25.0-87.9] years, P < .001) with cancers closer to the anal verge (median [range] height from anal verge, 5.5 [0.0-15.0] vs 7.0 [0.0-13.0] cm). All 22 local regrowths in the WW group were detected on routine surveillance and treated by salvage surgery (20 total mesorectal excisions plus 2 transanal excisions). Pelvic control after salvage surgery was maintained in 20 of 22 patients (91%). No pelvic recurrences occurred in the pCR group. Rectal preservation was achieved in 93 of 113 patients (82%) in the WW group (91 patients with no local regrowths plus 2 patients with local regrowths salvaged with transanal excision). At 5 years, overall survival was 73% (95% CI, 60%-89%) in the WW group and 94% (95% CI, 90%-99%) in the pCR group; disease-free survival was 75% (95% CI, 62%-90%) in the WW group and 92% (95% CI, 87%-98%) in the pCR group; and disease-specific survival was 90% (95% CI, 81%-99%) in the WW group and 98% (95% CI, 95%-100%) in the pCR group. A higher rate of distant metastasis was observed among patients in the WW group who had local regrowth vs those who did not have local regrowth (36% vs 1%, P < .001). Conclusions and Relevance A WW strategy for select rectal cancer patients who had a clinical complete response after neoadjuvant therapy resulted in excellent rectal preservation and pelvic tumor control; however, in the WW group, worse survival was noted along with a higher incidence of distant progression in patients with local regrowth vs those without local regrowth.
Relative effects of age on implant integration in a rat model: A longitudinal in vivo microct study

The effect of age on implant fixation in bone is not always considered during the design of preclinical models. The decision on animal's age is often related to practical or historical reasons, which ultimately may affect the reproducibility of results. This study aimed to quantify the effect of age by monitoring the fixation of contrast‐enhanced PEEK screws in rats, hypothesizing that the kinetics of fixation is impaired in older animals but that age effects are less severe than osteoporotic effects. The time course of implant fixation was investigated in healthy rats at 24, 40, and 60 weeks of age; and in ovariectomized rats. Implant fixation was monitored using in‐vivo microCT and dynamic histomorphometry during 1 month. The rats were euthanized 28 days post screw insertion. The data was analyzed both in absolute value and after normalization to baseline bone mass. In absolute terms, greater age had a detrimental effect on bone implant contact, bone fraction, implant stiffness, and bone remodeling but less than ovariectomy. Interestingly, once data was normalized to baseline bone mass this effect disappeared, suggesting that the physiologic response to implant placement was not affected by age. In conclusion, implant fixation kinetics is less affected by age than by baseline bone mass in this rat model. Animals of different ages can therefore be compared but data must be construed relatively to baseline bone mass and not in absolute terms. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 9999:1–12, 2018.
Consistency tradeoffs on distributed multi-datacentric systems

Distributed systems in the cloud computing context spread data across geographically remote datacenters to ensure always availability, scalability, and a best reactivity. Choosing latter properties in these systems leads to consistency issues (version conflicts, obsolete data, etc.); besides, most analytical solutions suggested for these issues are incomplete. SCOLCH proposes tradeoffs to achieve the required properties for service level agreement in cloud computing. Keywords— multi-datacentric systems; consistency; convergence; latency; availability
IL-9 exacerbates the development of chronic obstructive pulmonary disease through oxidative stress.

OBJECTIVE To investigate the role of IL-9 in chronic obstructive pulmonary disease (COPD), and to explore its potential mechanism. MATERIALS AND METHODS A mouse COPD model was established by exposure to cigarette smoke. COPD mice were then randomly assigned into two groups, including: the PBS group and the IL-9 antibody group. The above two groups were treated with phosphate-buffered saline (PBS) or IL-9 injection, respectively. The histopathological changes in lung tissues of mice were observed by hematoxylin-eosin (H&E) staining. Immunohistochemistry was performed to detect IL-9-positive (IL-9+) cells in lung tissues. Expression levels of IL-9, sIL-9R, STAT3, and p-STAT3 in peripheral blood of mice were determined by quantitative Real time-polymerase chain reaction (qRT-PCR), enzyme-linked immunosorbent assay (ELISA), and Western blot, respectively. In addition, the expression levels of superoxide dismutase (SOD), malondialdehyde (MDA), and reactive oxygen species (ROS) were detected. RESULTS H&E staining results showed that the airway wall structure of COPD mice in the PBS group was irregular. Ciliated columnar epithelium exhibited marked degeneration, necrosis and shedding. Besides, numerous inflammatory cell infiltration, narrowing and rupture of the alveolar septa, and larger cysts fused by adjacent alveoli were observed. H&E staining also indicated that the structure of alveolar epithelium was severely impaired in COPD mice. However, the pathological changes in lung tissues of mice in the IL-9 antibody group were much milder than those of the PBS group. Immunohistochemistry results showed a significant deposition of IL-9+ cells in the lung tissues of the PBS group. Meanwhile, the mRNA and protein levels of IL-9, sIL-9R, and p-STAT3 in the PBS group were also remarkably higher than those of the IL-9 antibody group. In addition, SOD content in the PBS group was significantly decreased, whereas the levels of MDA and ROS were significantly increased than those of the IL-9 antibody group. CONCLUSIONS IL-9 activated STAT3 and aggravated lung injury in COPD mice by increasing inflammatory and oxidative stress.
Serum Calprotectin in Adolescents With Inflammatory Bowel Disease—A Pilot Investigation

Objectives: Fecal calprotectin (FC) is a well-integrated parameter in the monitoring of adolescent patients with inflammatory bowel disease (IBD). However, measurement of FC is limited by day-to-day-variation and by the feces consistency. Furthermore, adolescents are often noncompliant to deliver fecal sampling leading to suboptimal monitoring. Consequently, we see the need of a substitute biomarker whenever measurement of FC fails and aimed to investigate serum calprotectin (SC) in adolescents with IBD. Methods: In cross sectional data from 19 ulcerative colitis (UC) patients <18 years old, a Spearman correlation was used to analyze the correlation between SC, FC, C-reactive protein (CRP) and endoscopic and symptom scores. In longitudinal data collected from 20 UC and Crohn disease (CD) patients (10–17 years old), Mixed Effect Models (MEM) were used to analyze the association between SC, FC, CRP, and symptom scores. Results: We found positive correlations between SC (19 samples) and the endoscopic score, symptom score, and CRP (r = 0.56, P = 0.01; r = 0.64, P = 0.003; r = 0.97, P < 0.0001). We found no significant correlation between SC and FC. In 27 samples from UC patients, the association of SC with FC and CRP were positive and significant (P = 0.004, estimate = 0.32; P = 0.0001, estimate = 0.002). The association between SC and symptom score was insignificant. In 49 samples from CD patients, the association between SC and CRP was significant (P = 0.02, estimate = 0.002) whereas associations between SC and FC and symptom score were insignificant. Conclusions: In the current pilot study, we found a correlation between SC and the endoscopically assessed inflammation in UC. SC may have the potential to improve disease monitoring of adolescent patients.
Altered brain volume and its relationship to characteristics of carotid plaques in asymptomatic patients

Abstract Carotid plaque is an aggregate marker of exposure to vascular risk factors, which are linked to structural brain changes. We investigated prestroke global and regional changes in brain volume in a carotid plaque population of cognitively healthy individuals and the association between carotid plaque characteristics and these changes. A total of 76 participants were divided into healthy control (HC, n = 28), vulnerable plaque (n = 27) and stable plaque groups (n = 21). All subjects underwent carotid ultrasound and brain magnetic resonance imaging (MRI). Voxel-based morphometry (VBM) was used to examine differences in regional gray matter volumes (rGMVs) among the different groups. The plaque group had a significantly lower mean total cerebral brain volume (TCBV) than the HC group (P = .03). Carotid intima-media thickness (CIMT) was negatively correlated with TCBV (r = -0.311, P = .006) and rGMV in the right thalamus (r = -0.589, P = .001). The rGMVs of the right middle occipital gyrus and bilateral lingual gyrus were significantly different between the unstable and stable groups. The gray-scale median (GSM) of the plaque and the total plaque risk score (TPRS) were correlated with the volume of the right middle occipital gyrus (r=-0.478, P = .001; r = 0.541, P = .001) and bilateral lingual gyrus (r = -0.419, P = .003; r = 0.288, P = .04). Carotid plaque is related to the volume of the brain parenchyma and right thalamus. The rGMVs of the right middle occipital gyrus and bilateral lingual gyrus differed between the vulnerable plaque and stable plaque groups, and the characteristics of carotid plaques may serve as indexes that reflect these changes
La musique est-elle un « neuro-protecteur » ?

L'ecoute et la pratique de la musique peuvent constituer un excellent moyen d'entretenir, voire developper, les competences cognitives, motrices, emotionnelles et sociales des seniors et de retarder ainsi les effets du vieillissement. Les travaux sur l'impact de la musique sur le vieillissement cerebral sont encore peu nombreux, mais leurs observations dans les cas de vieillissement pathologique sont prometteuses. La musique pourrait bientot devenir egalement un outil privilegie de prevention, luttant contre le vieillissement cognitif.
The Plastid Genome of Deschampsia cespitosa (Poaceae)

Plastid genome analysis of non-model organisms provides valuable information for basic research e.g., molecular evolutionary genomics, phylogeny and phylogeography. Deschampsia cespitosa is the most widespread species of the genus and it is a common grass that is found across Eurasia and North America. Scattered populations in regions of appropriate ecological conditions are also found in Australia, New Zealand and southern South America, where it is sympatric with D. antarctica. We analyzed the plastid genome of a sample of Deschampsia cespitosa of the Austrian Alps using high-throughput sequencing. The plastid (cp) genome shows the typical quadripartite structure with a length of 135,340 bp, comprising a large single-copy (LSC) region of 79,992 bp, a small single-copy (SSC) region of 12,572 bp and two inverted repeats (IR) regions of 21,388 bp each. It contains 115 genes, including 85 protein-coding genes, four ribosomal RNA genes and 30 transfer RNA genes. The GC content (%), number of repeats and microsatellites, RNA editing sites and codon usage were highly similar to those of D. antarctica. The results of this present study highlight the extremely conserved nature of the cp genome in this group, since the comparison involved individuals separated by about 13,000 km, from the Alps to Antarctica.
Detection and Quantification of Pythium tracheiphilum in Soil by Multiplex Real-Time qPCR.

In Canada, head lettuce (Lactuca sativa capitata) is extensively produced in the muck soils of southwestern Québec. However, yields are increasingly affected by various soilborne pathogens, including Pythium spp. , which cause wilt and damping off. In a survey conducted in Québec muck soils in 2010 and 2011, Pythium tracheiphilum Matta was identified as the predominant Pythium sp. in the root of head lettuce showing Pythium stunt symptoms. Therefore, to improve risk assessment and help further understanding of disease epidemiology, a specific and sensitive real-time quantitative polymerase chain reaction (qPCR) assay based on TaqMan-minor groove binder (MGB) technology was developed for P. tracheiphilum. The PCR primers along with a TaqMan-MGB probe were designed from the ribosomal internal transcribed spacer 2 region. A 100-bp product was amplified by PCR from all P. tracheiphilum isolates tested while no PCR product was obtained from 38 other Pythium spp. or from a selection of additional lettuce pathogens tested. In addition to P. tracheiphilum, the assay was multiplexed with an internal control allowing for the individual validation of each PCR. In artificially infested soils, the sensitivity of the qPCR assay was established as 10 oospores/g of dry soil. P. tracheiphilum was not detected in soils in which lettuce has never been grown; however, inoculum ranged from 0 to more than 200,000 oospores/g of dry soil in commercial lettuce fields. Also, disease incidence was positively correlated with inoculum concentration (r = 0.764). The results suggest that inoculum concentration should be considered when making Pythium stunt management decisions. The developed qPCR assay will facilitate reliable detection and quantification of P. tracheiphilum from field soil.
Robust Depth Estimation Using Auto-Exposure Bracketing

As the computing power of handheld devices grows, there has been increasing interest in the capture of depth information to enable a variety of photographic applications. However, under low-light conditions, most devices still suffer from low imaging quality and inaccurate depth acquisition. To address the problem, we present a robust depth estimation method from a short burst shot with varied intensity (i.e., auto-exposure bracketing) and/or strong noise (i.e., high ISO). Our key idea synergistically combines deep convolutional neural networks with a geometric understanding of the scene. We introduce a geometric transformation between optical flow and depth tailored for burst images, enabling our learning-based multi-view stereo matching to be performed effectively. We then describe our depth estimation pipeline that incorporates this geometric transformation into our residual-flow network. It allows our framework to produce an accurate depth map even with a bracketed image sequence. We demonstrate that our method outperforms the state-of-the-art methods for various datasets captured by a smartphone and a DSLR camera. Moreover, we show that the estimated depth is applicable for image quality enhancement and photographic editing.
Cyclophosphamide Use in Multiple Sclerosis: Levels Detected in Human Milk.

BACKGROUND Multiple sclerosis (MS) is a chronic autoimmune inflammatory neurological disease of the central nervous system. It is the most common immune-mediated disorder, affecting >2 million people worldwide. Cyclophosphamide is an alkylating agent commonly used to treat both malignancies and immune-mediated inflammatory nonmalignant processes. At present, there are no data available on its use in breastfeeding mothers. CASE REPORT In this study we report a 33-year-old mother who was suffering from MS. To treat her MS, stem cell transplantation protocol required preparation with multiple doses of cyclophosphamide. She had been exclusively breastfeeding for 6 months before undertaking this regimen. She voluntarily collected her milk samples at critical time points after the intravenous doses of 2.8 g cyclophosphamide for each of 4 days. Quantification of cyclophosphamide was determined using liquid chromatography coupled with tandem mass spectrometry. DISCUSSION Low levels in milk were determined for cyclophosphamide as the area under the curve was 364.1 μg. hour/mL on day 1 and 113.9 μg. hour/mL on day 4. Maximum concentration of cyclophosphamide was observed on day 1 at 40.82 μg/mL, which peaked at 4 hours. For 24 hours, the levels gradually receded to minimum concentrations. The average relative infant dose (RID) for a period of 4 days varied from 4.7% at day 1 to 0.9% at day 4. CONCLUSIONS Cyclophosphamide is transferred into breast milk in measurable quantities. This case report found RID of cyclophosphamide to be relatively low. However, great caution should be taken in counseling mothers regarding breastfeeding with this toxic drug.
Metabolic Syndrome Prediction Using Machine Learning Models with Genetic and Clinical Information from a Nonobese Healthy Population

The prevalence of metabolic syndrome (MS) in the nonobese population is not low. However, the identification and risk mitigation of MS are not easy in this population. We aimed to develop an MS prediction model using genetic and clinical factors of nonobese Koreans through machine learning methods. A prediction model for MS was designed for a nonobese population using clinical and genetic polymorphism information with five machine learning algorithms, including naïve Bayes classification (NB). The analysis was performed in two stages (training and test sets). Model A was designed with only clinical information (age, sex, body mass index, smoking status, alcohol consumption status, and exercise status), and for model B, genetic information (for 10 polymorphisms) was added to model A. Of the 7,502 nonobese participants, 647 (8.6%) had MS. In the test set analysis, for the maximum sensitivity criterion, NB showed the highest sensitivity: 0.38 for model A and 0.42 for model B. The specificity of NB was 0.79 for model A and 0.80 for model B. In a comparison of the performances of models A and B by NB, model B (area under the receiver operating characteristic curve [AUC] = 0.69, clinical and genetic information input) showed better performance than model A (AUC = 0.65, clinical information only input). We designed a prediction model for MS in a nonobese population using clinical and genetic information. With this model, we might convince nonobese MS individuals to undergo health checks and adopt behaviors associated with a preventive lifestyle.
Meshing and rendering of patient-specific deformation models with application to needle insertion simulation

Tissue deformation is common during many medical interventions. An accurate simulation of these procedures necessitates accounting for tissue displacements by modeling tissue deformation and medical tool interaction. In minimally-invasive procedures, due to lack of visibility, physicians rely on haptic feedback and medical imaging to assess the immediate anatomical configuration and relative medical tool position. These procedures are often difficult to learn and therefore extensive training becomes essential. Computerized training systems offer an alternative to cadavers and training on patients. To accurately model the tissue deformation, most such systems require a mesh representation of the anatomy. To replicate the medical imaging feedback offered during procedures, a realistic image simulation approach is also needed. In this thesis, a novel energy-based meshing technique taking medical images and producing desirable meshes for the finite element method is introduced. This method employs an image-based discretization energy combined with a geometry-based element quality energy. The former promotes each mesh element to cover similar intensity image regions, while the latter ensures the element suitability for finite element simulation. A method that can mimic realistic B-mode ultrasound images under deformation is also presented in this thesis. This method first maps the pixels of an image from a deformed mesh configuration back to the nominal configuration, and then interpolates them in a B-mode voxel volume reconstructed a priori. Needle insertion is involved in several medical procedures. These percutaneous procedures will benefit significantly from advances in simulating needle-tissue interaction, for which a 3D model is proposed in this thesis. Simulating needle flexibility is achieved fast and accurately using a novel approach employing torsional springs. The needle insertion simulation with haptic feedback is presented for a training scenario for prostate brachytherapy, where simulated ultrasound images coupled with deformation are also displayed. A scheme to generate patient models for this system is also devised using both the conventional meshing techniques in the literature and the proposed variational meshing method.