Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved Risk Prediction Calculator for Sentinel Node Positivity in Patients With Melanoma: The Melanoma Institute Australia Nomogram.

PURPOSE For patients with primary cutaneous melanoma, the risk of sentinel node (SN) metastasis varies according to several clinicopathologic parameters. Patient selection for SN biopsy can be assisted by National Comprehensive Cancer Network (NCCN) and ASCO/Society of Surgical Oncology (SSO) guidelines and the Memorial Sloan Kettering Cancer Center (MSKCC) online nomogram. We sought to develop an improved online risk calculator using alternative clinicopathologic parameters to more accurately predict SN positivity. PATIENTS AND METHODS Data from 3,477 patients with melanoma who underwent SN biopsy at Melanoma Institute Australia (MIA) were analyzed. A new nomogram was developed by replacing body site and Clark level from the MSKCC model with mitotic rate, melanoma subtype, and lymphovascular invasion. The predictive performance of the new nomogram was externally validated using data from The University of Texas MD Anderson Cancer Center (n = 3,496). RESULTS The MSKCC model receiver operating characteristic curve had a predictive accuracy of 67.7% (95% CI, 65.3% to 70.0%). The MIA model had a predictive accuracy of 73.9% (95% CI, 71.9% to 75.9%), a 9.2% increase in accuracy over the MSKCC model (P < .001). Among the 2,748 SN-negative patients, SN biopsy would not have been offered to 22.1%, 13.4%, and 12.4% based on the MIA model, the MSKCC model, and NCCN or ASCO/SSO criteria, respectively. External validation generated a C-statistic of 75.0% (95% CI, 73.2% to 76.7%). CONCLUSION A robust nomogram was developed that more accurately estimates the risk of SN positivity in patients with melanoma than currently available methods. The model only requires the input of 6 widely available clinicopathologic parameters. Importantly, the number of patients undergoing unnecessary SN biopsy would be significantly reduced compared with use of the MSKCC nomogram or the NCCN or ASCO/SSO guidelines, without losing sensitivity. An online calculator is available at www.melanomarisk. org.au.
A new species of the theropod dinosaur Syntarsus from the Early Jurassic Kayenta Formation of Arizona

ABSTRACT Until now, Syntarsus was based on a single species, S. rhodesiensis, known only from southern Africa. The discovery of Syntarsus in North America adds significantly to the increasingly detailed resemblance of African and North American Early Jurassic terrestrial vertebrate faunas. The new species, Syntarsus kayentakatae, is based on a complete skull and partial skeleton, and more fragmentary remains of at least 16 additional individuals, all from a narrow stratigraphie interval in the Kayenta Formation. Syntarsus kayentakatae is diagnosed by parasagittal cranial crests and fusion of the fibula to the calcaneum in adults. Syntarsus is the most derived member of the newly diagnosed theropod taxon Ceratosauria, possessing 22 apomorphies that arose subsequent to the divergence of ceratosaurs from other theropods. Syntarsus shares 20 of these with Coelophysis bauri, one of the earliest well-known theropods. By their first appearance, probably late Carnian, ceratosaurs already possessed a history invol.
Genotyping of Treponema pallidum in Cuba (2018–2019): Increased Circulation of Recombinant Genotype and No New Treponema pallidum Subspecies endemicum Infection Among Syphilis Patients

Multilocus sequence typing of Cuban isolates of Treponema pallidum (2018–2019) revealed an increased frequency of the recombinant allelic profile 15.7. 3, no new infection by T. pallidum subspecies endemicum among syphilis patients, 81% of isolates harboring macrolide resistance mutations, and no 16S rDNA mutations potentially conferring tetracycline resistance. Objectives This study aimed to determine the allelic profiles of Treponema pallidum in patients confirmed with syphilis in Cuba (2018–2019) and to explore mutations leading to macrolide and tetracycline resistance. Methods Multilocus sequence typing and polymerase chain reaction of rrn loci (23S and 16S rDNA), followed by Sanger sequencing, were used to define the allelic profile of TPA and resistance mutations, respectively. Results Allelic profile 1.3. 1 and the recombinant profile were identified, with 15.7. 3 having an increased frequency. We did not detect the presence of the T. pallidum subspecies endemicum among syphilis patients, as in previous reports. A high frequency of macrolide-resistant strains and the absence of mutations potentially causing tetracycline resistance were found. Conclusions Understanding the current status of treponemal infection in Cuban patients provides insights into the syphilis epidemiology.
A systematic review of machine learning models for predicting outcomes of stroke with structured data

Background and purpose Machine learning (ML) has attracted much attention with the hope that it could make use of large, routinely collected datasets and deliver accurate personalised prognosis. The aim of this systematic review is to identify and critically appraise the reporting and developing of ML models for predicting outcomes after stroke. Methods We searched PubMed and Web of Science from 1990 to March 2019, using previously published search filters for stroke, ML, and prediction models. We focused on structured clinical data, excluding image and text analysis. This review was registered with PROSPERO (CRD42019127154). Results Eighteen studies were eligible for inclusion. Most studies reported less than half of the terms in the reporting quality checklist. The most frequently predicted stroke outcomes were mortality (7 studies) and functional outcome (5 studies). The most commonly used ML methods were random forests (9 studies), support vector machines (8 studies), decision trees (6 studies), and neural networks (6 studies). The median sample size was 475 (range 70–3184), with a median of 22 predictors (range 4–152) considered. All studies evaluated discrimination with thirteen using area under the ROC curve whilst calibration was assessed in three. Two studies performed external validation. None described the final model sufficiently well to reproduce it. Conclusions The use of ML for predicting stroke outcomes is increasing. However, few met basic reporting standards for clinical prediction tools and none made their models available in a way which could be used or evaluated. Major improvements in ML study conduct and reporting are needed before it can meaningfully be considered for practice.
ECOLOGICAL CHARACTERISTICS OF WETLANDS RECEIVINGAN INDUSTRIAL EFFLUENT

The primary objectives of this study were to evaluate the ecological characteristics of wetland ecosystems that had developed in response to oil sands effluent relative to reference wetland ecosystems and, from such an evaluation, to assess whether these wetlands were viable systems capable of integrating into the northern Canadian landscape. A secondary objective was to evaluate the use of several ecologically relevant endpoints as indicators of an ecosystem response to a known anthropogenic stress, in this case, wetlands receiving oil sands effluent. To achieve this, a suite of endpoints were compared between effluent-impacted wetlands and nonimpacted reference wetlands. Endpoints for comparison included: (1) benthic macroinvertebrate community structure, (2) chironomid density and biomass, (3) the incidence of chironomid mentum deformities, (4) the mutagenetic potential of sediment-dwelling chironomids, (5) growth and photosynthetic rate for the aquatic plant Typha latifolia (cattail), and (6) fish acu.
The effects of prey movement, size and colour in the attack/avoidance behaviour of the Tiger beetle Cephalota circumdata leonschaeferi (Cassola) (Coleoptera Cicindelidae)

An examination has been made of factors triggering attack behaviour in adult Cephalota circumdata leonschaeferi (Cassola), living in the coastal strip of the Orbetello Lagoon Nature Reserve. Coloured dummies (blue, white, brown, black, red, and green) of various sizes (3.8, 7.5, 15 and 30 mm) have been used to evaluate the role of the following stimuli: movement, size and colour. Attacks recorded with experiments carried out in absence of movement (3.83%) were markedly fewer than those in presence (57.26%) of movement. The size of bait most frequently attacked by Tiger beetles was the 7.5-mm long one (corresponding to 1/2 the size of the adult Cephalota). The largest bait (30 mm) was significantly less stimulating than the other three sizes. Red was the colour that most stimulated attack and white the least. Brown and black gave results more similar to those of red, whereas green and blue frequently displayed a significantly less stimulatory effect. The two sexes displayed differences of reaction to the b.
Family‐based treatment via videoconference: Clinical recommendations for treatment providers during COVID‐19 and beyond

Abstract The necessity to employ distance‐based methods to deliver on‐going eating disorder care due to the novel coronavirus (COVID‐19) pandemic represents a dramatic and urgent shift in treatment delivery. Yet, TeleHealth treatments for eating disorders in youth have not been adequately researched or rigorously tested. Based on clinical experience within our clinic and research programs, we aim to highlight the common challenges clinicians may encounter in providing family‐based treatment (FBT) via TeleHealth for children and adolescents with anorexia nervosa and bulimia nervosa. We also discuss possible solutions and offer practical considerations for providers delivering FBT in this format. Additional research in TeleHealth treatment for eating disorders in youth may lead to improved access, efficiency, and effectiveness of FBT delivered via videoconferencing.
Studies on N Mineralization from Soils Amended with Green Manures under the Influence of Two Different Moisture Regime

A laboratory experiment was conducted over 12 weeks to study the nitrogen (N) mineralization pattern and kinetics from nine locally available green manure (GM) at submergence and field capacity (FC), when incorporated into typical rice growing teesta alluvial soils of the district Coochbehar located at Terai Agro-climatic region of West Bengal. Rapid mineralization was evidenced by the fact that out of total N mineralized at the end of incubation, 20.43–100.59% and 27.60–76.17% released during 1st week at submergence and FC, respectively. After 12 weeks highest N was mineralized from C. sophera (162.57 mg kg−1 soil) and G. sepium (195.72 mg kg−1 soil) amended soil at submerge and FC moisture condition, respectively. At submergence, soils amended with I. cornea and V. ungiculata and at FC, G. sepium and E. indica amended soil exhibited most consistent trend of successive increase till the end with a few exception; whereas mean (of moisture regime) cumulative mineralization showed most consistency in case of V. ungiculata and C. sophera. Mean (of GM) cumulative mineralization was better at submergence over FC moisture regime during early period; whereas reverse was the trend during later period of incubation. Similar was the trend for individual GMs except C. sophera, G. sepium and I. cornea recording higher value at FC almost all throughout the incubation period. FC moisture regime recorded higher mineralization potential (N0) and lower rate constant (k) for all GMs; except N0 value for P. pinnata. Considering all these above C. sophera and V. ungiculata were identified as best GM species across moisture regime as well as at submergence; whereas at FC moisture regime G. sepium and E. indica were best performing GM species.
Cloning and expression of an α-2,8-polysialyltransferase (STX) from Xenopus laevis

Polysialic acid (polySia) is a carbohydrate structure found on neural cell adhesion molecules (N-CAM). Two polysialyltransferases (polySiaTs) that catalyze synthesis of polySia have been described, and designated PST-1/PST/ST8SiaIV and STX/ST8SiaII. We cloned a polySiaT (xSTX) from a nonmammalian vertebrate, Xenopus laevis . xSTX had 80% amino acid similarity to the rat STX. This clone induced polySia expression when transfected into polySia-negative COS-1 cells. Northern blot analysis of whole embryos at different stages of development revealed that xSTX mRNA was most abundantly expressed in premetamorphic stages. The relative level of xSTX and N-CAM mRNAs was also examined and found to change in parallel to the extent of polysialylation on N-CAM. In adult tissues, the expression of xSTX mRNA was restricted to brain, eye and heart, which also expressed polySia. These results suggest that xSTX is the major enzyme responsible for the synthesis of polysialylated N-CAM in embryos at certain stages of development and also in adult tissues.
The Type IX Secretion System Is Required for Virulence of the Fish Pathogen Flavobacterium psychrophilum

Bacterial cold-water disease, caused by F. psychrophilum, is a major problem for salmonid aquaculture. Little is known regarding the virulence factors involved in this disease, and control measures are inadequate. A targeted gene deletion method was adapted to F. psychrophilum and used to demonstrate the importance of the T9SS in virulence. Proteins secreted by this system are likely virulence factors and targets for the development of control measures. ABSTRACT Flavobacterium psychrophilum causes bacterial cold-water disease in wild and aquaculture-reared fish and is a major problem for salmonid aquaculture. The mechanisms responsible for cold-water disease are not known. It was recently demonstrated that the related fish pathogen, Flavobacterium columnare, requires a functional type IX protein secretion system (T9SS) to cause disease. T9SSs secrete cell surface adhesins, gliding motility proteins, peptidases, and other enzymes, any of which may be virulence factors. The F. psychrophilum genome has genes predicted to encode components of a T9SS. Here, we used a SacB-mediated gene deletion technique recently adapted for use in the Bacteroidetes to delete a core F. psychrophilum T9SS gene, gldN. The ΔgldN mutant cells were deficient for secretion of many proteins in comparison to wild-type cells. Complementation of the mutant with wild-type gldN on a plasmid restored secretion. Compared to wild-type and complemented strains, the ΔgldN mutant was deficient in adhesion, gliding motility, and extracellular proteolytic and hemolytic activities. The ΔgldN mutant exhibited reduced virulence in rainbow trout and complementation restored virulence, suggesting that the T9SS plays an important role in the disease. IMPORTANCE Bacterial cold-water disease, caused by F. psychrophilum, is a major problem for salmonid aquaculture. Little is known regarding the virulence factors involved in this disease, and control measures are inadequate. A targeted gene deletion method was adapted to F. psychrophilum and used to demonstrate the importance of the T9SS in virulence. Proteins secreted by this system are likely virulence factors and targets for the development of control measures.
Anti-Inflammatory Potential of n-3 Polyunsaturated Fatty Acids Enriched Hen Eggs Consumption in Improving Microvascular Endothelial Function of Healthy Individuals—Clinical Trial

The effects of consumption of n-3 polyunsaturated fatty acids (n-3 PUFAs) enriched hen eggs on endothelium-dependent and endothelium-independent vasodilation in microcirculation, and on endothelial activation and inflammation were determined in young healthy individuals. Control group (N = 21) ate three regular hen eggs/daily (249 mg n-3 PUFAs/day), and n-3 PUFAs group (N = 19) ate three n-3 PUFAs enriched hen eggs/daily (1053 g n-3 PUFAs/day) for 3 weeks. Skin microvascular blood flow in response to iontophoresis of acetylcholine (AChID; endothelium-dependent) and sodium nitroprusside (SNPID; endothelium-independent) was assessed by laser Doppler flowmetry. Blood pressure (BP), body composition, body fluid status, serum lipid and free fatty acids profile, and inflammatory and endothelial activation markers were measured before and after respective dietary protocol. Results: Serum n-3 PUFAs concentration significantly increased, AChID significantly improved, and SNPID remained unchanged in n-3 PUFAs group, while none was changed in Control group. Interferon-γ (pro-inflammatory) significantly decreased and interleukin-10 (anti-inflammatory) significantly increased in n-3 PUFAs. BP, fat free mass, and total body water significantly decreased, while fat mass, interleukin-17A (pro-inflammatory), interleukin-10 and vascular endothelial growth factor A significantly increased in the Control group. Other measured parameters remained unchanged in both groups. Favorable anti-inflammatory properties of n-3 PUFAs consumption potentially contribute to the improvement of microvascular endothelium-dependent vasodilation in healthy individuals.
Rice Adaptation to Aerobic Soils: Physiological Considerations and Implications for Agronomy

Abstract Aerobic culture is a water-saving technique for direct-seeded rice cultivation. Growing rice under continuously unsaturated soil conditions can maximize water-use efficiency and minimize both labor requirements and greenhouse-gas emissions. Under a temperate climate, aerobic culture can produce a rice yield greater than 9 t ha–1 especially in central Japan (11.4 t ha–1). Aerobic culture using large-scale center-pivot sprinklers is being established in the central United States, where yields can surpass 10 t ha–1. However, yields remain at less than 8 t ha–1 in the tropics. The high yield of Japanese aerobic culture is mainly attributed to vigorous nitrogen uptake during the reproductive stage, which allows rice plants to produce more spikelets and biomass. Fertilizer management for aerobic culture must satisfy both the nitrogen demand and control spikelet density to achieve an appropriate sink–source balance. Unfortunately, the poor development of the root system in rice limits its water uptake from unsaturated soil. Adaptive responses such as adventitious root emergence, lateral root branching, and deep root penetration would protect the plants against dehydration stress in aerobic culture. Intermediate plant height with a few large tillers rather than semi-dwarf stature with profuse tillering should be a suitable plant type for aerobic culture, and plants should show leaf expansion despite fluctuations of soil moisture. The development and identification of suitable genotypes and crop management options are underway worldwide for more resource-use efficient and productive aerobic rice culture.
Prevention of pressure ulcers among individuals cared for in the prone position: lessons for the COVID-19 emergency.

OBJECTIVE Pressure ulcers (PUs) involve the destruction of skin and underlying tissue due to prolonged pressure and shear forces. These ulcers are painful and significantly reduce a person's quality of life. PUs are also expensive to manage and impact negatively on the achievement of cost-effective, efficient care delivery. METHOD Prone positioning is a postural therapy that aims to enhance respiratory function through increasing oxygenation levels. In contemporary clinical practice, ventilation in the prone position is indicated for patients with severe acute respiratory distress syndrome. However, despite its advantages in terms of respiratory function, several studies have examined complications of prone position ventilation and have identified PUs (facial PUs as well as PUs on other weight-bearing areas of the body) as a frequent complication in patients who are already in a precarious medical situation. International data suggest that up to 57% of patients nursed in the prone position develop a PU. The aim of this clinical review is to identify and review evidence-based recommendations developed to facilitate the selection and application of preventive interventions aimed at reducing PU development in patients ventilated in the prone position. Given the current COVID-19 crisis, this review is timely as intensive care unit (ICU) patients with COVID-19 require ventilation in the prone position at a level that is disproportionate to the general intensive care population. Up to 28% of patients admitted to the ICU with confirmed infection due to severe COVID-19 are cared for in the prone position. The scope of this review is limited to adult individuals only. RESULTS The skin assessment should be undertaken before proning and following positioning the patient back into the supine position. Although it is essential to keep the skin clean and moisturised, using pH-balanced cleansers, there is inconsistency in terms of the evidence to support the type of moisturiser. Use of positioning devices in addition to repositioning is recommended to offload pressure points on the face and body. Further, using dressings such as hydrocolloids, transparent film and silicone may be of benefit in decreasing facial skin breakdown. CONCLUSION Given the importance of PU prevention in this cohort of patients, adopting a focused prevention strategy, including skin assessment and care, offloading and pressure redistribution, and dressings for prevention may contribute to a reduction in the incidence and prevalence of these largely preventable wounds.
Fungal Species Concepts in the Genomics Era.

The 140,000 or so fungal species reported so far are heterogeneously defined based on varying criteria such as morphological, physiological, mating, and/or molecular features. Incongruences are common among traits used to separating closely related species and it is often difficult to compare fungal taxonomic groups defined based on different species recognition criteria. Though DNA sequence-based classification and identification have been made, a consensus has not been reached, primarily due to intrinsic limitations in the proposed one or a few genes. Here, I argue that the fundamental reason for the observed inconsistencies is that speciation is a stochastic process with the emergence and fixation of different traits influenced differently by many non-deterministic factors such as population size, random mutation, mode(s) of reproduction, selection imposed by interacting biotic and abiotic factors, and chance events. Each species concept attempts to capture one or a few traits emerged in the continuous process of speciation. I propose that a genome sequence-based classification and identification system could unify and stabilize fungal taxonomy and help integrate taxonomy with other fields of fungal biology. The genomic species concept could be similarly argued for other groups of eukaryotic microbes as well as for plants and animals.
Revision of the family Carabodidae (Acari: Oribatida) VI. Mangabebodes kymatismosi gen. nov., sp. nov. and Antongilibodes paulae gen. nov., sp. nov. from Madagascar

This is the sixth in a series of revisions on the family Carabodidae, in which we describe and illustrate two new genera, Mangabebodes kymatismosi gen. nov., sp. nov. and Antongilibodes paulae gen. nov., sp. nov., both from the island of Madagascar. The work is based on adult specimens studied with the aid of optical and scanning electron microscopy. http://zoobank.org/urn:lsid:zoobank.org:pub:5D0FD938-0B9A-4594-8FFE-65A8DD2B8CC4