A protocol for annotation of total body photography for machine learning to analyze skin phenotype and lesion classification.

Introduction: Artificial Intelligence (AI) has proven effective in classifying skin cancers using dermoscopy images. In experimental settings, algorithms have outperformed expert dermatologists in classifying melanoma and keratinocyte cancers. However, clinical application is limited when algorithms are presented with 'untrained' or out-of-distribution lesion categories, often misclassifying benign lesions as malignant, or misclassifying malignant lesions as benign. Another limitation often raised is the lack of clinical context (e.g., medical history) used as input for the AI decision process. The increasing use of Total Body Photography (TBP) in clinical examinations presents new opportunities for AI to perform holistic analysis of the whole patient, rather than a single lesion. Currently there is a lack of existing literature or standards for image annotation of TBP, or on preserving patient privacy during the machine learning process. Methods: This protocol describes the methods for the acquisition of patient data, including TBP, medical history, and genetic risk factors, to create a comprehensive dataset for machine learning. 500 patients of various risk profiles will be recruited from two clinical sites (Australia and Spain), to undergo temporal total body imaging, complete surveys on sun behaviors and medical history, and provide a DNA sample. This patient-level metadata is applied to image datasets using DICOM labels. Anonymization and masking methods are applied to preserve patient privacy. A two-step annotation process is followed to label skin images for lesion detection and classification using deep learning models. Skin phenotype characteristics are extracted from images, including innate and facultative skin color, nevi distribution, and UV damage. Several algorithms will be developed relating to skin lesion detection, segmentation and classification, 3D mapping, change detection, and risk profiling. Simultaneously, explainable AI (XAI) methods will be incorporated to foster clinician and patient trust. Additionally, a publicly released dataset of anonymized annotated TBP images will be released for an international challenge to advance the development of new algorithms using this type of data. Conclusion: The anticipated results from this protocol are validated AI-based tools to provide holistic risk assessment for individual lesions, and risk stratification of patients to assist clinicians in monitoring for skin cancer.

Hyaluronan molecular weight distribution is associated with the risk of knee osteoarthritis progression.

OBJECTIVE: We investigated the relationship between the molecular weight (MW) distribution of hyaluronan (HA) in synovial fluid (SF) and risk of knee osteoarthritis (OA) progression. METHODS: HA MW was analyzed for 65 baseline knee SFs. At 3-year follow-up, knees were scored for change in joint space narrowing (JSN), osteophyte (OST) progression, or occurrence of total knee arthroplasty (TKA). HA MW distribution was analyzed using agarose gel electrophoresis (AGE), and its relationship to OA progression was evaluated using logistic regression. The association between HA MW and self-reported baseline knee pain was analyzed using Pearson's correlation coefficients. RESULTS: Knee OA was categorized as non-progressing (OST-/JSN-, 26 knees, 40%), or progressing based on OST (OST+/JSN-, 24 knees, 37%), OST and JSN (OST+/JSN+, 7 knees, 11%) or total knee arthroplasty (TKA, 8 knees, 12%). The MW distribution of HA in baseline SFs was significantly associated with the odds of OA progression, particularly for index knees. After adjusting for age, gender, BMI, baseline X-ray grade and pain, each increase of one percentage point in %HA below 1 million significantly increased the odds of JSN (odds ratios (OR) = 1.45, 95% CI 1.02-2.07), TKA or JSN (OR = 1.24, 95%CI 1.01-1.53) and the odds of any progression (OR = 1.16, 95% CI 1.01-1.32). HA MW distribution significantly correlated with pain. CONCLUSION: These data suggest that the odds of knee OA progression increases as HA MW distribution shifts lower and highlight the value of reporting MW distribution rather than just average MW values for HA.

Brachypodium distachyon as a model for defining the allergen potential of non-prolamin proteins.

Epitope databases and the protein sequences of published plant genomes are suitable to identify some of the proteins causing food allergies and sensitivities. Brachypodium distachyon, a diploid wild grass with a sequenced genome and low prolamin content, is the closest relative of the allergen cereals, such as wheat or barley. Using the Brachypodium genome sequence, a workflow has been developed to identify potentially harmful proteins which may cause either celiac disease or wheat allergy-related symptoms. Seed tissue-specific expression of the potential allergens has been determined, and intact epitopes following an in silico digestion with several endopeptidases have been identified. Molecular function of allergen proteins has been evaluated using Gene Ontology terms. Biologically overrepresented proteins and potentially allergen protein families have been identified.

From crop domestication to super-domestication.

Research related to crop domestication has been transformed by technologies and discoveries in the genome sciences as well as information-related sciences that are providing new tools for bioinformatics and systems' biology. Rapid progress in archaeobotany and ethnobotany are also contributing new knowledge to understanding crop domestication. This sense of rapid progress is encapsulated in this Special Issue, which contains 18 papers by scientists in botanical, crop sciences and related disciplines on the topic of crop domestication. One paper focuses on current themes in the genetics of crop domestication across crops, whereas other papers have a crop or geographic focus. One feature of progress in the sciences related to crop domestication is the availability of well-characterized germplasm resources in the global network of genetic resources centres (genebanks). Germplasm in genebanks is providing research materials for understanding domestication as well as for plant breeding. In this review, we highlight current genetic themes related to crop domestication. Impressive progress in this field in recent years is transforming plant breeding into crop engineering to meet the human need for increased crop yield with the minimum environmental impact - we consider this to be 'super-domestication'. While the time scale of domestication of 10 000 years or less is a very short evolutionary time span, the details emerging of what has happened and what is happening provide a window to see where domestication might - and can - advance in the future.

[Initial experience with transpalpebral orbital lipectomy]. / Erfahrungen mit transpalpebraler orbitaler Lipektomie.

PURPOSE: The aim of this study was to evaluate the short-term effectiveness of transpalpebral orbital lipectomy. METHOD: Using a transpalpebral approach, 2.0-6.5 ml connective tissue was removed from 50 orbits of 33 patients with mild to severe Graves' orbitopathy (25 females, 8 males) over a 5-year period. Indications for surgery comprised cosmetic correction of exophthalmos (27/33 patients), corneal damage (5/33), and rapid bilateral deterioration of visual acuity in 1 patient. RESULTS: In 27 patients undergoing correction for aesthetic purposes no change in visual acuity ensued; in 4 of 5 keratopathy patients an improvement in visual acuity was detected. Diplopia ceased in 4 of 13 patients, diminished in 3 of 13 cases, and constantly increased in 2 of 13 cases. The high intraocular pressure returned to normal in 8 of 13 patients. The proptosis was reduced at 3.2+/-1.3 mm. CONCLUSION: Transpalpebral orbital lipectomy is a low-risk, highly effective technique for orbital decompression in both acute and chronic cases of Graves' orbitopathy.

Binary transformation systems based on 'shooter' mutants of Agrobacterium tumefaciens: a simple, efficient and universal gene transfer technology that permits marker gene elimination.

A simple transformation procedure with a positive selection scheme using the expression of the isopentenyl transferase ( ipt) gene of transfer DNA (T-DNA) 'shooter' mutants of Agrobacterium tumefaciens was elaborated. After comparing several 'shooter' mutants we found that particular strains frequently produced phenotypically normal shoots after co-culturing with tobacco leaf explants. Shoots selected for normal phenotype showed apical dominance and could be rooted with the same efficiency as non-transformed shoots. When binary vectors were introduced into these strains, stably integrated binary vector T-DNA sequences were found in some regenerants, which were produced under non-selective conditions on growth-regulator-free medium. Such phenotypically normal transformants typically lacked a stably integrated ipt gene. Normal looking shoots could also be produced in tomato, muskmelon and sweet pepper.

Replacement of the coat protein gene of plum pox potyvirus with that of zucchini yellow mosaic potyvirus: characterization of the hybrid potyvirus.

Infectious hybrid virus was generated by replacing part of the coat protein gene of plum pox potyvirus with that of the zucchini yellow mosaic potyvirus. This viable hybrid contains 84.5% of zucchini yellow mosaic potyvirus coat protein gene while the rest of the sequence was derived from plum pox potyvirus. Changing the coat protein gene between these two viruses had no effect on the experimental host range. Pathogenicity, stability and replication capacity of the hybrid virus were nearly identical to the parent viruses.

[Examination of silane ceramic systems by differential thermoanalysis]. / Fogászatban alkalmazott szilánkerámia rendszerek differenciál termoanalitikai vizsgálata.

In the present study two silane adhesive agents (Silicoup, Heraeus/Kulzer, and Monobond-S, Vivadent) and one type ceramic (VITA VKM 68) and their interface reactions were tested by thermo-analysis. The ceramic powder is thermally inactive. Using the two different silane solutions with the same ceramic type different thermical characteristics were found despite the same base material (gamma-methacryloxi-propyl-trimethoxi-silane). This can probably be attributed to the different configurations of the polycondensates.

Synthesis of (-)-strand RNA from the 3' untranslated region of plant viral genomes expressed in transgenic plants upon infection with related viruses.

When expressed in transgenic tobacco plants, transgene mRNA that includes the 3' untranslated region (3' UTR) of Lettuce mosaic virus served as template for synthesis of complementary (-)-strand RNA following an infection by Tobacco etch virus, Tobacco vein mottle virus or Pepper mottle virus, but not when infected with Cucumber mosaic virus. Deletion of the 3' UTR from the transgene abolished the synthesis of (-)-strand transcripts. Similar results were obtained in transgenic tobacco plants expressing mRNA that includes the RNA3 3' UTR of Cucumber mosaic virus when infected with Tomato aspermy virus. These results show that the viral RNA-dependent RNA polymerase of several potyviruses and Tomato aspermy virus have the ability to recognize heterologous 3' UTRs when included in transgene mRNAs, and to use them as transcription promoters.

Cytogenetic profile of primary pituitary germinoma.

We present a case of a germinoma in the sellar region of a 10-year-old female patient who presented with a history of polydipsia, polyuria and visual disturbances. The tumor was resected and histologically analyzed. Interphase cytogenetics was performed using chromosome specific (peri)-centromeric DNA probes for all the somatic and X chromosomes on fresh frozen tissues. Fluorescent in situ cell hybridization demonstrated accumulated cytogenetic abnormalities involving significant alterations of chromosome 1, 4, 5/19 and 15. The child was treated postoperatively by radiation and now appears well with only minor neurological deficits. At 3-year follow-up no recurrent tumor mass could be demonstrated.

The role of elastoviscosity in the efficacy of viscosupplementation for osteoarthritis of the knee: a comparison of hylan G-F 20 and a lower-molecular-weight hyaluronan.

The objective of this 12-week, double-masked, randomized, multicenter study was to compare the elastoviscous properties of a high-molecular-weight viscosupplement, hylan G-F 20 (polymer concentration, 0.8%), with those of a lower-molecular-weight hyaluronan (LMW HA) product (polymer concentration, 1%) and to determine the relationship of elastoviscosity to efficacy in the treatment of patients with osteoarthritis (OA) of the knee. Patients had radiographically confirmed primary idiopathic OA of the knee (Larsen grades I to V) with pain despite other treatments. After a 2-week washout period, 70 patients (73 knees) received three 2-mL intra-articular injections of test solution at 1-week intervals. Thirty-eight patients (38 knees) received hylan G-F 20, and 32 patients (35 knees) received LMW HA. During the 12-week follow-up period, the primary outcome measures assessed by patients (using a visual analogue scale) were weight-bearing pain, most painful knee movement, and overall treatment response; the primary outcome measures assessed by study evaluators were weight-bearing pain and overall assessment of treatment. The dynamic elastoviscous properties of the test solutions were measured on an oscillating Couette-type rheometer. Hylan G-F 20 was more elastoviscous than the LMW HA at all frequencies measured (0.001 to 10 Hz). At the final evaluation, patients who received hylan G-F 20 had significantly better results on all primary outcome measures compared with those who received LMW HA. No systemic adverse events were reported. Local adverse events consisted of pain or swelling, noted in 2 of 38 knees injected with hylan G-F 20, and pain, noted in 1 of 35 knees injected with LMW HA (adverse event rates per injection, 1.8% and 0.9%, respectively). The difference in the incidence of adverse events between groups was not statistically significant. The higher-molecular-weight, more elastoviscous hylan G-F 20 had significantly greater pain-relieving effects than did the lower-molecular-weight, less elastoviscous hyaluronan.

Expression of betaig-h3 is lower than normal in keratoconus corneas but increases with scarring.

PURPOSE: Keratoconus is a progressive ectatic disease of the cornea. Despite extensive clinical and laboratory investigations, its pathogenesis remains unclear. In this study, we examined the localization of betaig-h3, a recently described extracellular matrix protein in keratoconus corneas both in the absence and presence of subepithelial scarring. METHODS: Two normal corneas and central corneal buttons of 10 patients with keratoconus were excised during perforating keratoplasty and examined, including one case with acute corneal hydrops. In one case, keratoconus was associated with Down syndrome. Immunodetection was done with an antipeptide antibody reacting with the N-terminal part of betaig-h3. RESULTS: We found decreased betaig-h3 levels in the basal epithelial layer and keratocytes of keratoconus corneas. In the scarred corneas, however, betaig-h3 levels were increased in the basal epithelial layers and in activated keratocytes at the places of scarring. In the cornea of the patient with Down syndrome, we found an additional betaig-h3-positive zone in the anterior stroma. CONCLUSIONS: The decreased levels of betaig-h3 corneas seem to be specific for keratoconus. Considering the putative role of betaig-h3 as a cellular-attachment protein, paucity of betaig-h3 in the corneal stroma may lead to decreased mechanical stability and contribute to the development of keratoconus.

Corrected TIMI frame count does not predict 30-day adverse outcomes after reperfusion therapy for acute myocardial infarction.

BACKGROUND: Thrombolysis in Myocardial Infarction (TIMI) flow grading is limited by subjectivity and imprecision. The corrected TIMI frame count (cTFC) has been proposed to obviate these problems. We sought to validate the utility of the cTFC in predicting adverse clinical outcomes after reperfusion therapy. METHODS AND RESULTS: We used angiographic core laboratory data from the Intravenous nPA for Treating Infarcting Myocardium Early Study (lanoteplase versus alteplase) to assess the predictive capacity of both final TIMI flow and cTFC on 30 day-composite adverse outcome (death, reinfarction, and new or worsening congestive heart failure). Only 390 angiograms of 586 were analyzable for cTFC; 33.4% of angiograms could not be analyzed for cTFC because filling of distal landmarks was not visualized for technical reasons such as inadequate panning. The interobserver correlation for determination of the cTFC was 0.99 and the intraobserver correlation was 0.97. The cTFC in the group with adverse outcomes was 49 +/- 34; in the group without adverse outcomes, it was 44 +/- 31 (P =.27). Of note, the TIMI flow correlated with adverse outcome in the overall group of patients (P =.018, area under the receiver-operator characteristic curve [c] = 0. 590) as well as in the group of patients with cines analyzable for cTFC (P =.025, c = 0.600). The independent correlates of adverse outcomes were age (P <.001), heart rate (P =.001), TIMI flow grade (P =.027), and infarct location (P =.038) but not cTFC. CONCLUSIONS: The cTFC did not predict adverse outcomes in this population of patients but did show excellent reproducibility within our core laboratory.

Molecular evidence for the existence of two distinct subgroups in cucumber mosaic cucumovirus.

Infectious full-length cDNA clones from the genomic RNAs of a subgroup II cucumber mosaic cucumovirus strain (Trk7) were obtained. Sequence analysis of the whole genome revealed strong homology (99%) to the genome of Q-CMV, the only subgroup II strain whose entire genomic nucleotide sequence had been available in the database, and an overall 75% homology to those of subgroup I strains. We provide sequence comparisons of different parts of 1a, 2a and 2b proteins of Cucumovirus species, and propose phylogenetic trees based on these protein sequences.

Immunohistochemical detection of betaIG-H3 in scarring human corneas.

BACKGROUND: BetaIG-H3 is a recently described extracellular matrix protein that is present in various organs. In rabbit corneas, increased betaIG (the rabbit form of betaIG-H3) mRNA levels were shown during corneal development and wound healing. In this study, we investigated the localization of betaIG-H3 protein in scarring human corneas. METHODS: Corneal buttons obtained during keratoplasty were examined. Immunohistological detection using a polyclonal antipeptide antibody against the betaIG-H3 protein was performed on 24 pathological corneas (9 ulcerations, 8 alkali burns, 2 perforating injuries, 5 bullous keratopathy) and 2 normal corneas. RESULTS: In normal corneas, strong staining was present in the basal layer of the epithelium and in the endothelium; the stromal fibers showed faint, uniform immunoreactivity. In all scarring corneas, the epithelium was usually thickened and all of its layers were reactive with the betaIG-H3 antibody. The cytoplasm of the stromal fibroblasts, as well as the stromal fibers around them also showed staining with the antibody. These changes were present in all scarring corneas, irrespective of the pathological process leading to scar formation. CONCLUSION: These results prove, at the protein level, the presence of increased amounts of betaIG-H3 at the sites of scarring in human corneas.

Corneal transplantation in children.

Authors discuss the special problems related to childhood keratoplasties. They evaluate the results of the keratoplasties carried out in children during the past 10 years in their service. They review the concerning literature and summarize their opinion on the corneal transplantations of this age group.

Stunting induced by cucumber mosaic cucumovirus-infected Nicotiana glutinosa is determined by a single amino acid residue in the coat protein.

R-CMV, a subgroup II strain of cucumber mosaic cucumovirus (CMV) induces a very strong stunting response in Nicotiana glutinosa plants, while Trk7-CMV causes green mosaic in this host. The genetic determinant of this phenotype was mapped to a 534-nucleotide region at the 3' end of RNA3 with biologically active, full-length cDNA clones of R-CMV and Trk7-CMV and RNA3 chimeras of the two strains. Within this region, R-CMV differs from Trk7-CMV by a single amino acid at position 193 in the coat protein. Changing the codon for Lys at this position to Asn or Ser, by site-directed mutagenesis, also changed the phenotype of the viruses from green mosaic to induction of stunting. Profound differences in both the spread and the accumulation of the viruses causing stunting and green mosaic were observed, although these did not correlate with the host specificity of stunting. Since expression of R-CMV coat protein with the PVX vector did not cause stunting, the data suggest that the presence of other CMV components is necessary for the induction of this symptom.