Comparing CNNs and PLSr for estimating wheat organs biophysical variables using proximal sensing

Estimation of biophysical vegetation variables is of interest for diverse applications, such as monitoring of crop growth and health or yield prediction. However, remote estimation of these variables remains challenging due to the inherent complexity of plant architecture, biology and surrounding environment, and the need for features engineering. Recent advancements in deep learning, particularly convolutional neural networks (CNN), offer promising solutions to address this challenge. Unfortunately, the limited availability of labeled data has hindered the exploration of CNNs for regression tasks, especially in the frame of crop phenotyping. In this study, the effectiveness of various CNN models in predicting wheat dry matter, nitrogen uptake, and nitrogen concentration from RGB and multispectral images taken from tillering to maturity was examined. To overcome the scarcity of labeled data, a training pipeline was devised. This pipeline involves transfer learning, pseudo-labeling of unlabeled data and temporal relationship correction. The results demonstrated that CNN models significantly benefit from the pseudolabeling method, while the machine learning approach employing a PLSr did not show comparable performance. Among the models evaluated, EfficientNetB4 achieved the highest accuracy for predicting above-ground biomass, with an R² value of 0.92. In contrast, Resnet50 demonstrated superior performance in predicting LAI, nitrogen uptake, and nitrogen concentration, with R² values of 0.82, 0.73, and 0.80, respectively. Moreover, the study explored multi-output models to predict the distribution of dry matter and nitrogen uptake between stem, inferior leaves, flag leaf, and ear. The findings indicate that CNNs hold promise as accessible and promising tools for phenotyping quantitative biophysical variables of crops. However, further research is required to harness their full potential.

To What Extent Does Yellow Rust Infestation Affect Remotely Sensed Nitrogen Status?

The utilization of high-throughput in-field phenotyping systems presents new opportunities for evaluating crop stress. However, existing studies have primarily focused on individual stresses, overlooking the fact that crops in field conditions frequently encounter multiple stresses, which can display similar symptoms or interfere with the detection of other stress factors. Therefore, this study aimed to investigate the impact of wheat yellow rust on reflectance measurements and nitrogen status assessment. A multi-sensor mobile platform was utilized to capture RGB and multispectral images throughout a 2-year fertilization-fungicide trial. To identify disease-induced damage, the SegVeg approach, which combines a U-NET architecture and a pixel-wise classifier, was applied to RGB images, generating a mask capable of distinguishing between healthy and damaged areas of the leaves. The observed proportion of damage in the images demonstrated similar effectiveness to visual scoring methods in explaining grain yield. Furthermore, the study discovered that the disease not only affected reflectance through leaf damage but also influenced the reflectance of healthy areas by disrupting the overall nitrogen status of the plants. This emphasizes the importance of incorporating disease impact into reflectance-based decision support tools to account for its effects on spectral data. This effect was successfully mitigated by employing the NDRE vegetation index calculated exclusively from the healthy portions of the leaves or by incorporating the proportion of damage into the model. However, these findings also highlight the necessity for further research specifically addressing the challenges presented by multiple stresses in crop phenotyping.

In-Field Wheat Reflectance: How to Reach the Organ Scale?

The reflectance of wheat crops provides information on their architecture or physiology. However, the methods currently used for close-range reflectance computation do not allow for the separation of the wheat canopy organs: the leaves and the ears. This study details a method to achieve high-throughput measurements of wheat reflectance at the organ scale. A nadir multispectral camera array and an incident light spectrometer were used to compute bi-directional reflectance factor (BRF) maps. Image thresholding and deep learning ear detection allowed for the segmentation of the ears and the leaves in the maps. The results showed that the BRF measured on reference targets was constant throughout the day but varied with the acquisition date. The wheat organ BRF was constant throughout the day in very cloudy conditions and with high sun altitudes but showed gradual variations in the morning under sunny or partially cloudy sky. As a consequence, measurements should be performed close to solar noon and the reference panel should be captured at the beginning and end of each field trip to correct the BRF. The method, with such precautions, was tested all throughout the wheat growing season on two varieties and various canopy architectures generated by a fertilization gradient. The method yielded consistent reflectance dynamics in all scenarios.

Wheat Ear Segmentation Based on a Multisensor System and Superpixel Classification

The automatic segmentation of ears in wheat canopy images is an important step to measure ear density or extract relevant plant traits separately for the different organs. Recent deep learning algorithms appear as promising tools to accurately detect ears in a wide diversity of conditions. However, they remain complicated to implement and necessitate a huge training database. This paper is aimed at proposing an easy and quick to train and robust alternative to segment wheat ears from heading to maturity growth stage. The tested method was based on superpixel classification exploiting features from RGB and multispectral cameras. Three classifiers were trained with wheat images acquired from heading to maturity on two cultivars at different levels of fertilizer. The best classifier, the support vector machine (SVM), yielded satisfactory segmentation and reached 94% accuracy. However, the segmentation at the pixel level could not be assessed only by the superpixel classification accuracy. For this reason, a second assessment method was proposed to consider the entire process. A simple graphical tool was developed to annotate pixels. The strategy was to annotate a few pixels per image to be able to quickly annotate the entire image set, and thus account for very diverse conditions. Results showed a lesser segmentation score (F1-score) for the heading and flowering stages and for the zero nitrogen input object. The methodology appeared appropriate for further work on the growth dynamics of the different wheat organs and in the frame of other segmentation challenges.

Global Wheat Head Detection 2021: An Improved Dataset for Benchmarking Wheat Head Detection Methods

The Global Wheat Head Detection (GWHD) dataset was created in 2020 and has assembled 193,634 labelled wheat heads from 4700 RGB images acquired from various acquisition platforms and 7 countries/institutions. With an associated competition hosted in Kaggle, GWHD_2020 has successfully attracted attention from both the computer vision and agricultural science communities. From this first experience, a few avenues for improvements have been identified regarding data size, head diversity, and label reliability. To address these issues, the 2020 dataset has been reexamined, relabeled, and complemented by adding 1722 images from 5 additional countries, allowing for 81,553 additional wheat heads. We now release in 2021 a new version of the Global Wheat Head Detection dataset, which is bigger, more diverse, and less noisy than the GWHD_2020 version.

Five-year mortality in patients with diabetic foot ulcer during 2009-2010 was lower than expected

AIM

Mortality rates are decreasing in patients with diabetes. However, as this observation also concerns patients with diabetic foot ulcer (DFU), additional data are needed. For this reason, our study evaluated the 5-year mortality rate in patients with DFU during 2009-2010 and identified risk factors associated with mortality.

METHODS

Consecutive patients who attended a clinic for new DFU during 2009-2010 were followed until healing and at 1 year. Data on mortality were collected at year 5. Multivariate Cox proportional-hazards model was used to identify mortality risk factors.

RESULTS

A total of 347 patients were included: mean age was 65±12 years, diabetes duration was 16 [10; 27] years; 13% were on dialysis; and 7% had an organ transplant. At 5 years, 49 patients (14%) were considered lost to follow-up. Total mortality rate at 5 years was 35%, and 16% in patients with neuropathy. On multivariate analyses, mortality was positively associated with: age [hazard ratio (HR): 1.05 (1.03-1.07), P<0.0001]; duration of diabetes [HR: 1.02 (1.001-1.03], P=0.03]; PEDIS perfusion grade 2 vs. 1 [HR: 2.35 (1.28-4.29), P=0.006)]; PEDIS perfusion grade 3 vs. 1 [HR: 3.14 (1.58-6.24), P=0.001); and ulcer duration at year 1 [HR 2.09 (1.35-3.22), P=0.0009].

CONCLUSION

Mortality rates were not as high as expected despite the large number of comorbidities, suggesting that progress has been made in the health management of these patients. In particular, patients with neuropathic foot ulcer had a survival rate of 84% at 5 years.

The course of apathy in late-life depression treated with electroconvulsive therapy; a prospective cohort study

OBJECTIVES

Apathy, a lack of motivation, is frequently seen in older individuals, with and without depression, with substantial impact on quality of life. This prospective cohort study of patients with severe late-life depression treated with electroconvulsive therapy (ECT) aims to study the course of apathy and the predictive value of vascular burden and in particular white matter hyperintensities on apathy course.

METHODS

Information on apathy (defined by a score of >13 on the Apathy Scale), depression severity, vascular burden, and other putative confounders was collected in at 2 psychiatric hospitals on patients with late-life depression (aged 55 to 87 years, N = 73). MRI data on white matter hyperintensities were available in 52 patients. Possible risk factors for apathy post-ECT were determined using regression analyses.

RESULTS

After treatment with ECT, 52.0% (26/50) of the depression remitters still suffered from clinically relevant apathy symptoms. In the entire cohort, more patients remained apathetic (58.9%) than depressed (31.5%). Presence of apathy post-ECT was not associated with higher age, use of benzodiazepines, or severity of apathy and depression at baseline. Less response in depressive symptomatology after ECT predicted post-treatment apathy. The presence of vascular disease, diabetes mellitus and smoking, and white matter hyperintensities in the brain was not associated with post-treatment apathy.

CONCLUSIONS

Apathy may perpetuate in individual patients, despite remission of depressive symptoms. In this cohort of patients with late-life depression, post-ECT apathy is not associated with white matter hyperintensities.

In silico clinical trials for pediatric orphan diseases

To date poor treatment options are available for patients with congenital pseudarthrosis of the tibia (CPT), a pediatric orphan disease. In this study we have performed an in silico clinical trial on 200 virtual subjects, generated from a previously established model of murine bone regeneration, to tackle the challenges associated with the small, pediatric patient population. Each virtual subject was simulated to receive no treatment and bone morphogenetic protein (BMP) treatment. We have shown that the degree of severity of CPT is significantly reduced with BMP treatment, although the effect is highly subject-specific. Using machine learning techniques we were also able to stratify the virtual subject population in adverse responders, non-responders, responders and asymptomatic. In summary, this study shows the potential of in silico medicine technologies as well as their implications for other orphan diseases.

[Macro replantation of upper extremity. Update and review of the long-term functional results]

Confronted with increasing problems of financing in health care, some question the relevance of certain interventions of high technicality. Today, the limiting factor for practitioners is not any longer situated at the technical and technological level (the survival of macro replantations is assured in 85-90%) but moves slowly and surely towards the economic level. It is true that medicine has a price and that if a technique is expensive, it should at least be justified at the human level and superior to other less expensive therapeutic options which are available. In this article, we will first focus on the long-term outcome of patients and also on the functional benefit which brings them replantation compared to patients who underwent a regularization of their stump and possibly a reconstruction enabling them to be correctly fitted with a prosthesis.

Current views on calcium phosphate osteogenicity and the translation into effective bone regeneration strategies

Calcium phosphate (CaP) has traditionally been used for the repair of bone defects because of its strong resemblance to the inorganic phase of bone matrix. Nowadays, a variety of natural or synthetic CaP-based biomaterials are produced and have been extensively used for dental and orthopaedic applications. This is justified by their biocompatibility, osteoconductivity and osteoinductivity (i.e. the intrinsic material property that initiates de novo bone formation), which are attributed to the chemical composition, surface topography, macro/microporosity and the dissolution kinetics. However, the exact molecular mechanism of action is unknown. This review paper first summarizes the most important aspects of bone biology in relation to CaP and the mechanisms of bone matrix mineralization. This is followed by the research findings on the effects of calcium (Ca²⁺) and phosphate (PO₄³⁻) ions on the migration, proliferation and differentiation of osteoblasts during in vivo bone formation and in vitro culture conditions. Further, the rationale of using CaP for bone regeneration is explained, focusing thereby specifically on the material's osteoinductive properties. Examples of different material forms and production techniques are given, with the emphasis on the state-of-the art in fine-tuning the physicochemical properties of CaP-based biomaterials for improved bone induction and the use of CaP as a delivery system for bone morphogenetic proteins. The use of computational models to simulate the CaP-driven osteogenesis is introduced as part of a bone tissue engineering strategy in order to facilitate the understanding of cell-material interactions and to gain further insight into the design and optimization of CaP-based bone reparative units. Finally, limitations and possible solutions related to current experimental and computational techniques are discussed.

Exposing the third chromosome of Burkholderia cepacia complex strains as a virulence plasmid

The Burkholderia cepacia complex (Bcc) consists of 17 closely related species of opportunistic bacterial pathogens, which are particularly problematic for cystic fibrosis patients and immunocompromised individuals. Bcc genomes consist of multiple replicons, and each strain sequenced to date has three chromosomes. In addition to genes thought to be essential for survival, each chromosome carries at least one rRNA operon. We isolated three mutants during a transposon mutagenesis screen that were non-pathogenic in a Caenorhabditis elegans infection model. It was demonstrated that these mutants had lost chromosome 3 (c3), and that the observed attenuation of virulence was a consequence of this. We constructed a c3 mini-replicon and used it to cure c3 from strains of several Bcc species by plasmid incompatibility, resulting in nine c3-null strains covering seven Bcc species. Phenotypic characterization of c3-null mutants revealed that they were attenuated in virulence in multiple infection hosts (rat, zebrafish, C. elegans, Galleria mellonella and Drosophila melanogaster), that they exhibited greatly diminished antifungal activity, and that c3 was required for d-xylose, fatty acid and pyrimidine utilization, as well as for exopolysaccharide production and proteolytic activity in some strains. In conclusion, we show that c3 is not an essential chromosomal element, rather a large plasmid that encodes virulence, secondary metabolism and other accessory functions in Bcc bacteria.

Designing optimal calcium phosphate scaffold-cell combinations using an integrative model-based approach

Bone formation is a very complex physiological process, involving the participation of many different cell types and regulated by countless biochemical, physical and mechanical factors, including naturally occurring or synthetic biomaterials. For the latter, calcium phosphate (CaP)-based scaffolds have proven to stimulate bone formation, but at present still result in a wide range of in vivo outcomes, which is partly related to the suboptimal use and combination with osteogenic cells. To optimize CaP scaffold selection and make their use in combination with cells more clinically relevant, this study uses an integrative approach in which mathematical modeling is combined with experimental research. This paper describes the development and implementation of an experimentally informed bioregulatory model of the effect of calcium ions released from CaP-based biomaterials on the activity of osteogenic cells and mesenchymal stem cell driven ectopic bone formation. The amount of bone formation predicted by the mathematical model corresponds to the amount measured experimentally under similar conditions. Moreover, the model is also able to qualitatively predict the experimentally observed impaired bone formation under conditions such as insufficient cell seeding and scaffold decalcification. A strategy was designed in silico to overcome the negative influence of a low initial cell density on the bone formation process. Finally, the model was applied to design optimal combinations of calcium-based biomaterials and cell culture conditions with the aim of maximizing the amount of bone formation. This work illustrates the potential of mathematical models as research tools to design more efficient and cell-customized CaP scaffolds for bone tissue engineering applications.

[Patient complaints in a hospital emergency department in Belgium]

Patients express their dissatisfaction through complaints. This study analyzed the frequency and chief complaints of patients presenting to the emergency department (ED). The end point was find ways to improve patient satisfaction after their ED visit. In this retrospective, seven years study, we reviewed 155 chief complaints of patients presenting to the ED of a university hospital. The chief complaints were either from the patients or a family member. One hundred and fifty five chief complaints collected from 496.816 patients presenting to the ED were reviewed over a period of seven years. Complaints case rate was 3.1 per 10.000 visits. Complaints came from patients between the age of 20 to 60 years old (75.0 percent). Complains involved a physician (79.0 percent). The complaints were related a lack of communication (39.0 percent), long waiting time (14.0 percent), wrong diagnosis (22.0 percent), wrong treatment (13.0 percent) and ED disposition of the patient (12.0 percent). Two types of pathology represented more than 15 percent of the complaints: the traumatology (22.0 percent) and the psychiatry (17.0 percent). The traumatology and psychiatry represented respectively 30.0 percent and 10.0 percent of ED visits. Most complaints were addressed and resolved through a hospital mediator, Chief of service or Chief of staff. The rate of complains is low. Most complaints can be prevented if the physician improves communication with patients.

[The anatomical laboratory: a tool for the trial of the new therapeutic procedures]

Since September 2009, the new anatomical department is located on the CHU building. This modern anatomical laboratory is an effective tool to design the new therapeutic procedures and to teach these procedures to practitioners.

The Ti plasmid of Agrobacterium tumefaciens harbors an attM-paralogous gene, aiiB, also encoding N-Acyl homoserine lactonase activity

The Agrobacterium tumefaciens C58 genome contains three putative N-acyl homoserine lactone (acyl-HSL) hydrolases, which are closely related to the lactonase AiiA of Bacillus. When expressed in Escherichia coli, two of the putative acyl-HSL hydrolases, AttM and AiiB, conferred the ability to degrade acyl-HSLs on the host. In Erwinia strain 6276, the lactonases reduced the endogenous acyl-HSL level and the bacterial virulence in planta.

[How I treat ... facial paralysis by hypoglosso-facial anastomosis]

Thirteen patients underwent a hypoglosso- or a spino-facial nerve anastomosis between 1990 and 1996. Facial palsy was the result of surgery in 12 cases and of radiosurgery in 1 case. The mean interval between facial palsy and anastomosis was 12 months. Facial nerve function is determined on the basis of clinical examination according to the classification of House-Brackmann and our own evaluation. According to House, 10 patients are classified grade III and 3 grade IV. Our evaluation defines in 10 grade III, 7 good results and 3 fair results. As far as the good results are concerned, the mean interval between palsy and anastomosis is short (< 3 months). The permanent eating and swallowing dysfunctions are consecutive to multiple cranial nerve deficits. The post-paralysis hemifacial spasm is facilitated by prolongated electric stimulations.

[Hypothenar hammer syndrome]

The hypothenar hammer syndrome is an uncommon but underestimated lesion of the cubital artery caused by repetitive trauma at the level of the hamate bone. It characteristically occurs in patients with a history of manual work as metal workers, carpenters and motor mechanics. We present a case of a patient who developed this syndrome following intensive use of a dig. Clinical finding, diagnosis and treatment are discussed.

Carpal tunnel syndrome in childhood: report of five new cases

Carpal tunnel syndrome is a condition rarely encountered during the growth period. We describe five new cases in two large Belgian university hospitals. One case concerned a 2-year-old child suffering from disseminated angiomatosis, an association not previously reported. Another case of mild severity corresponded to the classic association of trigger fingers and carpal tunnel syndrome. The third case was posttraumatic, and the last two cases were of the familial type that previously has been reported in four families. We discuss these observations and briefly review the literature.

[Rapid determination of bactericidal kinetics by evaluating intracellular adenosine-triphosphate in bioluminescence]

Killing kinetics measurement is usually time-consuming and tedious. Bioluminescent adenosine-triphosphate (ATP) assay, after intracellular nucleotide release by bacterial lysis, selects very quickly normal from antibiotic-modified and dead bacteria. Two simultaneous assays are performed with more and less strong lysis reagents (nucleotide releasing bacterial NRB, nucleotide releasing somatic NRS, Lumac). Bioluminescence produced in a luciferine - luciferase system is measured with Biocounter M 2010 luminometer. Differential values of two assays reflect the intracellular ATP fraction of strongest bacteria in tested cultures. Killing curves of some beta lactamines (aminopenicillin and cephalosporins) were studied with active Escherichia coli and Streptococcus pneumoniae cultures. Bactericidal action was seen within few hours, and similar variations of intracellular ATP fraction and numbers of colony-forming units obtained by reference method were observed. This method, well-suited to large series of assays and very rapid (intracellular ATP assay within one minute), performs detailed killing kinetics in real time.

[Current treatment of fresh lesions of the flexor tendons]

Different aspects of primary treatment of flexor tendon lesions are reviewed. Of outstanding importance are: adequate setting and instruments plus meticulous repair with fine material, avoidance of traumatic manipulation of structures and anatomical repair, use of dynamic mobilisation of reconstructed tendons within a team of well informed and motivated therapists.

[Current emergency treatment of lesions of the flexor tendons: anatomical, biomechanical and cicatricial aspects]

Emergency treatment of flexor tendon lesion in 1988: anatomic biomechanical and healing characteristics. Flexor tendon surgery in 1988 must take into account detailed anatomic knowledge as well as healing and biomechanical properties of flexor tendons. Application of standardised surgical technics allows reliable treatment when the surgeon is familiar with these technics and the basic knowledge they suppose. The authors detail the technics and certain details with practical goals.

Intrinsic fasciotomy. When and why?

Major trauma to the upper extremity may lead to ischemic contracture of various muscle groups, sometimes including the intrinsic muscles of the hand. The clinical consequence of such necrotic fibrosis of the intrinsics is clawing of the digits with marked stiffness. After a short anatomical review of the fascias of the intrinsics, indications and operative techniques are discussed, in parallel with clinical cases. Intrinsic fasciotomy thus appears to be a major step in the prevention of digital clawing, when associated with early physiotherapy.

The denervated first dorsal interosseous muscle flap: a case report

Coverage of a dorsal defect on the hand of a child with exposed extensor tendons was provided by a denervated first dorsal interosseous muscle and splitthickness skin grafting. We do not recommend routine use of the first dorsal interosseous muscle as a flap; however, its use in cases in which the muscle has been denervated would seem justified.

Pregnancy complicated by insulinoma. Case report

An insulinoma was excised during pregnancy. The tumor was located by radiography and severe hypoglycaemia made it necessary to administer diazoxide to the mother. The out come in the pregnancy was satisfactory. The rationale and risks of giving diazoxide in pregnancy are discussed.