Back to the Roots: Agrobacterium-Specific Phages Show Potential to Disinfect Nutrient Solution from Hydroponic Greenhouses.

Agrobacterium biovar 1 is a soilborne plant pathogen with the ability to colonize the irrigation system of greenhouses, causing hairy root disease (HRD). Currently, management focuses on using hydrogen peroxide to disinfect the nutrient solution, but due to the emergence of resistant strains, its efficacy and sustainability are questioned. Using a relevant collection of pathogenic Agrobacterium biovar 1 strains, OLIVR1 to 6, six phages specific to this pathogen and belonging to three different genera were isolated from Agrobacterium biovar 1-infected greenhouses. All phages were named OLIVR, referring to their location of isolation, Onze-Lieve-Vrouwe-Waver, and were characterized by whole-genome analysis, confirming their strictly lytic lifestyle. They remained stable under greenhouse-relevant conditions. To assess the efficacy of the phages, their ability to disinfect greenhouse nutrient solution inoculated with agrobacteria was tested. Each of the phages infected their host, but their ability to decrease the bacterial concentration differed. For instance, OLIVR1 reduced the bacterial concentration with 4 log units without phage resistance emerging. While OLIVR4 and OLIVR5 were also infectious in nutrient solution, they did not always decrease the bacterial load below the limit of detection, and phage resistance emerged. Finally, the mutations causing phage resistance by receptor modification were identified. For OLIVR4-resistant Agrobacterium isolates, but not for OLIVR5-resistant isolates, motility decreased. Together, these data show the potential of some of these phages as disinfectant of nutrient solution, and they might be a valuable tool to tackle HRD. IMPORTANCE Hairy root disease, caused by rhizogenic Agrobacterium biovar 1 is a rapidly emerging bacterial disease worldwide. It affects tomatoes, cucumbers, eggplant, and bell pepper, causing high yield losses in hydroponic greenhouses. Recent findings suggest that the current management practices, mainly focusing on UV-C and hydrogen peroxide to disinfect contaminated water, have a questionable efficacy. Hence, we investigate the potential of phages as a biological means of preventing this disease. Using a diverse collection of Agrobacterium biovar 1, we isolated three different phage species that together infect 75% of the collection. Since these phages are strictly lytic, while remaining both stable and infectious under greenhouse-relevant conditions, they might be suitable candidates for biological control.

Isolation, characterization and genome analysis of an orphan phage FoX4 of the new Foxquatrovirus genus.

The growing interest in the therapeutic application of bacteriophages leads to a drastic increase in the number of sequenced genomes. Luckily, recent insights in phage taxonomy facilitate the classification of phages in a comprehensive and data-driven manner as recently proposed by the International Committee on Taxonomy of Viruses. In this research, we present the taxonomical classification of a novel, narrow host range Xanthomonas phage FoX4, isolated from a Brussels sprouts field in Belgium infested with Xanthomonas campestris pv. campestris. The phage has a limited ability to lyse a bacterial culture, yet adsorbs efficiently to its host. Based on its genome sequence and low similarity to previously described phages, the phage comprises the novel phage genus Foxquatrovirus.

Bacteriophage therapy as a treatment strategy for orthopaedic-device-related infections: where do we stand?

Antibiotic resistance represents a key challenge of the 21st century. Since the pipeline of new antibiotics in development is limited, the introduction of alternative antimicrobial strategies is urgently required. Bacteriophage therapy, the use of bacterial viruses to selectively kill bacterial pathogens, is re-emerging as a potential strategy to tackle difficult-to-treat and multidrug-resistant pathogens. The last decade has seen a surge in scientific investigation into bacteriophage therapy, including targeting orthopaedic-device-related infections (ODRIs) in several successful case studies. However, pharmacological data, knowledge on the interplay with the immune system and, especially in ODRIs, the optimal local application strategy and treatment outcomes remain scarce. The present review reports the state-of-the-art in bacteriophage therapy in ODRIs and addresses the hurdles in establishing bacteriophage therapy under good clinical practice guidelines. These hurdles include a lack of data concerning bacteriophage production, processing, administration and dosing, as well as follow-up clinical monitoring reports. To overcome these challenges, an integrated clinical approach is required, supported by comprehensive legislature to enable expansive and correctly implemented clinical trials.

How robust are clinical trials in primary and secondary ankle sprain prevention?

OBJECTIVES: Determine the statistical stability of RCTs examining primary and secondary prevention of ankle sprains. METHODS: Databases were searched to August 2023. We included parallel design RCTs, using conservative interventions for preventing ankle sprain, reporting dichotomous injury event outcomes. Statistical stability was quantified using Fragility Index (FI) and Fragility Quotient (FQ). Subgroup analyses were undertaken to test if FI varied based on by study objective, original approach to analysis (frequency vs time to event), follow-up duration, and pre-registration. RESULTS: 3559 studies were screened with 45 RCTs included. The median number of events required to change the statistical significance (FI) was 4 (IQR 1-6). FI was similar regardless of study objective, original analysis, follow-up duration, and pre-registration status. Median (IQR) FQ was 0.015 (0.005-0.046), therefore reversing events <2 patients/100 would alter significance. In 80% of studies the number of patients lost to follow-up was greater than the FI. CONCLUSION: RCTs informing primary and secondary prevention of ankle sprain are fragile. Only a small percentage of outcome event reversals would reverse study significance, and this is often exceeded by the number of drop outs. Robust reporting of dichotomous outcomes requires the use P values and key metrics such as FI or FQ.

Draft Genome Sequences of 27 Rhizogenic Agrobacterium Biovar 1 Strains, the Causative Agent of Hairy Root Disease.

Rhizogenic Agrobacterium biovar 1 strains are important plant pathogens that cause hairy root disease in Cucurbitaceae and Solanaceae crops cultivated under hydroponic conditions. In contrast to tumorigenic agrobacteria, only a few genome sequences of rhizogenic agrobacteria are currently available. Here, we report the draft genome sequences of 27 rhizogenic Agrobacterium strains.

The BOLD correlates of the visual P1 and N1 in single-trial analysis of simultaneous EEG-fMRI recordings during a spatial detection task.

Simultaneous EEG-fMRI measurements can combine the high spatial resolution of fMRI with the high temporal resolution of EEG. Therefore, we applied this approach to the study of peripheral vision. More specifically, we presented visual field quadrant fragments of checkerboards and a full central checkerboard in a simple detection task. A technique called "integration-by-prediction" was used to integrate EEG and fMRI data. In particular, we used vectors of single-trial ERP amplitude differences between left and right occipital electrodes as regressors in an ERP-informed fMRI analysis. The amplitude differences for the regressors were measured at the latencies of the visual P1 and N1 components. Our results indicated that the traditional event-related fMRI analysis revealed mostly activations in the vicinity of the primary visual cortex and in the ventral visual stream, while both P1 and N1 regressors revealed activation of areas in the temporo-parietal junction. We conclude that simultaneous EEG-fMRI in a spatial detection task can separate visual processing at 100-200 ms from stimulus onset from the rest of the information processing in the brain.

Cobalt and silver nanocoatings for reactor dosimetry.

Activation foils are an important tool for the characterization of neutron fields. Some of the materials that are used in these foils have large interaction cross-sections that cause unwanted self-shielding effects. In practice experimenters minimize these effects by using aluminium alloys. An alternative approach can be a nanocoating of a pure material on a carrier. The validity of this approach is investigated in this work. Nanocoatings can be more flexible compared to alloys and can probably reduce the number of required post-irradiation gamma spectrometry measurements. Cobalt and silver nanocoatings were deposited by physical vapour deposition on nickel and aluminium carrier foils. The nanocoatings were tested in two irradiation campaigns in the Belgian Reactor 1 at SCK CEN. By depositing nanocoatings with different thickness and determining the corresponding number of activated atoms the inherent flexibility of the technique is demonstrated. When the dosimeters were punched from the carrier foils, the metal cylindrical punch damaged the nanocoatings which increased the spread on the number of atoms between different dosimeters. This is prevented by including a Ti interlayer of 5 nm between the carrier and the cobalt and silver layers. It was shown that this results in a coating with good homogeneity or minimal spread. This study shows that applying nanocoatings on a carrier is a valid technique to make dosimeters.

The relation between visual orienting functions, daily visual behaviour and visuoperceptual performance in children with (suspected) cerebral visual impairment.

BACKGROUND: Children with cerebral visual impairment (CVI) present heterogeneous visual orienting functions (VOF) and higher-order perception. Multiple assessment methods evaluate CVI, but the relations between them remain unclear. AIM: To investigate the relations between VOF and (1) daily life behaviour and (2) visuoperceptual tests in children with (suspected) CVI. METHODS AND PROCEDURES: VOF were tested with a validated eye tracking-based paradigm. Visual perception was assessed using the children's visual impairment test for 3- to 6-year olds (CVIT 3-6) and (retrospective) visuoperceptual dimension results. Caregivers completed the Flemish cerebral visual impairment questionnaire (FCVIQ) and an expert panel scored relations between VOF and the other methods. We compared experts' survey responses with data-based results (linear mixed models and correlations). OUTCOMES AND RESULTS: Fourty-four children (23 boys, 21 girls; median age = 7y11mo, SD = 2y7mo) participated. Twenty-one experts completed the survey. Slower VOF was significantly associated with (1) object and face processing impairments, (2) visual (dis)interest, (3) worse visual spatial perception (to local motion and form stimuli), and (4) worse CVIT 3-6 object and scene recognition (to cartoon stimuli). CONCLUSIONS AND IMPLICATIONS: Integration of VOF with existing visual assessments provides a better clinical picture of CVI and can prevent misdiagnosing children as inattentive, incapable, or unmotivated.

Shared neural resources between left and right interlimb coordination skills: the neural substrate of abstract motor representations.

Functional magnetic resonance imaging was used to reveal the shared neural resources between movements performed with effectors of the left versus right body side. Prior to scanning, subjects extensively practiced a complex coordination pattern involving cyclical motions of the ipsilateral hand and foot according to a 90 degrees out-of-phase coordination mode. Brain activity associated with this (nonpreferred) coordination pattern was contrasted with pre-existing isodirectional (preferred) coordination to extract the learning-related brain networks. To identify the principal candidates for effector-independent movement encoding, the conjunction of training-related activity for left and right limb coordination was determined. A dominantly left-lateralized parietal-to-(pre)motor activation network was identified, with activation in inferior and superior parietal cortex extending into intraparietal sulcus and activation in the premotor areas, including inferior frontal gyrus (pars opercularis). Similar areas were previously identified during observation of complex coordination skills by expert performers. These parietal-premotor areas are principal candidates for abstract (effector-independent) movement encoding, promoting motor equivalence, and they form the highest level in the action representation hierarchy.

Inferotemporal neurons represent low-dimensional configurations of parameterized shapes.

Behavioral studies with parameterized shapes have shown that the similarities among these complex stimuli can be represented using a low number of dimensions. Using psychophysical measurements and single-cell recordings in macaque inferotemporal (IT) cortex, we found an agreement between low-dimensional parametric configurations of shapes and the representation of shape similarity at the behavioral and neuronal level. The shape configurations, computed from both the perceived and neuron-based similarities, revealed a low number of dimensions and contained the same stimulus order as the parametric configurations. However, at a metric level, the behavioral and neural representations deviated consistently from the parametric configurations. These findings suggest an ordinally faithful but metrically biased representation of shape similarity in IT.

Effects of perceptual learning in visual backward masking on the responses of macaque inferior temporal neurons.

Learning is critical for fast and efficient object recognition in primates. To understand the neuronal correlates of behavioral improvements due to training, we recorded the responses of single neurons in the inferior temporal (IT) cortex of monkeys that were trained to recognize briefly presented, backward-masked objects. First we investigated training effects that are specific to the objects shown during training and that do not transfer to untrained objects. Only one of two monkeys tested showed object-specific training effects at the behavioral level, and only this monkey showed a transient object-specific increase in object selectivity for trained compared with untrained backward-masked objects. However, in each monkey a substantial part of the training effect transferred to untrained objects. To investigate the neural correlates of these object-independent training effects, we compared the neural responses to masked objects in trained monkeys to the responses in untrained monkeys. Training was associated with a reduction of the responses to the irrelevant masking patterns. These findings suggest that extensive training in recognizing backward-masked objects results in neural changes that reduce IT responses to the interfering irrelevant masking patterns and enhance the processing of the relevant objects.

Characteristics and models of human symmetry detection.

Symmetry is everywhere - in natural objects, from crystals to living organisms, in manufactured articles of many kinds, and in art works from all cultures. Symmetry is a salient visual property that is detected efficiently and rapidly by the human visual system. In this paper, several decades of experimental research on human symmetry detection are reviewed. By examining the effects of several factors on symmetry detection, this research has revealed some important characteristics of how humans perceive symmetry. These characteristics constrain the general principles of putative underlying mechanisms and models of human symmetry detection. For example, the orientation of the axis of symmetry and its location in the visual field have effects that suggest that the bilateral symmetry of the visual system at cortical levels of the brain might partly determine the salience of vertical mirror symmetry. At the same time, there is a surprisingly high degree of flexibility and robustness that remains to be explained. Thus, symmetry provides a major challenge to model human flexibility and efficiency within the constraints of the biology of the visual system.

The effect of perceptual grouping on haptic numerosity perception.

We used a haptic enumeration task to investigate whether enumeration can be facilitated by perceptual grouping in the haptic modality. Eight participants were asked to count tangible dots as quickly and accurately as possible, while moving their finger pad over a tactile display. In Experiment 1, we manipulated the number and organization of the dots, while keeping the total exploration area constant. The dots were either evenly distributed on a horizontal line (baseline condition) or organized into groups based on either proximity (dots placed in closer proximity to each other) or configural cues (dots placed in a geometric configuration). In Experiment 2, we varied the distance between the subsets of dots. We hypothesized that when subsets of dots can be grouped together, the enumeration time will be shorter and accuracy will be higher than in the baseline condition. The results of both experiments showed faster enumeration for the configural condition than for the baseline condition, indicating that configural grouping also facilitates haptic enumeration. In Experiment 2, faster enumeration was also observed for the proximity condition than for the baseline condition. Thus, perceptual grouping speeds up haptic enumeration by both configural and proximity cues, suggesting that similar mechanisms underlie perceptual grouping in both visual and haptic enumeration.

Effects of physical connectivity on the representational unity of multi-part configurations.

While physical connection strongly supports perceptual integration of visual elements or parts into single objects, concavities along an object's contour strongly induce segmentation of objects into different parts. By means of a matching task, we examine whether the segmentation of connected parts and the grouping of disconnected parts imply differences in representational unity. All match trials consisted of either two identical configurations or two 180 degrees rotated versions of an otherwise identical configuration, whereas mismatch trials had one misoriented part. Results show that the 180 degrees matches with the physically disconnected parts were relatively slower than similar matches with physically connected parts, although the connections could be minimal (deep concavities, corner to edge connection). This suggests that the mental operation required for the 180 degrees match has more difficulty with the disconnected parts, indicating a measurably lower degree of representational unity.

Lorazepam but not diazepam impairs identification of pictures on the basis of specific contour fragments.

We tested the effects of lorazepam 0.038 mg/kg and diazepam 0.3 mg/kg on the identification of pictures of everyday objects that were specifically modified to examine the role of different parts of the external contour. By pressing the space bar of a computer keyboard, observers could add 1% of the total contour of each picture until it was recognized. Identification thresholds were measured in three display conditions, depending on where along the contour the addition of contour pixels started. In the minima condition, stimuli were initially displayed with only minima (i.e., locations along the contour where negative curvature is strongest); all parts with negative curvature were then built up gradually from the minima and only later on were the fragments with positive curvature shown until the contour became closed at the maxima (i.e., locations where positive curvature is strongest). In the maxima condition, initially only the maxima were displayed, with all positive contour built up first and then the negative curvature until the minima were reached. In the inflections condition, the points along the contour shown first were inflections (i.e., points where curvature is locally zero because the sign of curvature changes there) and contour was built up by adding parts of positive and negative curvature at both sides of each inflection until the extrema (minima and maxima) were reached to close the contour of the picture. In general, picture identification was more difficult (i.e., a larger portion of the contour was required) in the minima condition than in the maxima and the inflections conditions. The diazepam group did not differ significantly from the placebo group, while the lorazepam group had significantly lower performance in all three display conditions. Results are discussed in relation to previous research showing impaired perceptual integration and impaired implicit memory under lorazepam influence.

Effect of benzodiazepine on temporal integration in object perception.

RATIONALE: Though various psychometrical tests indicate that benzodiazepines affect vigilance, few studies have been conducted to assess the effect of benzodiazepines on attentional processes. OBJECTIVE: We used a RSVP (Rapid Serial Visual Presentation) procedure to investigate the effect of benzodiazepines on the attentional blink effect. It refers to the difficulty in detecting a probe following identification of a target within a temporal window of 500 ms. METHOD: Three experimental groups were tested (placebo, lorazepam and diazepam). Sequences of 15 pictures were centrally displayed for 50 ms each. In a dual-task condition, observers were instructed (1) to identify the target (the single picture on a blue background) and (2) to detect the presence of a probe. In the single-task condition, subjects were asked to detect the probe. The serial position of the probe relative to the target was varied. RESULTS: Performance was equivalent for the three groups in the single-task condition. In the dual-task condition, the attentional blink was increased in magnitude and duration for benzodiazepine-treated subjects, especially diazepam, than for placebo-treated subjects. A large number of intrusions (a tendency to report as target the name of a picture preceding the target) were observed in the benzodiazepine-treated groups. CONCLUSION: The results indicate that benzodiazepines impair visual integration in the temporal domain. This extends previous findings that benzodiazepine impairs visual integration in the spatial domain. The results also suggest that benzodiazepine increase time to disengage attention from a first to a second target.

Skewed symmetry: a nonaccidental property used to perceive visual forms.

Mathematically, skewed symmetry is a nonaccidental property because it can be interpreted as bilateral symmetry in depth viewed from a nonorthogonal angle. To find out whether this is a useful property in the perception of visual forms, 4 experiments were designed in which the Ss had to determine whether 2 symmetric or random patterns were the same regardless of possible affine transformations between them. The results provided mixed evidence: Although there was always a large symmetry advantage, skewed symmetry was only perceived as bilateral symmetry in depth for dot patterns with higher order types of symmetry (Experiment 1), when the dots were connected to form closed polygons (Experiments 2 and 4), or when they were surrounded by a frame to enhance their planarity (Experiment 3). In other cases, Ss relied on local groupings on the basis of proximity or curvilinearity, which are qualitatively affine invariant.

Matching multicomponent objects from different viewpoints: mental rotation as normalization?

Novel multicomponent objects were created, and 3 distractors were created for each object by changing the relations between the parts of the object. In a set of 5 experiments, target objects were presented as a motion sequence of multiple views or as a single view. Participants were asked to determine whether an image of an object, viewed from another viewpoint, was the same as the target object. The axis of rotation was aligned with one of the environmental axes or with the main axis of the object. The effects of viewpoint on performance imply that the matching of objects is viewpoint dependent and requires a process of normalization to undo the differences between the perceptual description and the stored object descriptions. The lack of a systematic effect of the axis of rotation, however, suggests that this normalization is best understood as not involving a 3-D transformation of stored 3-D object models.

Minimal information to determine affine shape equivalence.

Participants judged the affine equivalence of 2 simultaneously presented 4-point patterns. Performance level (d') varied between 1.5 and 2.7, depending on the information available for solving the correspondence problem (insufficient in Experiment 1a, superfluous in Experiment 1b, and minimal in Experiments 1c, 2a, 2b) and on the exposure time (unlimited in Experiments 1 and 2a and 500 ms in Experiment 2b), but it did not vary much with the complexity of the affine transformation (rotation and slant in Experiment 1 and same plus tilt in Experiment 2). Performance in Experiment 3 was lower with 3-point patterns than with 4-point patterns, whereas blocking the trials according to the affine transformation parameters had little effect. Determining affine shape equivalence with minimal-information displays is based on a fast assessment of qualitatively or quasi-invariant properties such as convexity/ concavity, parallelism, and collinearity.

The viewpoint-dependency of veridicality: psychophysics and modelling.

Human observers were shown projected angles, embedded in solid cross-like figures and were asked whether these projected angles could be the projection of an orthogonal angle in 3-D space (i.e. whether the two legs of the cross were orthogonal to each other). We found that performance depended on the viewpoint at which the angle was viewed: Both slant (i.e. the angle between the normal of the target angle relative to the plane of projection) and roll (i.e. the rotation around the normal of the target angle) had a systematic effect on the proportion of errors when observers were shown non-orthogonal angles. With orthogonal angles, however, this effect was absent (i.e. very low error rate with no systematic effect of slant and roll). Instead of assuming a viewpoint-dependent bias towards orthogonality, a computational analysis of the task, using a Bayesian approach, and a computer simulation showed that the viewpoint-dependency can be modelled by a fixed set of biases in order to constrain the set of possible scenes that could give rise to the projection.