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Abstract Objectives Recent advances in bio-inspired navigation have sparked interest in the phenomenon of skylight polarization. This interest stems from the potential of skylight-based orientation sensors, which performance can be simulated using physical models. However, the effectiveness of machine learning algorithms in this domain relies heavily on access to large datasets for training. Although there are several databases of simulated images in literature, there remains a lack of publicly available annotated real-world color polarimetric images of the sky across various weather conditions. Data description We present here a dataset obtained from a long-term experimental setup designed to collect polarimetric images from a stand-alone camera. The setup utilizes a Division-of-Focal-Plane polarization camera equipped with a fisheye lens mounted on a rotative telescope mount. Furthermore, we obtained the sensor’s orientation within the East-North-Up (ENU) frame from a geometrical calibration and an algorithm provided with the database. To facilitate further research in this area, the present sample dataset spanning two months has been made available on a public archive with manual annotations as required by deep learning algorithms. The images were acquired at 10 min intervals and were taken with various exposure times ranging from 33µs to 300ms.

Abstract The Maintenance of Lipid Asymmetry (Mla) pathway is a multicomponent system found in all gram-negative bacteria that contributes to virulence, vesicle blebbing and preservation of the outer membrane barrier function. It acts by removing ectopic lipids from the outer leaflet of the outer membrane and returning them to the inner membrane through three proteinaceous assemblies: the MlaA-OmpC complex, situated within the outer membrane; the periplasmic phospholipid shuttle protein, MlaC; and the inner membrane ABC transporter complex, MlaFEDB, proposed to be the founding member of a structurally distinct ABC superfamily. While the function of each component is well established, how phospholipids are exchanged between components remains unknown. This stands as a major roadblock in our understanding of the function of the pathway, and in particular, the role of ATPase activity of MlaFEDB is not clear. Here, we report the structure of E. coli MlaC in complex with the MlaD hexamer in two distinct stoichiometries. Utilising in vivo complementation assays, an in vitro fluorescence-based transport assay, and molecular dynamics simulations, we confirm key residues, identifying the MlaD β6-β7 loop as essential for MlaCD function. We also provide evidence that phospholipids pass between the C-terminal helices of the MlaD hexamer to reach the central pore, providing insight into the trajectory of GPL transfer between MlaC and MlaD.

Abstract The advantageous versatility of hexapod robots is often accompanied by high power consumption, while animals have evolved an energy efficient locomotion. However, there are a lack of methods able to compare and apply animals’ energetic optimizations to robots. In this study, we applied our method to a full servomotor-based hexapod robot to evaluate its energetic performance. Using an existing framework based on the laws of thermodynamics, we estimated four metrics using a dedicated test bench and a simulated robotic leg. We analyzed the characteristics of a single leg to shape the energetic profile of the full robot to a given task. Energy saving is improved by 10% through continuous duty factor adjustment with a 192% increase in power maximization. Moreover, adjusting the robot’s velocity by the step length and associating this with gait switching, reduces the power loss by a further 10% at low-speed locomotion. However, unlike in animals, only one unique optimal operating point has been revealed, which is a disadvantage caused by the low energetic efficiency of servomotor-based hexapods. Thus, these legged robots are severely limited in their capacity to optimally adjust their locomotion to various tasks—a counter-intuitive conclusion for a supposedly versatile robot.

Abstract Treatment of Clostridioides difficile infection (CDI) is expensive and complex, with a high proportion of patients suffering infection relapse (20–35%), and some having multiple relapses. A healthy, unperturbed gut microbiome provides colonisation resistance against CDI through competition for nutrients and space. However, antibiotic consumption can disturb the gut microbiota (dysbiosis) resulting in the loss of colonisation resistance allowing C. difficile to colonise and establish infection. A unique feature of C. difficile is the production of high concentrations of the antimicrobial compound para-cresol, which provides the bacterium with a competitive advantage over other bacteria found in the gut. p-cresol is produced by the conversion of para-Hydroxyphenylacetic acid (p-HPA) by the HpdBCA enzyme complex. In this study, we have identified several promising inhibitors of HpdBCA decarboxylase, which reduce p-cresol production and render C. difficile less able to compete with a gut dwelling Escherichia coli strain. We demonstrate that the lead compound, 4-Hydroxyphenylacetonitrile, reduced p-cresol production by 99.0 ± 0.4%, whereas 4-Hydroxyphenylacetamide, a previously identified inhibitor of HpdBCA decarboxylase, only reduced p-cresol production by 54.9 ± 13.5%. To interpret efficacy of these first-generation inhibitors, we undertook molecular docking studies that predict the binding mode for these compounds. Notably, the predicted binding energy correlated well with the experimentally determined level of inhibition, providing a molecular basis for the differences in efficacy between the compounds. This study has identified promising p-cresol production inhibitors whose development could lead to beneficial therapeutics that help to restore colonisation resistance and therefore reduce the likelihood of CDI relapse.

This review article aims to address common research questions in passive polarized vision for robotics. What kind of polarization sensing can we embed into robots? Can we find our geolocation and true north heading by detecting light scattering from the sky as animals do? How should polarization images be related to the physical properties of reflecting surfaces in the context of scene understanding? This review article is divided into three main sections to address these questions, as well as to assist roboticists in identifying future directions in passive polarized vision for robotics. After an introduction, three key interconnected areas will be covered in the following sections: embedded polarization imaging; polarized vision for robotics navigation; and polarized vision for scene understanding. We will then discuss how polarized vision, a type of vision commonly used in the animal kingdom, should be implemented in robotics; this type of vision has not yet been exploited in robotics service. Passive polarized vision could be a supplemental perceptive modality of localization techniques to complement and reinforce more conventional ones.

Abstract When attempting to land on a ship deck tossed by the sea, helicopter pilots must make sure that the helicopter can develop sufficient lift to be able to safely touchdown. This reminder of affordance theory led us to model and study the affordance of deck-landing-ability, which defines whether it is possible to land safely on a ship deck depending on the helicopter's available lift and the ship’s deck heave movements. Two groups of participants with no piloting experience using a laptop helicopter simulator attempted to land either a low-lifter or a heavy-lifter helicopter on a virtual ship deck by either triggering a pre-programmed lift serving as the descent law if it was deemed possible to land, or aborting the deck-landing maneuver. The deck-landing-ability was manipulated by varying the helicopter's initial altitude and the ship's heave phase between trials. We designed a visual augmentation making visible the deck-landing-ability, and thus enabling participants to maximize the safety of their deck-landing attempts and reduce the number of unsafe deck-landing. The visual augmentation presented here was perceived by participants as a means of facilitating this decision-making process. The benefits were found to have originated from the clear-cut distinction it helped them to make between safe and unsafe deck-landing windows and the display of the optimal time for initiating the landing.

Summary: Following acute genotoxic stress, both normal and tumorous stem cells can undergo cell-cycle arrest to avoid apoptosis and later re-enter the cell cycle to regenerate daughter cells. However, the mechanism of protective, reversible proliferative arrest, “quiescence,” remains unresolved. Here, we show that mitophagy is a prerequisite for reversible quiescence in both irradiated Drosophila germline stem cells (GSCs) and human induced pluripotent stem cells (hiPSCs). In GSCs, mitofission (Drp1) or mitophagy (Pink1/Parkin) genes are essential to enter quiescence, whereas mitochondrial biogenesis (PGC1α) or fusion (Mfn2) genes are crucial for exiting quiescence. Furthermore, mitophagy-dependent quiescence lies downstream of mTOR- and PRC2-mediated repression and relies on the mitochondrial pool of cyclin E. Mitophagy-dependent reduction of cyclin E in GSCs and in hiPSCs during mTOR inhibition prevents the usual G1/S transition, pushing the cells toward reversible quiescence (G0). This alternative method of G1/S control may present new opportunities for therapeutic purposes.

IntroductionAlteration in endothelial function during sepsis is thought to play a key role in the progression of organ failure. We herein compared plasma concentrations of endothelial activation biomarkers vascular endothelial growth factor (VEGF), hyaluronan (HA), plasminogen activator inhibitor-1 (PAI-1) and von Willebrand factor (vWF), as well as inflammatory mediator concentrations (IL-6, IL-8, IL-10, C-reactive protein and monocyte chemoattractant protein-1) in dogs with sepsis to healthy dogs.MethodsThis study was a multicenter observational clinical trial conducted at two university teaching hospitals from February 2016 until July 2017. The study included 18 client-owned dogs hospitalized with sepsis and at least one distant organ dysfunction, as well as 20 healthy dogs. Plasma biomarker concentrations were measured using ELISA. Severity of illness in dogs with sepsis was calculated using the 5-variable acute physiologic and laboratory evaluation (APPLEFAST) score. Biomarker concentrations were compared between septic and healthy dogs using linear models.ResultsSeptic peritonitis was the most frequent source of sepsis (11/18; 61%), followed by pneumonia (4/18; 22%). Ten dogs (56%) had only 1 organ dysfunction, whereas 3 dogs (17%) had 2, 3 (17%) had 3, 1 (6%) had 4 and 1 (6%) had 5 organ dysfunctions. The median APPLEFAST score in the septic dogs was 28.5 (Q1-Q3, 24–31). Mean plasma concentrations of all endothelial and inflammatory biomarkers, except vWF, were higher in the sepsis cohort than in controls. The mean endothelial biomarker concentrations in the septic cohort ranged from ~2.7-fold higher for HA (difference in means; 118.2 ng/mL, 95% credible limit; 44.5–221.7) to ~150-fold for VEGF (difference in means; 76.6 pg./mL, 95% credible limit; 33.0–143.4), compared to the healthy cohort. Fifteen dogs with sepsis (83%) died; 7 (46%) were euthanized and 8 (53%) died during hospitalization.ConclusionDogs with naturally occurring sepsis and organ dysfunction had higher mean concentrations of biomarkers of endothelial activation and inflammation compared to healthy dogs, broadening our understanding of the pathophysiology of sepsis secondary to endothelial dysfunction.

Abstract Background Disseminated aspergillosis (DA) in dogs has a guarded prognosis and there is a lack of a gold standard treatment protocol. Objective To retrospectively assess survival times and factors influencing survival times. Animals Dogs diagnosed with DA from January 2007 to June 2017. Methods Disseminated aspergillosis case data were retrieved from 13 Australian veterinary referral centers, with a diagnosis confirmed with culture or PCR. Factors influencing survival time after diagnosis were quantified using a Cox proportional hazards regression model. Results Thirty‐four dogs met the study inclusion criteria. Twenty‐two dogs were treated with antifungal treatment and 12 dogs received no antifungal treatment. Accounting for censoring of dogs that were either still alive on the date of data collection or were loss to follow‐up, dogs treated with itraconazole alone (n = 8) had a median survival time (MST) of 63 (95% CI: 20−272) days compared to 830 (95% CI: 267‐1259) days for the n = 14 dogs that received multimodal antifungal therapy (χ2 test statistic 8.6; df = 1; P

ParA is an ATPase involved in the segregation of newly replicated DNA in bacteria. Here, structures of a ParA filament bound to DNA and of ParA in various nucleotide states offer insight into its conformational changes upon DNA binding and filament assembly, including the basis for ParA’s cooperative binding to DNA.

Daniel Mann et al. describe a higher-resolution structure of the maintenance of lipid asymmetry inner membrane complex (MlaBDEF) in the Gram-negative pathogen, Acinetobacter baumannii. With this improved structural map, the authors clarify the secondary structure elements of MlaE helices and report on potential lipid dynamics by the MLA system that could inform the development of future therapeutics against A. baumannii infection.

Abstract In this work, we present an approach to cross-link cellulose nanofibrils (CNFs) with various metallic cations (Fe3+, Al3+, Ca2+, and Mg2+) to produce inks suitable for three-dimensional (3D) printing application. The printability of each hydrogel ink was evaluated, and several parameters such as the optimal ratio of Mn+:TOCNF:H2O were discussed. CNF suspensions were produced by mechanical disintegration of cellulose pulp with a microfluidizer and then oxidized with 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO). Finally, metal cations were introduced to the deprotonated TEMPO-oxidized CNF (TOCNF) suspension to cross-link the nanofibrils and form the corresponding hydrogels. The performances of each gel-ink were evaluated by rheological measurements and 3D printing. Only the gels incorporated with divalent cations Ca2+ and Mg2+ were suitable for 3D printing. The 3D printed structures were freeze-dried and characterized with Fourier transform infrared spectroscopy (FT-IR) and Scanning Electron Microscopy (SEM). The better interaction of the TOCNFs with the divalent metallic cations in terms of printability, the viscoelastic properties of the inks, and the variation trends owing to various metal cations and ratios are discussed.

FliD forms a cap complex at the tip of bacterial flagella and is essential for flagellum filament assembly. Here, the authors present the cryo-EM structure of the Campylobacter jejuni cap complex, revealing a pentameric assembly of FliD and further show that the C. jejuni flagellum filament is 11-stranded.

The bacterial flagellum is a complex, self-assembling macromolecular machine that powers bacterial motility. It plays diverse roles in bacterial virulence, including aiding in colonization and dissemination during infection. The flagellum consists of a filamentous structure protruding from the cell, and of the basal body, a large assembly that spans the cell envelope. The basal body is comprised of over 20 different proteins forming several concentric ring structures, termed the M- S- L- P- and C-rings, respectively. In particular, the MS rings are formed by a single protein FliF, which consists of two trans-membrane helices anchoring it to the inner membrane and surrounding a large periplasmic domain. Assembly of the MS ring, through oligomerization of FliF, is one of the first steps of basal body assembly. Previous computational analysis had shown that the periplasmic region of FliF consists of three structurally similar domains, termed Ring-Building Motif (RBM)1, RBM2, and RBM3. The structure of the MS-ring has been reported recently, and unexpectedly shown that these three domains adopt different symmetries, with RBM3 having a 34-mer stoichiometry, while RBM2 adopts two distinct positions in the complex, including a 23-mer ring. This observation raises some important question on the assembly of the MS ring, and the formation of this symmetry mismatch within a single protein. In this study, we analyze the oligomerization of the individual RBM domains in isolation, in the Salmonella enterica serovar Typhimurium FliF ortholog. We demonstrate that the periplasmic domain of FliF assembles into the MS ring, in the absence of the trans-membrane helices. We also report that the RBM2 and RBM3 domains oligomerize into ring structures, but not RBM1. Intriguingly, we observe that a construct encompassing RBM1 and RBM2 is monomeric, suggesting that RBM1 interacts with RBM2, and inhibits its oligomerization. However, this inhibition is lifted by the addition of RBM3. Collectively, this data suggest a mechanism for the controlled assembly of the MS ring.

How do bees perceive altitude changes so as to produce safe displacements within their environment? It has been proved that humans use invariants, but this concept remains little-known within the entomology community. The use of a single invariant, the optical speed rate of change, has been extensively demonstrated in bees in a ground-following task. Recently, it has been demonstrated that another invariant, the splay angle rate of change, could also be used by bees to adjust their altitude. This study aims to understand how bees use these invariants when they are available simultaneously. This issue has been addressed using an experimental setup providing discordant information to bees. We have shown that when the two invariants were available, bees performed ground-following tasks relying primarily on optical speed rate of change. Conversely, when optical speed rate of change was less easily accessible, splay angle rate of change was prioritized, unless the bees perceive danger. Taken together, these results illustrate how the joint use of several invariants allows bees to produce adaptive behaviors.

This paper presents a strategy to convert hydrophilic cellulose nanofibrils (CNF) into a highly cross-linked hydrophobic network with inorganic nanoparticles to develop a gel ink suitable for gel 3D printing. The CNF were chemically modified initially through a single-electron transfer-living radical polymerization (SET-LRP) of stearyl acrylate (SA) in the presence of the surface-modified cobalt iron oxide (CoFe2O4, CFO) nanoparticles. The modified CFO nanoparticles provide their multifunctional properties, such as magnetic and electrochemical, to the CNF hybrid network and, at the same time, act as cross-linking agents between the nanocellulose fibrils, while the grafted poly-stearyl acrylate (PSA) introduces a strong hydrophobicity in the network. A suitable gel ink form of this CNF–PSA–CFO material for gel 3D printing was achieved together with a certain solvent. Some test structure prints were directly obtained with the CNF–PSA–CFO gel and were used to evaluate the consolidation of such 3D objects through solvent exchange and freeze-drying while also keeping the magnetic and electrochemical properties of CFO in the CNF-based composite intact. The pristine CNF and CFO particles and the CNF–PSA–CFO were characterized by FTIR, SEM, XPS, TGA, VSM, and CV measurements.

This work aims to produce a 3D-printable bio-based filament composed of high-density polyethylene (HDPE) and chemically modified cellulose nanofibrils. Printing using HDPE as a raw material is challenging due to its massive shrinkage and warping problems. This paper presents a new method to overcome those difficulties by enhancing the mechanical properties and achieving better print quality. This was achieved using modified cellulose nanofibrils (CNFs) as fillers. Firstly, CNF was converted to a CNF-based macroinitiator through an esterification reaction, followed by a surface-initiated single-electron transfer living radical polymerization (SI-SET-LRP) of the hydrophobic monomer stearyl acrylate. Poly stearyl acrylate-grafted cellulose nanofibrils, CNF-PSAs, were synthesized, purified and characterized with ATR-FTIR, 13C CP-MAS NMR, FE-SEM and water contact angle measurements. A composite was successfully produced using a twin-screw extruder with a CNF-PSA content of 10 wt.%. Mechanical tests were carried out with tensile testing. An increase in the mechanical properties, up to 23% for the Young’s modulus, was observed. A morphologic analysis also revealed the good matrix/CNF compatibility, as no CNF aggregates could be observed. A reduction in the warping behavior for the composite filament compared to HDPE was assessed using a circular arc method. The 3D printing of complex objects using the CNF-PSA/HDPE filament resulted in better print quality when compared to the object printed with neat HDPE. Therefore, it could be concluded that CNF-PSA was a suitable filler for the reinforcement of HDPE, thus, rendering it suitable for 3D printing.

Helicopter landing on a ship is a visually regulated "rendezvous" task during which pilots must use fine control to land a powerful rotorcraft on the deck of a moving ship tossed by the sea while minimizing the energy at impact. Although augmented reality assistance can be hypothesized to improve pilots’ performance and the safety of landing maneuvers by guiding action toward optimal behavior in complex and stressful situations, the question of the optimal information to be displayed to feed the pilots’ natural information-movement coupling remains to be investigated. Novice participants were instructed to land a simplified helicopter on a ship in a virtual reality simulator while minimizing energy at impact and landing duration. The wave amplitude and related ship heave were manipulated. We compared the benefits of two types of visual augmentation whose design was based on either solving cockpit-induced visual occlusion problems or strengthening the online regulation of the deceleration by keeping the current

Chronic enteropathies are a common problem in dogs, but many aspects of the pathogenesis remain unknown, making the therapeutic approach challenging in some cases. Environmental factors are intimately related to the development and perpetuation of gastrointestinal disease and the gut microbiome has been identified as a contributing factor. Previous studies have identified dysbiosis and reduced bacterial diversity in the gastrointestinal microbiota of dogs with chronic enteropathies. In this case-controlled study, we use flow cytometry and 16S rRNA sequencing to characterise bacteria highly coated with IgA or IgG in faecal samples from dogs with chronic enteropathy and evaluated their correlation with disease and resolution of the clinical signs. IgA and IgG-coated faecal bacterial counts were significantly higher during active disease compared to healthy dogs and decreased with the resolution of the clinical signs. Characterisation of taxa-specific coating of the intestinal microbiota with IgA and IgG showed marked variation between dogs and disease states, and different patterns of immunoglobulin enrichment were observed in dogs with chronic enteropathy, particularly for Erysipelotrichaceae, Clostridicaceae, Enterobacteriaceae, Prevotellaceae and Bacteroidaceae, families. Although, members of these bacterial groups have been associated with strong immunogenic properties and could potentially constitute important biomarkers of disease, their significance and role need to be further investigated.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread in humans in almost every country, causing the disease COVID-19. Since the start of the COVID-19 pandemic, research efforts have been strongly directed towards obtaining a full understanding of the biology of the viral infection, in order to develop a vaccine and therapeutic approaches. In particular, structural studies have allowed to comprehend the molecular basis underlying the role of many of the SARS-CoV-2 proteins, and to make rapid progress towards treatment and preventive therapeutics. Despite the great advances that have been provided by these studies, many knowledge gaps on the biology and molecular basis of SARS-CoV-2 infection still remain. Filling these gaps will be the key to tackle this pandemic, through development of effective treatments and specific vaccination strategies.

To date, numerous studies have demonstrated the fundamental role played by optic flow in the control of goal-directed displacement tasks in insects. Optic flow was first introduced by Gibson as part of their ecological approach to perception and action. While this theoretical approach (as a whole) has been demonstrated to be particularly suitable for the study of goal-directed displacements in humans, its usefulness in carrying out entomological field studies remains to be established. In this review we would like to demonstrate that the ecological approach to perception and action could be relevant for the entomologist community in their future investigations. This approach could provide a conceptual and methodological framework for the community in order to: (i) take a critical look at the research carried out to date, (ii) develop rigorous and innovative experimental protocols, and (iii) define scientific issues that push the boundaries of the current scientific field. After a concise literature review about the perceptual control of displacement in insects, we will present the framework proposed by Gibson and suggest its added value for carrying out research in the field of behavioral ecology in insects.

This review article aims to address common research questions in hexapod robotics. How can we build intelligent autonomous hexapod robots that can exploit their biomechanics, morphology, and computational systems, to achieve autonomy, adaptability, and energy efficiency comparable to small living creatures, such as insects? Are insects good models for building such intelligent hexapod robots because they are the only animals with six legs? This review article is divided into three main sections to address these questions, as well as to assist roboticists in identifying relevant and future directions in the field of hexapod robotics over the next decade. After an introduction in section (1), the sections will respectively cover the following three key areas: (2) biomechanics focused on the design of smart legs; (3) locomotion control; and (4) high-level cognition control. These interconnected and interdependent areas are all crucial to improving the level of performance of hexapod robotics in terms of energy efficiency, terrain adaptability, autonomy, and operational range. We will also discuss how the next generation of bioroboticists will be able to transfer knowledge from biology to robotics and vice versa.

Pulsed thermography is a commonly used non-destructive testing method and is increasingly studied for the assessment of advanced materials such as carbon fibre-reinforced polymer (CFRP). Different processing approaches are proposed to detect and characterize anomalies that may be generated in structures during the manufacturing cycle or service period. In this study, matrix decomposition using Robust PCA via Inexact-ALM is investigated as a pre- and post-processing approach in combination with state-of-the-art approaches (i.e., PCT, PPT and PLST) on pulsed thermography thermal data. An academic sample with several artificial defects of different types, i.e., flat-bottom-holes (FBH), pull-outs (PO) and Teflon inserts (TEF), was employed to assess and compare defect detection and segmentation capabilities of different processing approaches. For this purpose, the contrast-to-noise ratio (CNR) and similarity coefficient were used as quantitative metrics. The results show a clear improvement in CNR when Robust PCA is applied as a pre-processing technique, CNR values for FBH, PO and TEF improve up to 164%, 237% and 80%, respectively, when compared to principal component thermography (PCT), whilst the CNR improvement with respect to pulsed phase thermography (PPT) was 77%, 101% and 289%, respectively. In the case of partial least squares thermography, Robust PCA results improved not only only when used as a pre-processing technique but also when used as a post-processing technique; however, this improvement is higher for FBHs and POs after pre-processing. Pre-processing increases CNR scores for FBHs and POs with a ratio from 0.43% to 115.88% and from 13.48% to 216.63%, respectively. Similarly, post-processing enhances the FBHs and POs results with a ratio between 9.62% and 296.9% and 16.98% to 92.6%, respectively. A low-rank matrix computed from Robust PCA as a pre-processing technique on raw data before using PCT and PPT can enhance the results of 67% of the defects. Using low-rank matrix decomposition from Robust PCA as a pre- and post-processing technique outperforms PLST results of 69% and 67% of the defects. These results clearly indicate that pre-processing pulsed thermography data by Robust PCA can elevate the defect detectability of advanced processing techniques, such as PCT, PPT and PLST, while post-processing using the same methods, in some cases, can deteriorate the results.

Small-angle X-ray scattering (SAXS) often includes an unwanted background, which increases the required measurement time to resolve the sample structure. This is undesirable in all experiments, and may make measurement of dynamic or radiation-sensitive samples impossible. Here, we demonstrate a new technique, applicable when the scattering signal is background-dominated, which reduces the requisite exposure time. Our method consists of exploiting coherent interference between a sample with a designed strongly scattering `amplifier'. A modified angular correlation function is used to extract the symmetry of the interference term; that is, the scattering arising from the interference between the amplifier and the sample. This enables reconstruction of the sample's symmetry, despite the sample scattering itself being well below the intensity of background scattering. Thus, coherent amplification is used to generate a strong scattering term (well above background), from which sample scattering is inferred. We validate this method using lithographically defined test samples.

Abstract Studies on insects’ visual guidance systems have shed little light on how learning contributes to insects’ altitude control system. In this study, honeybees were trained to fly along a double-roofed tunnel after entering it near either the ceiling or the floor of the tunnel. The honeybees trained to hug the ceiling therefore encountered a sudden change in the tunnel configuration midways: i.e. a "dorsal ditch". Thus, the trained honeybees met a sudden increase in the distance to the ceiling, corresponding to a sudden strong change in the visual cues available in their dorsal field of view. Honeybees reacted by rising quickly and hugging the new, higher ceiling, keeping a similar forward speed, distance to the ceiling and dorsal optic flow to those observed during the training step; whereas bees trained to follow the floor kept on following the floor regardless of the change in the ceiling height. When trained honeybees entered the tunnel via the other entry (the lower or upper entry) to that used during the training step, they quickly changed their altitude and hugged the surface they had previously learned to follow. These findings clearly show that trained honeybees control their altitude based on visual cues memorized during training. The memorized visual cues generated by the surfaces followed form a complex optic flow pattern: trained honeybees may attempt to match the visual cues they perceive with this memorized optic flow pattern by controlling their altitude.

Dimensional reduction methods have significantly improved the simplification of Pulsed Thermography (PT) data while improving the accuracy of the results. Such approaches reduce the quantity of data to analyze and improve the contrast of the main defects in the samples contributed to their popularity. Many works have been proposed in the literature mainly based on improving the Principal Component Thermography (PCT). Recently the Independent Component Analysis (ICA) has been a topic of attention. Many different approaches have been proposed in the literature to solve the ICA. In this paper, we investigated several recent ICA methods and evaluated their influence on PT data compared with the state-of-the-art methods. We conducted our evaluation on reference CFRP samples with known defects. We found that ICA outperform PCT for small and deep defects. For other defects ICA results are often not far from the results obtained by PCT. However, the frequency of acquisition and the ICA methods have a great influence on the results.

The ability to measure small deformations or strains is useful for understanding many aspects of materials. Here, an alternate analysis of speckle x-ray diffraction peaks is presented in which the systematic shifts of the speckles are analyzed allowing for strain (or flow) patterns to be inferred. This speckle tracking technique measures strain patterns with an accuracy similar to x-ray single crystal measurements but in amorphous or highly disordered materials.

The emergence and prevalence of drug resistance demands streamlined strategies to identify drug resistant variants in a fast, systematic and cost-effective way. Methods commonly used to understand and predict drug resistance rely on limited clinical studies from patients who are refractory to drugs or on laborious evolution experiments with poor coverage of the gene variants. Here, we report an integrative functional variomics methodology combining deep sequencing and a Bayesian statistical model to provide a comprehensive list of drug resistance alleles from complex variant populations. Dihydrofolate reductase, the target of methotrexate chemotherapy drug, was used as a model to identify functional mutant alleles correlated with methotrexate resistance. This systematic approach identified previously reported resistance mutations, as well as novel point mutations that were validated in vivo. Use of this systematic strategy as a routine diagnostics tool widens the scope of successful drug research and development.

The flagellum is a large proteinaceous organelle found at the surface of many bacteria, whose primary role is to allow motility through the rotation of a long extracellular filament. It is an essential virulence factor in many pathogenic species, and is also a priming component in the formation of antibiotic-resistant biofilms. The flagellum consists of the export apparatus on the cytosolic side; the basal body and rotor, spanning the bacterial membrane(s) and periplasm; and the hook-filament, that protrudes away from the bacterial surface. Formation of the basal body MS ring region, constituted of multiple copies of the protein FliF, is one of the initial steps of flagellum assembly. However, the precise architecture of FliF is poorly understood. Here, I report a bioinformatics analysis of the FliF sequence from various bacterial species, suggesting that its periplasmic region is composed of three globular domains. The first two are homologous to that of the type III secretion system injectisome proteins SctJ, and the third possesses a similar fold to that of the sporulation complex component SpoIIIAG. I also describe that Chlamydia possesses an unusual FliF protein, lacking part of the SctJ homology domain and the SpoIIIAG-like domain, and fused to the rotor component FliG at its C-terminus. Finally, I have combined the sequence analysis of FliF with the EM map of the MS ring, to propose the first atomic model for the FliF oligomer, suggesting that FliF is structurally akin to a fusion of the two injectisome components SctJ and SctD. These results further define the relationship between the flagellum, injectisome and sporulation complex, and will facilitate future structural characterization of the flagellum basal body.

The T3SS injectisome is a syringe-shaped macromolecular assembly found in pathogenic Gram-negative bacteria that allows for the direct delivery of virulence effectors into host cells. It is composed of a "basal body", a lock-nut structure spanning both bacterial membranes, and a "needle" that protrudes away from the bacterial surface. A hollow channel spans throughout the apparatus, permitting the translocation of effector proteins from the bacterial cytosol to the host plasma membrane. The basal body is composed largely of three membrane-embedded proteins that form oligomerized concentric rings. Here, we report the crystal structures of three domains of the prototypical Salmonella SPI-1 basal body, and use a new approach incorporating symmetric flexible backbone docking and EM data to produce a model for their oligomeric assembly. The obtained models, validated by biochemical and in vivo assays, reveal the molecular details of the interactions driving basal body assembly, and notably demonstrate a conserved oligomerization mechanism.

The HIV-1 viral infectivity factor (Vif) neutralizes cell-encoded antiviral APOBEC3 proteins by recruiting a cellular ElonginB (EloB)/ElonginC (EloC)/Cullin5-containing ubiquitin ligase complex, resulting in APOBEC3 ubiquitination and proteolysis. The suppressors-of-cytokine-signalling-like domain (SOCS-box) of HIV-1 Vif is essential for E3 ligase engagement, and contains a BC box as well as an unusual proline-rich motif. Here, we report the NMR solution structure of the Vif SOCS–ElonginBC (EloBC) complex. In contrast to SOCS-boxes described in other proteins, the HIV-1 Vif SOCS-box contains only one α-helical domain followed by a β-sheet fold. The SOCS-box of Vif binds primarily to EloC by hydrophobic interactions. The functionally essential proline-rich motif mediates a direct but weak interaction with residues 101–104 of EloB, inducing a conformational change from an unstructured state to a structured state. The structure of the complex and biophysical studies provide detailed insight into the function of Vif's proline-rich motif and reveal novel dynamic information on the Vif–EloBC interaction.

The assumption of basic properties, like self-regulation, in simple transcriptional regulatory networks can be exploited to infer regulatory motifs from the growing amounts of genomic and meta-genomic data. These motifs can in principle be used to elucidate the nature and scope of transcriptional networks through comparative genomics. Here we assess the feasibility of this approach using the SOS regulatory network of Gram-positive bacteria as a test case. Using experimentally validated data, we show that the known regulatory motif can be inferred through the assumption of self-regulation. Furthermore, the inferred motif provides a more robust search pattern for comparative genomics than the experimental motifs defined in reference organisms. We take advantage of this robustness to generate a functional map of the SOS response in Gram-positive bacteria. Our results reveal definite differences in the composition of the LexA regulon between Firmicutes and Actinobacteria, and confirm that regulation of cell-division inhibition is a widespread characteristic of this network among Gram-positive bacteria.

The human immunodeficiency virus type-1 (HIV-1) Rev protein regulates the nuclear export of intron-containing viral RNAs by recruiting the CRM1 nuclear export receptor. Here, we employed a combination of functional and phylogenetic analyses to identify and characterize a species-specific determinant within human CRM1 (hCRM1) that largely overcomes established defects in murine cells to the post-transcriptional stages of the HIV-1 life cycle. hCRM1 expression in murine cells promotes the cytoplasmic accumulation of intron-containing viral RNAs, resulting in a substantial stimulation of the net production of infectious HIV-1 particles. These stimulatory effects require a novel surface-exposed element within HEAT repeats 9A and 10A, discrete from the binding cleft previously shown to engage Rev's leucine-rich nuclear export signal. Moreover, we show that this element is a unique feature of higher primate CRM1 proteins, and discuss how this sequence has evolved from a non-functional, ancestral sequence.