Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthetic bottom-up approach reveals the complex interplay of Shigella effectors in regulation of epithelial cell death

Significance The virulence of numerous bacterial pathogens is dependent on nanomachines that inject tens of proteins (effectors) into host cells. Effectors are often functionally redundant or act in an additive manner to usurp cellular processes, limiting their characterization via traditional top-down loss-of-function assays. To overcome this issue, we developed an innovative synthetic bottom-up platform to conduct gain-of-function screens. These screens identified previously missed Shigella effectors that inhibit induced epithelial cell death, an important arm of the host innate immune system triggered in response to invading pathogens. Our studies provide new mechanistic insight into the sophisticated strategies by which Shigella effectors interact with the host to enable this pathogen to establish a replicative niche within the cytosol of infected epithelial cells. Over the course of an infection, many Gram-negative bacterial pathogens use complex nanomachines to directly inject tens to hundreds of proteins (effectors) into the cytosol of infected host cells. These effectors rewire processes to promote bacterial replication and spread. The roles of effectors in pathogenesis have traditionally been investigated by screening for phenotypes associated with their absence, a top-down approach that can be limited, as effectors often act in a functionally redundant or additive manner. Here we describe a synthetic Escherichia coli-based bottom-up platform to conduct gain-of-function screens for roles of individual Shigella effectors in pathogenesis. As proof of concept, we screened for Shigella effectors that limit cell death induced on cytosolic entry of bacteria into epithelial cells. Using this platform, in addition to OspC3, an effector known to inhibit cell death via pyroptosis, we have identified OspD2 and IpaH1.4 as cell death inhibitors. In contrast to almost all type III effectors, OspD2 does not target a host cell process, but rather regulates the activity of the Shigella type III secretion apparatus limiting the cytosolic delivery (translocation) of effectors during an infection. Remarkably, by limiting the translocation of a single effector, VirA, OspD2 controls the timing of epithelial cell death via calpain-mediated necrosis. Together, these studies provide insight into the intricate manner by which Shigella effectors interact to establish a productive intracytoplasmic replication niche before the death of infected epithelial cells.
Hand Posture Recognition: IR, IMU and sEMG

Hands are important anatomical structures for musical performance, and recent developments in input device technology have allowed rather detailed capture of hand gestures using consumer-level products. While in some musical contexts, detailed hand and finger movements are required, in others it is sufficient to communicate discrete hand postures to indicate selection or other state changes. This research compared three approaches to capturing hand gestures where the shape of the hand, i.e. the relative positions and angles of finger joints, are an important part of the gesture. A number of sensor types can be used to capture information about hand posture, each of which has various practical advantages and disadvantages for music applications. This study compared three approaches, using optical, inertial and muscular information, with three sets of 5 hand postures (i.e. static gestures) and gesture recognition algorithms applied to the device data, aiming to determine which methods are most effective.
Hydrothermal synthesis of bismuth oxybromide–bismuth oxyiodide composites with high visible light photocatalytic performance for the degradation of CV and phenol

This is the first report on a series of BiOpBrq/BiOmIn heterojunctions that were prepared using controlled hydrothermal methods. The compositions and morphologies of the BiOpBrq/BiOmIn could be controlled by adjusting some growth parameters, including reaction pH value, temperature, time, and KBr/KI molar ratio. The photocatalytic efficiency of the powder suspensions was evaluated by measuring crystal violet (CV) and phenol concentrations. Both the photocatalytic process and the photosensitized process were found to work concurrently. The quenching effects of various scavengers and EPR indicated that the reactive O2˙− played a major role and ˙OH and h+ played minor roles. The photocatalytic activity of the BiOpBrq/BiOmIn heterojunctons reached the maximum rate constant of 0.5285 (or 0.4713) h−1, 10 times higher than that of P25–TiO2, 14 times higher than that of BiOBr, and 6 times higher than that of BiOI.
The use of fungal entomopathogens as endophytes in biological control: a review

ABSTRACT Fungal entomopathogens have been proposed as environmentally friendly alternatives to chemical control. Unfortunately, their effectiveness continues to be limited by their susceptibility to ultraviolet (UV) light and low moisture. A relatively recent development, the use of fungal entomopathogens as endophytes, might overcome the traditional obstacles impeding the widespread adoption of fungal entomopathogens and also provide a novel alternative for management of insect pests and plant pathogens. In addition, some fungal entomopathogens could also function as biofertilizers. Eighty-five papers covering 109 individual fungal entomopathogen studies involving 12 species in six genera are reviewed. Thirty-eight plant species in 19 families were studied, with maize, common bean, and tomato being the most investigated. Of the 85 papers, 39 (46%) examined the effects of fungal entomopathogen endophytism on 33 insect species in 17 families and eight orders. Thirty-four (40%) examined plant response to endophytism, corresponding to 20 plant species. Various inoculation techniques (e.g., foliar sprays, soil drenching, seed soaking, injections, etc.) are effective in introducing fungal entomopathogens as endophytes, but colonization appears to be localized and ephemeral. The field of insect pathology will not substantially profit from dozens of additional studies attempting to introduce fungal entomopathogens into a wider array of plants, without attempting to understand the mechanisms underlying endophytism, the responses of the plant to such endophytism, and the consequent responses of insect pests and plant pathogens. This review presents several areas that should receive focused attention to increase the probability of success for making this technology an effective alternative to chemical control.
State-Space Adaptive Nonlinear Self-Interference Cancellation for Full-Duplex Communication

Full-duplex transmission comprises the ability to transmit and receive at the same time on the same frequency band. It allows for more efficient utilization of spectral resources, but raises the challenge of strong self-interference (SI). Cancellation of SI is generally implemented as a multi-stage approach. This paper proposes a novel adaptive SI cancellation algorithm in the digital domain based on Kalman filter theory that creates the following advances: first, the number of unknowns of the nonlinear SI model in cascade structure is significantly reduced compared to the conventional Hammerstein parallel model since it decouples the identification of linear and nonlinear elements; second, the remote signal-of-interest (SoI) is explicitly considered in the algorithm since the Kalman filter approach tunes its adaptation by the SoI power or performs successive cancellation; third, temporal variations of the SI channel are covered by a composite state-space model. In our simulation results, we analyze the performance by evaluating residual interference, system identification accuracy, and communication rate. We show that our Kalman filter solution in cascade structure delivers good performance with low computational complexity. In this configuration, the performance lines up with that of the monolithic (parallel) Kalman filter or the recursive-least squares (RLS) algorithms with parallel Hammerstein models. We implement our algorithm as a component of a practical prototype that demonstrates the benefits of a slender algorithmic design like the proposed cascade structure.
A Hybrid Resonant ZCS PWM Converter for Renewable Energy Sources Connecting to MVDC Collection System

To relieve the tail current effect of insulated-gate bipolar transistors which are preferred in high-power applications, an approach of zero-current-switching (ZCS) for main switches is presented in this paper. Different from the large turn-off current of the main switches of the conventional zero-voltage and zero-current-switching (ZVZCS) full-bridge (FB) dc–dc converter, small turn-off current of auxiliary circuit is introduced to achieve ZCS for main switches, where the auxiliary circuit also delivers a small portion power and can realize ZVZCS. Hence, high efficiency can be achieved with the switching loss lowered remarkably. Furthermore, a hybrid resonant FB dc–dc converter is proposed, the operation principle and parameters design rules of which are analyzed in detail. A 200 V-2 kV/3 kW experimental platform has been built to verify the feasibility and performance of the proposed ZCS approach, as well as the proposed converter.
OnNetwork+: Network Delay-Aware Management for Mobile Systems

Network errors such as packet losses consume large amounts of energy. We analyzed the reason for this through measurements using the latest smartphones and full-system simulation. We found that on packet losses the smartphones maintain high frequencies for CPU without doing useful work. To address this problem, we propose a method for reducing the energy consumption by lowering the performance level by exploiting a dynamic voltage and frequency scaling mechanism when long network delays are expected. According to our experiments, our method reduces the total energy consumption of web browsing on two different smartphones by up to 10.0% and 11.5%, respectively.
Changes in the fractionation profile of Al, Ni, and Mo during bioleaching of spent hydroprocessing catalysts with Acidithiobacillus ferrooxidans

ABSTRACT Spent hydroprocessing catalysts are known to contain a variety of potentially toxic metals and therefore studies on the bioavailability and mobility of these metals are critical for understanding the possible environmental risks of the spent catalysts. This study evaluates the different chemical fractions/forms of aluminium (Al), nickel (Ni), and molybdenum (Mo) in spent hydroprocessing catalyst and the changes they undergo during bioleaching with Acidithiobacillus ferrooxidans. In the spent catalyst (prior to bioleaching), Al was primarily present in its residual form, suggesting its low environmental mobility. However, Ni comprised mainly an exchangeable fraction, indicating its high environmental mobility. Molybdenum was mainly in the oxidizable form (47.1%), which indicated that highly oxidizing conditions were required to liberate it from the spent catalyst. During bioleaching the exchangeable, reducible and oxidizable fractions of all the metals were leached, whereas the residual fractions remained largely unaffected. At the end of bioleaching process, the metals remaining in the bioleached sample were predominantly in the residual fraction (98.3–99.5%). The ‘risk assessment code’ (RAC) and IR analysis also demonstrated that the environmental risks of the bioleached residue were significantly lower compared to the untreated spent catalyst. The results of this study suggest that bioleaching is an effective method in removing the metals from spent catalysts and the bioleached residue poses little environmental risk.
Some ecological problem with overhead power transmission lines with high current-carrying capacity

Overhead lines create problems with exploitation of ground along them. These problems are related not only to the lowest distances between lines and other facilities but also to electric and magnetic fields intensities. The main aim of paper is estimation of such the weather conditions, that the highest permissible values of magnetic field intensity is exceeded near power transmission lines with high current-carrying capacity.
GeoStreams: A Survey

Positional data from small and mobile Global Positioning Systems has become ubiquitous and allows for many new applications such as road traffic or vessel monitoring as well as location-based services. To make these applications possible, for which information on location is more important than ever, streaming spatial data needs to be managed, mined, and used intelligently. This article provides an overview of previous work in this evolving research field and discusses different applications as well as common problems and solutions. The conclusion indicates promising directions for future research.
The Protein Composition of the Oculor Zonules

Bovine and human zonules were found to be composed of noncollagenous acidic glycoprotein with a high cysteine content, double that previously reported. In reduced zonular fractions the most prominent peptide had a molecular weight (MW) of approximately 70,000. Lesser quantities of 170,000, 50,000, and 35,000 dalton peptides were also present and a variable number of lower MW bands, depending upon the degree of reduction and denaturation. A fraction of bovine zonules soluble in low ionic strength buffers contained primarily a peptide of approximately 50,000 daltons, often present as a doublet. Amino acid and hexosamine content of these two fractions was consistent with the presence of at least two different glycoconjugates, one a proteoglycan. Carbohydrate analysis of whole zonules suggested that these glycoconjugates include a sialofucose-containing glycoprotein and a lesser quantity of xylose-containing proteoglycan. The amino acid profile and peptide content of the zonules resembled that of elastic tissue microfibrils, increasing further the possibility of a close relationship between these two fibrils. Invest Ophthalmol Vis Sci 24:119-123, 1983
Cntr: Lightweight OS Containers

Container-based virtualization has become the de-facto standard for deploying applications in data centers. However, deployed containers frequently include a wide-range of tools (e.g., debuggers) that are not required for applications in the common use-case, but they are included for rare occasions such as in-production debugging. As a consequence, containers are significantly larger than necessary for the common case, thus increasing the build and deployment time. CNTR provides the performance benefits of lightweight containers and the functionality of large containers by splitting the traditional container image into two parts: the "fat" image--containing the tools, and the "slim" image -- containing the main application. At run-time, CNTR allows the user to efficiently deploy the "slim" image and then expand it with additional tools, when and if necessary, by dynamically attaching the "fat" image. To achieve this, CNTR transparently combines the two container images using a new nested namespace, without any modification to the application, the container manager, or the operating system. We have implemented CNTR in Rust, using FUSE, and incorporated a range of optimizations. CNTR supports the full Linux filesystem API, and it is compatible with all container implementations (i.e., Docker, rkt, LXC, systemd-nspawn). Through extensive evaluation, we show that CNTR incurs reasonable performance overhead while reducing, on average, by 66.6% the image size of the Top-50 images available on Docker Hub.
New paradigm for rapid achievement of appropriate therapy in special populations: coupling antibiotic dose optimization rapid microbiological methods

ABSTRACT Introduction: Some special patient populations (e.g. critically ill, burns, hematological malignancy, post-major surgery, post-major trauma) have characteristics that lead to higher rates of failure and mortality associated with infection. Choice of effective antibiotics and optimized doses are challenging in these patients that are commonly infected by multidrug-resistant pathogens. Areas covered: A review of the importance of diagnosis and the place of newer microbiological methods (e.g. whole-genome sequencing) to ensure rapid transition from empiric to directed antibiotic therapy is provided. The effects of pathophysiological changes on antibiotic pharmacokinetics are also provided. Expert opinion: Product information dosing regimens do not address the pharmacokinetic alterations that can occur in special patient populations and increase the likelihood of therapeutic failure and the emergence of bacterial resistance. Altered dosing approaches, supplemented with the use of dosing software and therapeutic drug monitoring, may be needed to ensure optimal antibiotic exposure and better therapeutic outcomes in these patients with severe infection. Dose optimization needs to be coupled with advanced microbiological techniques that enable rapid microbiological identification and characterization of resistance mechanism to ensure that maximally effective directed therapy can be chosen.
Motor innervation and proprioceptors of the mouthparts in the worker honey bee apis mellifera. II. Maxillary and labial nerves

Sensory and motor innervation of the proboscis by branches of the maxillary and labial nerves of the worker honey bee has been investigated in specimens stained vitally by methylene blue or viewed by scanning electron microscopy. A chordotonal organ consisting of a single scolopidium is present in the maxillary palp. Flexion of the maxillary palp occurs only passively, induced by the flexion of the galea. This chordotonal organ may function as a proprioceptor for the movement of the galea. Another chordotonal organ exists in the prementum of the labium. It contains, on the average, 12 sensory cells and presumably responds to the bending of the labial palp. A nerve‐net of bipolar cells arises from the sensory branches of the maxillary nerve. Free nerve endings derived from the periphery of this nerve‐net expand broadly on the intersegmental membranes connected to the stipes. The right and left nerves to the dilator muscles of the salivarium exchange branches, resulting in the reciprocal innervation of each muscle.
Effect of Socioeconomic Status and Underlying Disease on the Association between Ambient Temperature and Ischemic Stroke

Purpose Inconsistent findings have been reported regarding the effect of ambient temperature on ischemic stroke. Furthermore, little is known about how underlying disease and low socioeconomic status influence the association. We, therefore, investigated the relationship between ambient temperature and emergency department (ED) visits for ischemic stroke, and aimed to identify susceptible populations. Materials and Methods Using medical claims data, we identified ED visits for ischemic stroke during 2005–2009 in Seoul, Korea. We conducted piecewise linear regression analyses to find optimum ambient temperature thresholds in summer and winter, and estimated the relative risks (RR) and 95% confidence intervals (CI) per a 1℃ increase in temperature above/below the thresholds, adjusting for relative humidity, holidays, day of the week, and air pollutant levels. Results There were 63564 ED visits for ischemic stroke. In summer, the risk of ED visits for ischemic stroke was not significant, with the threshold at 26.8℃. However, the RRs were 1.055 (95% CI, 1.006–1.106) above 25.0℃ in medical aid beneficiaries and 1.044 (1.007–1.082) above 25.8℃ in patients with diabetes. In winter, the risk of ED visits for ischemic stroke significantly increased as the temperature decreased above the threshold at 7.2℃. This inverse association was significant also in patients with hypertension and diabetes mellitus above threshold temperatures. Conclusion Ambient temperature increases above a threshold were positively associated with ED visits for ischemic stroke in patients with diabetes and medical aid beneficiaries in summer. In winter, temperature, to a point, and ischemic stroke visits were inversely associated.
Functional osteology of the avian wrist and the evolution of flapping flight

The avian wrist is extraordinarily adapted for flight. Its intricate osteology is constructed to perform four very different, but extremely important, flight‐related functions. (1) Throughout the downstroke, the cuneiform transmits force from the carpometacarpus to the ulna and prevents the manus from hyperpronating. (2) While gliding or maneuvering, the scapholunar interlocks with the carpometacarpus and prevents the manus from supinating. By employing both carpal bones simultaneously birds can lock the manus into place during flight. (3) Throughout the downstroke‐upstroke transition, the articular ridge on the distal extremity of the ulna, in conjuction with the cuneiform, guides the manus from the plane of the wing toward the body. (4) During take‐off or landing, the upstroke of some heavy birds exhibits a pronounced flick of the manus. The backward component of this flick is produced by reversing the wrist mechanism that enables the manus to rotate toward the body during the early upstroke. The upward component of the flick is generated by mechanical interplay between the ventral ramus of the cuneiform, the ventral ridge of the carpometacarpus, and the ulnocarpo‐metacarpal ligament.
Hub Protein Controversy: Taking a Closer Look at Plant Stress Response Hubs

Plant stress responses involve numerous changes at the molecular and cellular level and are regulated by highly complex signaling pathways. Studying protein-protein interactions (PPIs) and the resulting networks is therefore becoming increasingly important in understanding these responses. Crucial in PPI networks are the so-called hubs or hub proteins, commonly defined as the most highly connected central proteins in scale-free PPI networks. However, despite their importance, a growing amount of confusion and controversy seems to exist regarding hub protein identification, characterization and classification. In order to highlight these inconsistencies and stimulate further clarification, this review critically analyses the current knowledge on hub proteins in the plant interactome field. We focus on current hub protein definitions, including the properties generally seen as hub-defining, and the challenges and approaches associated with hub protein identification. Furthermore, we give an overview of the most important large-scale plant PPI studies of the last decade that identified hub proteins, pointing out the lack of overlap between different studies. As such, it appears that although major advances are being made in the plant interactome field, defining hub proteins is still heavily dependent on the quality, origin and interpretation of the acquired PPI data. Nevertheless, many hub proteins seem to have a reported role in the plant stress response, including transcription factors, protein kinases and phosphatases, ubiquitin proteasome system related proteins, (co-)chaperones and redox signaling proteins. A significant number of identified plant stress hubs are however still functionally uncharacterized, making them interesting targets for future research. This review clearly shows the ongoing improvements in the plant interactome field but also calls attention to the need for a more comprehensive and precise identification of hub proteins, allowing a more efficient systems biology driven unraveling of complex processes, including those involved in stress responses.