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Bacteroides, the prominent bacteria in the human gut, play a crucial role in degrading complex polysaccharides. Their abundance is influenced by phages belonging to theCrassviralesorder. Despite identifying over 600Crassviralesgenomes computationally, only few have been successfully isolated. Continued efforts in isolation of moreCrassviralesgenomes can provide insights into phage-host-evolution and infection mechanisms. We focused on wastewater samples, as potential sources of phages infecting variousBacteroideshosts. Sequencing, assembly, and characterization of isolated phages revealed 14 complete genomes belonging to three novelCrassviralesspecies infectingBacteroides cellulosilyticusWH2. These species,Kehishuvirussp. ‘tikkala’ strain Bc01,Kolpuevirussp. ‘frurule’ strain Bc03, and ‘Rudgehvirus jaberico’ strain Bc11, spanned two families, and three genera, displaying a broad range of virion productions. Upon testing all successfully culturedCrassviralesspecies and their respective bacterial hosts, we discovered that they do not exhibit co-evolutionary patterns with their bacterial hosts. Furthermore, we observed variations in gene similarity, with greater shared similarity observed within genera. However, despite belonging to different genera, the three novel species shared a unique structural gene that encodes the tail spike protein. When investigating the relationship between this gene and host interaction, we discovered evidence of purifying selection, indicating its functional importance. Moreover, our analysis demonstrated that this tail spike protein binds to the TonB-dependent receptors present on the bacterial host surface. Combining these observations, our findings provide insights into phage-host interactions and present threeCrassviralesspecies as an ideal system for controlled infectivity experiments on one of the most dominant members of the human enteric virome.

 

Abstract Accreting protoplanets are windows into planet formation processes, and high-contrast differential imaging is an effective way to identify them. We report results from the Giant Accreting Protoplanet Survey (GAPlanetS), which collected H α differential imagery of 14 transitional disk host stars with the Magellan Adaptive Optics System. To address the twin challenges of morphological complexity and point-spread function instability, GAPlanetS required novel approaches for frame selection and optimization of the Karhounen–Loéve Image Processing algorithm pyKLIP . We detect one new candidate, CS Cha “c,” at a separation of 68 mas and a modest Δmag of 2.3. We recover the HD 142527 B and HD 100453 B accreting stellar companions in several epochs, and the protoplanet PDS 70 c in 2017 imagery, extending its astrometric record by nine months. Though we cannot rule out scattered light structure, we also recover LkCa 15 “b,” at H α ; its presence inside the disk cavity, absence in Continuum imagery, and consistency with a forward-modeled point source suggest that it remains a viable protoplanet candidate. Through targeted optimization, we tentatively recover PDS 70 c at two additional epochs and PDS 70 b in one epoch. Despite numerous previously reported companion candidates around GAplanetS targets, we recover no additional point sources. Our moderate H α contrasts do not preclude most protoplanets, and we report limiting H α contrasts at unrecovered candidate locations. We find an overall detection rate of ∼36 − 22 + 26 % , considerably higher than most direct imaging surveys, speaking to both GAPlanetS’s highly targeted nature and the promise of H α differential imaging for protoplanet identification. 

Abstract Pseudoalteromonas (BB2-AT2) is a ubiquitous marine heterotroph, often associated with labile organic carbon sources in the ocean (e.g. phytoplankton blooms and sinking particles). Heterotrophs hydrolyze exported photosynthetic materials, components of the biological carbon pump, with the use of diverse metalloenzymes containing zinc (Zn), manganese (Mn), cobalt (Co), and nickel (Ni). Studies on the metal requirements and cytosolic utilization of metals for marine heterotrophs are scarce, despite their relevance to global carbon cycling. Here, we characterized the Zn, Mn, Co, and Ni metallome of BB2-AT2. We found that the Zn metallome is complex and cytosolic Zn is associated with numerous proteins for transcription (47.2% of the metallome, obtained from singular value decomposition of the metalloproteomic data), translation (33.5%), proteolysis (12.8%), and alkaline phosphatase activity (6.4%). Numerous proteolytic enzymes also appear to be putatively associated with Mn, and to a lesser extent, Co. Putative identification of the Ni-associated proteins, phosphoglucomutase and a protein in the cupin superfamily, provides new insights for Ni utilization in marine heterotrophs. BB2-AT2 relies on numerous transition metals for proteolytic and phosphatase activities, inferring an adaptative potential to metal limitation. Our field observations of increased alkaline phosphatase activity upon addition of Zn in field incubations suggest that such metal limitation operates in sinking particulate material collected from sediment traps. Taken together, this study improves our understanding of the Zn, Mn, Co, and Ni metallome of marine heterotrophic bacteria and provides novel and mechanistic frameworks for understanding the influence of nutrient limitation on biogeochemical cycling. 

This work provides quantitative tests of the extent of violation of two inequalities applicable to qubits coupled into Bell states, using IBM's publicly accessible quantum computers. Violations of the inequalities are well established. Our purpose is not to test the inequalities, but rather to determine how well quantum mechanical predictions can be reproduced on quantum computers, given their current fault rates. We present results for the spin projections of two entangled qubits, along three axes A , B , and C , with a fixed angle θ between A and B and a range of angles θ ′ between B and C . For any classical object that can be characterized by three observables with two possible values, inequalities govern relationships among the probabilities of outcomes for the observables, taken pairwise. From set theory, these inequalities must be satisfied by all such classical objects; but quantum systems may violate the inequalities. We have detected clear-cut violations of one inequality in runs on IBM's publicly accessible quantum computers. The Clauser–Horne–Shimony–Holt (CHSH) inequality governs a linear combination S of expectation values of products of spin projections, taken pairwise. Finding S > 2 rules out local, hidden variable theories for entangled quantum systems. We obtained values of S greater than 2 in our runs prior to error mitigation. To reduce the quantitative errors, we used a modification of the error-mitigation procedure in the IBM documentation. We prepared a pair of qubits in the state |00〉, found the probabilities to observe the states |00〉, |01〉, |10〉, and |11〉 in multiple runs, and used that information to construct the first column of an error matrix M . We repeated this procedure for states prepared as |01〉, |10〉, and |11〉 to construct the full matrix M , whose inverse is the filtering matrix. After applying filtering matrices to our averaged outcomes, we have found good quantitative agreement between the quantum computer output and the quantum mechanical predictions for the extent of violation of both inequalities as functions of θ ′. 

This project seeks to investigate the under addressed issue of indoor environmental quality (IEQ) and the impacts these factors can have on human health. The recent COVID-19 pandemic has once again brought to the forefront the importance of maintaining a healthy indoor environment. Specifically, the improvement of indoor air flow has shown to reduce the risk of airborne virus exposure. This is extremely important in the context of hospitals, which contain high concentrations of atrisk individuals. Thus, the need to create a healthy indoor space is critical to improve public health and COVID-19 mitigation efforts. To create knowledge and provide insight on environmental qualities in the hospital setting, the authors have designed and built an interface to deploy in the University of Virginia Hospital Emergency Department (ED). The interface will display room-specific light, noise, temperature, CO 2 , humidity, VOC, and PM 2.5 levels measured by the low-cost Awair Omni sensor. These insights will assist ED clinicians in mitigating disease-spread and improving patient health and satisfaction while reducing caregiver burden. The team addressed the problem through agile development involving localized sensor deployment and analysis, discovery interviews with hospital clinicians and data scientists throughout, and the implementation of a human-design centered Django interface application. Furthermore, a literature survey was conducted to ascertain appropriate thresholds for the different environmental factors. Together, this work demonstrates opportunities to assist and improve patient care with environmental data. 

Abstract Aberrant neural oscillations hallmark numerous brain disorders. Here, we first report a method to track the phase of neural oscillations in real-time via endpoint-corrected Hilbert transform (ecHT) that mitigates the characteristic Gibbs distortion. We then used ecHT to show that the aberrant neural oscillation that hallmarks essential tremor (ET) syndrome, the most common adult movement disorder, can be transiently suppressed via transcranial electrical stimulation of the cerebellum phase-locked to the tremor. The tremor suppression is sustained shortly after the end of the stimulation and can be phenomenologically predicted. Finally, we use feature-based statistical-learning and neurophysiological-modelling to show that the suppression of ET is mechanistically attributed to a disruption of the temporal coherence of the aberrant oscillations in the olivocerebellar loop, thus establishing its causal role. The suppression of aberrant neural oscillation via phase-locked driven disruption of temporal coherence may in the future represent a powerful neuromodulatory strategy to treat brain disorders.