bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hypsochromic shift of phyC complements the inhibition of hypocotyl elongation under moderate red/far-red light
Authors: Yoshihara Shizue , Okajima Koji , Tokutomi Satoru 
Published: March 2024

AbstractPhytochrome (phy) is a plant photoreceptor that regulates various photomorphogenesis, and occurs in two forms, a red light (R)-absorbing form (Pr) and a far-red light (FR)-absorbing form (Pfr). Absorption spectral analyses of the photosensory module (PSM) showed that phyC in the Pr ofArabidopsis thaliana,Solanum lycopersicumandZea maysexhibited the absorption maxima shift toward shorter wavelengths (hypsochromic shift) compared with those of phyA and phyB. Substitution of the chromophore-binding domain complemented the hypsochromic shift in the spectra of phyC in the Pr. The effect of the hypsochromic shift on the inhibition of hypocotyl elongation was studied under R/FR ratio from 0.5-10. PhyB was revealed to play a major role in inhibition, and phyC showed a complementary role under R/FR <2.0. This may result from the activation peak of the phyC PSM, which was hypsochromically shifted compared with that of the phyB PSM from the Pr to Pfr. The leaf-filtered light measurement suggested that phyC enables plants to receive more R and contributes to survival in the field. Under low R/FR conditions, the activation efficiency of phyC was greater than that of phyB, suggesting that the hypsochromic shift of phyC is necessary for the robust growth of angiosperms.HighlightAngiosperm phyC with hypsochromically shifted activation inhibit hypocotyl elongation under relatively low red/far-red light conditions, in which phyB is not fully functional.
AllTheBacteria - all bacterial genomes assembled, available and searchable
Authors: Hunt Martin , Lima Leandro , Anderson Daniel , Hawkey Jane , Shen Wei , Lees John , Iqbal Zamin 
Published: March 2024

AbstractThe bacterial sequence data publicly available at the global DNA archives is a vast source of information on the evolution of bacteria and their mobile elements. However, most of it is either unassembled or inconsistently assembled and QC-ed. This makes it unsuitable for large-scale analyses, and inaccessible for most researchers to use. In 2021 Blackwell et al therefore released a uniformly assembled set of 661,405 genomes, consisting of all publicly available whole genome sequenced bacterial isolate data as of November 2018, along with various search indexes. In this study we extend that dataset up to August 2024, more than tripling the number of genomes. We also expand the scope, as we begin a global collaborative project to generate annotations for different species as desired by different research communities.In this study we describe the project as of release 2024-08, comprising 2,440,377 assemblies (including the 661k dataset). All 2.4 million have been uniformly reprocessed for quality criteria and to give taxonomic abundance estimates with respect to the GTDB phylogeny. We also provide antimicrobial resistance (AMR) gene and mutation annotation via AMRFinderPlus. Using an evolution-informed compression approach, the full set of genomes is just 130Gb in batched xz archives. We also provide multiple search indexes and a method for alignment to the full dataset. Finally, we outline plans for future annotations to be provided in further releases.
Risk assessment predicts most of the salmonellosis risk in raw chicken parts is concentrated in those few products with high-levels of high-virulent serotypes ofSalmonella
Authors: Kim Minho , Barnett-Neefs Cecil , Chavez Ruben A. , Kealey Erin , Wiedmann Martin , Stasiewicz Matthew J. 
Published: March 2024

AbstractSalmonellaprevalence has reduced in U.S. raw poultry products since adopting prevalence-basedSalmonellaperformance standards, but human illnesses did not reduce proportionally. We used Quantitative Microbial Risk Assessment to evaluate public health risks of raw chicken parts contaminated with different levels of allSalmonellaand specific high- and low-virulent serotypes. LognormalSalmonellalevel distributions were fitted using data from 2012 USDA-FSIS Baseline Survey and 2023 USDA-FSIS HACCP verification sampling data. Three different dose-response (DR) models were used: Single DR for all serotypes, reduced virulence for Kentucky, multiple serotype- specific DR models. All scenarios found risk concentrated in the few products with highSalmonellalevels. Using a single DR model with Baseline data (μ=-3.19, σ=1.29), 68% and 37% of illnesses were attributed to the 0.7% and 0.06% of products > 1 and 10 CFU/gSalmonella, respectively. More recent HACCP data (μ=-4.85, σ=2.44) showed that 99.9% and 99.6% of illnesses were attributed to the 2.3% and 0.8% of products > 1 and 10 CFU/gSalmonella, respectively. Scenarios with serotype-specific DR models showed more concentrated risk at higher levels. Baseline data showed 91.5% and 63.7% and HACCP data showed >99.9% and 99.9% of illnesses were attributed to products > 1 and 10 CFU/gSalmonella, respectively. Regarding serotypes, 0.003% and 0.3% of illnesses were attributed to the 0.2% and 0.7% of products with > 1 CFU/g of Kentucky, respectively, while 69% and 78.7% of illnesses were attributed to the 0.3% and 1.2% of products > 1 CFU/g containing either Enteritidis, Infantis, or Typhimurium using Baseline or HACCP input data, respectively. These results suggest public health risk in chicken parts is concentrated in the few finished products with high-levels and specifically high- levels of high-virulent serotypes. Low-virulent serotypes, such as Kentucky, are predicted to contribute to extremely few human cases.
Cell type-specific dynamics of prefrontal gamma synchrony during flexible behavior
Authors: Phensy Aarron J. , Hagopian Lara L. , Sohal Vikaas S. 
Published: March 2024

AbstractThe prefrontal cortex (PFC) is required for many cognitive processes that are disrupted in conditions such as schizophrenia. The PFC is composed of neuronal networks which are organized by both local microcircuitry and inter-regional projections, within which precisely tuned neuronal activity generates appropriate cognitive responses. Parvalbumin-positive interneurons (PVI) play an integral role by synchronizing select networks to oscillations in the gamma frequency range (∼30-100 Hz). Synchronized gamma oscillations seem to facilitate information transfer between neurons and across regions. In particular, our lab has previously shown that PVI-generated gamma oscillations in the left and right prefrontal cortices become synchronized during cognitive tasks and this synchronization is necessary for animals to learn rule shifts. Here, we examine how this synchrony propagates through prefrontal circuits using novel genetically encoded voltage indicators (GEVIs) to examine gamma oscillations in specific populations of deep layer projection neurons targeting either the mediodorsal thalamus (PFC-MD) or dorsal striatum (PFC-DS). We first designed a novel analysis which found that PVI exhibit inter-hemispheric gamma synchrony immediately (within seconds) following trial outcomes, during a specific subset of trials associated with the adoption of a new behavioral strategy. PFC-MD neurons did not exhibit gamma synchrony during these outcome periods, but did synchronize during the pre-decision period of the next trial. Furthermore, pre-decision gamma synchrony in PFC-MD neurons was dependent on PVI and did not occur in PFC-DS neurons. Together, our findings suggest that gamma synchrony is transmitted from PVI to PFC-MD neurons during rule shifts in a task-phase and cell type-specific manner to facilitate the updating of behavioral strategies.
Precision-based causal inference modulates audiovisual temporal recalibration
Authors: Li Luhe , Hong Fangfang , Badde Stephanie , Landy Michael S. 
Published: March 2024

AbstractCross-modal temporal recalibration guarantees stable temporal perception across ever-changing environments. Yet, the mechanisms of cross-modal temporal recalibration remain unknown. Here, we conducted an experiment to measure how participants’ temporal perception was affected by exposure to audiovisual stimuli with consistent temporal delays. Consistent with previous findings, recalibration effects plateaued with increasing audiovisual asynchrony and varied by which modality led during the exposure phase. We compared six observer models that differed in how they update the audiovisual temporal bias during the exposure phase and whether they assume modality-specific or modality-independent precision of arrival latency. The causal-inference observer shifts the audiovisual temporal bias to compensate for perceived asynchrony, which is inferred by considering two causal scenarios: when the audiovisual stimuli have a common cause or separate causes. The asynchrony-contingent observer updates the bias to achieve simultaneity of auditory and visual measurements, modulating the update rate by the likelihood of the audiovisual stimuli originating from a simultaneous event. In the asynchrony-correction model, the observer first assesses whether the sensory measurement is asynchronous; if so, she adjusts the bias proportionally to the magnitude of the measured asynchrony. Each model was paired with either modality-specific or modality-independent precision of arrival latency. A Bayesian model comparison revealed that both the causal-inference process and modality-specific precision in arrival latency are required to capture the nonlinearity and asymmetry observed in audiovisual temporal recalibration. Our findings support the hypothesis that audiovisual temporal recalibration relies on the same causal-inference processes that govern cross-modal perception.
Altered circadian rhythm, sleep, andrhodopsin 7-dependent shade preference during diapause inDrosophila melanogaster
Authors: Meyerhof Geoff T. , Easwaran Sreesankar , Bontempo Angela E. , Montell Craig , Montell Denise J. 
Published: March 2024

AbstractTo survive adverse environments, many animals enter a dormant state such as hibernation, dauer, or diapause. VariousDrosophilaspecies undergo adult reproductive diapause in response to cool temperatures and/or short day-length. While it is known that flies are less active during diapause, an in-depth understanding of diapause effects on circadian rhythms and sleep is lacking. Here we show that, in diapause-inducing conditions,Drosophila melanogasterexhibit altered circadian activity profiles, including a severely reduced morning activity peak and an advanced evening activity peak. Consequently, the flies have a single activity peak at a time similar to when non-diapausing flies have a siesta. Temperatures ≤15 °C, rather than short day-length, primarily drive the behavior. At cool temperatures, flies also rapidly enter a deep sleep state that lacks the sleep cycles of flies at higher temperatures and requires particularly high levels of stimulation for arousal. Furthermore, we show that at 18–25 °C, flies prefer to siesta in the shade, a preference that is virtually eliminated at 10 °C. Resting in the shade is driven by an aversion to blue light, sensed by rhodopsin 7 (Rh7) outside of the eyes. Flies at 10 °C show neuronal markers of elevated sleep pressure, including increased expression of Bruchpilot and elevated Ca2+in the R5 ellipsoid body neurons. Therefore sleep pressure might overcome blue light aversion. Thus at temperatures known to cause reproductive arrest, preserve germline stem cells, and extend lifespan,Drosophila melanogasterare prone to deep sleep and exhibit dramatically altered – yet rhythmic – daily activity patterns.Significance statementClimate change is impacting many animals, including insects. In diverse organisms, adverse environments trigger dormancy programs such as hibernation and diapause. Fruit flies undergo diapause to survive winter. Here we develop new methods and show that the same cool temperatures that delay fruit fly reproduction and extend lifespan, also promote deep sleep. Cool flies rapidly fall asleep and are difficult to arouse. Once awake, they immediately fall back to sleep. Whereas in warm environments, midday blue light drives flies to siesta in the shade, in cool temperatures the need to sleep overwhelms light-aversion, reducing shade preference. Animals that adjust their behavior directly to temperature, rather than day length, may be more resilient to a changing climate.
Improved functions for non-linear sequence comparison using SEEKR
Authors: Li Shuang , Eberhard Quinn , Ni Luke , Calabrese J. Mauro 
Published: March 2024

AbstractSEquence Evaluation throughk-mer Representation (SEEKR) is a method of sequence comparison that utilizes sequence substrings calledk-mers to quantify non-linear similarity between nucleic acid species. We describe the development of new functions within SEEKR that enable end-users to estimate p-values that ascribe statistical significance to SEEKR-derived similarities as well as visualize different aspects ofk-mer similarity. We apply the new functions to identify chromatin-enriched long noncoding RNAs (lncRNAs) that harborXIST-like sequence fragments and show that several of these fragments are bound byXIST-associated proteins. We also highlight the best practice of using RNA-Seq data to evaluate support for lncRNA annotations prior to their in-depth study in cell types of interest.
High-throughput Screening of Compounds against Autoluminescent NonreplicatingMycobacterium tuberculosisunder Diverse Conditions
Authors: Tian Xirong , Ma Wanli , Yusuf Buhari , Li Chunyu , Hameed H.M. Adnan , Wang Xinyue , Zhong Nanshan , Hu Jinxing , Zhang Tianyu 
Published: March 2024

ABSTRACTThe screening of new anti-mycobacterial chemicals is primarily focused on inhibiting the active growing bacteria. However, a major challenge in tuberculosis control is the ability ofMycobacterium tuberculosisto enter a nonreplicating state for extended periods, rendering it resistant to many clinical drugs and complicating eradication efforts. Existing low-oxygen-recovery assays designed for screening compounds targeting nonreplicatingM. tuberculosishave limitations, including the colony-forming unit counting for non-luminousM. tuberculosisand the instability of the free plasmid carryingluxABgenes in luminescentM. tuberculosis, along with exogenous substrate requirements for light producing. Moreover, these assays fail to accurately replicate the growth conditions of nonreplicatingM. tuberculosis in vitro, thus resulting in less convincing results. To address these challenges, we have developed an autoluminescence-based, cholesterol-enriched culture evaluation model to assess 17 anti-tuberculosis drugs of different classes against nonreplicatingM. tuberculosis. Our findings indicate that the relative light unit, measured in real-time, serves as a reliable surrogate marker for colony-forming unit, which typically becomes available one month later. This suggests the utility of our model for the rapid determination of drug susceptibility dynamically. The autoluminescentM. tuberculosis, harbouringluxCDABEgene cluster within its genome, can emit blue-green light stably and autonomously without requiring an external substrate supplement. The minimal inhibitory concentrations of all the drugs tested under anaerobic conditions are significantly different from that detected in aerobic environment. Our model allows for rapid, precise, and efficient assessment of drug activity under anaerobic conditions, thereby enabling a more comprehensive evaluation of anti-mycobacterial efficacy. Overall, our model represents a significant advancement in anti-tuberculosis drug discovery and pharmaceutical development.
The functional anatomy of nociception: effective connectivity in chronic pain and placebo responders
Authors: Nara Sanjeev , Baliki Marwan N. , Friston Karl J. , Ray Dipanjan 
Published: March 2024

AbstractThere is growing recognition of cortical involvement in nociception. The present study is motivated by predictive coding formulations of pain perception that stress the importance of top-down and bottom-up information flow in the brain. It compares forward and backward effective connectivity - estimated from resting-state fMRI - between chronic osteoarthritic patients and healthy control subjects. Additionally, it assesses differences in effective connectivity between placebo responders and non-responders and asks whether these differences can be used to predict pain perception and placebo response. To assess hierarchical processing in nociception, we defined two primary cortical regions: primary somatosensory cortex (SSC) and posterior insula (PI) (primary interoceptive cortex) and lateral frontal pole (FP1), a terminal relay station of the pain processing pathways. The directed (effective) connectivity within and between these regions were estimated using spectral dynamic causal modeling (DCM). 56 osteoarthritis patients and 18 healthy controls were included in the analysis. Within the patient group, effective connectivity was compared between placebo responders and non-responders.In osteoarthritic patients, contra control group, forward connectivity from SSC to FP1 and from PI to FP1 was enhanced in the left hemisphere. Backward connections from FP1 to SSC were more inhibitory. Intrinsic (i.e., inhibitory recurrent or self-connectivity) of left FP1 increased. In placebo responders compared to non-responders, forward connections from bilateral SSC to PI, left SSC to FP1, left PI to left FP1 were more inhibitory. In addition, self-connections of bilateral PI and top-down connections from right FP1 to right SSC were disinhibited; whereas self-connections of right FP1 became increasingly inhibitory. We confirmed the robustness of these results in a leave-one-out cross-validation analysis of (out-of-sample) effect sizes. Overall, effective extrinsic and intrinsic effective connectivity among higher and lower cortical regions involved in pain processing emerges as a promising and quantifiable candidate marker of nociception and placebo response. The significance of these findings for clinical practice and neuroscience are discussed in relation to predictive processing accounts of placebo effects and chronic pain.
Pf bacteriophages hinder sputum antibiotic diffusion via electrostatic binding
Authors: Chen Qingquan , Cai Pam , Chang Tony Hong Wei , Burgener Elizabeth , Kratochvil Michael J. , Gupta Aditi , Hargil Aviv , Secor Patrick R. , Nielsen Josefine Eilsø , Barron Annelise E. , Milla Carlos , Heilshorn Sarah C. , Spakowitz Andy , Bollyky Paul L. 
Published: March 2024

AbstractDespite great progress in the field, chronicPseudomonas aeruginosa(Pa) infections remain a major cause of morbidity and mortality in patients with cystic fibrosis, necessitating treatment with inhaled antibiotics. Pf phage is a filamentous bacteriophage produced byPathat has been reported to act as a structural element inPabiofilms. Pf presence has been associated with resistance to antibiotics and poor outcomes in cystic fibrosis, though the underlying mechanisms are unclear. Here, we have investigated how Pf phages and sputum biopolymers impede antibiotic diffusion using human sputum samples and fluorescent recovery after photobleaching. We demonstrate that tobramycin interacts with Pf phages and sputum polymers through electrostatic interactions. We also developed a set of mathematical models to analyze the complex observations. Our analysis suggests that Pf phages in sputum reduce the diffusion of charged antibiotics due to a greater binding constant associated with organized liquid crystalline structures formed between Pf phages and sputum polymers. This study provides insights into antibiotic tolerance mechanisms in chronicPainfections and may offer potential strategies for novel therapeutic approaches.TeaserPf phages and sputum polymers reduce antibiotic diffusion via electrostatic interactions and liquid crystal formation.
Reconfigurable multi-component nanostructures built from DNA origami voxels
Authors: Luu Minh Tri , Berengut Jonathan F. , Daljit Singh Jasleen Kaur , Coffi Dit Glieze Kanako , Turner Matthew , Skipper Karuna , Meppat Sreelakshmi , Fowler Hannah , Close William , Doye Jonathan P.K. , Abbas Ali , Wickham Shelley F.J. 
Published: March 2024

AbstractIn cells, proteins rapidly self-assemble into sophisticated nanomachines. Bio-inspired self-assembly approaches, such as DNA origami, have achieved complex 3D nanostructures and devices. However, current synthetic systems are limited by lack of structural diversity, low yields in hierarchical assembly, and challenges in reconfiguration. Here, we develop a modular system of DNA origami ‘voxels’ with programmable 3D connections. We demonstrate multifunctional pools of up to 12 unique voxels that can assemble into many shapes, prototyping 50 structures. Multi-step assembly pathways with sequential reduction in conformational freedom were then explored to increase yield. Voxels were first assembled into flexible chains and then folded into rigid structures, increasing yield 100-fold. Furthermore, programmable switching of local connections between flexible and rigid states achieved rapid and reversible reconfiguration of global structures. We envision that foldable chains of DNA origami voxels can be integrated with scalable assembly methods to achieve new levels of complexity in reconfigurable nanomaterials.
Silica seed particles improve the efficiency and throughput of nanoparticle acoustic trapping
Authors: Havers Megan , Baasch Thierry , Lenshof Andreas , Evander Mikael , Laurell Thomas 
Published: March 2024

Silica has rarely been used as a seed particle material in acoustic trapping of nanoparticles. Here we use fluorescent nanoparticles, which are frequently used as a model system, to demonstrate that throughput and nanoparticle trapping efficiency can be improved by using silica seed particles as opposed to traditionally used polystyrene seed particles. The 10 times larger dipole scattering coefficient of silica seed particles compared with polystyrene seed particles in water leads to a higher retention force against fluid flow and thus enables higher throughput. Seed particles retained at an actuation voltage of approximately 10 V p.p. can withstand flow rates up to 2100 ± 200 µl/min for silica and 200 ± 50 µl/min for polystyrene. Furthermore, silica is found to be 40%–2000% more efficient (number of trapped nanoparticles as measured by fluorescent intensity) than polystyrene seed particles in trapping 270-nm polystyrene nanoparticles from suspensions of 1010–1011 particles/ml. Moreover, after enriching nanoparticles into a silica seed particle cluster, the washing flow rate can be increased from 30 µl/min to 200 µl/min (the flow rate at which polystyrene clusters are unstable), halving the total sample processing time without losing the silica seed particle cluster or compromising the nanoparticle trapping efficiency. Thus, material properties (particularly density) of the seed particles are critical to both nanoparticle trapping efficiency and throughput.

Published by the American Physical Society
2024
Incommensurate charge density wave order in
U2Ti
Authors: Stevens Callum R. , Hermann Andreas , Huxley Andrew , Wermeille Didier 
Published: March 2024

Density functional theory predicted that the ground state of U2Ti should undergo a Peierls-like doubling of its unit cell along the c axis on cooling from high temperature [G. Kaur , ]. We report x-ray diffraction, heat capacity, and resistivity measurements showing that with decreasing temperature the transition from the parent hexagonal structure occurs in two steps, via an incommensurate state below TICDW=71(1) K which then undergoes a lock-in transition to the predicted commensurate Peierls-like state at TCCDW=46(3) K. The signatures of the upper transition in thermodynamic and transport measurements are weak, meaning that similar incommensurate charge density waves (ICDWs) preceding CDWs might occur more widely in other systems but elude detection. The collinear nature of both the ICDW and Peierls-like states we report is much simpler than more complex incommensurate states seen in α−U, which may in time provide greater insight into the mechanism for ICDW formation.

Published by the American Physical Society
2024