Sal

Abstract

Complex molecules-mediated interactions, which are based on the bidirectional information exchange between microbes and human cells, enable the defense against diseases and health maintenance. Recently, diverse single-direction interactions based on active metabolites, immunity factors, and quorum sensing signals have largely been summarized separately. In this review, according to a simplified timeline, we proposed the framework of Molecules-mediated Bidirectional Interactions (MBI) between microbe and humans to decipher and understand their intricate interactions systematically. About the microbe-derived interactions, we summarized various molecules, such as short-chain fatty acids, bile acids, tryptophan catabolites, and quorum sensing molecules, and their corresponding human receptors. Concerning the human-derived interactions, we reviewed the effect of human molecules, including hormones, cytokines, and other circulatory metabolites on microbial characteristics and phenotypes. Finally, we discussed the challenges and trends for developing and deciphering molecule-mediated bidirectional interactions and their potential applications in the guard of human health.

Abstract

Bolitoglossa digitigrada Wake, Brame and Thomas, 1982 was described from a few kilometers upstream from the Rio Santa Rosa, Ayacucho Region, Peru, at 1000 m a.s.l. in the Eastern Amazonian Montane Forest. Besides the type specimens, no additional collections or sightings of B. digitigrada had been reported for 43 years, and there is no information about its phylogenetic position inside its group. During a field expedition conducted in October 2022, we found four individuals of B. digitigrada in a corn and banana field near the community of San Jose, approximately 2.7 km from the type locality. Here, we provide information about living specimens, update description of coloration in life, elevation, and evaluate the phylogenetic relationships of B. digitigrada with a molecular phylogeny based on a 16S rRNA sequence.

The server's images are stored and served using object storage.

The object storage provider has sent a message stating that they will perform a 12-hour migration tomorrow, March 10th, from 8:00 AM – 8:00 PM CET, so downtime of the object storage service is expected. Site images will likely not be displayed during this time.

In these past days users have reported issues with image uploads. I suspect that the issue is related to this same migration. If so, images should be back and the upload issue resolved by tomorrow night. If uploads are still causing problems I will investigate further.

Abstract

Cognitive maps confer animals with flexible intelligence by representing spatial, temporal and abstract relationships that can be used to shape thought, planning and behaviour. Cognitive maps have been observed in the hippocampus1, but their algorithmic form and learning mechanisms remain obscure. Here we used large-scale, longitudinal two-photon calcium imaging to record activity from thousands of neurons in the CA1 region of the hippocampus while mice learned to efficiently collect rewards from two subtly different linear tracks in virtual reality. Throughout learning, both animal behaviour and hippocampal neural activity progressed through multiple stages, gradually revealing improved task representation that mirrored improved behavioural efficiency. The learning process involved progressive decorrelations in initially similar hippocampal neural activity within and across tracks, ultimately resulting in orthogonalized representations resembling a state machine capturing the inherent structure of the task. This decorrelation process was driven by individual neurons acquiring task-state-specific responses (that is, ‘state cells’). Although various standard artificial neural networks did not naturally capture these dynamics, the clone-structured causal graph, a hidden Markov model variant, uniquely reproduced both the final orthogonalized states and the learning trajectory seen in animals. The observed cellular and population dynamics constrain the mechanisms underlying cognitive map formation in the hippocampus, pointing to hidden state inference as a fundamental computational principle, with implications for both biological and artificial intelligence.

A spy tan egg pretends to be on the same emotional wavelength as other tan eggs

Sietske A.L. van Till and Eline M. Bunnik (2024) have recently expressed a concern about science miscommunication regarding human brain organoids. They worry that the mereological fallacy is often being committed when the possibility of brain organoid psychological capacities such as consciousness and intelligence are considered, especially by bioethicists discussing the moral status of human brain organoids. Focusing specifically on one psychological capacity, namely consciousness, this article begins with a brief introduction to van Till and Bunnik’s concern about the mereological fallacy as it relates to brain organoids. It is then shown that whether the mereological fallacy is being committed depends on commitments in philosophy of mind about how consciousness relates to the brain and its neural mechanisms. This is demonstrated by appealing to two different example views about the ontology of consciousness embraced by J.J.C. Smart’s type identity theory and a version of hylomorphism. The article ends with a discussion of how neurobiological theories of consciousness can be intertwined with ontological commitments about consciousness that have significant implications for HBOs. An awareness of this can yield a philosophically informed application of neurobiological theories to the topic of whether HBOs could be conscious.

Abstract

While observational studies and small pilot trials suggest that vitamin D, omega-3 and exercise may slow biological aging, larger clinical trials testing these treatments individually or in combination are lacking. Here, we report the results of a post hoc analysis among 777 participants of the DO-HEALTH trial on the effect of vitamin D (2,000 IU per day) and/or omega-3 (1 g per day) and/or a home exercise program on four next-generation DNA methylation (DNAm) measures of biological aging (PhenoAge, GrimAge, GrimAge2 and DunedinPACE) over 3 years. Omega-3 alone slowed the DNAm clocks PhenoAge, GrimAge2 and DunedinPACE, and all three treatments had additive benefits on PhenoAge. Overall, from baseline to year 3, standardized effects ranged from 0.16 to 0.32 units (2.9–3.8 months). In summary, our trial indicates a small protective effect of omega-3 treatment on slowing biological aging over 3 years across several clocks, with an additive protective effect of omega-3, vitamin D and exercise based on PhenoAge.

Abstract

Cacao and chocolate production is a global industry worth around $133 billion. Full sun cultivation is a modern approach aimed at increasing yields. We evaluated six cacao clones (PS 1319, CCN 10, CCN 51, PH 16, SJ 02, and CP 49) grown under full sun conditions to assess their leaf physiology, leaf structure, yield, and yield components. Leaf physiology was measured through seven gas exchange parameters, while leaf structure was analyzed using eight measurements. For fruit and seed, we evaluated seven yield components. The clones showed differences in gas exchange. Clones PH 16 and PS 1319 had higher net photosynthetic rates per unit of leaf area (A), transpiration rates, and lower leaf internal CO2 concentrations. These A high values suggest the clones are well-acclimatized to full sun cultivation. Water availability, nutrient supply, and appropriate plant architecture also contributed to this acclimatization. Under high light intensity, the potential quantum yield of photosystem II indicated no photoinhibition, and adaptations in the photosynthetic apparatus were observed, such as lower pigment concentration in clone PH 16. Clones differed in specific leaf area (SLA) and stomatal density (SD). CCN 51 had a higher SLA, while SJ 02 had a higher SD. A significant negative correlation (-0.89) was found between dry bean yield and leaf-to-air water vapor pressure deficit (VpdL), suggesting that VpdL is a crucial parameter for selecting high-performance clones for fertigated full sun cultivation. Yields ranged from 1,220 kg/ha (CCN 10) to 2,900 kg/ha (CCN 51). Full sun cacao farms have high yield potential due to a combination of cloning, management practices, and adequate water and nutrient availability.

Abstract

This paper presents design and analysis of an optical memory and counter based on ultra-compact temporal integrators (INTs) using a graphene hybrid plasmonic add-drop ring resonator (GHP-ADRR) and pulley-type ring resonator (GHP-PRR) for optical signal processing. Due to the valuable features of graphene hybrid plasmonic technology, the footprint of these INTs is equal to 4 × 3.5 µm2 for GHP-ADRR and 5.4 × 3.6 µm2 for GHP-PRR. Also, the performance of the INTs has been analyzed by the three-dimensional finite-difference time-domain method in the frequency and time domains, and the accuracy of the results has been compared with those of the math counterparts and also key specifications of the first-order temporal INTs including phase jump, insertion loss, 3 dB bandwidth, rise time, integration time window, and energy efficiency have been investigated. Based on the results, both circuits have better performance than the photonic counterparts. Furthermore, the performance of these INTs has been evaluated in detail as a high-speed optical memory and counter. It has been illustrated that due to the greater quality factor of the GHP-PRR, this circuit has more accuracy for realizing the first-order integration, optical memory, and counter than the GHP-ADRR-based INT.

Found a photos of ferns that I took during a visit to Cascadas Tulimán, in Puebla, Mexico, back in 2022.

Here is the biome:

I never got to identifying them, so any any input on potential IDs is welcome!

Abstract

We present ErAs:In(Al)GaAs-based terahertz transceiver modules, comprising transmitter and receiver components integrated on a single chip. The transceiver module is employed in a two-port single-path (TxRx-Rx) or 1.5-port pulsed free space photonic vector network analyzer setup, wherein the second receiver is an individual ErAs:InGaAs photoconductor. This configuration allows for simultaneous extraction of transmission and reflection coefficients or scattering parameters S21 and S11. The system achieves a peak dynamic range of ~59 dB for S21 and ~43 dB for S11 at a bandwidth reaching ~3.5 THz for the transmission and ~2.5 THz for the reflection path. These values are obtained by averaging over 500 traces at a scan rate of 4 Hz. The system exhibits superior frequency coverage compared to commercially available electronic vector network analyzers, thus offering a compact, cost-effective, broadband characterization solution for the benchmarking of terahertz devices and components.