Miracle-dz/UniFAR-FTUs huggingface dataset:
Immediate early genes as a molecular switch for lasting vulnerability following pubertal stress in mice

Why individuals have negative consequences following stress is a complex phenomenon that is dictated by individual factors, the timing of stress within the lifespan, and when the consequences are measured. Women who undergo adverse childhood experiences are at risk for lasting biological consequences, including affective and stress dysregulation. We have shown that pubertal adversity is associated with a blunted glucocorticoid response within the hypothalamic-pituitary-adrenal axis in both peripartum humans and mice. In mice, we examined puberty-stress reprogramming in the paraventricular nucleus (PVN) of the hypothalamus, which initiates the HPA axis response. We found that pubertal stress led to an upregulation of six immediate early genes (IEGs) in the PVN of adult, pregnant mice. Separately, we showed that the pregnancy-associated hormone allopregnanolone is necessary and sufficient to produce the blunted stress response phenotype in pubertally stressed mice. Here, we examined the response of the IEGs in the PVN to the primary disruption of pubertal stress in early adolescence and to the secondary disruption of increased allopregnanolone in pregnancy. We found that in adult female, but not male, mice previously stressed during puberty, intra-PVN allopregnanolone was sufficient to recapitulate the pubertal stress associated baseline IEG expression profile. We also examined baseline IEG expression during adolescence, where we found that IEGs have sex-specific developmental trajectories that were disrupted by pubertal stress. Altogether, these data establish that IEGs can act as a key molecular switch that leads to increased vulnerability to negative outcomes in adult, pubertally stressed animals. Understanding how the factors that produce vulnerability combine throughout the lifespan will further our understanding of the etiology of negative outcomes and will help guide both the nature and timing of potential treatments.
Evolution of hind limb morphology of Titanosauriformes (Dinosauria, Sauropoda) analyzed via 3D Geometric Morphometrics reveals wide-gauge posture as an exaptation for gigantism

The sauropod hind limb was the main support that allowed their gigantic body masses and a wide range of dynamic stability adaptations. It was closely related to the position of the centre of masses of their multi-ton barrel-shaped bodies, and experienced one of the most noticeable posture changes during macronarian evolution. Deeply branched macronarians achieved increasingly arched hind limbs in what is known as wide-gauge posture. However, it is not clear if this evolutionary trend is related to the evolutionary cascade toward gigantism even though some titanosaurians were the largest terrestrial vertebrates that ever existed. We tested evolutionary changes in hind limb morphology in the Macronaria phylogenetic tree by 3D geometric morphometrics. The macronarian hind limb does become progressively more arched toward deeply-branched groups, specifically Saltasauridae. However, there is morphological convergence between different macronarian subclades. Wide-gauge posture does not correlate with changes in body size deeper in the macronarian evolutionary tree, and acted as an exaptation to gigantism. Despite some titanosaurian subclades becoming some of the largest vertebrates, there is a phyletic body size decrease in Macronaria.
The determination of the three-dimensional distribution of rain from the Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar

This paper describes a recent development in rainfall estimation using satellite-flown and ground-based radars. The Tropical Rainfall Measuring Mission (TRMM) Precipitation Radar (PR), its algorithms and data processing are discussed. The ground validation algorithms and processing of the ground-based radar reflectivity data are explained. The estimates of attenuation-corrected radar reflectivity factor and rainfall rate are given at each resolution cell of the PR. The estimated near-surface rainfall rate and average rainfall rate at the altitudes of 2 km are calculated for each beam position. The TRMM PR profiling algorithm and processing of the PR reflectivity for rain distribution are explained. The TRMM rain products and their geophysical parameters are derived from the measurements from the satellite and ground-based radar. The derived geophysical parameters include vertical rain and hydrometeor profile, rain type, radar back-scatter cross-section, raindrop size distribution, rain gauge rain rates and 5-day and monthly average rain rates. For validation purposes the instantaneous and climatological comparison of the rain estimates from both the Precipitation Radar and ground-based radar at Melbourne, Florida, was carried out on the basis of rain type; i.e. convective/stratiform, vertical structure and rain maps. The error sources in rain profile retrieval from space-borne radar; i.e. the PR and ground-based radar with their algorithm limitations are discussed. A second set of data, this time for an area where no simultaneous ground data are available has also been analysed; the data were chosen for the three-dimensional rain distribution over some parts of India. The issues such as discrimination of rain from surface clutter, calibration accuracy and sensitivity of precipitation radar and discrimination of rain echo from noise are discussed.
Possible identification of local deposits of Cl2SO2 on Io from NIMS/Galileo spectra

[1] Starting from the recent discovery of chlorine ions in Io's plasma torus, we searched for evidence of Cl-bearing species at the surface of the satellite. We have identified Cl2SO2, with possible contribution by ClSO2, as candidates for the absorber(s) of the 3.92 μm band locally present in NIMS/Galileo spectra of the reddish deposits south of Marduk's volcanic center. Low-temperature laboratory measurements of the infrared spectra of several Cl and S-bearing molecules in the solid state, coupled with radiative transfer modeling, first allowed us to select four candidate molecules. Their abundance and stability at Io's surface have been tested through formation, condensation, and destruction scenarios using volcanic and atmospheric models completed with chemical and thermodynamical data. In particular, the sublimation rates of solid Cl2SO2 and SO2 have been measured to study the selective condensation of these species. Cl2SO2 diluted at ∼1% in a millimeter thick layer of solid SO2 is the favorite candidate for the 3.92 μm band. We strongly favor a formation process of this molecule by heterogeneous reaction of Cl atoms on SO2 ice condensing on plume particles or at Io's surface. The high Cl2SO2 abundance observed implies that a Cl-rich volcanic eruption ([Cl − (Na + K)]/S > 0.015) occurred at Marduk. ClSO2 is a potential additional contributor to the band. Pure H2S is safely discarded as it is extremely unstable at Io's surface but an upper limit of 0.01% is derived for H2S diluted in SO2. Finally, chemical constraints allow us to firmly exclude H2S2. We also suggest that Cl2S may be an alternative explanation for the reddish coloration of some volcanic deposits.
Garnet-spinel intergrowths in ultrahigh-temperature granulite, Eastern Ghats, India: Possible evidence of an early Tschermak-rich orthopyroxene during prograde metamorphism

Abstract UHT metamorphosed aluminous granulites from the Eastern Ghats Belt, India, contain contrasting mineral assemblages in closely spaced domains. Reaction textures and mineral chemistry in one domain are consistent with prograde metamorphism. A unique intergrowth texture is found in garnet porphyroblasts from the other domain. Lamellar to vermicular intergrowth of spinel solid-solution occurs in garnet, particularly in the central part of the porphyroblast. Locally, sapphirine, overgrowing spinel, is also intergrown with garnet. Three possible mechanisms are discussed to account for the garnet-spinel intergrowth: (1) from early stabilized orthopyroxene + sillimanite; (2) spinel forming pseudomorphs after early sillimanite inclusions in garnet; and (3) from an early stabilized hypothetical, highly aluminous orthopyroxene involving a complex reaction between the (Fe,Mg)-Tschermak and Fe3+-Tschermak components. Sapphirine is produced by a reaction involving spinel and aluminous pyroxene. Regardless of the exact mechanism, available thermodynamic data suggest that all such reactions presumably occurred due to loading and/or heating during prograde metamorphism consistent with the conclusion from the other domain. Such an intergrowth texture has not been reported previously in aluminous granulite parageneses, but these could provide crucial information regarding the prograde segment of the metamorphic evolution of deep crustal rocks.
Investigating the Rescue Potential of Fecal Microbiota Transplants in Anorexia Nervosa using Antibiotic-treated Mice in a Split Group Cross-Over Study

Anorexia nervosa (AN) is a complex and serious mental disorder, which may affect individuals of all ages and sex, but primarily affecting young women. The disease is characterized by a disturbed body image, restrictive eating behavior, and a lack of acknowledgment of low body weight. The underlying causes of AN remain largely unknown, and current treatment options are limited to psychotherapy and nutritional support. This paper investigates the impact of Fecal Microbiota Transplants (FMT) from AN patients on food intake, body weight, behavior, and gut microbiota in antibiotic-treated mice. Two rounds of FMT were performed using AN and control (CO) donors. During the second round of FMT, a subset of mice received FMT from a different donor type. This split-group cross-over design was chosen to demonstrate any recovery effect of FMT from a healthy donor. The first FMT, from AN donors, resulted in lower food intake in mice without affecting body weight. After FMT2, serum analysis revealed higher levels of appetite-influencing hormones (PYY and leptin) in mice receiving AN-GM. Gut microbiota analysis showed significant differences between AN and CO mice after FMT1, before cross-over. Specific bacterial genera and families Ruminococcaceae, Lachnospiraceae, and Faecalibacterium showed different abundances in AN and CO receiving mice. Behavioral tests showed decreased locomotor activity in AN mice after FMT1. Overall, the results suggest that AN-GM may contribute to altered food intake and appetite regulation, which can be ameliorated with FMT from a healthy donor potentially offering FMT as a supportive treatment for AN.
Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability

Existing single cell bisulfite-based DNA methylation analysis is limited by low DNA recovery, and the measurement of 5hmC at single-base resolution remains challenging. Here we present a bisulfite-free single-cell whole-genome 5mC and 5hmC profiling technique, named Cabernet, which can characterize 5mC and 5hmC at single-base resolution with high genomic coverage. Cabernet utilizes Tn5 transposome for DNA fragmentation, which enables the discrimination between different alleles for measuring hemi-methylation status. Using Cabernet, we revealed the 5mC, hemi-5mC and 5hmC dynamics during early mouse embryo development, uncovering genomic regions exclusively governed by active or passive demethylation. We show that hemi-methylation status can be used to distinguish between pre– and post-replication cells, enabling more efficient cell grouping when integrated with 5mC profile. The property of Tn5 naturally enables Cabernet to achieve high-throughput single-cell methylome profiling, where we probed mouse cortical neurons and embryonic day 7.5 (E7.5) embryos, and constructed the library for thousands of single cells at high efficiency, demonstrating its potential for analyzing complex tissues at substantially low cost. Together, we present a new way of high-throughput methylome and hydroxymethylome detection at single-cell resolution, enabling efficient analysis of epigenetic status of biological systems with complicated nature such as neurons and cancer cells. Significance Statement Most of current methylation profiling techniques rely on bisulfite treatment, which suffers low DNA recovery. The technique proposed in this study, named Cabernet, can be used to measure 5mC and 5hmC at single-base resolution with high genomic coverage. By using Tn5 transposome, hemi-methylation status can be measured and high-throughput methylome profiling can be achieved. Together, it provides an efficient way to analyze the epigenetic landscape of complicated biological systems.
Automated Surface-Based Segmentation of Deep Gray Matter Regions Based on Diffusion Tensor Images Reveals Unique Age Trajectories Over the Healthy Lifespan

Many studies have demonstrated unique trajectories of deep gray matter (GM) volumes over development and aging, suggesting but not measuring microstructural alterations over the lifespan. Only a few studies have measured diffusion tensor imaging (DTI) parameters in deep GM or reported these values across a wide age range in a large cohort. To enable efficient DTI studies of deep GM in large cohorts without the need of T1-weighted images, an automated segmentation technique is proposed here that works solely on parametric maps calculated from DTI. The algorithm segments the globus pallidus, striatum, thalamus, hippocampus and amygdala per hemisphere by deforming 3D models of these structures to their boundaries visible on the contrast provided by diffusion tensor maps and images alone. This new DTI-only method is compared against standard T1-weighted image segmentation for (i) 1.25 mm isotropic diffusion data from the Human Connectome Project (HCP) test-retest cohort (n=44) and (ii) 1.5 mm isotropic test-retest diffusion data from a local normative study (n=24). Dice coefficients of voxel overlap between methods in the HCP test-retest cohort were high (>0.7) for 7 of 10 structures, but were low for the left globus pallidus (0.54) and left/right amygdala (0.67, 0.69). The proposed DTI-only segmentation qualitatively appeared more accurate and yielded smaller volumes than T1w for 8/10 structures in both cohorts, with the exception of the globus pallidus which showed larger volumes in the HCP test-retest data but lower volumes in the local normative study data. The DTI-only segmentation method was then applied to two local single site development/aging ‘lifespan’ cohorts (cohort 1: n=365 5-90 years, cohort 2: n= 164 5-74 years) to assess age changes in volume, fractional anisotropy (FA) and mean diffusivity (MD). In both cohorts, MD trajectories were quadratic for all five structures, decreasing slightly and then increasing after ∼30-35 years. In cohort #1, FA trajectories remained flat from 5 to ∼25 years and then started to decrease for the globus pallidus and hippocampus and over 5 to 90 years, FA decreased linearly for amygdala, increased linearly for striatum, and remained constant for the thalamus. In the second cohort, using an alternate acquisition protocol, the FA trajectories of all 5 structures across all ages were similar, except for the globus pallidus and thalamus which both increased in value from 5 ∼ 20 years and likely reflect differences in acquisition details. Notably, the development and aging trajectories for DTI were distinct from those of the deep GM volumes. The proposed automated deep GM segmentation method on DTI-only will facilitate the analysis of deep GM DTI (currently ignored in nearly all studies despite the data there within the field-of-view) and will be advantageous particularly for studies that do not have a T1-weighted scan, as in many clinical populations.
The effects of resistance training on denervated myofibers, senescent cells, and associated protein markers in middle-aged adults

Denervated myofibers and senescent cells are hallmarks of skeletal muscle aging. However, sparse research has examined how resistance training affects these outcomes. We investigated the effects of unilateral leg extensor resistance training on denervated myofibers, senescent cells, and associated protein markers in middle-aged participants (MA, 55±8 years old, 17 females, 9 males). We obtained vastus lateralis (VL) muscle cross-sectional area (mCSA), VL biopsies, and strength assessments before and after training. Fiber cross-sectional area (fCSA), satellite cells (Pax7+), denervated myofibers (NCAM+), senescent cells (p16+ or p21+), senescence-related proteins, and senescence-associated secretory phenotype (SASP) proteins were analyzed from biopsied muscle. Leg extensor peak torque increased after training (p<0.001), while VL mCSA trended upward (p=0.082). No significant changes were observed for fCSA, NCAM+ myofibers, or senescent (p16+ or p21+) cells, albeit satellite cells increased after training (p=0.037). While >90% satellite cells were not p16+ or p21+, most p16+ and p21+ cells were Pax7+ (>90% on average). Training altered 13/46 proteins related to muscle-nerve communication (all upregulated, p<0.05) and 10/19 proteins related to cellular senescence (9 upregulated, p<0.05). Only 1/17 SASP proteins increased with training (IGFBP-3, p=0.031). In conclusion, resistance training upregulates proteins associated with muscle-nerve communication in MA participants but does not alter NCAM+ myofibers. Moreover, while training increases senescence-related proteins in skeletal muscle, this coincided with an increase in satellite cells but not alterations in senescent cell content or SASP proteins. Hence, we interpret these collective findings as resistance training being an unlikely inducer of cellular senescence in humans.
Basic Density, Tracheid Length and Strength Properties of Juvenile and Mature Wood of Pinus patula Grown in Tanzania

SYNOPSIS More than 70% of Tanzanian plantations consist of conifers, 60% of which are Pinus patula plantations. Juvenile wood is one of the most important sources of variability. The proportion of juvenile wood in the stems of 27-year-old Pinus patula trees is considerable (weighted mean proportion of 49%). Juvenile wood has lower basic density, shorter tracheid length and inferior strength properties when compared to mature wood. Reporting average values does not give a true picture of differences existing between juvenile and mature wood, and this could lead to hazards.
Biofilm growth and the related changes in the physical properties of a porous medium: 2. Permeability

Growth of a biofilm in a porous medium reduces the total volume and the average size of the pores. The change in the pore size distributions is easily quantified when certain geometric assumptions are made. Existing models of permeability or of relative permeability can be manipulated to yield estimates of the resulting reduction in permeability as a function of biofilm thickness. The associated reductions in porosity and specific surface can be estimated as well. Based on a sphere model of the medium, the Kozeny-Carman permeability model predicts physically realistic results for this problem. Using a cut-and-random-rejoin-type model of the medium, the permeability model of Childs and Collis-George yields qualitatively reasonable results for this problem, as does a generalization of the relative permeability model of Mualem. Permeability models of Kozeny-Carman and of Millington and Quirk lead to unrealistic results for a cut-and-random-rejoin-type medium. The Childs and Collis-George and the Mualem models predict that the permeability reduction for a given volume of biomass is greatest when the porous medium has uniform pore sizes.
A first estimation of SMOS-based ocean surface T-S diagrams

A first estimation of satellite-based ocean surface T-S diagrams is performed by using SMOS Sea Surface Salinity (SSS) and OSTIA Sea Surface Temperature (SST) and comparing them with in situ measurements interpolated fields obtained by the Argo-buoys for the North Atlantic and over the entire year 2011. The key objectives at the base of this study are: (1) To demonstrate the feasibility of generating routinely satellite-derived surface T-S diagrams, obviating the lack of extensive sampling of the surface open ocean, (2) To display the T-S diagrams variability and the distribution/dynamics of SSS, altogether with SST and the relative density with respect to in situ measurements, and (3) To assess the SMOS SSS data added value in detecting geophysical signals not sensed/resolved by the Argo measurements. To perform the latter analysis, the satellite-Argo mismatches have been overlapped with geophysical parameters of precipitation rates, surface heat and freshwater fluxes and wind speed data. Ongoing and future efforts focus on enlarging the study area and the temporal frame of the analysis and aim at developing a method for the systematic identification of surface water masses formation areas by remotely sensed data.
Late-Holocene teleconnections between tropical Pacific climatic variability and precipitation in the western USA: evidence from proxy records

Decadal to multidecadal fluctuations between drought and relatively more moist conditions are a defining characteristic of precipitation variability in the western USA. In an attempt to better understand the forcing mechanisms responsible for producing this variability, relationships between proxy indices of tropical climatic variability and precipitation-related reconstructions in the western USA are examined. The tropical proxies include the δ18O record from the Quelccaya ice cap (southern subtropical Andes) and the lacustrine sedimentation record from Laguna Pallcacocha (near-equatorial Andes). The precipi tation-related records are tree-ring reconstructions of river flow, drought severity and precipitation over the contiguo USA. One new finding is a consistent relation between decadal variability in El Niñno activity and precipitation-related proxies through much of the western USA during the past 1200 years. Surpris ingly, the proxy records do not show a systematic link between inferred El Niñno activity and precipitation in the interior Southwest USA. A second new result is the existence of relationships at decadal to multidecadal timescales between fluctuations in Quelccaya δ18O, precipitation-related proxies from the western USA, and proxy records from the Pacific Basin. This finding links the Quelccaya record to the transhemi spheric Pacific decadal-scale climatic variability documented from proxy records by Villalba et al. (2001), and suggests that similar changes in the large-scale circulation changes accompany both the decadal and multidecadal signals. A composite constructed using gridded proxy precipitation constructed on the basis of decadal-scale fluctuations in inferred-El Niñno activity shows a pattern rather different to Niñno-based teleconnection maps for the instrumental record. In the proxy-based composite, positive values cover much of the extreme western, west central and southeastern USA, with negative values in the central Mis sissippi Valley. The interior Southwest shows essentially no response. A second composite based on multi decadal variability in Quelccayaδ18O shows a well-developed dipole pattern across the western USA with opposing centres in the interior Southwest and Northwest. It is suggested that this dipole pattern results from multidecadal variability in tropical Pacific SSTs and resulting changes in the strength of the Northeast Pacific High and the latitudinal distribution of cool season westerlies across the eastern North Pacific and western USA.