Miracle-dz/UniFAR-FTUs huggingface dataset:
Sea lamprey nests promote the diversity of benthic macroinvertebrate assemblages

The habitat heterogeneity hypothesis states that increased habitat heterogeneity promotes species diversity through increased availability of ecological niches. We aimed at describing the local-scale effects of nests of the sea lamprey (Petromyzon marinus L.) as ecosystem engineer on macroinvertebrate assemblages. We hypothesized that increased streambed physical heterogeneity caused by sea lamprey spawning would modify invertebrate assemblages and specific biologic traits and promote reach-scale diversity. We sampled thirty lamprey nests of the Nive River in three zones: the unmodified riverbed (control) and zones corresponding to the nest: the area excavated (pit) and the downstream accumulation of pebbles and cobbles (mound). The increased habitat heterogeneity created by lamprey was traduced by biological heterogeneity with a reduced density of invertebrates (1160 to 6540 individuals per m2 in control, 680 to 6460 individuals per m2 in pit and 1980 to 6240 individuals per m2 in mound) and number of taxa (23.5 ± 3.9 taxa for control, 18.6 ± 3.9 taxa in pit and 21.2 ± 4.5 taxa for mound) in the pit compared to other zones. However the overall taxa diversity in nest increased with 82 ± 14 taxa compared to the 69 ± 8 taxa estimated in control zone. Diversity indices were consistent with the previous results indicating a loss of α diversity in pit but a higher β diversity between a pit and a mound than between two control zones, especially considering Morisita index accounting for taxa abundance. Trait analysis showed high functional diversity within zones with a reduced proportion of collectors, scrapers, shredders, litter/mud preference and small invertebrates in mound, while the proportion of “slabs, blocks, stones and pebbles” preference and largest invertebrates increased. Pit presented the opposite trend, while control had globally intermediate trait proportions. Our results highlight important effects on species and functional diversity due to habitat heterogeneity created by a nest-building species, what can ultimately influence food webs and nutrient processes in river ecosystems.
DeepVariant calling provides insights into race diversity and its implication for sorghum breeding

Due to evolutionary divergence, sorghum race populations exhibit vast genetic and morphological variations. A k-mer-based sorghum race sequence comparison identified the conserved k-mers of all sorghum race accessions and the race-specific genetic signatures identified the gene variability in 10,321 genes (PAVs). To understand the sorghum race structure, diversity and domestication, deep learning-based variant calling approach was employed in a set of genotypic data derived from a diverse panel of 272 sorghum accessions. The data resulted in 1.7 million high-quality genome-wide SNPs and identified selective signature (both positive and negative) regions through a genome-wide scan with different (iHS and XP-EHH) statistical methods. We discovered 2,370 genes associated with selection signatures including 179 selective sweep regions distributed over 10 chromosomes. Localization of these regions undergoing selective pressure with previously reported QTLs and genes revealed that the signatures of selection could be related to the domestication of important agronomic traits such as biomass and plant height. The developed k-mer signatures will be useful in the future to identify the sorghum race and SNP markers assist in plant breeding programs.
Deterministic and Probabilistic Evaluation of Retrofit Alternatives for a Five-Story Flat-Slab RC Building

The effectiveness of seismic retrofitting applied to enhance seismic performance was assessed for a five-story reinforced concrete (RC) flat-slab building structure in the central United States. In addition to this, an assessment of seismic fragility that relates the probability of exceeding a performance level to the earthquake intensity was conducted. The response of the structure was predicted using nonlinear static and dynamic analyses with synthetic ground motion records for the central U.S. region. In addition, two analytical approaches for nonlinear response analysis were compared. FEMA 356 (ASCE 2000) criteria were used to evaluate the seismic performance of the case study building. Two approaches of FEMA 356 were used for seismic evaluation: global-level and member-level using three performance levels (Immediate Occupancy, Life Safety and Collapse Prevention). In addition to these limit states, punching shear drift limits were also considered to establish an upper bound drift capacity limit for collapse prevention. Based on the seismic evaluation results, three possible retrofit techniques were applied to improve the seismic performance of the structure, including addition of shear walls, addition of RC column jackets, and confinement of the column plastic hinge zones using externally bonded steel plates. Seismic fragility relationships were developed for the existing and retrofitted structure using several performance levels. Fragility curves for the retrofitted structure were compared with those for the unretrofitted structure. For development of seismic fragility curves, FEMA global drift limits were compared with the drift limits based on the FEMA member-level criteria. In addition to this, performance levels which were based on additional quantitative limits were also considered and compared with FEMA drift limits. Finally, recommendations are made for implementing the seismic fragility analysis results into MAEviz, the damage visualization module developed by the MidAmerica Earthquake Center.
Dissecting errors made in response to externally- and internally-driven visual tasks in the common marmosets and humans

Various visual paradigms in oculomotor research have been used for studying the neural processes of eye movement, cognitive control, attention and neurological disorders. However, we usually analyse data collected from humans or over-trained non-human primates (NHPs), focusing only on successful trials, whereas error trials are usually excluded. These errors may repetitively show up in diseases, but their interpretation would be difficult due to the absence of records taken from healthy controls. In the current study, we aimed to analyse both correctly and incorrectly performed trials in both marmosets and humans. We trained marmosets to perform the gap saccade task and the oculomotor delayed response task. We also collected data from human subjects who performed identical tasks. We categorised error trials into three different groups, based on the time when an incorrect response occurred. We also interpreted possible causes by analysing saccade reaction time, saccade landing position and task history. Despite the rareness of human error, we found that marmosets and humans showed remarkably similar behaviour in error and success. We also found that successful saccades in the gap saccade task had always the highest peak velocity in both species, reflecting faster sensorimotor processing for correct responses. Our results suggest that marmosets and humans might share similar neural processing for successful and unsuccessful oculomotor behaviour, making them a suitable model for studying human behaviour. More importantly, analysing error trials in sync with successful ones will provide further insights into the cognitive and sensorimotor processes. NEW AND NOTEWORTHY This is the first detailed report focusing on analysing both error and successful trials in oculomotor tasks. We proposed nomenclatures and a generalizable way of grouping and analysing error trials. Our results also indicate that marmosets can be a promising experimental candidate for oculomotor research because they replicate the saccade properties of error and success seen in humans. This will help set the baseline measurements to study brain disorders using NHP and understand the neural mechanisms from a different perspective.
NUDT6, the Antisense Protein of FGF2 Gene, Plays a Depressogenic Role by Promoting Inflammation and Suppressing Neurogenesis without Altering FGF2 Signaling

Fibroblast growth factor-2 (FGF2) is involved in the regulation of affective behavior and shows antidepressant effects through Akt and ERK1/2 pathways. NUDT6 is a protein encoded from FGF2 gene’s antisense strand and its role in the regulation of affective behavior is unclear. Here, we show that increasing NUDT6 expression in the hippocampus results in depression-like behavior in rats without changing FGF2 levels or activating its downstream effectors, Akt and ERK1/2. Instead, NUDT6 acts by inducing inflammatory signaling, specifically by increasing S100A9 levels, activating NF-κB and rising microglia number along with a reduction in neurogenesis. Conversely, inhibition of hippocampal NUDT6 expression by shRNA results in antidepressant effects and increases neurogenesis without altering FGF2 levels. Together these findings suggest that NUDT6 may play a role in major depression by inducing a proinflammatory state and serve as a novel therapeutic target for antidepressant development. This is the first report of an antisense protein acting through a different mechanism of action than regulation of its sense protein. The opposite effects of NUDT6 and FGF2 on depression-like behavior may serve as a mechanism to fine-tune affective behavior. Our findings open up new venues for studying the differential regulation and functional interactions of sense and antisense proteins in neural function and behavior as well as in neuropsychiatric disorders.
Graph pangenome reveals functional, evolutionary, and phenotypic significance of human nonreference sequences

Thousands of DNA sequences in global populations are not present in the human reference genome, named nonreference sequence (NRS). Long-read sequencing (LRS) technologies enable better discovery of NRS with large length, particularly in repetitive regions. Here, we de novo assembled 539 genomes in five genetically divergent human populations sequenced by LRS technology and identified 5.1 million NRSs. These NRSs were merged into 45,284 nonredundant NRSs, of which 66.2% were novel. 78.5% of NRSs were repeat sequences, such as VNTR and STR. 38.7% of NRSs were common in the five populations, 35.6% were population specific, while 21.3% were ancestral and present in nonhuman primates. 144 NRS hotspots spanned 141 Mb of the human genome and many NRSs contained known functional domains or intersected with coding genes. Based on graph-based pangenome, we detected 565 transcript expression quantitative trait loci on NRSs, of which 467 were novel. We also detected 39 NRS candidates for adaptive selection within the human population related to the language system and diabetes. GWAS revealed 14 NRSs significantly associated with eight phenotypes, such as anaemia. Furthermore, we identified 154 NRSs in strong linkage disequilibrium with 258 phenotype-associated SNPs in the GWAS catalogue. Our work expands the landscape of human NRS and provides novel insights into functions of NRS to facilitate evolutionary and biomedical research.
Immunogenicity and Protective Efficacy of a SARS-CoV-2 mRNA Vaccine Encoding Secreted Non-Stabilized Spike Protein in Mice

Establishment of an mRNA vaccine platform in low- and middle-income countries (LMICs) is important to enhance vaccine accessibility and ensure future pandemic preparedness. Here, we describe the preclinical studies of a SARS-CoV-2 mRNA encoding prefusion-unstabilized ectodomain spike protein encapsulated in lipid nanoparticles (LNP) “ChulaCov19”. In BALB/c mice, ChulaCov19 at 0.2, 1, 10, and 30 μg given 2 doses, 21 days apart, elicited robust neutralizing antibody (NAb) and T cells responses in a dose-dependent relationship. The geometric mean titer (GMT) of micro-virus neutralizing (micro-VNT) antibody against wild-type virus was 1,280, 11,762, 54,047, and 62,084, respectively. Higher doses induced better cross-neutralizing antibody against Delta and Omicron variants. This elicited specific immunogenicity was significantly higher than those induced by homologous prime-boost with inactivated (CoronaVac) or viral vector (AZD1222) vaccine. In heterologous prime-boost study, mice primed with either CoronaVac or AZD1222 vaccine and boosted with 5 μg ChulaCov19 generated NAb 7-fold higher against wild-type virus (WT) and was also significantly higher against Omicron (BA.1 and BA.4/5) than homologous CoronaVac or AZD1222 vaccination. AZD1222-prime/mRNA-boost had mean spike-specific IFNγ positive T cells of 3,725 SFC/106 splenocytes, which was significantly higher than all groups except homologous ChulaCov19. Challenge study in human-ACE-2-expressing transgenic mice showed that ChulaCov19 at 1 μg or 10 μg protected mice from COVID-19 symptoms, prevented SARS-CoV-2 viremia, significantly reduced tissue viral load in nasal turbinate, brain, and lung tissues 99.9-100%, and without anamnestic of Ab response which indicated its protective efficacy. ChulaCov19 is therefore a promising mRNA vaccine candidate either as a primary or a boost vaccination and has entered clinical development.
Balancing true and false detection of intermittent sensory targets by adjusting the inputs to the evidence accumulation process

Decisions about noisy stimuli are widely understood to be made by accumulating evidence up to a decision bound that can be adjusted according to task demands. However, relatively little is known about how such mechanisms operate in continuous monitoring contexts requiring intermittent target detection. Here, we examined neural decision processes underlying detection of 1-second coherence-targets within continuous random dot motion, and how they are adjusted across contexts with Weak, Strong, or randomly Mixed weak/strong targets. Our prediction was that decision bounds would be set lower when weak targets are more prevalent. Behavioural hit and false alarm rate patterns were consistent with this, and were well-captured by a bound-adjustable leaky accumulator model. However, beta-band EEG signatures of motor preparation contradicted this, instead indicating lower bounds in the Strong-target context. We thus tested two alternative models in which decision bound dynamics were constrained directly by Beta measurements, respectively featuring leaky accumulation with adjustable leak, and non-leaky accumulation of evidence referenced to an adjustable sensory-level criterion. We found that the latter model best explained both behaviour and neural dynamics, highlighting novel means of decision policy regulation and the importance of neurally-informed modelling.
Enterococcal Linear Plasmids Adapt to Enterococcus faecium and Spread within Multidrug-Resistant Clades

Antimicrobial resistance (AMR) of bacterial pathogens, including enterococci, is a global concern, and plasmids are crucial for spreading and maintaining AMR genes. Plasmids with linear topology were identified recently in clinical multidrug-resistant enterococci. ABSTRACT Antimicrobial resistance (AMR) of bacterial pathogens, including enterococci, is a global concern, and plasmids are crucial for spreading and maintaining AMR genes. Plasmids with linear topology were identified recently in clinical multidrug-resistant enterococci. The enterococcal linear-form plasmids, such as pELF1, confer resistance to clinically important antimicrobials, including vancomycin; however, little information exists about their epidemiological and physiological effects. In this study, we identified several lineages of enterococcal linear plasmids that are structurally conserved and occur globally. pELF1-like linear plasmids show plasticity in acquiring and maintaining AMR genes, often via transposition with the mobile genetic element IS1216E. This linear plasmid family has several characteristics enabling long-term persistence in the bacterial population, including high horizontal self-transmissibility, low-level transcription of plasmid-carried genes, and a moderate effect on the Enterococcus faecium genome alleviating fitness cost and promoting vertical inheritance. Combining all of these factors, the linear plasmid is an important factor in the spread and maintenance of AMR genes among enterococci.
Microphysiological vascular malformation model reveals a role of dysregulated Rac1 and mTORC1/2 in lesion formation

Somatic activating mutations of PIK3CA are associated with the development of vascular malformations (VMs). Here, we describe a microfluidic model of PIK3CA-driven VMs consisting of human umbilical vein endothelial cells (HUVECs) expressing PIK3CA activating mutations embedded in 3D hydrogels. We observed enlarged and irregular vessel phenotypes, consistent with clinical signatures and concomitant with PI3K-driven upregulation of Rac1/PAK, MEK/ERK, and mTORC1/2 signaling. We observed differential effects between Alpelisib, a PIK3CA inhibitor, and Rapamycin, an mTORC1 inhibitor, in mitigating matrix degradation and vascular network topology. While both drugs are effective in preventing vessel enlargement, Alpelisib suppressed mTORC2-dependent AKT1 phosphorylation and MEK/ERK signaling. Rapamycin failed to reduce MEK/ERK and mTORC2 activity and resulted in vascular hyperbranching, while inhibiting PAK, MEK1/2, and mTORC1/2 signaling mitigates abnormal growth and vascular dilation. Collectively, these findings establish an in vitro platform for modeling VMs and confirm a role of dysregulated Rac1/PAK and mTORC1/2 signaling in PIK3CA-driven VMs.
White matter structural bases for predictive tapping synchronization

We determined the intersubject association between rhythmic entrainment abilities of human subjects during a synchronization continuation tapping task (SCT) and the macro and microstructural properties of their superficial (SWM) and deep (dWM) white matter. Diffusion-weighted images were obtained from 32 subjects who also performed the SCT with auditory or visual metronomes and five tempos ranging from 550 to 950 ms. We developed a method to determine the fiber density of U-fibers running tangentially to the cortex. Notably, the right audiomotor system showed individual differences in the density of U-fibers that were correlated with the degree of predictive entrainment across subjects. These correlations were selective for the synchronization epoch with auditory metronomes and were specific for tempos around 1.5 Hz. In addition, there was a significant association between predictive rhythmic entrainment and the density and bundle diameter of the corpus callosum (CC), forming a chronotopic map where behavioural correlations of short and long intervals were found with the anterior and posterior portions of the CC. Finally, the fiber bundle cross-section of the arcuate fasciculus, the CC, and the Superior Longitudinal Fasciculus showed a significant correlation with the mean asynchronies of the auditory SCT. These findings suggest that the structural properties of the SWM and dWM in the audiomotor system support the predictive abilities of subjects during rhythmic tapping, where the density of cortical U-fibers are linked to the preferred tapping tempo, and the bundle properties of CC define an interval selective topography that has an anterior posterior gradient.
Ecology and age, but not genetic ancestry, predict fetal loss in a wild baboon hybrid zone.

OBJECTIVES Pregnancy failure represents a major fitness cost for any mammal, particularly those with slow life histories such as primates. Here, we quantified the risk of fetal loss in wild hybrid baboons, including genetic, ecological, and demographic sources of variance. We were particularly interested in testing the hypothesis that hybridization increases fetal loss rates. Such an effect would help explain how baboons may maintain genetic and phenotypic integrity despite interspecific gene flow. MATERIALS AND METHODS We analyzed outcomes for 1020 pregnancies observed over 46 years in a natural yellow baboon-anubis baboon hybrid zone. Fetal losses and live births were scored based on records of female reproductive state and the appearance of live neonates. We modeled the probability of fetal loss as a function of a female's genetic ancestry (the proportion of her genome estimated to be descended from anubis [vs. yellow] ancestors), age, number of previous fetal losses, dominance rank, group size, climate, and habitat quality using binomial mixed effects models. RESULTS Female genetic ancestry did not predict fetal loss. Instead, the risk of fetal loss is elevated for very young and very old females. Fetal loss is most robustly predicted by ecological factors, including poor habitat quality prior to a home range shift and extreme heat during pregnancy. DISCUSSION Our results suggest that gene flow between yellow and anubis baboons is not impeded by an increased risk of fetal loss for hybrid females. Instead, ecological conditions and female age are key determinants of this component of female reproductive success.
RTEL-1 and DNA polymerase theta promote subtelomeric DNA synthesis and telomere fusion in C. elegans

Interstitial telomere sequences (ITS) are degenerate telomere tracts scattered along chromosome arms whose functions are not well understood. We found that critically shortened telomeres of C. elegans telomerase mutants initiate DNA synthesis within ITS tracts that were close to or far from a telomere. Some ITS tracts were targeted recurrently. RTEL-1 dismantles T-loops and recombination intermediates, and DNA polymerase theta (POLQ-1) promotes end-joining using short segments of microhomology. In telomerase mutants, RTEL-1 and POLQ-1 promoted telomere fusion and DNA synthesis at subtelomeric ITS tracts. RTEL-1 is known to suppress homologous recombination, and we found that RTEL-1 similarly suppressed POLQ-1-mediated double-strand break repair. Mutation signatures characteristic of repair by POLQ-1 occurred during initiation of subtelomeric DNA synthesis and at subsequent template shifting events. We propose that RTEL-1 and POLQ-1 play distinct essential roles in subtelomeric DNA synthesis, a process that may contribute significantly to telomere fusion and tumor genome evolution.
DECAY PROPERTIES OF THE E HYPERON AND E RESONANCES

A sample of 2500 {Xi}{sup -} and 500 {Xi}{sup 0} hyperons, produced in {Xi}K, {Xi}K{pi}, and {Xi}K{pi}{pi} final states by K{sup -} (in H{sub 2}) at incident momenta of 1.7 to 2.7 BeV/c, has been analyzed. The data are from an exposure (K-63) of 26 events/{mu}b in the 72-inch bubble chamber; approximately 85% of the {Xi}{sup -} events and 60% of the {Xi}{sup 0} events have been analyzed. For the {Xi}, they determine the spin and decay parameters a{sub {Xi}} and {Phi}{sub {Xi}} = tan{sup -1} ({beta}{sub {Xi}}/{Gamma}{sub {Xi}}). Combining their data with 900 {Xi}{sup -} and 150 {Xi}{sup 0} events from an earlier experiment (K-72), they obtain the following results: (1) {Xi} spin - J = 1/2 favored over J = 3/2 by {approx} 2.5 standard deviations; (2) {Xi} decay parameters (assuming a{sub {Lambda}} = 0.647 {+-} 0.048) - a{sub {Xi}{sup -}} = -0.398 {+-} 0.041, {Phi}{sub {Xi}{sup -}} = 9.8{sup o} {+-} 9.0{sup o}; a{sub {Xi}{sup 0}} = -0.413 {+-} 0.104. They observe {Xi}*(1530) and {Xi}*(1817); their data are insufficient for analysis of suggested {Xi}* resonances at 1705 and 1933 MeV. They measure the {Xi}*(1530) electromagnetic mass difference {Delta}m = m({Xi}*{sup -}) = m({Xi}*{sup 0}) = 2.0 {+-}more » 3.2 MeV. Using data, part of which has already been described, they find for {Xi}*(1530): J {ge} 3/2 favored over J = 1/2 (the J = 1/2 hypothesis is {approx} 3.5% as probable as the J = 3/2 hypothesis); J{sup P} = 3/2{sup +} favored over 3/2{sup -} by {approx} 2.8 standard deviations. For {Xi}*(1817) decaying into {Xi}*(1530) + {pi}, the hypotheses J{sup P} = 1/2{sup +}, 1/2{sup -}, 3/2{sup -}, 5/2{sup +}, 7/2{sup -}, etc. (corresponding to {ell} = 1, 2, 0 and 2, 1 and 3, and 2 and 4, respectively) are favored over other hypotheses, but results are inconclusive due to large background. « less