Miracle-dz/UniFAR-FTUs huggingface dataset:
Pelage Variation and Morphometrics of Closely Related Callithrix Marmoset Species and Their Hybrids

Background Hybrids are expected to show greater phenotypic variation than their parental species, yet how hybrid phenotype expression varies with genetic distances in closely-related parental species remains surprisingly understudied. Here we study pelage and morphometric trait variation in anthropogenic hybrids vailable at the end of the article between four species of Brazilian Callithrix marmosets, a relatively recent primate radiation. Marmoset species are distinguishable by pelage phenotype and morphological specializations for eating tree exudates. Here, we (1) describe qualitative phenotypic pelage differences between parental species and hybrids; (2) test whether significant quantitative differences exist between parental and hybrid morphometric phenotypes; and (3) determine which hybrid morphometic traits show heterosis, dysgenesis, trangression, or intermediacy relative to the parental trait. For morphometric traits, we investigated both cranial and post-cranial traits, particularly as most hybrid morphological studies focus on the former instead of the latter. Finally, we estimate mitogenomic distances between marmoset species from previously published data. Results Marmoset hybrid facial and overall body pelage variation reflected novel combinations of coloration and patterns present in parental species. In morphometric traits, C. jacchus and C. penicillata were the most similar to each other, while C. aurita was the most distinct, and C. geoffroyi trait measures fell between these other species. Only three traits in C. jacchus x C. penicillata hybrids showed heterosis. We observed heterosis and dysgenesis in several traits of C. penicillata x C. geoffroyi hybrids. Transgressive segregation was observed in hybrids of C. aurita and the other species. These hybrids were also C. aurita-like for a number of traits. Genetic distance was closest between C. jacchus and C. penicillata and farthest between C. aurita and the other species. Conclusion We attributed significant morphometric differences between marmoset species to variable levels of morphological specialization for exudivory in these species. Our results suggest that intermediate or parental species-like hybrid traits relative to the parental trait values are more likely in crosses between species with relatively lesser genetic distance. More extreme phenotypic variation is more likely in parental species with greater genetic distance, with transgressive traits appearing in hybrids of the most genetically distant parental species. We further suggest that less developmental disturbances can be expected in hybrids of more recently diverged parental species, and that future studies of hybrid phenotypic variation should investigate selective pressures on Callithrix cranial and post-cranial morphological traits.
Drifting population dynamics with transient resets characterize sensorimotor transformation in the monkey superior colliculus

To produce goal-directed eye movements known as saccades, we must channel sensory input from our environment through a process known as sensorimotor transformation. The behavioral output of this phenomenon (an accurate eye movement) is straightforward, but the coordinated activity of neurons underlying its dynamics is not well understood. We searched for a neural correlate of sensorimotor transformation in the activity patterns of simultaneously recorded neurons in the superior colliculus (SC) of three male rhesus monkeys performing a visually guided, delayed saccade task. Neurons in the intermediate layers produce a burst of spikes both following the appearance of a visual (sensory) stimulus and preceding an eye movement command, but many also exhibit a sustained activity level during the intervening time (“delay period”). This sustained activity could be representative of visual processing or motor preparation, along with countless cognitive processes. Using a novel measure we call the Visuomotor Proximity Index (VMPI), we pitted visual and motor signals against each other by measuring the degree to which each session’s population activity (as summarized in a low-dimensional framework) could be considered more visual-like or more motor-like. The analysis highlighted two salient features of sensorimotor transformation. One, population activity on average drifted systematically toward a motor-like representation and intermittently reverted to a visual-like representation following a microsaccade. Two, activity patterns that drift to a stronger motor-like representation by the end of the delay period may enable a more rapid initiation of a saccade, substantiating the idea that this movement initiation mechanism is conserved across motor systems.
Biomolecular condensates modulate membrane lipid packing and hydration

Membrane wetting by biomolecular condensates recently emerged as a key phenomenon in cell biology, playing an important role in a diverse range of processes across different organisms. However, an understanding of the molecular mechanisms behind condensate formation and interaction with lipid membranes is still missing. To study this, we exploited the properties of the dyes ACDAN and LAURDAN as nano-environmental sensors in combination with phasor analysis of hyperspectral and lifetime imaging microscopy. Using glycinin as a model condensate-forming protein and giant vesicles as model membranes, we obtained vital information on the process of condensate formation and membrane wetting. Our results reveal that glycinin condensates display differences in water dynamics when changing the salinity of the medium as a consequence of rearrangements in the secondary structure of the protein. Remarkably, analysis of membrane-condensates interaction with protein as well as polymer condensates indicated a correlation between increased wetting affinity and enhanced lipid packing. This is demonstrated by a decrease in the dipolar relaxation of water across all membrane-condensate systems, suggesting a general mechanism to tune membrane packing by condensate wetting.
Inversion mode n-channel GaAs field effect transistor with high-k/metal gate

Highly effective passivation of GaAs surface is achieved by a thin amorphous Si (a-Si) cap, deposited by plasma enhanced chemical vapor deposition method. Capacitance voltage measurements show that carrier accumulation or inversion layer is readily formed in response to an applied electrical field when GaAs is passivated with a-Si. High performance inversion mode n-channel GaAs metal-oxide-semiconductor field-effect transistors (MOSFETs) were fabricated with an a-Si/high-k/metal gate stack. Drain current in saturation region of 220mA∕mm with a mobility of 885cm2∕Vs were obtained at a gate overdrive voltage of 3.25V in MOSFETs with 5μm gate length.
Metabolic rewiring of the probiotic bacterium Lacticaseibacillus rhamnosus GG contributes to cell-wall remodeling and antimicrobials production

Lacticaseibacillus rhamnosus GG (LGG) is a Gram-positive beneficial bacterium that resides in the human intestinal tract and belongs to the family of lactic acid bacteria (LAB). This bacterium is a widely used probiotic and was suggested to provide numerous benefits for human health. However, as in most LAB strains, the molecular mechanisms that mediate the competitiveness of probiotics under different diets remain unknown. Fermentation is a fundamental process in LAB, allowing the oxidation of simple carbohydrates (e.g., glucose, mannose) for energy production under conditions of oxygen limitation, as in the human gut. Our results indicate that fermentation reshapes the metabolome, volatilome, and proteome architecture in LGG. Furthermore, fermentation alters cell envelope remodeling and peptidoglycan biosynthesis, which leads to altered cell wall thickness, aggregation properties, and cell wall composition. In addition, fermentable sugars induced secretion of known and novel metabolites and proteins targeting the enteric pathogens Enterococcus faecalis and Salmonella Enterica serovar Typhimurium. Overall, our results link the common metabolic regulation of cell wall remodeling, aggregation to host tissues, biofilm formation in probiotic strains, and connect the production of antimicrobial effectors with metabolome reprogramming. These findings provide novel insights into the role of nutrition in the establishment of LGG in the gastrointestinal tract.
RNAP promoter search and transcription kinetics in live E. coli cells

Bacterial transcription has been studied extensively in vitro, which has provided indepth insight regarding transcription mechanisms. However, the live cell environment may impose different rules on transcription than the homogenous and simplified in vitro environment. How an RNA polymerase (RNAP) molecule searches rapidly through the vast nonspecific chromosomal DNA in the three-dimensional nucleoid space and binds a specific promoter sequence remains elusive. The kinetics of transcription in vivo could also be impacted by specific cellular environments including nucleoid organization and nutrient availability. In this work, we investigated the promoter search dynamics and transcription kinetics of RNAP in live E. coli cells. Using single-molecule tracking (SMT) and fluorescence recovery after photobleaching (FRAP) and combining with different genetic, drug inhibition, and growth conditions, we observed that RNAP’s promoter search is facilitated by nonspecific DNA interactions and largely independent of nucleoid organization, growth condition, transcription activity, or promoter classes. RNAP’s transcription kinetics, however, is sensitive to these conditions and mainly modulated at the levels of actively engaged RNAP and the promoter escape rate. Our work establishes a foundation for further mechanistic studies of bacterial transcription in live cells.
The effects of nutritional level and body condition score on cytokines in seminal plasma of beef bulls

Introduction High quality semen is essential for reproductive efficiency. Nutrition and environmental factors impact the ejaculate components, like cytokines, that are essential for pregnancy establishment. We hypothesized that differing nutritional periods and body condition scores would affect seminal plasma cytokine concentrations of bulls. Methods Mature Angus bulls (n=11) were individually housed and randomly assigned to either over-fed (n=5) or restricted (n=6) treatment pathways. Bulls were fed different volumes of a single ration creating 8 individual treatment periods. Body weight and body condition scores were taken every 14 d to manage intake volumes. Ejaculates were collected every 84 d to determine seminal plasma cytokine profiles. A complete randomized design was used to evaluate seminal plasma cytokines after each nutritional treatment. Initial cytokine concentrations and volume of the ejaculate were included as covariates. Results All cytokines returned to initial concentrations following maintenance treatments at an ideal body condition score of 6. Nutritional treatments affected (P ≤ 0.05) IFN-γ, IL-8, MIP-1α, MIP-1β, TNF-α, IL-1β, and VEGF-A. However, TNF-α, IFN-γ, and MIP-1α had the greatest impact on cytokine profile. Discussion Nutritional levels and adiposity altered seminal plasma cytokine concentrations which could potentially impact the inflammatory balance of the uterus and the immune responses necessary for pregnancy establishment.
The genetic architecture of the human skeletal form

The human skeletal form underlies our ability to walk on two legs, but unlike standing height, the genetic basis of limb lengths and skeletal proportions is less well understood. Here we applied a deep learning model to 31,221 whole body dual-energy X-ray absorptiometry (DXA) images from the UK Biobank (UKB) to extract 23 different image-derived phenotypes (IDPs) that include all long bone lengths as well as hip and shoulder width, which we analyzed while controlling for height. All skeletal proportions are highly heritable (∼40-50%), and genome-wide association studies (GWAS) of these traits identified 179 independent loci, of which 102 loci were not associated with height. These loci are enriched in genes regulating skeletal development as well as associated with rare human skeletal diseases and abnormal mouse skeletal phenotypes. Genetic correlation and genomic structural equation modeling indicated that limb proportions exhibited strong genetic sharing but were genetically independent of width and torso proportions. Phenotypic and polygenic risk score analyses identified specific associations between osteoarthritis (OA) of the hip and knee, the leading causes of adult disability in the United States, and skeletal proportions of the corresponding regions. We also found genomic evidence of evolutionary change in arm-to-leg and hip-width proportions in humans consistent with striking anatomical changes in these skeletal proportions in the hominin fossil record. In contrast to cardiovascular, auto-immune, metabolic, and other categories of traits, loci associated with these skeletal proportions are significantly enriched in human accelerated regions (HARs), and regulatory elements of genes differentially expressed through development between humans and the great apes. Taken together, our work validates the use of deep learning models on DXA images to identify novel and specific genetic variants affecting the human skeletal form and ties a major evolutionary facet of human anatomical change to pathogenesis.
The Embryonic Origin of Primordial Germ Cells in the Tardigrade Hypsibius exemplaris

Primordial germ cells (PGCs) give rise to gametes – cells necessary for the propagation and fertility of diverse organisms. Current understanding of PGC development is limited to the small number of organisms whose PGCs have been identified and studied. Expanding the field to include little-studied taxa and emerging model organisms is important to understand the full breadth of the evolution of PGC development. In the phylum Tardigrada, no early cell lineages have been identified to date using molecular markers. This includes the PGC lineage. Here, we describe PGC development in the model tardigrade Hypsibius exemplaris. The four earliest-internalizing cells (EICs) exhibit PGC-like behavior and nuclear morphology. The location of the EICs is enriched for mRNAs of conserved PGC markers wiwi1 (water bear piwi 1) and vasa. At early stages, both wiwi1 and vasa mRNAs are detectable uniformly in embryos, which suggests that these mRNAs do not serve as localized determinants for PGC specification. Only later are wiwi1 and vasa enriched in the EICs. Finally, we traced the cells that give rise to the four PGCs. Our results reveal the embryonic origin of the PGCs of H. exemplaris and provide the first molecular characterization of an early cell lineage in the tardigrade phylum. We anticipate that these observations will serve as a basis for characterizing the mechanisms of PGC development in this animal.
Systematic assessment of the contribution of structural variants to inherited retinal diseases

Despite increasing success in determining genetic diagnosis for patients with inherited retinal diseases (IRDs), mutations in about 30% of the IRD cases remain unclear or unsettled after targeted gene panel or whole exome sequencing. In this study, we aimed to investigate the contributions of structural variants (SVs) to settling the molecular diagnosis of IRD with whole-genome sequencing (WGS). A cohort of 755 IRD patients whose pathogenic mutations remain undefined was subjected to WGS. Four SV calling algorithms including include MANTA, DELLY, LUMPY, and CNVnator were used to detect SVs throughout the genome. All SVs identified by any one of these four algorithms were included for further analysis. AnnotSV was used to annotate these SVs. SVs that overlap with known IRD-associated genes were examined with sequencing coverage, junction reads, and discordant read pairs. PCR followed by Sanger sequencing was used to further confirm the SVs and identify the breakpoints. Segregation of the candidate pathogenic alleles with the disease was performed when possible. In total, sixteen candidate pathogenic SVs were identified in sixteen families, including deletions and inversions, representing 2.1% of patients with previously unsolved IRDs. Autosomal dominant, autosomal recessive, and X-linked inheritance of disease-causing SVs were observed in 12 different genes. Among these, SVs in CLN3, EYS, PRPF31 were found in multiple families. Our study suggests that the contribution of SVs detected by short-read WGS is about 0.25% of our IRD patient cohort and is significantly lower than that of single nucleotide changes and small insertions and deletions.
Phylogenetic Comparative Approach Reveals Evolutionary Conservatism, Ancestral Composition, and Integration of Vertebrate Gut Microbiota

How host-associated microbial communities evolve as their hosts diversify remains equivocal: How conserved is their composition? What was the composition of ancestral microbiota? Do microbial taxa covary in abundance over millions of years? Multivariate phylogenetic models of trait evolution are key to answering similar questions for complex host phenotypes, yet they are not directly applicable to relative abundances, which usually characterize microbiota. Here, we extend these models in this context, thereby providing a powerful approach for estimating phylosymbiosis (the extent to which closely related host species harbor similar microbiota), ancestral microbiota composition, and integration (evolutionary covariations in bacterial abundances). We apply our model to the gut microbiota of mammals and birds. We find significant phylosymbiosis that is not entirely explained by diet and geographic location, indicating that other evolutionary-conserved traits shape microbiota composition. We identify main shifts in microbiota composition during the evolution of the two groups and infer an ancestral mammalian microbiota consistent with an insectivorous diet. We also find remarkably consistent evolutionary covariations among bacterial orders in mammals and birds. Surprisingly, despite the substantial variability of present-day gut microbiota, some aspects of their composition are conserved over millions of years of host evolutionary history.
An Application of Causal Bandit to Content Optimization

Amazon encompasses a large number of discrete businesses such as Retail, Advertising, Fresh, Business (B2B e-commerce), andPrimeVideo, mostofwhichmaintainapresenceacrossitse-commercewebsite. Theyproducecontentforourcustomers that belong to diverse content types such as merchandising (e.g. product recommendations), product advertisements (e.g. sponsored products and display ads), program adoption banners (e.g. Amazon Fresh), and consumption (e.g. Prime Video). When customers visit a web page on the website, it triggers a content allocation process where we determine the specific content to show in regions of customer shopping experience on that web page. Content produced by the aforementioned businesses then needs to be arbitrated during this process. We present a causal bandit based framework to address the problem of content optimization in this context. The framework is responsible for fairly balancing the differing objectives and methods of these businesses, and selecting the right content to display to the customers at the right time. It does so with thegoalofimprovingtheoverallsite-widecustomershoppingexperience. Inthispaper, wepresentourcontentoptimization framework, describe its components, demonstrate the framework’s effectiveness through online randomized experiments, and share learnings from deploying and testing the framework in production.
A physical model and experimental testbed for real‐time simulation of flute‐like instruments

In the last decades, a wealth of experimental data has been gathered concerning sound production in flute‐like instruments. These data have driven the development and fine tuning of analytical models for the physical processes involved. Here, a number of these results are integrated into a real‐time physical model of a flute‐like instrument. The model proposed is one‐dimensional and driven by a single input pressure. The system was designed in the spirit of a laboratory testbed, where geometric and performance parameters can be controlled in real time, and in which important physical quantities can be viewed in real time, either in the time domain or frequency domain. In this way, the user may observe and validate the behavior of variables that would otherwise be hidden in the feedback loop. Additionally, the system was designed in a modular fashion, so as to allow independent substitution and adjustment of any of the model blocks. So as to allow real‐time implementation and parameter control, a novel tim.
Bilinear transformation of infinite-dimensional state-space systems and balanced realizations of nonrational transfer functions

The bilinear transform maps the open right half plane to the open unit disk and is therefore a suitable tool for carrying over results for continuous-time systems to discrete-time systems and vice versa. Corresponding state-space formulae are widely used and well understood for the case of finite-dimensional systems. In this paper infinite-dimensional generalizations of these formulae are studied for a general class of infinite-dimensional state-space systems. In particular, it is shown that reachability and observability are carried over and that the reachability and observability gramians are preserved under this transformation. Young showed that a wide class of nonrational discrete-time transfer functions admit a balanced state-space representation. It is shown that this result carries over to the continuous-time situation via the bilinear transformation.
Wake formation behind a rolling sphere

Experimental flow visualizations are presented depicting the flow behind a spherical body moving on a plane wall. In the Reynolds number range of 100<Re<350, four distinct wake modes occur which are dependent on the imposed rotation rate of the body. Five different rotation rates are examined: two with forward rolling, one with pure translation (zero rotation), and two with reversed rolling. As the sphere undergoes forward rolling, steady and unsteady wake modes are observed which bear similarities to the flow behind an isolated sphere in a free stream. However, for cases with reversed and zero rotation of the sphere, a new antisymmetric wake mode is discovered.
Epitaxial growth of ferromagnetic ultrathin MnGa films with perpendicular magnetization on GaAs

We have successfully grown ferromagnetic MnGa ultrathin films on GaAs substrates by molecular beam epitaxy. Reflection high energy electron diffraction and cross‐sectional transmission electron microscopy show that monocrystalline MnGa films are grown with the c axis of the tetragonal unit cell normal to the (001) GaAs substrates. Both magnetization measurements by vibrating sample magnetometer and extraordinary Hall effect (EHE) measurements indicate perpendicular magnetization, with the remnant magnetization of 225 emu/cm3 and EHE resistivity in the range of 0.5–4 μΩ cm at room temperature. The material possesses properties ideal for certain nonvolatile magnetic memory coupled with underlying III‐V circuitry.