Miracle-dz/UniFAR-FTUs huggingface dataset:
Self-organised pattern formation in the developing neural tube by a temporal relay of BMP signalling

Developing tissues interpret dynamic changes in morphogen activity to generate cell type diversity. To quantitatively study BMP signalling dynamics in the vertebrate neural tube, we developed a new ES cell differentiation system tailored for growing tissues. Differentiating cells form striking self-organised patterns of dorsal neural tube cell types driven by sequential phases of BMP signalling that are observed both in vitro and in vivo. Data-driven biophysical modelling showed that these dynamics result from coupling fast negative feedback with slow positive regulation of signalling by the specification of an endogenous BMP source. Thus, in contrast to relays that propagate morphogen signalling in space, we uncover a BMP signalling relay that operates in time. This mechanism allows rapid initial concentrationsensitive response that is robustly terminated, thereby regulating balanced sequential cell type generation. Altogether, our study provides an experimental and theoretical framework to understand how signalling dynamics are exploited in developing tissues.
Darwin’s “neuters” and the evolution of the sex continuum in a superorganism

Ant castes are an amazing example of phenotypic plasticity. In worker-destined embryos of the ant Cardiocondyla obscurior, the default female developmental trajectory is interrupted even before the gonadal precursor cells acquire a sexual identity. miRNA and mRNA expression in embryos reveal three distinct phenotypic entities: males, females, and “neuters”, as Darwin coined the worker caste in “On the Origin of Species”. Based on these results we propose that haplodiploidy, in conjunction with insect sex determination, allows for the expression of a third dimension on the sex continuum, thus facilitating the evolution of individuals which develop traits their parents do not have. One sentence summary Sex and caste differentiation begin during the same embryonic developmental window in the ant Cardiocondyla obscurior.
Proteome-wide base editor screens to assess phosphorylation site functionality in high-throughput

Signaling pathways that drive gene expression are typically depicted as having a dozen or so landmark phosphorylation and transcriptional events. In reality, thousands of dynamic post-translational modifications (PTMs) orchestrate nearly every cellular function, and we lack technologies to find causal links between these vast biochemical pathways and genetic circuits at scale. Here, we describe “signaling-to-transcription network” mapping through the development of PTM-centric base editing coupled to phenotypic screens, directed by temporally-resolved phosphoproteomics. Using T cell activation as a model, we observe hundreds of unstudied phosphorylation sites that modulate NFAT transcriptional activity. We identify the phosphorylation-mediated nuclear localization of the phosphatase PHLPP1 which promotes NFAT but inhibits NFκB activity. We also find that specific phosphosite mutants can alter gene expression in subtle yet distinct patterns, demonstrating the potential for fine-tuning transcriptional responses. Overall, base editor screening of PTM sites provides a powerful platform to dissect PTM function within signaling pathways.
Population size shapes trade-off dilution and adaptation to a marginal niche unconstrained by sympatric habitual conditions

Niche expansion remains significantly understudied in sympatric scenarios where marginal and habitual niches are simultaneously available. Devoid of spatial constraints, such conditions impose selection to maintain fitness in habitual (high-productivity) niches while adapting to marginal (low-productivity) niches. Hence, habitual niche composition should constrain adaptation to marginal niches. This remains untested. Similarly, it is unknown if larger populations expand their niches better. We tested these hypotheses using experimental evolution with Escherichia coli and found that larger populations consistently adapted better to both marginal and habitual niches. Whereas the habitual niche composition (constant versus fluctuating environments; environmental fluctuations varying in both predictability and speed) significantly shaped fitness in habitual niches, surprisingly, it failed to constrain adaptation to the marginal niche. Curiously, two negatively correlated habitual niches can still each be positively correlated with the marginal niche. This allows the marginal niche to dilute trade-offs between habitual niches, thereby enabling costless niche expansion.
VaxSeer: Selecting influenza vaccines through evolutionary and antigenicity models

Current vaccines provide limited protection against rapidly evolving viruses. For example, the flu vaccine’s effectiveness has averaged below 40% for the past five years. Today, clinical outcomes of vaccine effectiveness can only be assessed retrospectively. Since vaccine strains are selected at least six months ahead of flu season, prospective estimation of their effectiveness is crucial but remains under-explored. In this paper, we propose an in-silico method named VaxSeer that selects vaccine strains based on their coverage scores, which quantifies expected vaccine effectiveness in future seasons. This score considers both the future dominance of circulating viruses and antigenic profiles of vaccine candidates. Based on historical WHO data, our approach consistently selects superior strains than the annual recommendations. Finally, the prospective coverage score exhibits a strong correlation with retrospective vaccine effectiveness and reduced disease burden, highlighting the promise of this framework in driving the vaccine selection process.
SUMO chains depolymerization induces slender to stumpy differentiation in T. brucei bloodstream parasites

Trypanosoma brucei are extracellular protozoan parasites transmitted by tsetse flies that cause sleeping sickness in humans and nagana in cattle. Inside the mammalian host, differentiation from a bloodstream replicative slender form into a quiescent stumpy form allows the persistence of the parasite and the spread of the infection. SUMOylation is a reversible and dynamic post-translational modification of proteins that regulates diverse nuclear processes, such as DNA replication, repair and transcription. SUMO can be attached to its target proteins either as a single monomer or forming polymeric chains. We found that transgenic cell lines able to conjugate SUMO just as a monomer are attenuated in vivo. SUMO chain mutant monomorphic parasites display relapsing and remitting waves of parasitemia, at variance with wild-type parasites that cause unremitting parasitemia and mice death. Furthermore, when mice are infected with an analogous SUMO chain mutant generated in a differentiation-competent pleomorphic background, stumpy cells can be observed at unusually low parasitemia values. Our study reveals that SUMO depolymerization could represent a coordinated signal triggered during a quiescence activation program.
Theta activity discriminates high-level, species-specific body processes

Among social stimuli that trigger rapid reactions, body images occupy a prominent place. Given that bodies carry information about other agents’ intentions, actions and emotional expressions, a foundational question concerns the neural basis of body processing. Previous fMRI studies have investigated this but were not yet able to clarify the time course and its functional significance. The present EEG study investigated the role of slow oscillatory cortical activity in body processing and species-specificity. Human participants viewed naturalistic images of human and monkey bodies, faces, and objects, along with mosaic-scrambled versions to control for low-level visual features. Analysis of event-related theta power (4 – 7 Hz) combined with data-driven methods revealed a strong, body-evoked neural response that is specific to human bodies and likely originates from a widespread cortical region during a time window of 150 – 550 ms after the onset of the body image. Our results corroborate recent research proposing a widespread, species-specific cortical network of human body processing. We submit that this network may play an essential role in linking body processes to movement intentions.
Targeted Metagenomic Databases Provide Improved Analysis of Microbiota Samples

We introduce Moonbase, a flexible pipeline that can be used to build targeted, project-specific, databases in order to improve the accuracy of taxonomic detection and quantification in complex microbial communities. Moonbase was evaluated using synthetic metagenomic samples and compared against existing methods including MetaPhlAn3 and generalized Kraken2 databases. Our results indicate that Moonbase significantly improves species precision and quantification, outperforming marker genes and generalized databases. Construction of a phylogenetic tree from 16S data of genomes in Moonbase allows for the incorporation of UniFrac-type phylogenetic information into diversity calculations of samples. We demonstrate the resulting analysis has increased statistical power in distinguishing microbial communities. This study highlights the continual evolution of metagenomic tools with the goal of improving metagenomic analysis and highlights the potential of the Moonbase pipeline.
A UTO P EPTIDE ML: A UTOMATED M ACHINE L EARNING FOR B UILDING T RUSTWORTHY P EPTIDE B IOACTIVITY P REDICTORS

Automated machine learning (AutoML) solutions can bridge the gap between new computational advances and their real-world applications by enabling experimental scientists to build trustworthy models. Here, we consider the design of such a tool for developing peptide bioactivity predictors. We analyse different design choices concerning data acquisition and negative class definition, homology partitioning for the construction of independent evaluation sets, the use of protein language models as a general sequence representation method, and model selection and hyperparameter optimisation. Finally, we integrate the conclusions drawn from this study into AutoPeptideML, an end-to-end, user-friendly application that enables experimental researchers to build trustworthy models, facilitating compliance with community guidelines. The source code, documentation, and data are available in the project GitHub repository: https: //github.com/IBM/AutoPeptideML . Additionally, we have established a dedicated web-server, accessible at: http://peptide.ucd. ie/AutoPeptideML .
Insights into vision from interpretation of a neuronal wiring diagram

What insects can see has been probed by over a century of behavioral experiments. Motion and color vision have also been studied through neurophysiology in insect brains. Here I study form vision by interpreting a neuronal wiring diagram of the Drosophila optic lobe. The Dm3 “line amacrine” cells are shown to divide into three cell types with oriented dendrites, and to be connected with three TmY cell types, also with oriented dendrites. All six cell types are predicted to respond selectively to oriented visual stimuli, with preferred orientation defined by dendrite orientation. Their receptive fields are predicted by mapping input from other cell types that chiefly convey information from single facets of the compound eye. Dm3 to Dm3 and TmY connectivity is approximated by cross-orientation inhibition and TmY to TmY connectivity by iso-orientation excitation. Both connectivity motifs were previously hypothesized for mammalian visual cortex. Two of the TmY types target a novel type of LC10 cell, which leads by multiple pathways to brain regions that support learning of visual form. Based on the spatial organization of TmY to TmY and LC10 connectivity, I conjecture that flies may see illusory contours and corners.
Developing a Subjective Measure of the Quality of City Life (QCL) : The Case of Seoul*

Measuring the quality of city life (QCL) is important for city marketing given that QCL influences the city brand image and resident‐ city relationship. Despite its importance, most previous measures of community well‐being were developed in the context of small towns, and limited attention has been given to a subjective mea sure of QCL in the context of a large city. This study develops and tests a subjective measure of quality of city life (QCL) in the context of a large metropolitan city. Quality of c ity life (QCL) refers to the degree of need satisfaction and feelings of happiness one experiences during the course of city life. The results from a survey of 507 residents from 25 major districts in Seoul indicate that the QCL measure has convergent and discriminate validity. The results also indicate that QCL has predictive validity in relation to satisf action with city services, trust in the city government, word ‐of‐ mouth communication, and a sense of citizen pride. The managerial and policy implications of this study are discussed.
Arterial mechanics, extracellular matrix, and smooth muscle differentiation in carotid arteries deficient for Rac1

Stiffening of the extracellular matrix (ECM) occurs after vascular injury and contributes to the injury-associated proliferation of vascular smooth muscle cells (SMCs). ECM stiffness also activates Rac-GTP, and SMC Rac1 deletion strongly reduces the proliferative response to injury in vivo. However, ECM stiffening and Rac can affect SMC differentiation, which, in itself, can influence ECM stiffness and proliferation. Here, we used pressure myography and immunofluorescence analysis of mouse carotid arteries to ask if the reported effect of Rac1 deletion on in vivo SMC proliferation might be secondary to a Rac effect on basal arterial stiffness or SMC differentiation. The results show that Rac1 deletion does not affect the abundance of arterial collagen-I, -III, or -V, the integrity of arterial elastin, or the arterial responses to pressure, including the axial and circumferential stretch-strain relationships that are assessments of arterial stiffness. Medial abundance of alpha-smooth muscle actin and smooth muscle-myosin heavy chain, markers of the SMC differentiated phenotype, were not statistically different in carotid arteries containing or deficient in Rac1. Nor did Rac1 deficiency have a statistically significant effect on carotid artery contraction to KCl. Overall, these data argue that the inhibitory effect of Rac1 deletion on in vivo SMC proliferation reflects a primary effect of Rac1 signaling to the cell cycle rather than a secondary effect associated with altered SMC differentiation or arterial stiffness.
Pipe flow through a fractal orifice

Direct numerical simulations (DNS) in combination with an immersed boundary (IB) method have been used for the study of a pipe flow through different orifice plates. Test simulations have been performed for the validation of a plain turbulent pipe flow at a Reynolds number of Re = 5300. The addition of an orifice plate causes the flow structure to change, depending on the type of flow that is used. Simulations have been performed with five different orifice geometries for a laminar flow, Re = 1, and a turbulent flow, Re = 4300. The orifices have a porosity of 0.4 and exhibit the shape of a circle, a square and the first three generations of the Koch snowflake. In the case of a laminar flow, the viscous forces are significant in a relative large area close to the walls, causing the largest axial velocities at the center of the pipe. The geometries with the largest perimeter exhibit the largest centerline velocity and the largest pressure drop. Turbulent flow simulations show high velocities close to the wall slightly before and inside the orifice plate. Behind the orifice plate, the amount of backflow and forward traveling flow is the largest for the circular orifice which probably causes the highest turbulent kinetic energy and the largest pressure drop. Besides the flow structure, the mixing properties are studied by inserting circular contours of passive particles. The evolution of the contour generates information about the stretchand fold mechanism around the different orifice plates.
CONSERVATION OF POLISH RED CATTLE

Polish Red cattle are the most conserved breed of cattle in Poland. The current population of Polish Red cows is estimated to be approximately 30000, of which only 1321 animals accounted for the active population in the year 2005. of these, approximately 500 cows (spread over 60 farms) are included in the genetic resources conservation programme. This survey was conducted among 100 breeders of Polish Red cattle, 94 of them were from the Malopolska region. Average area of surveyed farms was 44.2 ha, but this value was overstated by 3 farms with areas of 700, 260 and 160 ha respectively. However, the overwhelming majority of farms (84%) were small ones with area of less than 20 ha. Also, majority of all farms (79%)) had less than 20 Polish Red cows. Among the farms availing the “Conservation of Farm Animal Breeds” package, the overwhelming majority (92%) had up to 10 cows only. And cattle were the only animal species reared in majority of farms (63) most of which (92%) also had other cattle breeds (mainly Polish Holstein-Friesian of Black-and-White and Red-and-White variety). The farms surveyed represent the future of Polish Red cattle breeding in Poland which are largely dependent on government subsidies. In case subsidies were lifted or even limited, as many as 80% of the farmers were of the opinion to abandon Polish Red cows in favour of breeds that are more efficient and economically profitable.
Gender and Collaboration

We document persistent gender disparities in economics. The fraction of women in economics has grown significantly over the last forty years but the difference in research output between men and women remains large. There are significant differences in the co-authorship networks of men and women: women have fewer collaborators, collaborate more often with the same co-authors, and a higher fraction of their co-authors are co-authors of each other. Both men and women exhibit homophily in their co-authorship relations. Finally, women collaborate with more senior co-authors. Similar output and collaboration patterns obtain in sociology. JEL Codes: D8, D85, J7, J16, O30
Effect of Implementing Indwelling Urinary Catheter Maintenance Care Nursing Guidelines on Catheter Associated Urinary Tract Infection Occurence in Intensive Care Unit

: Catheter Associated Urinary Tract Infection (CAUTI) is widespread Health Acquired Infection that influence patient’s welfare and duration of hospitalization. Aim: Determine effect of implementing Indwelling Urinary Catheter (IUC) maintenance nursing care guidelines on CAUTI occurance in intensive care unit (ICU). Design: A quasi-experimental design pretest and post-test phase was used . Setting: The study was conducted in ICU affiliated to Suez Canal University Hospital. Tools : Three tools utilized in this study; nurses’ knowledge questionnaire regarding IUC maintenance nursing care guidelines, nurses´ practice e observational checklist and patient observational assessment sheet. Result: The nurses total score for both knowledge and practice improved significantly after implementation of IUC maintenance nursing care guidelines (p-value= 000). Also, nurses’ knowledge and practice founded to be correlated positively to each other during both pretest phase and post-test phase (p-value= .000, .006) respectively. Improving nurses´ practice to more than one-fold result in decreasing CAUTI from decrease from 54.48 to 31.9 per 1000 catheter day. Conclusion: IUC maintenance nursing care guidelines enhance nurses’ knowledge and practice and decrease CAUTI rate in Suez Canal University Hospital ICU.
Fabrication and testing of crop waste Ceiba Pentandra Shell Powder reinforced biodegradable composite �lms

Ceiba Pentandra Shell Powder (CPSP) bio waste is chosen as a bio �ller combined with Polyvinyl Alcohol (PVA) as a matrix to make bio�lms to increase the exploitation of bio waste materials and reduce the use of plastic materials. The fabricated bio�lms endured the structural, thermal, microstructural, mechanical, UV barrier, opacity, water absorption, and soil burial properties. FTIR plots indicated no signi�cant chemical reaction or formation of new functional groups during an interaction between PVA and CPSP. XRD diffractograms represented the crystallinity index (35.3, 38.6, 42.3, 46.4 and 48.5%) and crystalline size (18.14, 20.89, 23.23, 24.87and 26.34 nm) of bio�lms increased with CPSP loading (5–25 wt. %). The PVA/CPSP �lms are thermally stable up to 322 ℃ . The peak highs of AFM images showed that the �lms surface roughness gradually increased from 94.75 nm (5 wt. % CPSP) to 320.17 nm (25 wt. % CPSP). The FESEM micrographs clarify the homogenous distribution of CPSP materials in the PVA matrix. Tensile strength and tensile modulus are noticeably increased by 26.32% and 37.92%, respectively, due to the loading of CPSP from 5 wt. % to 20 wt. % in the PVA matrix. The PVA/CPSP �lms outperform than pure PVA �lms in UV shielding (350–450 nm). The 59% of weight loss of �lms was estimated during 60 days of burial time. Overall, PVA/ CPSP (5–25 wt. %) �lms are biodegradable and have promising applications as good packaging material.
Feeding Impact of Yellow Maize Variety “Pool 8A” On Egg Production in Layers

: An experiment was carried out at Rubirizi farm in the College of Agriculture Animal Science and veterinary Medicine (CAVM) of the University of Rwanda, to evaluate the effects of feeding a yellow maize variety pool 8A based-diet on egg production in layers. A total number of 60 pullets were randomly divided into two lots of 30 pullets, and each lot was made of three sub-groups of ten pullets arranged in a complete randomized design and data were collected during ten weeks from July to October 2013. The parameters studied were the laying rate, feed conversion ratio, feed intake, rate of broken eggs, and weight of eggs, and egg yolk colour index. The inclusion ratio of both types of maize (white and yellow) was the same (47%) and all other ingredients were similar in two ration formulation. A proximate analysis of both maize based-diets and eggs produced was carried out in laboratory of CAVM-Busogo campus. Data were analyzed using GenStat with a one-way ANOVA. The proximate analysis revealed that yellow maize recorded high protein content (9.18%) than white maize (7.48%). Pullets fed with yellow maize based-diet recorded an average weekly laying rate of 89.7% while those fed on white maize recorded 87% but the difference were not significant (P>0.05). There was no significant difference (P>0.05) between the average daily feed intake of 110.7g/day/hen for white maize based-diet while it was 110.2g/day/hen. The feed conversion ratio tended to be the same, 2.2 for pullets fed on yellow maize based-diet and 2.3 for those fed on white maize based-diet. Eggs from layers fed with a yellow maize based-diet had a higher yolk colour score (8= yellow) than those from white maize based-diet (11= pale yellow) index evaluated using colour charts comparison.