Miracle-dz/UniFAR-FTUs huggingface dataset:
India’s Burgeoning Food Subsidies: How Much can we Blame the Food Corporation of India?

The Food Subsidy Bill of the Government of India has increased manifold in the past decades. The Food Corporation of India (FCI) is responsible for ensuring that the subsidy reaches both the producers through the support prices and to the consumers through the Public Distribution System (PDS). The high economic costs of the Food Corporation, along with low PDS prices contributes to the rising food subsidy bill. Some parts of this economic costs are within the purview of the FCI while others are completely outside its domain. Hence this paper attempts to ascertain the factors leading to the increasing food subsidy and the extent to which these are attributable to the FCI. We find that, in fact, some of the major components of the economic costs, which are leading to rising food subsidy, are not within the control of the FCI and to that extent, the parastatal can be absolved of the blame. The villain of the piece appears to be the support price policy of the government and some components of the economic cost of FCI, which are outside the purview of the FCI. The paper also delves into analysing the cost components of FCI in an attempt to assess the performance of the parastatal itself. Sussidi alimentari crescenti in India: quanto possiamo ritenere responsabile la Food Corporation of India? Il Food Subsidy Bill del governo indiano e cresciuto secondo molte modalita negli ultimi decenni. La Food Corporation of India (FCI) e responsabile della destinazione dei sussidi affinche siano assegnati ai produttori attraverso il sostegno ai prezzi ed ai consumatori tramite il Public Distribution System (PDS). Gli elevati costi della Food Corporation, insieme ai bassi prezzi del PDS, contribuiscono al sorgere del conto sussidi agli alimentari. Parte di questi costi rientrano nelle competenze della Food Corporation, mentre altri sono completamente al di la del suo ambito di attivita. A questo proposito questo lavoro cerca di individuare i fattori che portano ad un incremento dei sussidi alimentari e in che misura questi fattori siano attribuibili alla Food Corporation. Sono state riscontrate evidenze che alcune componenti dei costi che causano gli elevati sussidi non rientrano tra le competenze della Food Corporation e di conseguenza l’ente statale non ne puo essere ritenuto responsabile. I responsabili sembrerebbero essere la politica di sostegno ai prezzi condotta dal governo e alcune componenti di costo che sono al di fuori delle competenze della Corporation stessa. Questo studio approfondisce anche l’analisi delle componenti di costo della Food Corporation nel tentativo di valutare l’efficienza dell’ente stesso.
Estimating Waiting Distances Between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent

Genomes are composed of a mosaic of segments inherited from different ancestors, each separated by past recombination events. Consequently, genealogical relationships among multiple genomes vary spatially across different genomic regions. Expectations for the amount of genealogical variation among unlinked (uncorrelated) genomic regions is well described for either a single population (coalescent) or multiple structured populations (multispecies coalescent). However, the expected similarity among genealogies at linked regions of a genome is less well characterized. Recently, an analytical solution was derived for the expected distribution of waiting distances between changes in genealogical trees spatially across a genome for a single population with constant effective population size. Here we describe a generalization of this result, in terms of the expected distribution of waiting distances between changes in genealogical trees and topologies, for multiple structured populations with branch-specific effective population sizes (i.e., under the multispecies coalescent). Our solutions establish an expectation for genetic linkage in multispecies datasets and provide a new likelihood framework for linking demographic models with local ancestry inference across genomes.
Bayesian inference reveals a complex evolutionary history of belemnites

Belemnites are an extinct group of Mesozoic coleoid cephalopods, common in Jurassic and Cretaceous marine sedimentary rocks. Despite their significance, their total group phylogeny has rarely been considered in recent decades. In contrast, most researchers restricted the assignment of families to one of the two usually recognized subgroups, the Belemnitina and the Belemnopseina. As for many fossil cephalopods, researchers have been reluctant to employ modern phylogenetic methods to illuminate belemnites’ evolutionary history. To overcome the “dead end” of belemnite systematics, we performed the first tip-dated Bayesian analysis of belemnite phylogeny. In our analysis, the Aulacoceratida are found as the monophyletic sister group to belemnites. The Sinobelemnitidae are resolved as paraphyletic and fall outside the Belemnitina and Belemnopseina, which make up the remaining belemnites. Belemnitina is restricted to Jurassic species with generally no or apical furrows. Holcobelidae are the earliest branching Belemnopseina. Cylindroteuthids sensu lato (including Oxyteuthidae) are nested within Belemnopseina, contrary to the common hypothesis placing them within the Belemnitina. Duvaliidae and Dicoelitidae are recovered as members of the Belemnopseina, but their precise relationship has to be evaluated based on more taxa and additional characters. We introduce the well-supported unranked clade Pseudoalveolata, which includes Dimitobelidae, Belemnitellidae, and members of the paraphyletic “Belemnopseidae”. The phylogeny presented here, based on reproducible and quantitative methods, contrasts with the usually applied authoritative “stratophenetic” approach to belemnite systematics, based on the overemphasis of single characters. This result is considered the basis for future studies on belemnite phylogeny, allowing for a rigorous testing of evolutionary hypotheses. PLAIN LANGUAGE SUMMARY Belemnites were common extinct cephalopods that were closely related to today’s squid and cuttlefish. The most common fossil remains of belemnites are bullet-shaped calcitic “cones” (rostrum) that cover their internal shells. Belemnites’ evolutionary history is not well known. Our study revealed an evolutionary tree of belemnites based on the statistical analysis of morphological features of the rostrum and calibrated to the known geological ages of the studied belemnite species. This approach was for the first time applied to belemnites and changed several aspects that were believed about their evolution.
Synergistic anti-phage activity of bacterial defence systems

Bacterial defence against phage predation involves diverse defence systems acting both individually and concurrently, yet their interactions remain poorly understood. We investigated >100 defence systems in 42,925 bacterial genomes and identified numerous instances of their non-random co-occurrence and mutual exclusion. For several pairs of defence systems significantly co-occurring in Escherichia coli strains, we demonstrate synergistic anti-phage activity, including tmn synergising with defence systems containing sensory switch ATPase domains. Some of the defence system pairs that are mutually exclusive in E. coli significantly co-occur in other taxa, and one tested mutually exclusive pair showed synergy. These findings demonstrate compatibility and synergy between defence systems, allowing bacteria to adopt flexible strategies for phage defence, driven by specific environmental pressures. The evolution of bacterial immune repertoires seems to be shaped largely by selection for resistance to host-specific phages rather than by negative epistasis.
CRISPRa screen identifies a role for c-KIT signaling in tamoxifen resistance, potentially through upregulation of ABC transporters

Resistance to endocrine therapy is a common problem in patients with estrogen receptor alpha (ERα) positive breast cancer. In this study, we took a non-biased genome-wide approach to identify novel mechanisms of endocrine resistance using a clustered regularly interspaced short palindromic repeats (CRISPR) activating (CRISPRa) screen. Results from the screen identified 109 candidate resistance-associated genes, with several of these genes, such as EGFR and SRC, having been previously associated with endocrine resistance. One candidate gene that has not been previously associated with endocrine resistance is the tyrosine kinase receptor, c-KIT. We further tested for associations between c-KIT and endocrine resistance and found that c-KIT overexpressing cells proliferate more rapidly in the presence of tamoxifen compared to control cell lines. To gain deeper insight into the potential role of c-KIT signaling in tamoxifen resistance, we next performed precision nuclear run-on and sequencing (PRO-seq) analysis of c-KIT overexpressing cells to identify downstream factors that may mediate the c-KIT response. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the overexpressed genes found that the only class of factors that was significantly induced by c-KIT was the ATP-binding cassette (ABC) transporters; specifically, ABCA1, ABCA4, and ABCG1. Interestingly, overexpression of two of these ABC transporters, ABCA1 and ABCG1, significantly correlated with worse prognosis in ERα+ breast cancer patients following endocrine therapy. We then tested for potential therapeutic effects of c-KIT inhibition on endocrine resistance and found that the c-KIT inhibitor Gleevec appears to synergize with tamoxifen to suppress MCF-7-S cell growth. Together, our findings support the hypothesis that c-KIT signaling promotes endocrine resistance via the induction of ABC transporter activity. Additionally, our studies suggest that inhibition of c-KIT signaling may represent a novel strategy for preventing or overcoming endocrine resistance in ERα+ patients.
Investigating the human and nonobese diabetic mouse MHC class II immunopeptidome using protein language modeling

Identifying peptides associated with the major histocompability complex class II (MHCII) is a central task in the evaluation of the immunoregulatory function of therapeutics and drug prototypes. MHCII-peptide presentation prediction has multiple biopharmaceutical applications, including the safety assessment of biologics and engineered derivatives in silico, or the fast progression of antigen-specific immunomodulatory drug discovery programs in immune disease and cancer. This has resulted in the collection of large-scale data sets on adaptive immune receptor antigenic responses and MHC-associated peptide proteomics. In parallel, recent deep learning algorithmic advances in protein language modelling (PLM) have shown potential in leveraging large collections of sequence data and improve MHC presentation prediction. Here, we train a compact transformer model (AEGIS) on human and mouse MHCII immunopeptidome data, including a preclinical murine model, and evaluate its performance on the peptide presentation prediction task. We show that the transformer performs on par with existing deep learning algorithms and that combining datasets from multiple organisms increases model performance. We trained variants of the model with and without MHCII information. In both alternatives, the inclusion of peptides presented by the I-Ag7 MHC class II molecule expressed by the non-obese diabetic (NOD) mice enabled for the first time the accuratein silico prediction of presented peptides in a preclinical type 1 diabetes model organism, which has promising therapeutic applications. 0.1 Availability and implementation The source code is available at https://github.com/Novartis/AEGIS.
Contrasting effects of Ksr2, an obesity gene, on trabecular bone volume and bone marrow adiposity

Pathological obesity and its complications are associated with an increased propensity for bone fractures. Humans with certain genetic polymorphisms at the kinase suppressor of ras2 (Ksr2) locus develop severe early-onset obesity and type 2 diabetes (T2D). Both conditions are phenocopied in mice with Ksr2 deleted, but whether this affects bone health remains unknown. Here we studied the bones of global Ksr2 null mice and found that Ksr2 negatively regulates femoral, but not vertebral, bone mass in two genetic backgrounds, while the paralogous gene, Ksr1, was dispensable for bone homeostasis. Mechanistically, KSR2 regulates bone formation by influencing adipocyte differentiation at the expense of osteoblasts in the bone marrow. Compared with Ksr2’s known role as a regulator of feeding by its function in the hypothalamus, pair feeding and osteoblast-specific conditional deletion of Ksr2 reveals that Ksr2 can regulate bone formation autonomously. Despite the gains in appendicular bone mass observed in absence of Ksr2, bone strength, as well as fracture healing response remains compromised in these mice. This study highlights the interrelationship between adiposity and bone health and provides mechanistic insights into how Ksr2, an adiposity and diabetic gene, regulates bone metabolism.
Contributions of adaptation and purifying selection to SARS-CoV-2 evolution

Continued evolution and adaptation of SARS-CoV-2 has lead to more transmissible and immune-evasive variants with profound impact on the course of the pandemic. Here I analyze the evolution of the virus over 2.5 years since its emergence and estimate rates of evolution for synonymous and non-synonymous changes separately for evolution within clades – well defined mono-phyletic groups with gradual evolution – and for the pandemic overall. The rate of synonymous mutations is found to be around 6 changes per year. Synonymous rates within variants vary little from variant to variant and are compatible with the overall rate of 7 changes per year (or 7.5 × 10−4 per year and codon). In contrast, the rate at which variants accumulate amino acid changes (non-synonymous mutation) was initially around 12-16 changes per year, but in 2021 and 2022 dropped to 6-9 changes per year. The overall rate of non-synonymous evolution, that is across variants, is estimated to be about 26 amino acid changes per year (or 2.7 × 10−3 per year and codon). This strong acceleration of the overall rate compared to within clade evolution indicates that the evolutionary process that gave rise to the different variants is qualitatively different from that in typical transmission chains and likely dominated by adaptive evolution. I further quantify the spectrum of mutations and purifying selection in different SARS-CoV-2 proteins and show that the massive global sampling of SARS-CoV-2 is sufficient to estimate site specific fitness costs across the entire genome. Many accessory proteins evolve under limited evolutionary constraint with little short term purifying selection. About half of the mutations in other proteins are strongly deleterious.
No evidence for cognitive impairment in an experimental rat model of knee osteoarthritis and associated chronic pain

Although chronic pain states have been associated with impaired cognitive functions, including memory and cognitive flexibility, the cognitive effects of osteoarthritis (OA) pain remain to be clarified. The aim of this study was to measure cognitive function in the mono-iodoacetate (MIA) rat model of chronic OA-like knee pain. We used young adult male Lister hooded rats, which are well suited for cognitive testing. Rats received either a unilateral knee injection of MIA (3mg/50µL) or saline as control. Joint pain at rest was assessed for up to 12 weeks using weight-bearing asymmetry, and referred pain at a distal site using determination of hindpaw withdrawal thresholds (PWT). The watermaze delayed-matching-to-place (DMP) test of rapid place learning, novel object recognition (NOR) memory assay and an operant response-shift and -reversal task were used to measure memory and behavioural flexibility. Open field locomotor activity, startle response, and prepulse inhibition (PPI) were also measured for comparison. MIA-injected rats showed markedly reduced weight-bearing on the injured limb, as well as pronounced cartilage damage and synovitis, but interestingly no changes in PWT. Rearing was reduced, but otherwise locomotor activity was normal and no changes in startle and PPI were detected. MIA-injected rats had intact watermaze DMP performance, suggesting no substantial change in hippocampal function, and there were no changes in NOR memory or performance on the operant task of behavioural flexibility. Our finding that OA-like pain does not alter hippocampal function, unlike other chronic pain conditions, is consistent with human neuroimaging findings.
Extreme sex chromosome differentiation, likely driven by inversion, contrasts with mitochondrial paraphyly between species of crowned sparrows

Sympatric species pairs provide researchers with the opportunity to study patterns of genomic differentiation during the late stages of speciation and to identify the genomic regions underlying reproductive isolation. The Golden-crowned Sparrow (Zonotrichia atricapilla) and the White-crowned Sparrow (Zonotrichia leucophrys) are broadly sympatric songbirds found in western North America. These sister species are phenotypically differentiated and largely reproductively isolated despite possessing similar mitochondrial genomes, likely due to recent mitochondrial introgression. We used a genotyping-by-sequencing (GBS) approach to determine the structure of nuclear genomic differentiation between these species and also between two hybridizing subspecies of Z. leucophrys, across more than 45,000 single nucleotide polymorphisms (SNPs). The two Z. leucophrys subspecies showed moderate levels of relative differentiation, as well as patterns consistent with a history of recurrent selection in both ancestral and daughter populations. Z. leucophrys and Z. atricapilla show high levels of relative differentiation and strong heterogeneity in the level of differentiation among different chromosomal regions, with a large portion of the Z chromosome showing highly elevated differentiation. Patterns of relative and absolute differentiation and linkage disequilibrium suggest a large inversion on the Z chromosome, with inversion haplotypes that segregate between Z. atricapilla and Z. leucophrys. While mitochondrial DNA differentiation is often emphasized in studies of speciation, differentiation between these Zonotrichia sparrows appears to have occurred first in the Z chromosome and secondarily in autosomes, followed by mitochondrial introgression. This putative inversion has implications for reproductive isolation between these species and adds to a growing body of evidence for the importance of inversions and the Z chromosome in speciation.
New relationships are not necessarily more variable: female degus are more consistent with strangers, male degus are less

When an organism explores a new environment or stimulus it varies its behavior to ensure proper sampling. As contingencies are learned, variance can give-way to routines and stereotypies. This phenomenon is common across species but has not been well studied in the social domain, in which the stimulus an animal investigates, another individual, may react negatively to unexpected behaviors. Here we investigate the effects of social familiarity on interaction variability in degus, female members of which are predisposed to form relationships with new, same-sex individuals. Degus were presented with a series of 20 minute, dyadic “reunion” sessions across days, interleaving exposures to familiar and unfamiliar same-sex conspecifics. We found that session-to-session variability in males was higher between strangers compared with cagemates, suggesting males may establish relationships by testing different social roles. In contrast, following an initial exposure, female strangers showed lower session-to-session change compared with cagemates, potentially establishing new relationships by maintaining behavioral norms. Social novelty did not appear to affect variability of interaction timing within a session. Given ecological pressures on female degus to form large, stable social networks, the data are consistent with the notion that higher behavioral variability across encounters is maladaptive for establishing cooperative peer relationships.
Power laws govern the abundance distribution of birds by rank

Only a few bird species are abundant. According to new data, a log left-skewed distribution, rather than a lognormal distribution, better adjusts to the abundance distribution of bird species. We look at the rank abundance distribution rather than the species abundance distribution and find three power laws that fit the tails using the same data.
In Vitro and In Vivo Activity of Gepotidacin against Drug-Resistant Mycobacterial Infections

Mycobacterial pathogens, including nontuberculous mycobacteria (NTM) and Mycobacterium tuberculosis, are pathogens of significant worldwide interest owing to their inherent drug resistance to a wide variety of FDA-approved drugs as well as causing a broad range of serious infections. Identifying new antibiotics active against mycobacterial pathogens is an urgent unmet need, especially those antibiotics that can bypass existing resistance mechanisms. ABSTRACT Mycobacterial pathogens, including nontuberculous mycobacteria (NTM) and Mycobacterium tuberculosis, are pathogens of significant worldwide interest owing to their inherent drug resistance to a wide variety of FDA-approved drugs as well as causing a broad range of serious infections. Identifying new antibiotics active against mycobacterial pathogens is an urgent unmet need, especially those antibiotics that can bypass existing resistance mechanisms. In this study, we demonstrate that gepotidacin, a first-in-class triazaacenapthylene topoisomerase inhibitor, demonstrates potent activity against M. tuberculosis and M. fortuitum, as well as against other clinically relevant NTM species, including fluoroquinolone-resistant M. abscessus. Furthermore, gepotidacin exhibits concentration-dependent bactericidal activity against various mycobacterial pathogens, synergizes with several drugs utilized for their treatment, and reduces bacterial load in macrophages in intracellular killing assays comparably to amikacin. Additionally, M. fortuitum ATCC 6841 was unable to generate resistance to gepotidacin in vitro. When tested in a murine neutropenic M. fortuitum infection model, gepotidacin caused a significant reduction in bacterial load in various organs at a 10-fold lower concentration than amikacin. Taken together, these findings show that gepotidacin possesses a potentially new mechanism of action that enables it to escape existing resistance mechanisms. Thus, it can be projected as a potent novel lead for the treatment of mycobacterial infections, particularly for NTM, where present therapeutic interventions are extremely limited.