Miracle-dz/UniFAR-FTUs huggingface dataset:
GOThresher: a program to remove annotation biases from protein function annotation datasets

Motivation Advances in sequencing technologies have led to a surge in genomic data, although the functions of many gene products coded by these genes remain unknown. While in-depth, targeted experiments that determine the functions of these gene products are crucial and routinely performed, they fail to keep up with the inflow of novel genomic data. In an attempt to address this gap, high-throughput experiments are being conducted in which a large number of genes are investigated in a single study. The annotations generated as a result of these experiments are generally biased towards a small subset of less informative Gene Ontology (GO) terms. Identifying and removing biases from protein function annotation databases is important since biases impact our understanding of protein function by providing a poor picture of the annotation landscape. Additionally, as machine learning methods for predicting protein function are becoming increasingly prevalent, it is essential that they are trained on unbiased datasets. Therefore, it is not only crucial to be aware of biases, but also to judiciously remove them from annotation datasets. Results We introduce GOThresher, a Python tool that identifies and removes biases in function annotations from protein function annotation databases. Implementation and Availability GOThresher is written in Python and released via PyPI https://pypi.org/project/gothresher/ and on the Bioconda Anaconda channel https://anaconda.org/bioconda/gothresher. The source code is hosted on GitHub https://github.com/FriedbergLab/GOThresher and distributed under the GPL 3.0 license. Contact {idoerg@iastate.edu | parnal@iastate.edu}
Origin of the Rare Hybrid Genus ×Trisetokoeleria Tzvelev (Poaceae) According to Molecular Phylogenetic Data

In our article, we analyzed new data on the origin of the hybrid genus ×Trisetokoeleria. According to the morphological criteria ×T. jurtzevii is a hybrid between Koeleria asiatica s. l. and Trisetum spicatum, ×T. taimyrica, and originated from Koeleria asiatica s. l. and Trisetum subalpestre, ×T. gorodkowii, a hybrid between Koeleria asiatica and Trisetum ruprechtianum. Later ×T. taimyrica was transferred to Koeleria. Parental taxa are prone to active hybridization themselves, thus, new methods of next-generation sequencing (NGS) were needed to clarify the relationships of these genera. For NGS we used the fragment 18S rDNA (part)–ITS1–5.8S rDNA (totally 441 accessions). We analyzed ITS1–5.8S rDNA–ITS2 region, trnL–trnF and trnK–rps16 from eight samples of the five species, using the Sanger method: ×Trisetokoeleria jurtzevii, ×T. taimyrica, Koeleria asiatica, Sibirotrisetum sibiricum (=Trisetum sibiricum), and Trisetum spicatum. We also studied the pollen fertility of ×Trisetokoeleria and its possible progenitors. Our data partly contradicted previous assumptions, based on morphological grounds, and showed us a picture of developed introgression within and between Koeleria and Trisetum. ×T. jurtzevii, a totally sterile hybrid formed rather recently. We can suppose that ×T. jurtzevii is a hybrid between K. asiatica and some Trisetum s. str. Species, but not T. spicatum. ×T. gorodkowii, a hybrid in the stage of primary stabilization; it has one unique ribotype related to T. spicatum s. l. The second parental species is unrelated to Trisetum ruprechtianum. ×T. taimyrica and is a stabilized hybrid species; it shares major ribotypes with the T. spicatum/T. wrangelense group and has a minor fraction of rDNA related to genus Deyeuxia s. l.
The Prevalence and Lived Experience of Pain in People Undertaking Dialysis

(1) Background: Pain is a prevalent and debilitating symptom associated with kidney failure. However, the impact of pain on quality of life remains unclear. We aimed to identify the prevalence, severity and characteristics of people undertaking dialysis impacted by pain and explore the lived experience of pain (2) Methods: A cross-sectional survey was administered to people undertaking haemodialysis or via telephone to those undertaking peritoneal and home haemodialysis in a single tertiary centre. Open-ended questions were analysed using thematic analysis. (3) Results: Responses were received from 131 participants (response rate 66.8%). Most were undergoing haemodialysis (87.0%). Pain was present in 92% (n = 121) of patients with 62% (n = 81) reporting pain as severe to excruciating. Common sites of pain were joints, muscle cramps, headaches, fistula pain, non-specific back pain and neuropathy. The overarching theme from the thematic analysis was that pain was a “debilitating and accepted burden” (4) Conclusions: Pain is highly prevalent, severe and debilitating in those on dialysis. There is a need for health care providers to be proactive and attentive to the management of pain. More research is needed to identify effective treatment approaches to decrease pain burden and improve the quality of life in those with kidney failure.
Cache-Efficient Approach for Index-Free Personalized PageRank

Personalized PageRank (PPR) measures the importance of vertices with respect to a source vertex. Since real-world graphs are evolving rapidly, PPR computation methods need to be index-free and fast. Unfortunately, existing index-free methods suffer from cache misses. They follow the state-of-the-art algorithm that first performs the Forward Push (FP) phase and subsequently runs the random walk Monte-Carlo simulation (MC) phase. Although existing methods succeed in reducing cache misses in the FP phase, an inefficient data layout limits their performance improvement. Besides, existing methods have overlooked the importance of reducing cache misses in the MC phase. In this paper, we propose a cache-efficient approach that accelerates both FP and MC phases. In the FP phase, we first reorder the data layout with low overheads. Specifically, we utilize the Breadth First Search result so that vertices near the source vertex are co-located on the reordered data layout. We subsequently perform optimized FP, namely Distance-Extension Forward Push (DEFP). By preferentially proceeding FP around the source vertex, DEFP improves memory access locality. In the MC phase, we perform optimized MC, namely Vertex-Centric Random Walk (VCRW). VCRW aggregates random walks at each vertex to eliminate redundant memory access for repeatedly obtaining neighbor vertices. We prove that most of the random walks can be aggregated while maintaining accuracy guarantees. Experimental results show that the proposed method is up to 4.7x faster than existing index-free methods and outperforms the state-of-the-art index-oriented method under rigorous accuracy guarantees.
Testing Long-Run Neutrality

Propositions about long run neutrality are at the heart of most macroeconomic models. Yet, since the 1970's when Lucas and Sargent presented powerful critiques of traditional neutrality tests, empirical researchers have made little progress on testing these propositions. In this paper we show that. in spite of the Lucas-Sargent critique. long run neutrality can be tested without specifying a complete model of economic activity. This is possible when the variables are integrated. In this case, permanent shifts in the historical data can be uncovered using VAR methods, and neutrality can be tested when there is a priori knowledge of one of the structural impact multipliers or one of the structural long run multipliers. In most circumstances such a priori knowledge is available. We use this framework to test four long run neutrality propositions: (i) the neutrality of money, (ii) the superneutrality of money. (iii) a vertical long run Phillips curve, and (iv) the Fisher effect. In each application, our a priori knowledge consists of a range of plausible values for the relevant impact and long run multipliers. We find that the U.S. postwar data are consistent with the neutrality of money and a vertical long run Phillips curve. but find evidence against the superneutrality of money and the long run Fisher relation. The sign of the estimated effect of money growth on output depends on the particular identifying assumption used. For a wide range of plausible identifying restrictions, nominal interest rates are found to move less than one-for-one with inflation in the long run. (This abstract was borrowed from another version of this item.) (This abstract was borrowed from another version of this item.) (This abstract was borrowed from another version of this item.) (This abstract was borrowed from another version of this item.) (This abstract was borrowed from another version of this item.) (This abstract was borrowed from another version of this item.)
Water-rich Disks around Late M Stars Unveiled: Exploring the Remarkable Case of Sz 114

We present an analysis of the JDISCS JWST/MIRI-MRS spectrum of Sz 114, an accreting M5 star surrounded by a large dust disk with a shallow gap at ∼39 au. The spectrum is molecule-rich; we report the detection of water, CO, CO2, HCN, C2H2, and H2. The only identified atomic/ionic transition is from [Ne ii] at 12.81 μm. A distinct feature of this spectrum is the forest of water lines with the 17.22 μm emission surpassing that of most mid-to-late M star disks by an order of magnitude in flux and aligning instead with disks of earlier-type stars. Moreover, the flux ratios of C2H2/H2O and HCN/H2O in Sz 114 also resemble those of earlier-type disks, with a slightly elevated CO2/H2O ratio. While accretional heating can boost all infrared lines, the unusual properties of Sz 114 could be explained by the young age of the source, its formation under unusual initial conditions (a large massive disk), and the presence of dust substructures. The latter delays the inward drift of icy pebbles and helps preserve a lower C/O ratio over an extended period. In contrast, mid-to-late M-star disks—which are typically faint, small in size, and likely lack significant substructures—may have more quickly depleted the outer icy reservoir and already evolved out of a water-rich inner disk phase. Our findings underscore the unexpected diversity within mid-infrared spectra of mid-to-late M-star disks, highlighting the need to expand the observational sample for a comprehensive understanding of their variations and thoroughly test pebble drift and planet formation models.
Relationship between Serum and Brain Carotenoids , α-Tocopherol , and Retinol Concentrations and Cognitive Performance in the Oldest Old from the Georgia Centenarian Study

Citation Johnson, E. J., R. Vishwanathan, M. A. Johnson, D. B. Hausman, A. Davey, T. M. Scott, R. C. Green, et al. 2013. “Relationship between Serum and Brain Carotenoids, α-Tocopherol, and Retinol Concentrations and Cognitive Performance in the Oldest Old from the Georgia Centenarian Study. ” Journal of Aging Research 2013 (1): 951786. doi:10.1155/2013/951786. http://dx.doi. org/10.1155/2013/951786.
Monitoring Tools and Strategies for Effective Electrokinetic Nanoparticle Treatment

Nanoparticles are increasingly being used by industry to enhance the outcomes of various chemical processes. In many cases, these processes involve over-dosages that compensate for particle losses. At best, these unique waste streams end up in landfills. This circumstance is inefficient and coupled with uncertain impacts on the environment. Pozzolanic nanoparticle treatments have been found to provide remarkable benefits for strength restoration and the mitigation of durability problems in ordinary Portland cement and concrete. These treatments have been accompanied by significant particle losses stemming from over-dosages and instability of the colloidal suspensions that are used to deliver these materials into the pore structure. In this study, new methods involving simple tools have been developed to monitor and sustain suspension stability. Turbidity measurement was introduced to monitor the progress of electrokinetic nanoparticle treatment. This tool made it possible to amend a given dosing strategy in real time while it remains possible to make effective treatment adjustments. By monitoring the particle stability and using pH and electric field controls to avoid suspension collapse, successful electrokinetic treatment dosage strategies were demonstrated using 20 nm NALCO 1056 alumina-coated silica particles. These trials indicated that turbidity measurements could track the visually imperceptible phenomena of particle flocking early on at the inception of its development. Suspensions of these nanoparticles were successfully delivered into 5 cm diameter by 10 cm tall hardended cement paste (HCP) specimens by monitoring fluid turbidity along with the specific gravity and using these values to guide the active management of the treatment dosage and pH. Under this new strategy, these losses were reduced to 5% as compared to the 80% losses associated with other treatment approaches. The relationship between the turbidity and the specific gravity was found to be linear. These plots indicated regions of turbidity and specific gravity that were associated with particle flocking. The tools, guidelines, and strategies developed in this work made it possible to manage efficient (low-particle-loss) electrokinetic nanoparticle treatments by signaling in real time when adjustments to electric field, pH, and particle dosage increments were needed.
In Silico Prediction of Physicochemical Properties

This report provides a critical review of computational models, and in particular (quantitative) structure-property relationship (QSPR) models, that are available for the prediction of physicochemical properties. The emphasis of the review is on the usefulness of the models for the regulatory assessment of chemicals, particularly for the purposes of the new European legislation for the Registration, Evaluation, Authorisation and Restriction of CHemicals (REACH), which entered into force in the European Union (EU) on 1 June 2007. It is estimated that some 30,000 chemicals will need to be further assessed under REACH. Clearly, the cost of determining the toxicological and ecotoxicological effects, the distribution and fate of 30,000 chemicals would be enormous. However, the legislation makes it clear that testing need not be carried out if adequate data can be obtained through information exchange between manufacturers, from in vitro testing, and from in silico predictions. The effects of a chemical on a living organism or on its distribution in the environment is controlled by the physicochemical properties of the chemical. Important physicochemical properties in this respect are, for example, partition coefficient, aqueous solubility, vapour pressure and dissociation constant. Whilst all of these properties can be measured, it is much quicker and cheaper, and in many cases just as accurate, to calculate them by using dedicated software packages or by using (QSPRs). These in silico approaches are critically reviewed in this report. LIST OF ABBREVIATIONS AIT Auto-ignition temperature ANN Artifical Neural Network Dow Octanol-water distribution coefficient EC European Commission ECB European Chemicals Bureau ECETOC European Centre for Ecotoxicology and Toxicology of Chemicals EPA Environmental Protection Agency F Fugacity ratio or Fischer Statistic GSE General Solubility Equation Ka Acid Dissociation Constant (often as pKa) Koc Organic carbon coefficient – measure of soil sorption Kom Organic matter coefficient – measure of soil sorption Kow Octanol-water partition coefficient MAE Mean absolute error MP Melting point MW Molecular Weight OECD Organisation for Economic Cooperation and Development Q 2 Cross-validated R 2 measure of predictive ability QSAR Quantitative Structure-Activity Relationship QSPR Quantitative Structure-Property Relationship R 2 Coefficient of determination – measure of goodness-of-fit REACH Registration Evaluation and Authorisation of Chemicals RMS Root mean square s Standard error of the estimate Saq Aqueous solubility SMILES Simplified Molecular Line Entry system Tb Boiling point TF Flash point Tm Melting point VP Vapour pressure
How Did We Get Here: The Best Vaccines Ever Facing the Highest Public Hesitancy?

mRNA vaccine technology is the most interesting final product of decades of research. This new platform for public health is simple to transfer to low-income countries and can be used against diverse agents, including cancer. It is environmentally clean, relatively low-cost, and does not use animals for its production. Most importantly, mRNA vaccines have been highly efficacious in avoiding serious disease and death from COVID-19. Yet, at the highest point of the pandemic, many voices, including some from prominent positions, opposed their use. Similarly, the Human Papillomavirus (HPV) vaccines, which are highly effective, very safe, and probably confer long life protection against its HPV types, faced strong parents’ hesitancy. Vaccine hesitancy has been the subject of extensive research, focusing primarily on factors associated with the public, the political environment, and messaging strategies. However, the issue of unfair worldwide access to the COVID-19 vaccines has recently sparked significant debate about the vaccine industry’s role. Recent data demonstrated that the system’s perceived unfairness with the masses is behind the growing populist anti-vaccine movements worldwide. The association between populism and antivaccine attitudes has been reported at country and individual levels. The anti-science attitudes behind vaccine hesitancy emerge when the scientist is not found credible due to the suspicion that they had monetary investments in pharmaceutical companies. Here, I argue that the obscurity of the vaccine market, but also its unfairness, are important factors contributing to vaccine hesitancy. The purpose of this commentary is to stimulate a review of current market regulations and to improve its transparency and fairness, particularly in the context of public health emergencies. By doing so, a new pandemic would find us better prepared. The general population and much of the healthcare community often ignore the years of dedicated work and substantial public funding that enabled the discovery and design of vaccines. Conversely, pharmaceutical companies often over-emphasize their investments in research and development. A decade ago, Marcia Angell provided a detailed breakdown of pharmaceutical expenses, revealing that marketing and administration costs were 2.5 times higher than research and development expenses; recently, Olivier Wouters confirmed the high expenditures of the pharmaceutical industry in lobbying and political campaign contributions. In this commentary, I will present the cases of HPV and COVID-19 vaccines as examples of when vaccines, instead of being public health goods, became market goods, creating large inequities and health costs. This failure is a structural cause behind more ideological vaccine hesitancy, less studied so far.
A Hybrid Channel Access Mechanism for NR-U to Improve the Coexistence Performance

The saturated licensed spectrum is insufficient to meet the increasing demand for data traffic, which paves the path for exploring new bands. Since the unlicensed bands are free of cost, efforts are made to offload the cellular data to unlicensed bands, which results in unlicensed versions of cellular technologies. New Radio Unlicensed (NR-U) is the unlicensed version of New Radio (NR). Since anyone can access unlicensed frequency, the devices follow listen before talk (LBT) to gain access to the unlicensed band. Unlike WiFi, the dominant technology in unlicensed bands, the cellular node can not transmit data immediately after the LBT procedure. The node has to wait for the next licensed slot boundary to occur since it is scheduled technology. However, the LBT procedure can end before the occurrence of slot boundary; the period after LBT to the slot bound boundary by sending a reservation signal (RS) or staying idle using a gap. The RS approach yields high fairness with less efficiency, whereas the gap-based approach gives better fairness with comparatively less fairness. To deal with the tradeoff in fairness and efficiency, we have proposed a hybrid channel access method that uses both gap and RS approaches. In the proposed method, the duration of RS is limited by a threshold, and the RS is transmitted as fragments. The proposed method achieves 54 % to 128 % higher fairness than the gap-based approach and 10 % to 28 % than the RS-based approach for the given simulation scenario.
A contest is a strategic interaction in which players compete for a prize by making irreversible outlays. Contest models are grounded on Tullock (1980) and the most comprehensive on contest theory

1. Introduction A contest is a strategic interaction in which players compete for a prize by making irreversible outlays. Contest models are grounded on Tullock (1980) and the most comprehensive on contest theory is Konrad (2009). The point of departure of this paper is that players in a contest may have mixed motives. On one hand, participants have the interest of winning the contest and taking the prize. On the other hand, they could be better off taking part in a contest which implies some cooperative behaviour. For example, players would be better off if the waste of resources used is less pronounced than the highest possible. This might be pursued whenever the players commit themselves to cooperate. In brief, it is possible to maintain that, albeit in a contest, players may behave both competitively and cooperatively. In particular, cooperative behaviour of players depends upon the behavioural environment to which they adapt so shaping their actions. That is, players are ecologically rational as in the definition provided by Smith (2008): " […] the behavior of an individual, a market, an institution, or other social system involving collectives of individuals is ecologically rational to the degree that it is adapted to the structure of its environment […] " 1. With specific regard to contests, in the presence of a cooperative environment the competition may be prevented from becoming extremely harmful and even socially wasteful. It is worth noting that players may have an interest in cooperation even if they still retain a proper willingness to win the contest. A fitting real-life example can be drawn from managerial competition within firms. In fact, in large firms the management may apply an internal competition between workers and managers in order to assign a promotion or to promote efficiency. In the presence of the harshest competition possible, players may put excessive efforts into the contest, thereby determining a detrimental and dissipative scenario for the firm. In such a case, a competitive structure reward scheme can be tempered by a cooperative structure in order to mitigate a possible pernicious impact of the contest. In fact, managers may have an interest in winning the contest for promotion, but they also may have the interest of avoiding unproductive and wasteful competition. In sum, we can say that players in the contest may have a payoff function which encloses both competitive and cooperative efforts. In other words, the …