Miracle-dz/UniFAR-FTUs huggingface dataset:
INTREPPPID - An Orthologue-Informed Quintuplet Network for Cross-Species Prediction of Protein-Protein Interaction

An overwhelming majority of protein-protein interaction (PPI) studies are conducted in a select few model organisms largely due to constraints in time and cost of the associated “wet lab” experiments. In silico PPI inference methods are ideal tools to overcome these limitations, but often struggle with cross-species predictions. We present INTREPPPID, a method which incorporates orthology data using a new “quintuplet” neural network, which is constructed with five parallel encoders with shared parameters. INTREPPPID incorporates both a PPI classification task and an orthologous locality task. The latter learns embeddings of orthologues that have small Euclidean distances between them and large distances between embeddings of all other proteins. INTREPPPID outperforms all other leading PPI inference methods tested on both the intra-species and cross-species tasks using strict evaluation datasets. We show that INTREPPPID’s orthologous locality loss increases performance because of the biological relevance of the orthologue data, and not due to some other specious aspect of the architecture. Finally, we introduce PPI.bio and PPI Origami, a web server interface for INTREPPPID and a software tool for creating strict evaluation datasets, respectively. Together, these two initiatives aim to make both the use and development of PPI inference tools more accessible to the community. GRAPHICAL ABSTRACT
Phylotranscriptomics reveals convergent behavioral evolution associated with shared and unique mechanisms in cavity-nesting songbirds

Uncovering the genomic bases of phenotypic adaptation is a major goal in biology, but this has been hard to achieve for complex behavioral traits. Here, we leverage the repeated, independent evolution of obligate cavity-nesting in birds to test the hypothesis that the shared pressure to compete for a limited breeding resource drives convergent behavioral evolution via convergent gene regulatory changes in the brain. Using behavioral assays in the field, hormonal measures of free-living subjects, and transcriptome-wide analyses of the brain in wild-captured males and females, we examined five species pairs across five avian families, each including one obligate cavity-nesting species and a related species with an open cup-nesting or otherwise more flexible nest strategy. Results support the hypothesis of behavioral convergence, with higher levels of territorial aggression in obligate cavitynesters, particularly among females. Levels of testosterone in circulation were not associated with nest strategy or aggression for either sex, but phylogenetic analyses of individual genes and co-regulated gene networks revealed some shared patterns of gene expression, including a nest strategy-related gene network shared across families and two separate networks linked to aggression only in females. Though associated with convergent behavioral evolution, these genes were not significantly enriched for particular functional pathways, and the scope of convergent gene expression evolution was limited to a small percent of the genome. Together, these observations indicate that replicated evolutionary changes in complex behavior arise via a combination of convergent and lineage-specific evolution of gene regulation. Significance Trait convergence has tremendous potential to reveal the proximate mechanisms by which natural selection generates evolutionary change. However, these investigations are often limited to traits with a simple and well-understood genetic basis, and less is known about the underpinnings of convergence in complex quantitative traits like many behaviors. Across five avian families with independent origins of obligate cavity-nesting, we find behavioral convergence, particularly among females, which display higher territorial aggression than their more flexibly-nesting relatives. We find both shared and unique patterns of brain gene expression, indicating that evolution follows diverse paths towards building an aggressive bird. These results highlight how complex behaviors can arise from a combination of repeated and independent molecular changes in response to shared ecological pressures.
Neuroestrogens facilitate male-typical behaviors by potentiating androgen receptor signaling in medaka

In rodents, estrogens aromatized from androgens in the brain, also known as neuroestrogens, are essential for the development of male-typical behaviors. In many other vertebrates including humans and teleost fish, however, androgens facilitate these behaviors directly via the androgen receptor without aromatization into estrogens. Here we report that male medaka fish lacking Cyp19a1b (a subtype of aromatase predominantly expressed in the brain) exhibit severely impaired male-typical mating and aggression, despite elevated brain androgen levels. These phenotypes can be rescued by estrogen administration, indicating that neuroestrogens are pivotal for male-typical behaviors even in non-rodents. Our results further suggest that neuroestrogens facilitate male-typical behaviors by potentiating androgen action in the brain via the direct stimulation of androgen receptor transcription, thereby revealing a previously unappreciated mechanism of action of neuroestrogens. We additionally show that female fish lacking Cyp19a1b are less receptive to male courtship and conversely court other females, highlighting the significance of neuroestrogens in establishing sex-typical behaviors in both sexes.
An approach to analysing plot scale infiltration and runoff responses to rainfall of fluctuating intensity

Simulated rainfall of fluctuating intensity was applied to runoff plots on bare dryland soils in order to explore a new method for analysing the non‐steady‐state responses of infiltration and overland flow. The rainfall events all averaged 10 mm/h but included intensity bursts of up to 70 mm/h and lasting 5–15 min, as well as periods of low intensity and intermittency of up to 25 min. Results were compared with traditional steady‐state estimates of infiltrability made under simulated rainfall sustained at a fixed intensity of 10 mm/h. Mean event infiltration rate averaged 13.6% higher under fluctuating intensities, while runoff ratios averaged only 63% of those seen under constant intensity. In order to understand the changing soil infiltrability, up to three affine Horton infiltration equations were fitted to segments of each experiment. All equations had the same final infiltrability fc, but adjusted values for coefficients f0 (initial infiltrability) and Kf (exponential decay constant) were fitted for periods of rainfall that followed significant hiatuses in rainfall, during which subsurface redistribution allowed near‐surface soil suction to recover. According to the fitted Horton equations, soil infiltrability recovered by up 10–24 mm/h during intra‐event rainfall hiatuses of 15 to 20‐min duration, contributing to higher overall event infiltration rates and to reduced runoff ratios. The recovery of infiltrability also reduced the size of runoff peaks following periods of low intensity rainfall, compared with the predictions based on single Horton infiltration equations, and in some cases, no runoff at all was recorded from late intensity peaks. The principal finding of this study is that, using a set of affine equations, the intra‐event time variation of soil infiltrability can be tracked through multiple intensity bursts and hiatuses, despite the lack of steady‐state conditions. Copyright © 2016 John Wiley & Sons, Ltd.
Application of PSInSAR for assessment of surface deformations in post_mining area _ case study of the former Walbrzych Hard Coal Basin (SW Poland)

The study presents results of surface displacements calculated with the PSInSAR technique for the area of the former Wałbrzych Hard Coal Basin (WHCB) in SW Poland. Underground mining of hard coal took place there until the late 90’ties of the 20 Century. In accordance with the present state of knowledge, secondary deformations are a common phenomenon on post-mining areas. The chosen monitoring technique has provided data and has allowed study surface movements in Wałbrzych in the post mining period, for which no other, conventional surveys were available. In the analysis radar images acquired by the ENVISAT satellite for the 458 track and for the 2002 – 2009 period have been used. The results of PSInSAR data processing indicate elevation of the surface within the boundaries of former mining areas, reaching up to +6 mm/yr and on average +4 mm/yr. We assume that the end of mine water drainage and restoration of Carboniferous ground water table is the main factor responsible for this process and observe delayed response of the rock mass. ARTICLE INFO
Biochemical and allelopathic features of Adonis vernalis, Allium ursinum, and Leucojum vernum in the M.M. Gryshko National Botanical Garden of the NAS of Ukraine

The article presents the results of a study on the content and dynamics of the accumulation of biogenic elements and brassinolides in plants of Adonis vernalis, Allium ursinum, and Leucojum vernum in Kyiv, Ukraine. Data is provided on allelopathic activity, content of macro- and microelements, phenolic compounds, and laccase activity in plants and the rhizosphere soil under the conditions of the M.M. Gryshko National Botanical Garden of the National Academy of Sciences of Ukraine (NBG). The plants from the collection of the NBG were used as objects of study in field experiments. The content of biogenic elements in plant tissues and soil was analyzed using an inductively coupled plasma spectrometer. The allelopathic analysis of soil was conducted using a direct bioassay method with Lepidium sativum seedlings as the test object. Phenolic compounds were extracted from the soil using the ion exchange (desorption) method. The content of brassinosteroids was measured spectrophotometrically at a wavelength of 450 nm. The content of laccase was measured spectrophotometrically at a wavelength of 530 nm.The results demonstrate that model plant species employ a wide range of physiological mechanisms throughout the vegetation period to enhance their resistance to abiotic factors. These mechanisms include maintaining potassium and calcium balance and utilizing hormonal compounds. Plants have been proven to have compensatory mechanisms in response to stress factors, substituting one biochemical marker of resistance with another. Both, brassinosteroids and silicon, contribute to the adaptive capacity of organisms.
Navigating Lung Cancer: Exploring Progress and Obstacles - A Comprehensive Review

Lung cancer persists as a significant global health dilemma, characterized by elevated incidence and mortality rates worldwide. Despite recent strides in diagnostic methodologies, screening approaches, and therapeutic modalities, lung cancer retains its status as the foremost cause of cancer-related fatalities internationally. The disease is predominantly categorized into two primary forms: small-cell carcinomas and the notably more prevalent non-small-cell carcinomas, constituting approximately 85% of cases. While smoking stands as the primary risk factor for lung cancer, accounting for 80-90% of related deaths, other factors such as dietary habits, air pollution, genetic predisposition, and prior lung conditions play substantial roles. Diagnostic procedures encompass a range of techniques, including radiography, sputum cytology, bronchoscopy, biomarker analysis, among others. The imperative for progress and refinement in diagnostic tools, especially for early detection and monitoring in high-risk demographics, underscores the urgency. Continual research and enhancement of surgical, systemic, and localized treatments are indispensable in the battle against lung cancer. Despite advancements, challenges persist in achieving timely diagnoses, particularly in high-risk groups, and augmenting overall survival rates. This comprehensive review delves into current research advancements in lung cancer, with specific focus on classification, patient well-being, risk factors, diagnostic methodologies, and treatment options.
Greenhouse gas emissions from Swedish consumption of meat, milk and eggs 1990 and 2005

SUMMARY The goal of this study was to estimate the greenhouse gas (GHG) emissions related to consumption of animal products in Sweden 1990 and 2005, using a life cycle perspective. The objectives were: ‐ to estimate total and per capita GHG emissions in Sweden caused by the consumption of meat, dairy products and eggs from 1990 and 2005 and ‐ to investigate whether present trends in consumption of animal food in Sweden are sustainable from a global warming perspective. Life cycle GHG emissions from the Swedish consumption of meat, dairy products and eggs 1990 and 2005 were analysed using LCA‐methodology. The analysis dealt with the phases of animal production as shown in Figure 2.1. Also imports were considered. The calculated GHG emissions include primary production (at the farm‐ gate), transports to and processes at food industry and finally, transport to a retailer which we assume to be in Stockholm. The sum of GHG emissions from these subsystems is here called the product´s Carbon footprint, CF. The Swedish consumption of meat has grown strongly during the period 1990‐2005, while consumption of dairy products and eggs has been relatively stable. Parallel with this, domestic animal production has decreased (with the exception of poultry meat) and consequently meat imports have increased significantly. Total GHG emissions from the consumption of dairy products decreased by ~14 % (close to 0.6 Mtons carbon dioxide equivalents, CO 2 e) between 1990 and 2005, and amounted to approximately 3.5 Mtons CO 2 e in 2005. The overall emission cut was an effect of efficiency gains in milk production while changes in consumption patterns were of minor significance. In 2005, the average consumption of fresh dairy products, cheese and milk powder was the source of emissions corresponding to approximately 380 kg CO 2 e per capita. Egg consumption was relative stable over the time‐period but import has increased due to a lowered domestic production. Total emissions from egg consumption were close to 0.18 Mtons CO 2 e in 2005 corresponding to ~20 kg CO 2 e per capita. Per capita GHG emissions caused by the consumption of all meat, milk and egg products increased by more than 16 % and reached ~ 1 100 kg CO 2 e per capita in 2005. This corresponds to an average increase of approximately 1 % GHG emissions per year between 1990 and 2005. This growth occured despite the fact that the production …
Ultramafic Rocks and the Upper Mantle

Cosmic abundances of elements and meteorite analogies indicate an ultrabasic mantle. Detailed review of ultramafic rocks in their varied associations suggests that representative mantle sample are included among oceanic and orogenic peridotites, and nodules in basalts and kimberlites. Extrapolation from rocks to mantle must be made with caution; their petrogenesis is complex and the mantle is heterogeneous. Twenty-seven estimates of mantle composition based on meteorite models, ultramafic rocks, and hypothetical peridotites are tabulated and compared with basalts in chemical variation diagrams. The three groups are separated by their alkali contents and stages of fractionation. Mantle estimates based on ultramafic rocks are low in alkalis to provide common basaltic magmas by simple subtraction, but they can yield high-pressure picritic liquids capable of fractionating during uprise to produce low-pressure basaltic types at the surface. Trace-element contents of ultramafic rocks and the upper mantle are not well determined. Models for the upper mantle are based on mineral facies determined experimentally for appropriate compositions, temperatures and pressures. Review of experimental data for the system peridotite-gabbro-water, correlated with geophysical data, suggests that the upper mantle is composed of peridotite with layers and pods of eclogite and residual or precipitated dunite and peridotite; with increasing depth, feldspathic peridotite (rarely occurring) is transformed to spinel peridotite and this to garnet-peridotite, at 50-75 kms depth. Garnet peridotite perists down to the Transition Zone at 350-400 kms, where pyroxene is dissolved by garnet, and olivine is transformed to a spinel-like phase. Eclogite is abundant from 80 to 150 kms depth. The low velocity zone begins at 75-100 kms where hornblende becomes unstable, producing traces of interstitial hydrous magma of andesitic composition within eclogite; within a peridotite mantle, interstitial hydrous magma may be alkalic (potassic).
International Migration through the Tourism Industry: Implications, Challenges, and Contradictions in South Africa

The tourism industry has advantages and disadvantages that are evident in South Africa. One of the disadvantages in Cape Town is the growth of particularly urban tourism that has displaced domestic tourists due to the high prices charged. The development of the domestic tourism market is challenged by the dominant unemployment, poverty, and inequality that are affecting the South African economy. Yet, tourism consumption requires the availability of discretionary income as a necessary condition to afford to procure and consume tourism offerings. Government support is visible in the industry as it has the ability to create jobs and opportunities for entrepreneurs. Even though three cities in South Africa, Cape Town, Durban, and Johannesburg, dominate the urban tourism market, this can also be reflected in the flight frequencies via Johannesburg, which is the regional hub for Southern Africa.
City of crisis (Preface)

ion from their use-values(.)If we make abstraction from its use-value, we abstract also from the material constituents and forms which make it a use value. It is no longer a table, a house, (.) or any other useful thing. All its sensuous characteristics are extinguished. (.) With the disappearance of the useful character of the products of labour, the useful character of the kinds of labour embodied in them also disappears; this in turn entails the disappearance of the dif ferent concrete forms of labour. They can no longer be distinguished, but are “The r ight to the city” in Athens during a cr isis era 193 all together reduced to the same kind of labour, human labour in the abstract. ”
Synthetic Biology in Biofuels Production

Increasing demand of biofuels is inevitable today considering the adverse impact of fossil fuels on environment, issue of its sustainability, rising price, and dependence on foreign countries. However, the question remains on how to produce biofuels in cost effective manner from the non-food resources. The non-food agricultural and forestry residues have recalcitrant biomass that is difficult to hydrolyze via enzymes, and presence of non-conventional pentose sugars and inhibitors makes the sugar fermentation into ethanol a formidable task. Besides, ethanol has its inherent issue of having low energy density and hygroscopic nature, encouraging scientists to look for alternative fuels, such as butanol and hydrocarbons. Algae are another non-food feedstock that is being explored for fuel production, but its low growth rate and low lipid yield in fluctuating environmental growth condition is of great concern. Synthetic biology with its new tools and applications is likely to play a central role in addressing these issues. Keywords: synthetic biology; biofuels; lignocellulosic biomass; metabolic engineering; feedstock engineering; microbial engineering; hydrolytic enzymes; algal fuels
Explaining to Students How Personality Differences Can Be Maintained in the Face of Directional Selection through Trait Covariation

Those of us who teach both personality psychology and evolutionary psychology must help students understand how individual differences in personality are maintained in the face of directive selection. A new study is offered to help explain the maintenance of personality variability over evolutionary time. Analysis of scores on the five major personality factors in two large data sets (Ns = 307,313 and 619,150) confirmed a prediction from socioanalytic theory that the most common two-score profiles occur within superfactors α and β, which affect coalition formation and status achievement, respectively (Hogan & Blickle, 2017). A parallel analysis of 1,718 representative English trait terms indicated that most trait terms fall at the intersection of two positive or two negative poles of the five factors, with five notable exceptions. The co-occurrence of negative and positive personality traits may help to explain how variability in personality is maintained over evolutionary time and is a good object lesson for students on how we are the result of blind evolution rather than intelligent design.
Killer cell immunoglobulin-like receptor (KIR) polymorphism : functional implications and clinical relevance.

NK cell function is regulated by Killer-cell Immunoglobulin-like Receptors (KIR) some of which recognise class I Major Histocompatibility Complex molecules. KIRs have been shown to exhibit a high degree of functional diversity which is generated at several levels. However, the functional relevance of this diversity remains largely unknown. This thesis describes our approach towards elucidating the functional relevance of KIR diversity. To study this we first compiled all known KIR sequences into a database. We developed bioinformatics tools to facilitate the study of these sequences and have made both the tools and database publicly accessible online. Subsequent efforts were directed towards investigating the structural impact of KIR polymorphism by means of molecular modelling software. The results that were generated by this approach have provided information with regards to the ligand binding properties of most activating KIR proteins. In addition, we have also developed a KIR gene typing system capable of detecting all known KIR genes as well as the alleles of five of the KIR proteins for which a ligand has been described. We have implemented this KIR typing system to three different sample panels: a reference panel of more than 100 B-lymphoblastoid cell lines (BLCL), a family based KIR haplotype segregation study and a cohort of 141 unrelated donor (UD) haematopoietic stem cell transplant pairs. Our investigations have allowed us to generate the largest KIR typing reference panel, to characterise the KIR profile of a Mexican Mestizo population and to investigate the clinical relevance of KIRs in UD-Haematopoietic Stem Cell Transplantation (HSCT). Our results demonstrate that the beneficial effect of NK alloreactivity in the Graft-versus-Host direction as predicted by Ruggeri's algorithm cannot be applied to the UD-HSCT setting. In addition, I describe our findings relating to the clinical role of KIR genes and alleles in the UD-HSCT cohort.
System for determining the quality of sleep

Embodiments of the present invention provide a distributed computer system and method for determining the quality of sleep of the user 340 during sleep. Distributed computer system, by detecting the change in the body posture of the user 340 during sleep, will determine the quality of sleep. Sleep quality will be determined by the feature vector associated with each position of the user 340 during sleep. Posture of the user will be determined by recording the body motion signal 200 caused by mechanical motion and muscle motion of the user's body. FIELD 1