Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of Signatures of Positive Selection That Have Shaped the Genomic Landscape of South African Pig Populations

Simple Summary Pigs are important in agriculture as they produce animal-based protein for human consumption. The analysis of selection signatures has implications for the maintenance and utilization of genetic diversity and can reveal genes associated with phenotypic traits, either as a result of natural or of artificial selection. Pig populations are poorly characterised in South Africa. Hence, studies aimed at evaluating genetic distinctiveness and pig breed diversity will contribute to developing a rational plan for population conservation programs among other applications. Abstract South Africa boasts a diverse range of pig populations, encompassing intensively raised commercial breeds, as well as indigenous and village pigs reared under low-input production systems. The aim of this study was to investigate how natural and artificial selection have shaped the genomic landscape of South African pig populations sampled from different genetic backgrounds and production systems. For this purpose, the integrated haplotype score (iHS), as well as cross population extended haplotype homozygosity (XP-EHH) and Lewontin and Krakauer’s extension of the Fst statistic based on haplotype information (HapFLK) were utilised. Our results revealed several population-specific signatures of selection associated with the different production systems. The importance of natural selection in village populations was highlighted, as the majority of genomic regions under selection were identified in these populations. Regions under natural and artificial selection causing the distinct genetic footprints of these populations also allow for the identification of genes and pathways that may influence production and adaptation. In the context of intensively raised commercial pig breeds (Large White, Kolbroek, and Windsnyer), the identified regions included quantitative loci (QTLs) associated with economically important traits. For example, meat and carcass QTLs were prevalent in all the populations, showing the potential of village and indigenous populations’ ability to be managed and improved for such traits. Results of this study therefore increase our understanding of the intricate interplay between selection pressures, genomic adaptations, and desirable traits within South African pig populations.
Embracing Personalized Strategies in Radiotherapy for Nasopharyngeal Carcinoma: Beyond the Conventional Bounds of Fields and Borders

Simple Summary In the dynamic landscape of nasopharyngeal carcinoma (NPC) management, this review delves into a spectrum of radiotherapy (RT) practices, ranging from meticulous target delineation to dose prescription and sophisticated treatment delivery. The paper accentuates the evolving landscape of tailored treatment strategies and the departure from conventional one-size-fits-all RT treatment. Noteworthy initiatives, such as volume-reduced RT and adaptive planning, in conjunction with the integration of biomarkers and functional imaging for risk stratification, are highlighted. These efforts aim to inform treatment intensification or de-escalation, advocating for a paradigm shift towards patient-centric NPC management. The research momentum exemplifies a collective commitment to advancing NPC treatment and improving the quality of life in NPC survivors. Abstract Radiotherapy is the primary treatment modality for non-metastatic nasopharyngeal carcinoma (NPC) across all TN-stages. Locoregional control rates have been impressive even from the 2D radiotherapy (RT) era, except when the ability to deliver optimal dose coverage to the tumor is compromised. However, short- and long-term complications following head and neck RT are potentially debilitating, and thus, there has been much research investigating technological advances in RT delivery over the past decades, with the primary goal of limiting normal tissue damage. On this note, with a plateau in gains of therapeutic ratio by modern RT techniques, future advances have to be focused on individualization of RT, both in terms of dose prescription and the delineation of target volumes. In this review, we analyzed the guidelines and evidence related to contouring methods, and dose prescription for early and locoregionally advanced (LA-) NPC. Next, with the preference for induction chemotherapy (IC) in patients with LA-NPC, we assessed the evidence concerning radiotherapy adaptations guided by IC response, as well as functional imaging and contour changes during treatment. Finally, we discussed on RT individualization that is guided by EBV DNA assessment, and its importance in the era of combinatorial immune checkpoint blockade therapy with RT.
Accumulation of metallic elements into the superficial peat layer of mires and wet mineral soils of Estonian forest land / Akumulacja metali w powierzchniowej warstwie gleb torfowych i wilgotnych glebach mineralnych ekosystemów leśnych Estonii

Abstract This article studied the extent of accumulation of aqua regia extractable metallic elements (Al, Mg, Pb, Zn, Hg, Cd) into peaty (histic) epipedon (EP) of fen soils, transitional bog soils, peaty gley soils and peaty podzols. The accumulation coefficients (Kac) of the elements in EP were estimated in relation of forest floor (FF, as an input) as a comparison to deeper levels (SS, as a past background). The study revealed that the extent of accumulation and its order depend on soil (peat) type or pedo-ecological conditions of peatification. In the forming of EP from FF, the concentrations of Al and Pb were increased on an average 2.5-5.0 times, but that of Hg increased significantly only in peaty soils (on an average 1.5-1.6 times). The contents of Zn were significantly decreased (Kac 0.1-0.5) in all soil groups. The comparison of EP peats concentrations with SS data demonstrated a considerable accumulation of Pb, Cd, Zn and Hg into thin (~20 cm) superficial peat layer. Streszczenie Z wykorzystaniem wody królewskiej badano stopień akumulacji metali (Al, Mg, Pb, Zn, Hg, Cd) w epipedonie torfów wysokich (EP), torfów przejściowych, oglejonych glebach torfowych oraz zabagnionych glebach bielicowych. Współczynnik akumulacji metali (Kac) w EP oszacowano w zależności od runa leśnego (FF, jako wkład) i w porównaniu do głębszych poziomów (SS, jako tło przeszłości). Stwierdzono, że stopień akumulacji metali jest uzależniony of typu gleby (torfu) oraz jej właściwości. W powstałym EP z FF stężenia Al i Pb zwiększyły się średnio 2.5-5.0 razy, natomiast Hg istotnie jedynie w glebach torfowych (średnio 1.5-1.6 razy). Istotnie zmniejszyły się (Kac 0.1-0.5 razy) zawartości Zn we wszystkich glebach. Porównując zawartości metali w EP z SS stwierdzono znaczącą akumulację Pb, Cd, Zn i Hg w (~20 cm) powierzchniowej warstwie torfowej.
Histopathological Spectrum and Molecular Characterization of Liver Tumors in the Setting of Fontan-Associated Liver Disease

Simple Summary Fontan-associated liver disease (FALD) is a late sequela of single ventricle palliation. The long-term consequences of Fontan’s physiology have a spectrum of outcomes resulting in chronic hepatic venous congestion, liver cirrhosis, hyperplastic nodules, and liver neoplasms that are both benign, such as hepatic adenoma (HA), and malignant, including hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC). To date, genetic and molecular studies of HCC/CC contextual to FALD are lacking. We report the molecular profile of the heterogeneous group of tumors observed in the FALDs (HA, HCC, and CC) we studied with the aim of comparing any differences with the same tumors without FALD and identifying possible recurrent variables, such as molecular alterations, that could be predictive of clinical outcome. Abstract Purpose: Univentricular heart is corrected with the Fontan procedure (FP). In the long term, so-called Fontan-associated liver diseases (FALDs) can develop. The aim of this study is to analyze the molecular profile of FALDs. Methods: FALDs between January 1990 and December 2022 were reviewed for histology and immunohistochemistry, laboratory data, and images. Targeted next generation sequencing (NGS), performed on the DNA and RNA of both neoplastic and non-lesional liver tissue, was applied. Results: A total of 31/208 nodules > 1 cm in diameter were identified on imaging, but a liver biopsy was available for five patient demonstrating the following: one hepatocellular adenoma (HA), two hepatocellular carcinomas (HCCs), one fibrolamellar carcinoma (FLC), and one intrahepatic cholangiocarcinoma (ICC). Molecular analysis showed a copy number alteration involving FGFR3 in three cases (two HCCs and one ICC) as well as one HCC with a hotspot mutation on the CTNNB1 and NRAS genes. Tumor mutational burden ranged from low to intermediate. A variant of uncertain significance in GNAS was present in two HCCs and in one ICC. The same molecular profile was observed in a non-lesional liver. A DNAJB1-PRKACA fusion was detected only in one FLC. Conclusions: Neoplastic FALDs show some unusual molecular profiles compared with non-Fontan ones. The presence of the same alterations in non-lesional cardiac cirrhosis could contribute to the development of FALD.
Metal-Based Nanoparticles for Cardiovascular Diseases

Globally, cardiovascular diseases (CVDs) are the leading cause of death and disability. While there are many therapeutic alternatives available for the management of CVDs, the majority of classic therapeutic strategies were found to be ineffective at stopping or significantly/additionally slowing the progression of these diseases, or they had unfavorable side effects. Numerous metal-based nanoparticles (NPs) have been created to overcome these limitations, demonstrating encouraging possibilities in the treatment of CVDs due to advancements in nanotechnology. Metallic nanomaterials, including gold, silver, and iron, come in various shapes, sizes, and geometries. Metallic NPs are generally smaller and have more specialized physical, chemical, and biological properties. Metal-based NPs may come in various forms, such as nanoshells, nanorods, and nanospheres, and they have been studied the most. Massive potential applications for these metal nanomaterial structures include supporting molecular imaging, serving as drug delivery systems, enhancing radiation-based anticancer therapy, supplying photothermal transforming effects for thermal therapy, and being compounds with bactericidal, fungicidal, and antiviral qualities that may be helpful for cardiovascular diseases. In this context, the present paper aims to review the applications of relevant metal and metal oxide nanoparticles in CVDs, creating an up-to-date framework that aids researchers in developing more efficient treatment strategies.
AN AUTOMATIC ANALYSIS OF MAJOR ELEMENTS IN SILICATE ROCKS WITH X-RAY FLUORESCENCE SPECTROMETER USING FUSED DISC SAMPLES

A rapid analysis of major elements in silicate rocks of various chemical composition has been investigated with an automatic X-ray fluorescence spectrometer, Rigaku IKF 3064, connected with micro computer NOVA 01, using fused disc samples. We obtained farely good results which are very close to wet chemical values, by employing separate calibrations and matrix corrections for different rock types such as silicic rocks (SiO2≥70 wt%) and intermediate to basic rocks (SiO5<70 wt%). Calibration for silicic rocks was based on 4 silicic rocks such as granite, granodiorite and rhyolite, and 12 composite samples prepared by mixing of standard samples, reagent SiO2 and A12O3. For intermediate to basic rocks, 45 rock samples including gabbro, basalt, andesite, granite, mudstone and claystone were used. Moreover, for the heighest accuracy, partial matrix corrections with a few elements were carried out as to Si, Al, Mn, and Mg for intermediate to basic rocks. Precision and accuracy of the analysis were checked by the measurements of 43 rock samples previously analysed by conventional wet chemical method and the statistical treatment of the data. Standard deviations of the analysis have been evaluated as 0.70-1.0 (SiO2), 0.04-0.06 (TiO2), 0.26-0.50 (A12O3), 0.18-0.60 (total iron as Fe2O3), 0.01 (MnO), 0.10-0.32 (MgO), 0.05-0.27 (CaO), 0.14-0.31 (Na2O), 0.06-0.07 (K2O), and 0.06-0.23 (P2O5).
Low-Coherence Homodyne Interferometer for Sub-Megahertz Fiber Optic Sensor Readout

This study proposes a method for interferometric fiber optic sensor readouts. The method utilizes the advantages of the active homodyne demodulation technique and low-coherence interferometry. The usage of the tandem low-coherence interferometer enables modulating the reference interferometer without any changes to the sensor. This achieves high sensitivity, high stability, and a wide frequency band. A sensitivity of up to 0.1 nm (RMS) in the frequency range of 5 kHz is demonstrated by detecting acoustic signals with a fiber Michelson interferometer as a sensor.
Sodium Channel Gene Variants in Fetuses with Abnormal Sonographic Findings: Expanding the Prenatal Phenotypic Spectrum of Sodium Channelopathies

Voltage-gated sodium channels (VGSCs) are responsible for the initiation and propagation of action potentials in the brain and muscle. Pathogenic variants in genes encoding VGSCs have been associated with severe disorders including epileptic encephalopathies and congenital myopathies. In this study, we identified pathogenic variants in genes encoding the α subunit of VGSCs in the fetuses of two unrelated families with the use of trio-based whole exome sequencing, as part of a larger cohort study. Sanger sequencing was performed for variant confirmation as well as parental phasing. The fetus of the first family carried a known de novo heterozygous missense variant in the SCN2A gene (NM_001040143.2:c.751G>A p.(Val251Ile)) and presented intrauterine growth retardation, hand clenching and ventriculomegaly. Neonatally, the proband also exhibited refractory epilepsy, spasms and MRI abnormalities. The fetus of the second family was a compound heterozygote for two parentally inherited novel missense variants in the SCN4A gene (NM_000334.4:c.4340T>C, p.(Phe1447Ser), NM_000334. 4:c.3798G>C, p.(Glu1266Asp)) and presented a severe prenatal phenotype including talipes, fetal hypokinesia, hypoplastic lungs, polyhydramnios, ear abnormalities and others. Both probands died soon after birth. In a subsequent pregnancy of the latter family, the fetus was also a compound heterozygote for the same parentally inherited variants. This pregnancy was terminated due to multiple ultrasound abnormalities similar to the first pregnancy. Our results suggest a potentially crucial role of the VGSC gene family in fetal development and early lethality.
To What Extent Is HbA1c Associated with Glycemic Variability in Patients with Type 1 Diabetes? A Retrospective, Noninterventional Study

Background: Glycemic variability (GV) is a novel parameter used in evaluating the quality of diabetes management. Current guidelines recommend the use of GV indexes alongside the traditional parameter to evaluate glycemic control: hemoglobin A1c (HbA1c). This study aims to evaluate the extent to which HbA1c explains the GV phenomena in patients with Type 1 diabetes (T1DM). Methods: In 147 patients with T1DM, associations between HbA1c and several GV indexes were analyzed. Results: Patients with an HbA1c < 7% had a lower median standard deviation of glycemia (60 vs. 48; p < 0.001), a lower coefficient of variation (34.1 vs. 38.0; p < 0.001), and a significantly increased median time in range (78 vs. 58; p < 0.001). HbA1c was positively correlated with the coefficient of variation (r = 0.349; p < 0.001) and the standard deviation (r = 0.656; p < 0.001) but reversely correlated with a lower time in range (r = −0.637; p < 0.001). Conclusions: HbA1c only partially explains the GV phenomena in patients with T1DM. The HbA1c value is associated more strongly with the time in range and standard deviation than with the coefficient of variation.
Acceleration of plasma in current sheet during substorm dipolarizations in the Earth's magnetotail: Comparison of different mechanisms

This work is devoted to the investigation of particle acceleration during magnetospheric dipolarizations. A numerical model is presented taking into account the four scenarios of plasma acceleration that can be realized: (A) total dipolarization with characteristic time scales of ≈3 min; (B) single peak value of the normal magnetic component B z occurring on the time scale of less than 1 min; (C) a sequence of rapid jumps of B z interpreted as the passage of a chain of multiple dipolarization fronts (DFs); and (D) the simultaneous action of mechanism (C) followed by the consequent enhancement of electric and magnetic fluctuations with the small characteristic time scale ≤1 s. In a frame of the model, we have obtained and analyzed the energy spectra of four plasma populations: electrons e−, protons H+, helium He+, and oxygen O+ ions, accelerated by the above-mentioned processes (A)–(D). It is shown that O+ ions can be accelerated mainly due to the mechanism (A); H+ and He+ ions (and to some extent electrons) can be more effectively accelerated due to the mechanism (C) than the single dipolarization (B). It is found that high-frequency electric and magnetic fluctuations accompanying multiple DFs (D) can strongly accelerate electrons e− and really weakly influence other populations of plasma. The results of modeling demonstrated clearly the distinguishable spatial and temporal resonance character of particle acceleration processes. The maximum particle energies depending on the scale of the magnetic acceleration region and the value of the magnetic field are estimated. The shapes of energy spectra are discussed.This work is devoted to the investigation of particle acceleration during magnetospheric dipolarizations. A numerical model is presented taking into account the four scenarios of plasma acceleration that can be realized: (A) total dipolarization with characteristic time scales of ≈3 min; (B) single peak value of the normal magnetic component B z occurring on the time scale of less than 1 min; (C) a sequence of rapid jumps of B z interpreted as the passage of a chain of multiple dipolarization fronts (DFs); and (D) the simultaneous action of mechanism (C) followed by the consequent enhancement of electric and magnetic fluctuations with the small characteristic time scale ≤1 s. In a frame of the model, we have obtained and analyzed the energy spectra of four plasma populations: electrons e−, protons H+, helium He+, and oxygen O+ ions, accelerated by the above-mentioned processes (A)–(D). It is shown that O+ ions can be accelerated mainly due to the mechanism (A); H+ and He+ ions (and to some exten.
Using Three-Dimensional Printing Technology to Solve Complex Primary Total Hip Arthroplasty Cases: Do We Really Need Custom-Made Guides and Templates? A Critical Systematic Review on the Available Evidence

The burden of osteoarthritis (OA) is around 300 million people affected worldwide, with the hip representing a commonly affected joint. Total hip arthroplasty (THA) has been used with notable success as a definitive treatment to improve pain and function in hip OA patients. The recent advent of new technologies, such as 3D printing, has pushed the application of these new concepts toward applications for the well-known THA. Currently, the evidence on the use of 3D printing to aid complex primary THA cases is still scarce. Methods: An extensive literature review was conducted to retrieve all articles centered on the use of 3D printing in the setting of primary THA. Results: A total of seven studies were included in the present systematic review. Four studies investigated the use of 3D-printed surgical guides to be used during surgery. The remaining three studies investigated the benefit of the use of 3D-printed templates of the pelvis to simulate the surgery. Conclusions: The use of 3D printing could be a promising aid to solve difficult primary total hip arthroplasty cases. However, the general enthusiasm in the field is not supported by high-quality studies, hence preventing us from currently recommending its application in everyday practice.
Investigation of the Effect of the Baric Formation Parameters on Free and Forced Oscillations of the Level and Flow in the Sea of Azov

The effect of inhomogeneous moving atmospheric pressure fields upon the flows, and free and forced oscillations of the Azov Sea level induced by constant wind is studied by the method of mathematical modeling. The hypothesis on the role of the resonance mechanism in arising of the extremely high amplitudes of the surge oscillations and seiches generated by a baric field moving at the velocity equal to that of a free long wave is tested. The equations of the applied mathematical model are described in general, transition to the curvilinear coordinates is shown, the model parameters chosen allowing for different physical factors are substantiated, and the features of the model numerical realization are explained. The information on the wind and atmospheric pressure fields used in the numerical experiments is given. The results of simulations of free oscillations in the Sea of Azov are discussed with the purpose to analyze the impact of the resonance characteristics related to the speed and time of the baric fields’ motion over the sea. The sea level deviations resulted from the calculations with constant pressure and those with passing of the inhomogeneous baric front are compared. It is revealed that at one and the same wind, the baric disturbances moving over the Sea of Azov induce the forced oscillations and after their forcing is stopped – free oscillations the amplitudes of which exceed those obtained at constant atmospheric pressure by 14%. It is shown that the baric front motion, speed and time of which are chosen based on the assumption on generation of the waves with maximum amplitudes, plays an important but not decisive role in formation of the currents’ structure and the level oscillations in the Sea of Azov.
Sexual Rewards and Costs in Heterosexual and Gay Hispanic Adults

The Interpersonal Exchange Model of Sexual Satisfaction proposes that sexual satisfaction can be explained by the balance of sexual rewards or costs exchange. The Interpersonal Exchange Model of Sexual Satisfaction Questionnaire (IEMSSQ) was developed from this model. The IEMSSQ includes the Reward/Costs Checklist (RCC). The RCC assesses different sexual exchanges that are categorized into sexual rewards and/or costs. Analyses and comparisons of sexual rewards and costs in the Hispanic cisgender population based on gender (man or woman) and sexual orientation (heterosexual and homosexual) with this measure have not been conducted. The main goal was to analyze and rank the sexual rewards, costs, and both, indicated by a sample of 1996 Hispanic partnered participants (heterosexual men, gay men, heterosexual women, and lesbians). The predominant sexual exchanges that were reported involved emotional aspects, both as rewards and costs. When participants indicated that the exchange was both a reward and a cost, they were referring to aspects specifically related to the sexual relationship itself. Heterosexual men and women had greater rewards and higher costs, respectively. Gay men obtained a greater number of items reported as rewards and costs. The results provide further insight into sexual satisfaction related to gender and sexual orientation.