Miracle-dz/UniFAR-FTUs huggingface dataset:
Free recombination within Helicobacter pylori (nucleotide sequencingyhorizontal genetic exchangeyevolutionylinkage equilibrium)

Sequences of three gene fragments ( flaA, flaB, and vacA) from Helicobacter pylori strains isolated from patients in Germany, Canada, and South Africa were analyzed for diversity and for linkage equilibrium by using the Ho- moplasy Test and compatibility matrices. Horizontal genetic exchange in H. pylori is so frequent that different loci and polymorphisms within each locus are all at linkage equilib- rium. These results indicate that H. pylori is panmictic. Comparisons with sequences from Escherichia coli, Neisseria meningitidis, and Drosophila melanogaster showed that recom- bination in H. pylori was much more frequent than in other species. In contrast, when multiple family members infected with H. pylori were investigated, some strains were indistin- guishable at all three loci. Thus, H. pylori is clonal over short time periods after natural transmission.
Assessing and monitoring coral reef sponges: Why and how?

Functional roles of sponges in coral reef ecosystems include: increasing coral survival by binding live corals to the reef frame and preventing access to their skeletons by excavating organisms; mediating regeneration of physically damaged reefs by temporary stabilization of carbonate rubble; reworking of solid carbonate through bioerosion; recycling nutrients and adding to primary production through microbial symbionts with special biochemical capabilities; clearing the water column of procaryotic plankton; serving as food for a variety of megafauna; and attracting support for responsible human stewardship of coral reefs with aesthetically appealing colors and morphologies. Nevertheless, sponges tend to be avoided in assessment and monitoring of coral reefs because they are not easy to quantify or identify, and because we have only recently begun to understand the importance of their many functional roles. As we gain more understanding of these roles of sponges in coral reefs, the need to carefully assess and monitor changes in sponges is becoming more clear. Focus on functional roles dictates choice of methods for assessing and monitoring sponges, as follows: (1) volume will generally be the most useful way to quantify sponge populations; (2) accurate identification to genus, family, or even order, combined with a brief description and reference to voucher specimens, is preferable to guesses on species names, in cases for which identification can't be verified by specialists; (3) permanently marked sites must be monitored over time in order to be able to detect community changes and to distinguish beneficial from detrimental effects of sponges on corals.
Protective effects of selenium and zinc on the brain acetyl cholinesterase activity in lead intoxified rat

Lead is a common toxic agent which impairs various organs functions of the body. The basis of this toxicity is believed to be the negative influence on enzymatic system of cells. In the past few years, increasing consideration has been given to interactions occurring between lead and some essential metals including Se and Zn. Based on the finding that some trace elements could reverse the toxicity of lead on tissue functions this work was performed to study the protective effects of Zn and Se against lead toxicity. Thus changes in acetyl cholinesterase (AchE) activity in brain regions were investigated in different conditions. Four groups of rats were chosen. In acute study, i.p. administration of Pb (13.5 mg/kg) for 2 weeks reduced the activity of AchE in the cortex by 28.7% but Pb in presence of Zn (0.5 mg/kg) and Se (0.4 mg/kg) inhibited AchE activity only by 11.5% and 25%, respectively, such inhibition in mid-brain were 44.7%, 18.2%, 32% and in the cerebellum 48.2%, 38.4% and 12.0%. In chronic study, animals were administered Pb alone (4 mg/kg) or in the presence of Se or Zn for 60 days. Following these treatments, AchE activities in the cortex were reduced by 41.5%, 22.0% and 39.6%, respectively. These inhibitions in mid-brain were 56.0%, 37.6%, 54.5% and in cerebellum 46.0%, 45.0%, 32.6%. It is concluded that lead had toxic effect on AchE activity in different brain regions and Zn and Se could reverse this inhibition to some extent.
Ethylene Is Not Essential for R-Gene Mediated Resistance but Negatively Regulates Moderate Resistance to Some Aphids in Medicago truncatula

Ethylene is important for plant responses to environmental factors. However, little is known about its role in aphid resistance. Several types of genetic resistance against multiple aphid species, including both moderate and strong resistance mediated by R genes, have been identified in Medicago truncatula. To investigate the potential role of ethylene, a M. truncatula ethylene- insensitive mutant, sickle, was analysed. The sickle mutant occurs in the accession A17 that has moderate resistance to Acyrthosiphon kondoi, A. pisum and Therioaphis trifolii. The sickle mutant resulted in increased antibiosis-mediated resistance against A. kondoi and T. trifolii but had no effect on A. pisum. When sickle was introduced into a genetic background carrying resistance genes, AKR (A. kondoi resistance), APR (A. pisum resistance) and TTR (T. trifolii resistance), it had no effect on the strong aphid resistance mediated by these genes, suggesting that ethylene signaling is not essential for their function. Interestingly, for the moderate aphid resistant accession, the sickle mutant delayed leaf senescence following aphid infestation and reduced the plant biomass losses caused by both A. kondoi and T. trifolii. These results suggest manipulation of the ethylene signaling pathway could provide aphid resistance and enhance plant tolerance against aphid feeding.
Endocrine Risk Factors of Endometrial Cancer: Polycystic Ovary Syndrome, Oral Contraceptives, Infertility, Tamoxifen

Endometrial cancer is the most common gynecologic cancer and is predominantly endocrine-related. The role of unopposed estrogen in the development of endometrial cancer has been investigated in numerous studies. Different reproductive factors such as younger age at menarche, late age at menopause, infertility, nulliparity, age of birth of the first child, and long-term use of unopposed estrogens during hormone replacement therapy have been associated with an increased risk of endometrial cancer. In contrast, there is a growing body of evidence for a protective role of oral contraceptives. Most of the published data on the association between infertility and polycystic ovary syndrome are inconclusive, whereas the effect of tamoxifen on the risk of endometrial cancer has been well established. With this review, we aim to summarize the evidence on the association between infertility, polycystic ovary syndrome, oral contraceptives, and tamoxifen and the development of endometrial cancer.
Mechanically Robust, Softening Shape Memory Polymer Probes for Intracortical Recording

While intracortical microelectrode arrays (MEAs) may be useful in a variety of basic and clinical scenarios, their implementation is hindered by a variety of factors, many of which are related to the stiff material composition of the device. MEAs are often fabricated from high modulus materials such as silicon, leaving devices vulnerable to brittle fracture and thus complicating device fabrication and handling. For this reason, polymer-based devices are being heavily investigated; however, their implementation is often difficult due to mechanical instability that requires insertion aids during implantation. In this study, we design and fabricate intracortical MEAs from a shape memory polymer (SMP) substrate that remains stiff at room temperature but softens to 20 MPa after implantation, therefore allowing the device to be implanted without aids. We demonstrate chronic recordings and electrochemical measurements for 16 weeks in rat cortex and show that the devices are robust to physical deformation, therefore making them advantageous for surgical implementation.
Qualitative accounts of PrEP discontinuation from the general population in Eswatini

Abstract People in receipt of pre-exposure prophylaxis (PrEP) for the prevention of HIV in Sub-Saharan Africa often discontinue taking the medication. We conducted 27 semi-structured interviews with men and women who had started PrEP but did not return to the clinic for a refill after a 1, 2 or 3-month period. These ‘discontinuation’ clients were enrolled in a PrEP demonstration project for the general population in nurse-led, public-sector, primary-care clinics in Eswatini. Reasons for discontinuation included changes to self-perceived HIV risk such as the end of pregnancy and absent partners. Others described PrEP as inaccessible when working away from home and many described difficulties relating to a daily pill regimen and managing side effects. Female clients described being prohibited from using PrEP by their partners and co-wives. From these results, we recommend that client-centred counselling stresses the prevention-effective adherence paradigm, which promotes PrEP use in risk periods that are identifiable and PrEP discontinuation when the risk period has finished. A national scale up of PrEP may mitigate problems accessing PrEP. Extended counselling and support could assist with adherence and the management of side effects. Education and support for partners and families of PrEP clients may also contribute to better PrEP continuation.
Guideline for Limb‐Salvage Treatment of Osteosarcoma

Osteosarcoma is the most common primary malignant bone tumor, occurring mainly in children and adolescents, and the limbs are the main affected sites. At present, limb‐salvage treatment is considered as an effective basic standard treatment for osteosarcoma of the limb. China has a vast territory, but the development of technology is not balanced,which requires sufficient theoretical coverage, strong technical guidance and the application of limb‐salvage treatment guidelines to the treatment of osteosarcoma. Therefore, to standardize and promote the development of limb‐salvage surgery technology and improve the success rate of limb‐salvage treatment, this guide systematically introduces limb‐salvage techniques for the treatment of patients with limb osteosarcoma through definition of limb‐salvage treatment, surgical methods, efficacy evaluation, postoperative treatment and prevention of complications, rehabilitation guidance, and follow‐up advice.
Rapid species identification of Sonoran pronghorn from fecal pellet DNA

The Sonoran pronghorn (Antilocapra americana sonoriensis) is a subspecies of pronghorn found exclusively in the Sonoran Desert of Arizona (USA) and Mexico. Sonoran pronghorn persist at low densities and are geographically isolated from other pronghorn populations. Numbers have declined in recent decades, but the population has rebounded from a low of fewer than 50 animals in 2003 to an estimated 159 individuals in 2012; however, little is known about population demographics beyond abundance estimates. We developed a species identification test that uses mitochondrial DNA (mtDNA) species-specific primers to distinguish between sympatric Sonoran pronghorn and mule deer (Odocoileus hemionus) using DNA extracted from fecal pellets. We accurately identified each species in 100% of the blood and tissue reference samples. We also evaluate the rate of DNA degradation in pronghorn fecal samples ranging from 1 day to 124 days old and document that mtDNA species identification success rates were 100% through day 14. Success rates dropped to 95% by day 21, 50% on day 60, and 10% by day 124. This new test will be a valuable tool for documenting the presence of Sonoran pronghorn across their current range and can also be used for other pronghorn populations. © 2014 The Wildlife Society.
Genetic polymorphisms −137 (G > C) (rs187238) and −607 (C > A) (rs1946518) and serum level of interleukin 18 in Fars ethnic groups with metabolic syndrome in Northern Iran

Abstract Introduction We aimed to determine the genetic polymorphisms and serum level of interleukin 18 in Fars ethnic groups. Material and methods 226 Fars ethnic groups were participated. The ATP III criteria were used to assess MS components. The SNPs of the IL-18 gene were determined with ARMS-PCR. Results The GG, GC, and CC genotypes of −137 were 50%, 40%, and 10%. The CC, CA, and AA genotypes of −607 were 45%, 37%, and 18%. The GG, GC, and CC genotypes of −137 were 44.20%, 43.40%, and 12.40%, and were 55.75%, 36.28%, and 7.97% in subjects with and without MS, respectively. The CC, CA, and AA genotypes of −607 were 48.70%, 37.20%, and 14.20% and were 41.60%, 37.20%, and 21.20% in both groups, respectively. Conclusion IL-18 gene may different in specific populations, different ethnic groups and geographic regions. The IL-18 polymorphisms might not be used as a marker of metabolic syndrome.
A note on the product of two matrices of index one

Abstract In this paper, we show some necessary and/or sufficient conditions so that AB and/or BA are core matrices, whenever A and B are core complex matrices (a matrix A is a core matrix, that is a matrix of index one, if ). More specifically, we also analyse some similar situations where A, B, AB and/or BA are diagonalizable matrices or EP matrices. Moreover, we provide, as an application, two results concerning the reverse order law for the Moore–Penrose inverse of the product of two matrices.
Sensitivity analysis of equilibrium in density‐dependent matrix population models

We consider the effects of parameter perturbations on a density-dependent population at equilibrium. Such perturbations change the dominant eigenvalue λ of the projection matrix evaluated at the equilibrium as well as the equilibrium itself. We show that, regardless of the functional form of density dependence, the sensitivity of λ is equal to the sensitivity of an effective equilibrium density , which is a weighted combination of the equilibrium stage densities. The weights measure the contributions of each stage to density dependence and their effects on demography. Thus, is in general more relevant than total density, which simply adds all stages regardless of their ecological properties. As log λ is the invasion exponent, our results show that successful invasion will increase , and that an evolutionary stable strategy will maximize . Our results imply that eigenvalue sensitivity analysis of a population projection matrix that is evaluated near equilibrium can give useful information about the sensitivity of the equilibrium population, even if no data on density dependence are available.
A Preliminary Evaluation of the Pro-Chondrogenic Potential of 3D-Bioprinted Poly(ester Urea) Scaffolds

Degeneration of articular cartilage (AC) is a common healthcare issue that can result in significantly impaired function and mobility for affected patients. The avascular nature of the tissue strongly burdens its regenerative capacity contributing to the development of more serious conditions such as osteoarthritis. Recent advances in bioprinting have prompted the development of alternative tissue engineering therapies for the generation of AC. Particular interest has been dedicated to scaffold-based strategies where 3D substrates are used to guide cellular function and tissue ingrowth. Despite its extensive use in bioprinting, the application of polycaprolactone (PCL) in AC is, however, restricted by properties that inhibit pro-chondrogenic cell phenotypes. This study proposes the use of a new bioprintable poly(ester urea) (PEU) material as an alternative to PCL for the generation of an in vitro model of early chondrogenesis. The polymer was successfully printed into 3D constructs displaying adequate substrate stiffness and increased hydrophilicity compared to PCL. Human chondrocytes cultured on the scaffolds exhibited higher cell viability and improved chondrogenic phenotype with upregulation of genes associated with type II collagen and aggrecan synthesis. Bioprinted PEU scaffolds could, therefore, provide a potential platform for the fabrication of bespoke, pro-chondrogenic tissue engineering constructs.
Pyrrocidine, a molecular off switch for fumonisin biosynthesis

Sarocladium zeae is a fungal endophyte of maize and can be found co-inhabiting a single seed with Fusarium verticillioides, a major mycotoxigenic food safety threat. S. zeae produces pyrrocidines A and B that inhibit the growth of F. verticillioides and may limit its spread within the seed to locations lacking S. zeae. Although coinhabiting single seeds, the fungi are generally segregated in separate tissues. To understand F. verticillioides’ protective physiological response to pyrrocidines we sequenced the F. verticillioides transcriptome upon exposure to purified pyrrocidine A or B at sub-inhibitory concentrations. Through this work we identified a F. verticillioides locus FvABC3 (FVEG_11089) encoding a transporter critical for resistance to pyrrocidine. We also identified FvZBD1 (FVEG_00314), a gene directly adjacent to the fumonisin biosynthetic gene cluster that was induced several thousand-fold in response to pyrrocidines. FvZBD1 is postulated to act as a genetic repressor of fumonisin production since deletion of the gene resulted in orders of magnitude increase in fumonisin. Further, pyrrocidine acts, likely through FvZBD1, to shut off fumonisin biosynthesis. This suggests that S. zeae is able to hack the secondary metabolic program of a competitor fungus, perhaps as preemptive self-protection, in this case impacting a mycotoxin of central concern for food safety.
The Structure of Amyloid Versus the Structure of Globular Proteins

The issue of changing the structure of globular proteins into an amyloid form is in the focus of researchers' attention. Numerous experimental studies are carried out, and mathematical models to define the essence of amyloid transformation are sought. The present work focuses on the issue of the hydrophobic core structure in amyloids. The form of ordering the hydrophobic core in globular proteins is described by a 3D Gaussian distribution analog to the distribution of hydrophobicity in a spherical micelle. Amyloid fibril is a ribbon-like micelle made up of numerous individual chains, each representing a flat structure. The distribution of hydrophobicity within a single chain included in the fibril describes the 2D Gaussian distribution. Such a description expresses the location of polar residues on a circle with a center with a high level of hydrophobicity. The presence of this type of order in the amyloid forms available in Preotin Data Bank (PDB) (both in proto- and superfibrils) is demonstrated in the present work. In this system, it can be assumed that the amyloid transformation is a chain transition from 3D Gauss ordering to 2D Gauss ordering. This means changing the globular structure to a ribbon-like structure. This observation can provide a simple mathematical model for simulating the amyloid transformation of proteins.
Two-Dimensional Carbon-Rich Conjugated Frameworks for Electrochemical Energy Applications.

Following a 15-year-long investigation on graphene, two-dimensional (2D) carbon-rich conjugated frameworks (CCFs) have drawn growing research interest as a new generation of multifunctional materials. Typical 2D CCFs include 2D π-conjugated polymers (also classified as 2D π-conjugated covalent organic frameworks) and 2D π-conjugated metal-organic frameworks, which are characterized by layer-stacked periodic frameworks with high in-plane π-conjugation. These unique structures endow 2D CCFs with regular porosities, large specific surface areas, and superior chemical stability. In addition, 2D CCFs exhibit certain notable properties (e.g., excellent electronic conductivity, designable topologies, and defined catalytic/redox-active sites), which have motivated increasing efforts to explore 2D CCFs for electrochemical energy applications. In this Perspective, the structural features and synthetic principles of 2D CCFs are briefly introduced. Moreover, we discuss recent achievements in 2D CCFs designed for various electrochemical energy conversion (electrocatalysis) and storage (supercapacitors and batteries) applications. Particular emphasis is placed on analyzing the precise structural regulation of 2D CCFs. Finally, we provide an outlook about the future development of synthetic 2D CCFs for electrochemical applications, which concerns novel monomer design, chemical methodology/strategy establishment, and a roadmap towards practical applications.
Genome wide distribution of G-quadruplexes and their impact on gene expression in malaria parasites

Mechanisms of transcriptional control in malaria parasites are still not fully understood. The positioning patterns of G-quadruplex (G4) DNA motifs in the parasite’s AT-rich genome, especially within the var gene family which encodes virulence factors, and in the vicinity of recombination hotspots, points towards a possible regulatory role of G4 in gene expression and genome stability. Here, we carried out the most comprehensive genome-wide survey, to date, of G4s in the Plasmodium falciparum genome using G4Hunter, which identifies G4 forming sequences (G4FS) considering their G-richness and G-skewness. We show an enrichment of G4FS in nucleosome-depleted regions and in the first exon of var genes, a pattern that is conserved within the closely related Laverania Plasmodium parasites. Under G4-stabilizing conditions, i.e., following treatment with pyridostatin (a high affinity G4 ligand), we show that a bona fide G4 found in the non-coding strand of var promoters modulates reporter gene expression. Furthermore, transcriptional profiling of pyridostatin-treated parasites, shows large scale perturbations, with deregulation affecting for instance the ApiAP2 family of transcription factors and genes involved in ribosome biogenesis. Overall, our study highlights G4s as important DNA secondary structures with a role in Plasmodium gene expression regulation, sub-telomeric recombination and var gene biology.
Accuracy and Reliability of Commercial Wrist-Worn Pulse Oximeter During Normobaric Hypoxia Exposure Under Resting Conditions

ABSTRACT Purpose: The present study analyzed peripheral blood oxygen saturation (SpO2) and heart rate (HR) measurements taken on the Garmin fēnix® 5X Plus watch, comparing them to measurements taken on a standard medical-grade pulse oximeter during normobaric hypoxia exposure under resting conditions. Methods: Thirteen women (mean ± SD: Age 20 ± 1 years, height 165 ± 5 cm, mass, 67 ± 9 kg) and ten men (mean ± SD: Age 21 ± 3 years, height 177 ± 6 cm, mass 78 ± 11 kg) sat inside a customized environmental chamber while the fraction of inspired oxygen (FIO2) was adjusted to simulate altitudes of 12,000; 10,000; 8,000; 6,000; and 900 ft. The novel commercial device (Garmin fēnix®) and a medical-grade pulse oximeter (Nonin® 7500) were used to measure SpO2 and HR in triplicate at each simulated altitude. Bland–Altman analyses were used to assess differences between methods. Results: Bland–Altman analysis indicated 3.3% bias for SpO2 measurements taken on the Garmin fēnix® at 12,000 ft of simulated altitude (limits of agreement: −1.9–8.6%). Mean differences in SpO2 measurements were smaller at the remaining simulated altitudes, where bias measurements ranged from 0.7% to 0.8%. The Garmin fēnix® also underestimated heart rate, but those discrepancies were minimal (bias measurements at all simulated altitude exposures were < 1.0 bpm). Conclusions: With the exception of readings taken at 12,000 ft of simulated altitude, the Garmin fēnix® exhibits minimal overestimation of SpO2 and minimal underestimation of HR during simulated altitude exposure. These data suggest the Garmin fēnix® watch may be a viable method to monitor SpO2 and HR under most ambient environmental conditions.