Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Multiplex Amplicon PCR Technology to Efficiently and Timely Generate Rift Valley Fever Virus Sequence Data for Genomic Surveillance

Rift Valley fever (RVF) is a febrile vector-borne disease endemic in Africa and continues to spread in new territories. It is a climate-sensitive disease mostly triggered by abnormal rainfall patterns. The disease is associated with high mortality and morbidity in both humans and livestock. RVF is caused by the Rift Valley fever virus (RVFV) of the genus Phlebovirus in the family Phenuiviridae. It is a tripartite RNA virus with three genomic segments: small (S), medium (M) and large (L). Pathogen genomic sequencing is becoming a routine procedure and a powerful tool for understanding the evolutionary dynamics of infectious organisms, including viruses. Inspired by the utility of amplicon-based sequencing demonstrated in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Ebola, Zika and West Nile viruses, we report an RVFV sample preparation based on amplicon multiplex polymerase chain reaction (amPCR) for template enrichment and reduction of background host contamination. The technology can be implemented rapidly to characterize and genotype RVFV during outbreaks in a near-real-time manner. To achieve this, we designed 74 multiplex primer sets covering the entire RVFV genome to specifically amplify the nucleic acid of RVFV in clinical samples from an animal tissue. Using this approach, we demonstrate achieving complete RVFV genome coverage even from samples containing a relatively low viral load. We report the first primer scheme approach of generating multiplex primer sets for a tripartite virus which can be replicated for other segmented viruses.
Biodegradation of Microtoxic Phenylpropanoids (Phenylpropanoic Acid and Ibuprofen) by Bacteria and the Relevance for Their Removal from Wastewater Treatment Plants

The NSAID ibuprofen (2-(4-isobutylphenyl)propanoic acid) and the structurally related 3-phenylpropanoic acid (3PPA), are widely used pharmaceutical and personal care products (PPCPs) which enter municipal waste streams but whose relatively low rates of elimination by wastewater treatment plants (WWTPs) are leading to the contamination of aquatic resources. Here, we report the isolation of three bacterial strains from a municipal WWTP, which as a consortium are capable of mineralizing ibuprofen. These were identified as the Pseudomonas citronellolis species, termed RW422, RW423 and RW424, in which the first two of these isolates were shown to contain the catabolic ipf operon responsible for the first steps of ibuprofen mineralization. These ipf genes which are associated with plasmids could, experimentally, only be transferred between other Sphingomonadaceae species, such as from the ibuprofen degrading Sphingopyxis granuli RW412 to the dioxins degrading Rhizorhabdus wittichii RW1, generating RW421, whilst a transfer from the P. citronellolis isolates to R. wittichii RW1 was not observed. RW412 and its derivative, RW421, as well as the two-species consortium RW422/RW424, can also mineralize 3PPA. We show that IpfF can convert 3PPA to 3PPA-CoA; however, the growth of RW412 with 3PPA produces a major intermediate that was identified by NMR to be cinnamic acid. This and the identification of other minor products from 3PPA allows us to propose the major pathway used by RW412 to mineralize 3PPA. Altogether, the findings in this study highlight the importance of ipf genes, horizontal gene transfer, and alternative catabolic pathways in the bacterial populations of WWTPs to eliminate ibuprofen and 3PPA.
THE FREQUENCY OF OCCURRENCE OF SPEECH SOUNDS IN SPOKEN ENGLISH

This paper presents some results of a study of the words used in telephone conversations. These show that many words have a much higher relative occurrence in conversation than in written matter, and that conversation in general is characterized by a more intensive use of its commonest words than written matter. Curves are presented showing the number of different words found among a given total number of words, not only in individual conversations but also in samples as high as 10,000 total words. Finally the paper shows the distribution of the fundamental sounds of speech in conversation and shows the differences in the relative occurrence of the speech sounds in conversation as compared with written matter, in nouns as compared with verbs, adjectives, etc., and in the few frequently used words as compared with the many infrequently used words. The results are based on about 80,000 recorded words.
Optic nerve head perfusion changes in eyes with proliferative diabetic retinopathy treated with intravitreal ranibizumab or photocoagulation: a randomized controlled trial

Background: Proliferative diabetic retinopathy (PDR) is a serious sight-threatening disease, and half of the patients with high-risk PDR can develop legal blindness within 5 years, if left untreated. This study was aimed at comparing panretinal photocoagulation (PRP) and intravitreal ranibizumab injections in terms of radial peripapillary capillary (RPC) density on optical coherence tomography angiography (OCTA) in patients with treatment-naive PDR. Methods: This open-label, prospective, randomized clinical trial included 50 patients with treatment-naive PDR with optic disc neovascularization and randomized them into two groups: group 1, with patients undergoing two sessions of PRP 2 weeks apart, and group 2, with patients received three intravitreal ranibizumab injections (0.5 mg) 1 month apart for 3 consecutive months. Patients underwent a full ophthalmological examination, including best-corrected distance visual acuity (BCDVA) measurement in the logarithm of minimal angle of resolution (logMAR) notation and OCTA before intervention and monthly after the last laser session or the first intravitreal ranibizumab injection for 3 months of follow-up. Visual field (VF) was tested at the beginning and end of 3 months. Results: Forty-two (84%) eyes completed the 3-month follow-up, including 22 eyes in the PRP group (88%) and 20 (80%) eyes in the ranibizumab group. The two groups were comparable in terms of demographic characteristics, diabetes duration, baseline BCDVA, glycated hemoglobin level, OCTA parameters, VF indices, and intraocular pressure (all P > 0.05). The RPC density change from baseline to the 3-month follow-up was significantly lower in the PRP group than in the ranibizumab group (mean difference in RPC density change: - 3.61%; 95% confidence interval: - 5.57% to - 1.60%; P = 0.001). The median (interquartile range) logMAR change from baseline to the 3-month follow-up (0.0 [0.2]) was significantly higher in the PRP group than in the ranibizumab group (- 0.15 [0.3]; P < 0.05). The median changes in central foveal thickness from baseline to the 3-month follow-up differed significantly between the two groups (P = 0.001). Conclusions: In eyes with PDR and neovascularization of the disc RPC density on OCTA increased in the ranibizumab group and decreased in the PRP group. Visual acuity gain was higher in the ranibizumab group than in the PRP group. Future multicenter trials addressing our limitations are required to verify the findings of this study.
Confusion noise level due to galactic and extragalactic binaries

We have revised our earlier rough estimate of the combined galactic and extragalactic binary confusion noise level curve for gravitational waves. This was done to correct some numerical errors and to allow for roughly three frequency bins worth of information about weaker sources being lost for each galactic binary signal that is removed from the data. The results are still based on the spectral amplitude estimates for different types of galactic binaries reported by Hils et al in 1990, and assume that the gravitational wave power spectral densities for other galaxies are proportional to the optical luminosities. The estimated confusion noise level drops to the LISA instrumental noise level at between roughly 3 and 8 mHz.
Magnetic Neutral Sheets in Evolving Fields - Part Two - Formation of the Solar Corona

It is shown in the previous paper that whenever twisted flux tubes are bundled together, they are subject to dynamical nonequilibrium and internal neutral point reconnection, causing rapid dissipation of their torsion. In the present paper we explore the consequences of this general dynamical dissipation in the magnetic fields that produce the active corona of the Sun. The footpoints of the field are continually manipulated by the subphotospheric convection, so that the lines of force are continually wrapped and rotated about each other. The dynamical dissipation of the wrapping and rotation transfers the work done on the footpoints directly into heat in the corona, at a rate estimated to be of the order of 10/sup 7/ ergs cm/sup -2/ s/sup -1/. The effect appears to be the principal source of heat to the visible corona. This general picture implies that all magnetic fields extending outward from convecting astronomical bodies produce intense heating of the tenuous outer atmospheres of these bodies, in general agreement with the observed fact of the universal activity of stars and galaxies.
A distributed event-triggered scheme for discrete-time multi-agent consensus with communication delays

This study mainly investigates the event-triggered data transmission in discrete-time multi-agent consensus problem with communication delays. A new distributed event-triggered scheme is proposed for the considered multi-agent network model. An action of the agent is triggered by an `event' which is a well-defined condition on the system state. For the proposed event-triggered protocol, the authors prove that the multi-agent network will achieve consensus asymptotically. Numerical examples are provided to demonstrate the effectiveness of the obtained theoretical results.
Functional imaging of the exposed brain

When the brain is exposed, such as after a craniotomy in neurosurgical procedures, we are provided with the unique opportunity for real-time imaging of brain functionality. Real-time functional maps of the exposed brain are vital to ensuring safe and effective navigation during these neurosurgical procedures. However, current neurosurgical practice has yet to fully harness this potential as it pre-dominantly relies on inherently limited techniques such as electrical stimulation to provide functional feedback to guide surgical decision-making. A wealth of especially experimental imaging techniques show unique potential to improve intra-operative decision-making and neurosurgical safety, and as an added bonus, improve our fundamental neuroscientific understanding of human brain function. In this review we compare and contrast close to twenty candidate imaging techniques based on their underlying biological substrate, technical characteristics and ability to meet clinical constraints such as compatibility with surgical workflow. Our review gives insight into the interplay between technical parameters such sampling method, data rate and a technique’s real-time imaging potential in the operating room. By the end of the review, the reader will understand why new, real-time volumetric imaging techniques such as functional Ultrasound (fUS) and functional Photoacoustic Computed Tomography (fPACT) hold great clinical potential for procedures in especially highly eloquent areas, despite the higher data rates involved. Finally, we will highlight the neuroscientific perspective on the exposed brain. While different neurosurgical procedures ask for different functional maps to navigate surgical territories, neuroscience potentially benefits from all these maps. In the surgical context we can uniquely combine healthy volunteer studies, lesion studies and even reversible lesion studies in in the same individual. Ultimately, individual cases will build a greater understanding of human brain function in general, which in turn will improve neurosurgeons’ future navigational efforts.
POSSIBLE RISKS IN AGRITOURISM AND WAYS TO OVERCOME THEM (BASED ON THE EXAMPLE OF THE GURIA REGION)

Agritourism activities are sometimes associated with certain risks, protection against which can be seen as one of the important factors contributing to the development of agritourism. The purpose of the article is to analyze the risks in agritourism on the example of Guria, one of the regions of Georgia, and to outline ways to overcome them. The document outlines the risks associated with overcrowding in tourist destinations, climate change, seasonality of tourism, spread of various pests/diseases of agricultural plants and animals, food safety, environmental and air pollution, improper waste management, financial support for agritourism, etc. Their solution often requires both individual and joint coordinated efforts of farmers, local governments and visitors themselves, resulting in the opportunity to offer tourists a variety of safe tourism products in the form of recreation, interesting attractions, and a better understanding of local life, which will make their stay more enjoyable, useful and interesting. The main results of the article are based on the data of our research, which was conducted by direct survey (questionnaire) in one of the regions of Georgia - Guria. The study determined that there are 566 farms in all three municipalities of the Guria region (281 in Ozurgeti municipality, 110 in Chokhatauri municipality, in Lanchkhut municipality - 175), 400 farmers took part in the study, 80 of whom are engaged in agritourism (41 in Ozurgeti municipality, 16 in Chokhataur municipality, 23 in Lanchkhut). The topic analyzes the peculiarities of the existing risk management and offers recommendations on measures to be implemented on the example of the Guria region.
Caveolin-1-Related Intervention for Fibrotic Lung Diseases

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal interstitial lung disease (ILD) for which there are no effective treatments. Lung transplantation is the only viable option for patients with end-stage PF but is only available to a minority of patients. Lung lesions in ILDs, including IPF, are characterized by alveolar epithelial cell (AEC) senescence and apoptosis and accumulation of activated myofibroblasts and/or fibrotic lung (fL) fibroblasts (fLfs). These composite populations of fLfs show a high rate of basal proliferation, resist apoptosis and senescence, and have increased migration and invasiveness. They also more readily deposit ECM proteins. These features eventuate in progressive destruction of alveolar architecture and loss of lung function in patients with PF. The identification of new, safer, and more effective therapy is therefore mandatory for patients with IPF or related ILDs. We found that increased caveolin-1 and tumor suppressor protein, p53 expression, and apoptosis in AECs occur prior to and then with the proliferation of fLfs in fibrotic lungs. AECs with elevated p53 typically undergo apoptosis. fLfs alternatively demonstrate strikingly low basal levels of caveolin-1 and p53, while mouse double minute 2 homolog (mdm2) levels and mdm2-mediated degradation of p53 protein are markedly increased. The disparities in the expression of p53 in injured AECs and fLfs appear to be due to increased basal expression of caveolin-1 in apoptotic AECs with a relative paucity of caveolin-1 and increased mdm2 in fLfs. Therefore, targeting caveolin-1 using a caveolin 1 scaffolding domain peptide, CSP7, represents a new and promising approach for patients with IPF, perhaps other forms of progressive ILD or even other forms of organ injury characterized by fibrotic repair. The mechanisms of action differ in the injured AECs and in fLfs, in which differential signaling enables the preservation of AEC viability with concurrent limitation of fLf expansion and collagen secretion. The findings in three models of PF indicate that lung scarring can be nearly abrogated by airway delivery of the peptide. Phase 1 clinical trial testing of this approach in healthy volunteers has been successfully completed; Phase 1b in IPF patients is soon to be initiated and, if successful, will be followed by phase 2 testing in short order. Apart from the treatment of IPF, this intervention may be applicable to other forms of tissue injury characterized by fibrotic repair.
Antenatal and Postnatal Sequelae of Oxidative Stress in Preterm Infants: A Narrative Review Targeting Pathophysiological Mechanisms

The detrimental effects of oxidative stress (OS) can start as early as after conception. A growing body of evidence has shown the pivotal role of OS in the development of several pathological conditions during the neonatal period, which have been therefore defined as OS-related neonatal diseases. Due to the physiological immaturity of their antioxidant defenses and to the enhanced antenatal and postnatal exposure to free radicals, preterm infants are particularly susceptible to oxidative damage, and several pathophysiological cascades involved in the development of prematurity-related complications are tightly related to OS. This narrative review aims to provide a detailed overview of the OS-related pathophysiological mechanisms that contribute to the main OS-related diseases during pregnancy and in the early postnatal period in the preterm population. Particularly, focus has been placed on pregnancy disorders typically associated with iatrogenic or spontaneous preterm birth, such as intrauterine growth restriction, pre-eclampsia, gestational diabetes, chorioamnionitis, and on specific postnatal complications for which the role of OS has been largely ascertained (e.g., respiratory distress, bronchopulmonary dysplasia, retinopathy of prematurity, periventricular leukomalacia, necrotizing enterocolitis, neonatal sepsis). Knowledge of the underlying pathophysiological mechanisms may increase awareness on potential strategies aimed at preventing the development of these conditions or at reducing the ensuing clinical burden.
A numerical model of a convective cell driven by non-uniform horizontal heating.

A numerical model of thermal convection for a two-dimensional laminar, non-linear, non-rotating, incompressible, viscous fluid contained in a rectangle and heated non-uniformly from below is investigated. Two studies are made, one for a stress free bottom boundary and the other for a constant applied stress along the bottom. The Boussinesq equations are integrated numerically by means of the explicit scheme of DuFort and Frankel (1953) and in each case the top and side boundaries are both insulating and rigid. In the first study the dependence of the cellular convective motion and isotherms upon the Prandtl number, F, and the horizontal Rayleigh number, Ra, is examined. A single asymmetric convective cell develops as the Rayleigh number is increased. The asymmetry and intensity of the circulation increase markedly with increasing horizontal Rayleigh number but respond slightly to changes in the Prandtl number. The bottom boundary layer thickness is also examined and is found to decrease as the Rayleigh number increases. In the second study, calculations are presented for a single Rayleigh number and Prandtl number and a moderate range in applied stress. The stress is applied in opposition to the thermal driving. As the stress increases, the thermal circulation weakens and the opposing circulation becomes stronger. The increase in stress results in a change from a thermal to a dual, containing both thermal and stress driven circulations of the same magnitude, to a stress driven circulation. Thesis Supervisor: Robert C. Beardsley Title: Assistant Professor of Oceanography IL____I___ _l _ _tl I-~UI-YII~ LLX I-U~. II -I -^--~-LI -Ln
Comparison between continuous and discrete frequency domain solution methods for structural steady state calculations with the finite element method

– Different solution methods, using finite element method in continuous and discrete frequency domain, are compared with each other in order to find the most appropriate method for the estimation of steady state vibrations in linear structural and mechanical problems. The purpose of this paper is to describe the procedures. , – The continuous and some relevant discrete frequency domain solution methods are compared by an analytical investigation as well as by the numerical examination of a simple model. Finally, results for a more relevant example using finite elements are presented. , – It is shown that the steady state computation using the continuous frequency domain system description delivers the exact solution for a given system. , – Based on the presented results, the use of continuous frequency domain system description is recommendable in most cases.
Combining Interior-Point and Pivoting Algorithms for Linear Programming

We propose a new approach to combine linear programming LP interior-point and simplex pivoting algorithms. In any iteration of an interior-point algorithm we construct a related LP problem, which approximates the original problem, with a known strictly complementary primal-dual solution pair. Thus, we can apply Megiddo's Megiddo, N. 1991. On finding primal-and dual-optimal bases. ORSA J. Comput.31 63-65. pivoting procedure to compute an optimal basis for the approximate problem in strongly polynomial time. We show that, if the approximate problem is constructed from an interior-point iterate sufficiently close to the optimal face, then any optimal basis of the approximate problem is an optimal basis for the original problem. If the LP data are rational, the total number of interior-point iterations to create such a sufficient approximate problem is bounded by a polynomial in the data size. We develop a modification of Megiddo's procedure and discuss several implementation issues in solving the approximate problem. We also report encouraging computational results for this combined approach.
On the global stability of two-dimensional, incompressible, elastic bars in uniaxial extension

When a rectangular bar is subjected to uniaxial tension, the bar usually deforms (approximately) homogeneously and isoaxially until a critical load is reached. A bifurcation, such as the formation of shear bands or a neck, may then be observed. One approach is to model such an experiment as the in-plane extension of a two-dimensional, homogeneous, isotropic, incompressible, hyperelastic material in which the length of the bar is prescribed, the ends of the bar are assumed to be free of shear and the sides are left completely free. It is shown that standard constitutive hypotheses on the stored-energy function imply that no such bifurcation is possible in this model due to the fact that the homogeneous isoaxial deformation is the unique absolute minimizer of the elastic energy. Thus, in order for a bifurcation to occur either the material must cease to be elastic or the stored-energy function must violate the standard hypotheses. The fact that no local bifurcations can occur under the assumptions used herein was known previously, since these assumptions prohibit the load on the bar from reaching a maximum value. However, the fact that the homogeneous deformation is the absolute minimizer of the energy appears to be a new result.