Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-1 subtype diversity and phylogenetic insight into non-B subtype transmission in Slovenia, 1989-2013.

INTRODUCTION Disease progression, drug resistance mutations, and treatment strategies may vary by HIV-1 subtype. This study determined HIV-1 subtypes circulating in Slovenia, a Central European country with an HIV-1 epidemic driven by men who have sex with men, focusing on molecular epidemiology of non-B subtypes. METHODS A total of 367 HIV-1 sequences were included. Subtype was assigned by employing eight different HIV subtyping tools coupled with maximum likelihood phylogenetic analyses. RESULTS The subtyping tools COMET, jpHMM, and REGA 3.0 exhibited the best performance on the dataset studied. Phylogenetic analyses showed a 14.7% prevalence of non-B subtypes, with subtype A detected most frequently (4.9%), followed by CRF02_AG (2.4%), subtype C (1.1%), subtypes D, G, and CRF01_AE (0.8% each), and subtypes F and CRF22_01A1 (0.3% each). A subtype could not be assigned to 12 sequences (3.3%), indicating potential unique recombinant forms. Non-B subtypes were significantly associated with a heterosexual route of transmission and infection acquired in Eastern Europe, Africa, or Asia. CONCLUSION In a country where subtype B is predominant, non-B subtypes were observed in one out of seven patients, a non-negligible proportion, which underlines the importance of systematic surveillance of HIV subtype diversity and the corresponding molecular epidemiology.
The Cost of Capital of Cross-Listed Firms

This paper analyses the cost of capital of firms with foreign equity listings. Our purpose is to shed light on the question whether international and domestic asset pricing models yield a different estimate of the cost of capital for cross-listed stocks. We distinguish between (i) the multifactor ICAPM of Solnik (1979) and Sercu (1980) including both the global market portfolio and exchange rate risk premia and (ii) the single factor domestic CAPM. We test for the significance of the cost of capital differential in a sample of 336 cross-listed stocks from nine countries in the period 1980–99. Our hypothesis is that the cost of capital differential is substantial for firms with international listings, as these are often large multinationals with a strong international orientation. We find that the asset pricing models yield a significantly different estimate of the cost of capital for only 12% of the cross-listed companies. The size of the cost of capital differential is around 50 basis points for the US, 80 basis points for the UK and 100 basis points for France.
THE EFFECT OF INDIVIDUAL PERCEPTIONS OF INTERNET CONNECTION QUALITY AND DIGITAL FINANCIAL SERVICES’ PLATFORM CREDIBILITY ON THE USAGE OF DIGITAL FINANCIAL SERVICES

Digital Financial Services (DFS) present an opportunity to expand financial access within society; however, DFS adoption remains relatively low in Indonesia. This study aims to assess how individual perceptions of internet connection quality and the credibility of DFS platforms influence their adoption in Indonesia. Utilizing data from the 2020 Digital Economy Household Survey (DEHS) and employing the probit and ordered probit estimation models, the research demonstrates a positive and significant relationship between perceptions of internet connection quality, DFS platform credibility, and the likelihood and frequency of DFS usage. Notably, a majority of DFS users fall under the "occasionally used" category, indicating usage ranging from 3 to 30 minutes per day. The study underscores the need for collaborative efforts to establish a well-distributed, trusted, and secure DFS ecosystem. This necessitates addressing regulatory frameworks, enhancing infrastructure, and improving public financial literacy to enhance user acceptance and utilization of DFS platforms.
Application of Multimodal MRI in the Early Diagnosis of Autism Spectrum Disorders: A Review

Autism spectrum disorder (ASD) is a neurodevelopmental disorder in children. Early diagnosis and intervention can remodel the neural structure of the brain and improve quality of life but may be inaccurate if based solely on clinical symptoms and assessment scales. Therefore, we aimed to analyze multimodal magnetic resonance imaging (MRI) data from the existing literature and review the abnormal changes in brain structural–functional networks, perfusion, neuronal metabolism, and the glymphatic system in children with ASD, which could help in early diagnosis and precise intervention. Structural MRI revealed morphological differences, abnormal developmental trajectories, and network connectivity changes in the brain at different ages. Functional MRI revealed disruption of functional networks, abnormal perfusion, and neurovascular decoupling associated with core ASD symptoms. Proton magnetic resonance spectroscopy revealed abnormal changes in the neuronal metabolites during different periods. Decreased diffusion tensor imaging signals along the perivascular space index reflected impaired glymphatic system function in children with ASD. Differences in age, subtype, degree of brain damage, and remodeling in children with ASD led to heterogeneity in research results. Multimodal MRI is expected to further assist in early and accurate clinical diagnosis of ASD through deep learning combined with genomics and artificial intelligence.
Self‐similar rupture implied by scaling properties of volcanic earthquakes occurring during the 2004‐2008 eruption of Mount St. Helens, Washington

We analyze a group of 6073 low‐frequency earthquakes recorded during a week‐long temporary deployment of broadband seismometers at distances of less than 3 km from the crater at Mount St. Helens in September of 2006. We estimate the seismic moment (M0) and spectral corner frequency (f0) using a spectral ratio approach for events with a high signal‐to‐noise (SNR) ratio that have a cross‐correlation coefficient of 0.8 or greater with at least five other events. A cluster analysis of cross‐correlation values indicates that the group of 421 events meeting the SNR and cross‐correlation criteria forms eight event families that exhibit largely self‐similar scaling. We estimate the M0 and f0 values of the 421 events and calculate their static stress drop and scaled energy (ER/M0) values. The estimated values suggest self‐similar scaling within families, as well as between five of eight families (i.e., M0∝f0−3 and ER/M0∝ constant). We speculate that differences in scaled energy values for the two families with variable scaling may result from a lack of resolution in the velocity model. The observation of self‐similar scaling is the first of its kind for such a large group of low‐frequency volcanic tectonic events occurring during a single active dome extrusion eruption.
Modeling biological-physical feedback mechanisms in marine systems

The marine biosphere is an active and important component of the Earth system. Biologically induced changes in physical oceanic properties through phytoplankton cause potential positive and negative feedbacks. In particular, surface floating cyanobacteria can increase light absorption and the albedo at the ocean surface and decrease momentum input by wind. In this thesis I study the feedbacks mediated by marine cyanobacteria on the physics of the upper ocean. Using the water column model GOTM, I set up a coupled biological-physical model to investigate local effects of the feedbacks on the mixed layer dynamics. Extending these one-dimensional studies, I use the general circulation model MITgcm and set up a three-dimensional coupled biological-physical model to study also non-local effects on the ocean circulation on a basin-wide scale. I show that the absorption feedback by phytoplankton leads to a surface warming and a subsurface cooling. The temperature differences caused by cyanobacteria are more pronounced than those caused by other phytoplankton. The positive absorption and wind feedbacks mediated by cyanobacteria are stronger than the negative albedo feedback. Cyanobacteria mediate a local shallowing of up to 30% of the surface mixed layer due to the absorption feedback and of around 10% due to the wind feedback. By warming the ocean surface and shallowing the mixed layer cyanobacteria locally lead to environmental conditions promoting their own growth. Due to the circulation, colder subsurface waters can be transported and thus also lead to a surface cooling at other locations. Increased absorption by phytoplankton and cyanobacteria affects the meridional overturning circulation. Reduced surface wind stress mediated by cyanobacteria leads to a distortion of the subtropical gyre and to reduced subtropical downwelling and equatorial upwelling. In a warmer environment the local effects of the absorption and the wind feedback are stronger than today. With increasing temperatures cyanobacteria shift northwards and lead to stronger effects of the biological-physical feedbacks in some regions, but weaker effects in other regions. Increasing temperatures might lead to a spread of cyanobacteria, if they are able to adapt to temperatures higher than 30 degrees C, and thus a larger ocean region would be affected by the induced feedbacks. Yet, the model studies do not indicate a substantial increase in the area covered by cyanobacteria. This thesis provides the first quantitative estimate of how surface floating cyanobacteria feed back on their physical environment. Overall, the results suggest that surface floating cyanobacteria and their feedbacks on light absorption and wind stress need to be taken into account in ocean models used for climate scenarios in order to capture changes in the dynamics of the upper ocean.
Autofluidization of pyroclastic flows propagating on rough substrates as shown by laboratory experiments

This study investigates the influence of the substrate surface roughness on the emplacement mechanisms of pyroclastic flows. We carried out laboratory experiments on gravitational flows generated from the release of initially fluidized or nonfluidized columns of fine particles (diameter d = 0.08 mm) in a horizontal channel. The roughness of the channel base was uniform in each experiment, created by gluing particles of diameter d0 = 0.08 to 6 mm to the base. Other things being equal, the flow runout distance increased with the channel base roughness (d0) to a maximum of about twice that of flows on a smooth substrate when d0 = 1.5–3 mm, before decreasing moderately at higher roughness values of d0 = 6 mm. Long runout originated mainly during the late stages of emplacement as flow deceleration was strongly reduced at high substrate roughness. This was caused by (partial) autofluidization due to an upward air flux escaping from the substrate interstices in which flow particles settled. Autofluidization was evidenced by high pore fluid pressure measurements at the base of initially nonfluidized flows and also by reduced flow runout when the interstices were initially partially filled so that less air was available. Furthermore, the runout distance of flows of large particles (d = 0.35 mm), which could not be fluidized by the ascending air flux, was independent of the substrate roughness. This study suggests that autofluidization caused by air escape from the interstices of a rough substrate is one important mechanism to explain the common long runout distance of pyroclastic flows even on subhorizontal topographies.
Mesquite removal and mulching impacts on herbage production on a semidesert grass-shrub rangeland

The objectives of our study were to determining the effects of velvet mesquite (Prosopis velutina) removal, control of the resulting basal sprouts, and mulching treatments on herbage production (standing biomass) and selected soil chemicals (nutrients) shown to affect herbage production on the Santa Rita Experimental Range. Mesquite control treatments consisted of overstory removal by chain saw with and without control of the resulting basal sprouts. Mulching treatments were applications of mesquite wood chips, commercial compost, or lopped-and-scattered mesquite branchwood. Mesquite removal resulted in increases for total herbage production and the production of native herbaceous species. Production of the nonnative Lehmann lovegrass (Eragrostis lehmanniana), the dominant herbaceous species, was unchanged. The mulching treatments did not affect herbage production. None of the treatments affected soil chemical properties thought to influence herbage production.
Assessment of Lime and Lemon Production in Nepal

A survey was undertaken to assess the state of art of production, scale of plantation and genetic diversity of lime and lemon in Nepal during 2000/01. Lime and lemon were extensively distributed throughout the mid hills stretching from Ilam district in the east to Darchula district in the far west of the country. Out of total plantations, 80 percent was lime plantations. Over 76 percent of lime and 23 percent of lemon trees were recently planted. Average size of holding was 45 trees per orchards for lime and lemon. Over 60 percent of orchards were grown as secondary enterprises. Most of the orchards were under rainfed conditions in marginal lands with poor management. Varieties were local landraces. The finding revealed that the maximum production of lime and lemon was 235 and 147 kg per tree per year, respectively. Off-season production was negligible. Blossom and fruit drops due to a long spell of drought and strong hailstorms during flowering and fruiting season as well as citrus green stink bug, shoot borer, leaf miner, lemon butterfly, and citrus aphid were the major problems. Similarly, die-back, citrus canker, gummosis, and tristiza virus were known as serious diseases in the country. The findings revealed a great potentiality of exploiting indigenous genetic resources and existing domestic market opportunities for both main as well as off-season lime production. This offers for viable economic opportunities to help improving economic conditions of small and commercial farmers particularly to the hill districts of the country. Keywords: Citrus, acid lime, germplasm, hill lemon. J. Inst. Agric. Anim. Sci. 23:49-58
Three‐dimensional seismic velocity structure around the focal area of the 1978 Miyagi‐Oki earthquake

We performed a 3D seismic tomography around the rupture area of the 1978 Miyagi‐Oki earthquake (M 7.4) using both onshore and offshore seismic station data. In our results, the subducting oceanic crust and the mantle wedge of the overriding plate were imaged as the landward dipping low P‐wave velocity (∼7.0 km/s) layer and the high velocity (∼8.0 km/s) layer above it, respectively. Most of the earthquakes were relocated along the plate boundary, including the mainshock and the aftershocks of 16 August 2005 Miyagi‐Oki earthquake (M 7.2). The relationship between spatial extents of the rupture areas of the 1978 and 2005 earthquakes and the velocity variation in the mantle wedge suggests that the heterogeneity of the upper plate delimits the extent of the rupture area of large (M > 7) interplate earthquakes.
Predicting prey availability for stream salmonids

iii ACKNOWLEDGEMENTS v TABLE OF CONTENTS vi LIST OF TABLES vii LIST OF FIGURES viii LIST OF APENDICES ix INTRODUCTION 1 MATERIALS AND METHODS 6 Study Site 6 Sampling Design 10 Laboratory Procedures 12 Statistical Analyses 15 RESULTS 17 Composition of the drift, benthic and salmonid diet samples 17 Total 18 Behavioral drifting invertebrates found within diet samples 19 Relationship between salmonid growth and the abundance of behavioral drifting invertebrates in the drift 21 DISCUSSION 28 REFERENCES 32
Mirror mode structures in the asymmetric Hermean magnetosheath: Hybrid simulations

Results of two global three‐dimensional hybrid simulations of the solar wind interaction with the Hermean magnetosphere are presented for southward and northward interplanetary magnetic field (IMF) orientations. Important dawn‐dusk asymmetries of the Hermean bow shock and magnetosheath are observed depending on the IMF orientation. For the southward IMF, the dawnside has a thicker magnetosheath with higher β values and slower bulk velocities compared to the duskside, whereas for the northward IMF, the duskside has a thicker and higher β magnetosheath with slower bulk velocities. Mirror mode activity consequently appears at the dawnside for the southward IMF and at the duskside for the northward IMF. A mechanism for the bow shock and magnetosheath asymmetries is proposed and discussed in the context of the Hermean and terrestrial magnetosheaths.
Lead isotope composition of Central American volcanoes: Influence of the Galapagos plume

Lead isotopic analyses of lavas from Central America, both along and behind the volcanic arc, help to clarify source components in the mantle wedge. Analysis of previous Pb isotopic data had implied that little or no marine sediment lead was added to the Central American source region, as all samples fell within the MORB field, in contrast to other information (e.g., Ba/La, 10Be, 87Sr/86Sr) that indicated a high subduction component. The data presented here include several analyses of local marine sediment, showing it to be exceptionally unradiogenic in Pb and thus permitting high sediment contributions to the mantle source region without significant changes in Pb isotopes. Combined Pb‐Nd and Pb‐Sr isotopic diagrams clearly illustrate the influence of crustal contamination for samples from Guatemala and Honduras, and of subducted sediment for all lavas of the volcanic front. Samples collected behind the volcanic front are derived from mixing between enriched and depleted mantle sources, and in central Costa Rica (extending to the back arc) overlap Pb, Sr and Nd isotope values for both Cocos Island and some components of the Galapagos hot spot. The restricted geographical occurrence of the enriched mantle signature in Central America, coupled with the persistence of the signal well into the back arc region, imply that these lavas are sampling Galapagos plume‐influenced mantle. The presence of this plume component beneath southern Central America and extending to the northeast beneath the Caribbean confirms a Galapagos hot spot origin for this part of Caribbean Plate.
Determination of Sex by Discriminant Function Analysis of Mandibles From two Croatian Archaeological Sites

Many morphologic characteristics and metric methods have been employed for sex determination. If there are only skulls or fragmented jaws available, identification of sex is made on differences in shape and size of the cranial morphological marks. In the present study, an attempt is made to establish standards for sex determination from fragmentary and complete mandibles from two archeological sites in Croatia. On each mandible 18 parameters were measured. Descriptive and multifactorial statistics were performed on the collected data and seven discriminant functions were generated. A discriminant function derived from nine mandibular variables provided 92.06% reliability in sex determination. Length of the mandibular body (males 88.34+/-4.67 mm ; females 81.41+/-3.04 mm), mandibular angle (males 118.47+/-6.16° ; females 125.63+/-5.37°) and minimum ramus breadth (males 31.26+/-2.94 mm ; females 28.36+/-2.15 mm) are detected as variables providing the best separation of the sexes. Results of this study show that mandibles can be used for determining sex, as stated in other similar studies.
Routine coagulation assays underestimate levels of antithrombin‐dependent drugs but not of direct anticoagulant drugs in plasma from patients with cirrhosis

There is increasing recognition that thrombotic complications may occur in patients with cirrhosis, and literature on antithrombotic treatment in these patients is rapidly emerging. Due to extensive haemostatic changes in patients with cirrhosis, careful monitoring of anticoagulant therapy may be required. Recent data suggest that plasma levels of low molecular weight heparin (LMWH) are substantially underestimated by the anti‐activated factor X (anti‐Xa) assay in patients with cirrhosis. We studied the in vitro recovery of antithrombin (AT)‐dependent and –independent anticoagulant drugs in plasma from 26 patients with cirrhosis and 30 healthy controls and found substantially reduced anti‐Xa levels when AT‐dependent anticoagulant drugs were added to the plasma of patients with cirrhosis. LMWH (0·2 U/ml) had the poorest recovery in plasma from patients with cirrhosis (0·13 ± 0·06 U/ml, compared to 0·23 ± 0·03 U/ml in controls, P < 0·0001), followed by unfractionated heparin and fondaparinux. In contrast, the recovery of rivaroxaban and dabigatran was identical between patients and controls. These data suggest that the anti‐Xa assay cannot be used to monitor AT‐dependent anticoagulant drugs in patients with cirrhosis, as it substantially underestimates drug levels. The direct factor Xa and IIa inhibitors, however, may be monitored through the respective anti‐Xa and anti‐IIa assays in patients with cirrhosis.
Modelling directivity effects of the October 31, 2002 (Mw=5.8)Molise, Southern Italy, earthquake

Acceleration time series recorded by the Italian Strong Motion Network (RAN) during the October 31, 2002 (Mw=5.8), Molise earthquake, are employed in order to investigate source effects on the ground motion in the epicentral area. We consider two different seismogenic sources: a fault model inferred from inversion of teleseismic, regional and local seismic signals [Vallée and Di Luccio, 2005], and a fault model based on seismotectonic data [Basili and Vannoli, 2005]. Both source studies suggest a deep location of the earthquake fault plane (ranging from 6.0 to 20.1 km and from 12.0 to 19.9 km, respectively), however, with considerably different fault lengths (5.2 and 10.5 km, respectively), and widths (14.2 and 8 km, respectively). Due to these differences, only the second model allows for effective horizontal unilateral rupture propagation. Finite fault effects are modelled by the Deterministic-Stochastic-Method (DSM) [Pacor et al., 2005], and the Hybrid Integral-Composite source model (HIC) [Gallovic and Brokesova, 2006]. In both methods k-square slip distributions on the faults are considered. We simulate the October 31, 2002 earthquake considering: 1) Vallée and Di Luccio [2005] faultwith a bilateral rupture propagation, and 2) Basili and Vannoli [2005] fault with unilateral directions of the rupture propagation. The spectral attenuation is modelled using a regional estimate of the quality factor [Castro et al., 2004] and k values estimated from acceleration records. Comparison between synthetic and recorded data at nearby stations (hypocentral distances < 60 km) performed in terms of frequency content and peak ground motion, favours the model with unilateral propagation of the rupture. Assuming the source model with unilateral rupture propagation, we utilize both asymptotic and full wave field methods in order to simulate ground shaking scenarios for an area extending up to 150 km epicentral distance. These results are then subjected to comparison with peak ground accelerations recorded in the far field.