Miracle-dz/UniFAR-FTUs huggingface dataset:
Rapid detection of cytochrome cd1-containing nitrite reductase encoding gene nirS with loop-mediated isothermal amplification assay

The cytochrome cd1-containing nitrite reductase, nirS, plays an important role in biological denitrification. Consequently, investigating the presence and abundance of nirS is a commonly used approach to understand the distribution and potential activity of denitrifying bacteria, in addition to denitrifier communities. Herein, a new molecular biology technique termed loop-mediated isothermal amplification (LAMP) was developed to rapidly detect nirS gene using those of Pseudomonas aeruginosa to optimize the assay. The LAMP assay relied on a set of four primers that were designed to recognize six target sequence sites, resulting in high target specificity. The specificity of the assay was confirmed by the lack of amplification when using DNA from 15 other bacterial species lacking nirS gene. The limit of detection for the LAMP assay under optimized conditions was 1.87 pg/reaction of genomic DNA, which was an order of magnitude lower than that required by conventional PCR assays. Moreover, a cell-template based LAMP assay was also developed for detecting nirS gene that directly used bacterial cells as template rather than genomic DNA. Only 1 h was needed from the addition of bacterial cells to the reaction to the verification of amplification success, and bulky and sophisticated equipment were not needed. Further, the nirS gene of P. aeruginosa in spiked seawater samples could be detected with both the DNA-template based LAMP assay and the cell-template based LAMP assay, thereby demonstrating the practicality of in-field use of them. In summary, the LAMP assays described here represent a rapid, user-friendly, and cost-effective alternative to conventional PCR.
Molecular Breeding of Sweetpotato Carotenoids

Sweetpotato [sweet potato; Ipomoea batatas (L.) Lam. ] is the seventh most valued food crop of the world. It has an inherent ability to grow under diverse agroecological and microclimatic zones ranging from tropical and subtropical zones to temperate areas with its tuberous roots enriched with the secondary metabolites of immense nutritional value. Among these, carotenoids are the most conspicuous one for having their use in nutritional, pharmaceutical, food, feed, aquaculture, and cosmetic industries. In food industries, carotenoids are used as food additives being antioxidants with attractive colors. Despite the immense economic importance, sweetpotato has received lesser attention in terms of its breeding with improved varieties. The conventional method of breeding by crossing has not been much successful due to the complexity of genome sterility and cross-incompatibility. Hence, the modern molecular breeding approaches, e.g. genetic, genomic, and metabolic (pathway) engineering, have been applied to this crop by some of researchers in Japan, Korea, and China to generate various cultivars with improved quantities and qualities of carotenoids. This has also opened a new gate for molecular breeders to engineer new sweetpotato cultivars enriched with carotenoids under current global scenario of dramatically rising climatic changes where novel food resources are bitterly needed, especially under alarmingly growing world population, the majority of which suffers from malnutrition.
A note on the effect of urbanization on temperature in Ibadan

The effects of urbanization on the temperature characteristics of a tropical city are examined. Twenty-year records of maximum, minimum and mean temperatures were extracted from four established meteorological stations in the Ibadan area. Three stations are within the urban region and the remaining one, which serves as the control station, is situated in a rural environment, outside the city. Analysis shows that the urban heat island effect of the city is clearly reflected in the magnitudes of night-time minimum and mean temperatures, whereas the day-time maximum temperature is slightly lower, in the city. There is no clear evidence of any change in the urban temperature excess over time. The heat island effects of the city are more noticeable towards the end of the dry season and in the early part of the rainy season. The mean heat island, as reflected by the night-time minimum temperature, is about 1.0 K during the dry season, and 0.5 K during the rainy season.
A Comparison of the Effects of Exchangeable Sodium and Potassium upon the Physical Condition of Soils

The effects of exchangeable sodium and of exchangeable potassium upon soil physical condition were compared by means of permeability ratio, air to water, and modulus of rupture determinations. The permeability ratio is a measure of the change in pore-size distribution due to the action of water and the modulus of rupture is a measure of soil crusting. The permeability ratio and modulus of rupture increased markedly with increasing exchangeable-sodium-percentage, whereas, increases in the exchangeable-potassium-percentage had little effect. The relation of the permeability ratio to exchangeable-sodium-percentage can be expressed by an exponential equation of the form, y = aeᵇˣ, whereas, the modulus of rupture is linearly related to exchangeable-sodium-percentage by the equation y' = mx + c. The parameters a, b, m and c of the respective equations are positively correlated with cation exchange capacity and total specific surface.
Spatial and temporal rainfall variability near the Amazon-Tapajós confluence

[1] Do the influences of river breezes or other mesoscale effects lead to a systematic river proximity bias in Amazon rainfall data? We analyzed rainfall for a network of 38 rain gauges located near the confluence of the Tapajos and Amazon rivers in the eastern Amazon Basin. Tipping bucket rain gauges worked adequately in the Amazon rainfall regime, but careful field calibration and comparison with collocated conventional rain gauges were essential to incorporate daily totals from our array into regional maps. Stations very near the large rivers miss the afternoon convective rain, as expected if a river breeze promotes subsidence over the river, but paradoxically, this deficiency is more than compensated by additional nocturnal rainfall at these locations. The NOAA Climate Prediction Center (CPC) Morphing technique (CMORPH) passive infrared inferred rainfall data do an adequate job of describing medium scale variability in this region, but some localized breeze effects are not resolved at 0.25° resolution. For areas inland from the rivers, nocturnal rainfall contributes less than half of total precipitation. A large-scale rainfall increase just to the west of Santarem manifests itself locally as a ‘tongue' of enhanced rain from along the wide area of open water at the Tapajos-Amazon confluence. The Amazon River breeze circulation affects rainfall more than does the Tapajos breeze, which moves contrary to the predominant wind. East of the riverbank, the effects of the Tapajos breeze extend only a few kilometers inland. Rainfall increases to the north of the Amazon, possibly the result of uplift over elevated terrain. Dry season rainfall increases by up to 30% going away from the Amazon River, as would be expected given breeze-induced subsidence over the river.
Mesoscale convective complexes in Africa

Abstract Digitized full-disk infrared satellite imagery from the European geostationary satellite (Meteosat) for 1986 and 1987 was used to construct a climatology of mesoscale convective complexes (MCCs) in Africa One hundred ninety-five systems formed over Africa and its near vicinity during the two-year study period. From this database, characteristics of African MCCs were calculated. The results indicate that these MCCs display many of the same characteristics as those found in the Americas, the Indian subcontinent, and the western Pacific region. The systems are predominantly nocturnal and tend to form over or in the immediate vicinity of land. Much of the activity occurs over the African Sahel. while comparatively little occurs over the equatorial rain forest. The average lifetime of African MCCs is about 11.5 h, whereas systems in the western Pacific region and the Americas last about 11 and 10 h, respectively. The size distributions of the African systems are also extremely similar to those of the .
Uncertainty assessment for contaminant leaching from flood water retention areas

A probabilistic framework was developed to quantify the risk of groundwater contamination by flood water seepage from retention areas. The involved flow and transport processes have been described and a mass balance model was developed to calculate the contaminant infiltration. During the model application the flood data (flood water depth, flood duration, etc.) were compiled in scenarios and were linked to the soil information in the retention area. The uncertainty of the saturated hydraulic conductivity and of the linear sorption coefficient of the topsoil was described in probability density functions generated from field data and literature values and can be used for Monte Carlo simulations to calculate the risk of groundwater contamination.
Counting synapses using FIB / SEM microscopy : a true revolution for ultrastructural volume reconstruction

on the number of synaptic profi les per unit area and their average cross-sectional length in ultrathin sections of tissue (Colonnier and Beaulieu, 1985). The other technique is the disector method, that is based on the number of synaptic profi les that are present in a reference section but that disappear in another section separated by a known distance (Sterio, 1984). Both methods rely on the analysis of a limited number of single sections and thus, the estimate of the number of synapses per unit volume may vary according to the sampling methods used in a particular study (DeFelipe et al., 1999). In addition, there is no general consensus regarding sampling procedures or the criteria to identify synapses. As a consequence, there are often discrepancies in the results obtained in different laboratories and they can be diffi cult to compare. In this context, the ideal approach would be to directly analyze samples reconstructed from serial sections. This can be achieved by conventional serial-section transmission electron microscopy (TEM), but this is a time consuming and technically demanding task, mainly due to the diffi culties in obtaining large numbers of correlative serial sections (see for example Harris et al., 2006; Hoffpauir et al., 2007). To overcome these problems, methods have been developed that avoid the need for ultrathin sectioning, such as serial section electron tomography (Soto et al., 1994). Other techniques facilitate the collection of serial ultrathin sections INTRODUCTION In the cerebral cortex there are two main morphological types of synapses, Gray’s type I and type II synapses (Gray, 1959) that correspond to the asymmetric and symmetric types of Colonnier, respectively (Colonnier, 1968; see also, Colonnier, 1981; Peters, 1987; Peters et al., 1991; Peters and Palay, 1996). In general, asymmetric synapses are considered to be excitatory (glutamatergic) and symmetric synapses inhibitory (GABAergic). Moreover, asymmetric synapses are much more abundant (75–95% of all neocortical synapses) than symmetric synapses (5–25%: for reviews, see Houser et al., 1984; White, 1989; DeFelipe and Fariñas, 1992; DeFelipe et al., 2002). Therefore, understanding the distribution, size and proportion of the two major cortical types of synapses is extraordinarily important in terms of function. Considerable effort has been dedicated to defi ne methods that accurately estimate the number of synapses in the cerebral cortex, as well as the changes that take place during the course of normal life, and under pathological or experimental conditions. As a result, stereological methods have been developed to estimate the threedimensional characteristics of synapses from two-dimensional observations, and to estimate their size and number in a given volume of tissue. Two of these stereological methods have been commonly used, one of which is a size-frequency method based Counting synapses using FIB/SEM microscopy: a true revolution for ultrastructural volume reconstruction
Evaluation of improved sheep breeds in pastoral areas of Yabello district, Southern Oromia, Ethiopia

This study was conducted at Yabello district of Borana zone with the objectives of evaluating the productive performance of the 25% Dorper crossbred and the local blackhead Somali sheep under agro pastoralists’ conditions, creating awareness, improving pastoralists’ knowledge and skill. The training was given to the selected pastoralists, development agents, and experts on the importance and management of the improved sheep. A total of four F1 50% Dorper crossbred were provided for the two established Pastoralists’ Research Groups (PRGs). Both quantitative and qualitative data were collected using appropriate methods. The quantitative data were analyzed using simple descriptive statistics and an independent sample t-test while qualitative were analyzed using pairwise ranking and narration methods. The result of the study indicated that 25% Dorper crossbred ram were significantly higher in birth weight, weight at 6 months, and yearling (marketable) weight at 12 months compared to the local blackhead Somali sheep. Moreover, Dorper crossbred had better marketability, weight, meat, drought, and disease resistance compared to their counterparts. As a result, all concerned parties should make 25% Dorper crosses more popular and scaled up in order to improve the productive performance of the local blackhead Somali sheep in the study areas.
Effects of differential cementation on the sonic velocities of upper cretaceous skeletal grainstones (Southeastern Netherlands)

ABSTRACT P-wave velocities measured in Cretaceous skeletal grainstones from Limburg, southeastern Netherlands, are significantly higher in moderately cemented samples than in poorly cemented samples from similar depositional facies. Petrography suggests that this relationship is due to differences in the extent of development of intergranular cementation as influenced by original grain mineralogy, rather than a significant difference in primary porosity. The time-average velocity equation for a calcite matrix fails to predict the cementation effect on sonic velocity at high porosities. Linear and nonlinear time-average regressions show strong correlation between velocity and porosity. Whether the underlying trend is linear or nonlinear is a fundamental question that cannot be determined with this data set. Comparison between carbonate grainstones and siliciclastic sandstones reveals that: (1) the grainstones have gradients in velocity-porosity space similar to those in siliciclastic arenites but have velocities that are up to 0.3 km/s higher than those in clean arenites and up to 0.8 km/s higher than in argillaceous arenites; and (2) grainstones develop a rigid framework that transports elastic waves at significantly higher porosities than arenites, 40-50% compared to 30-40%. Higher sonic velocity presumably results from the higher matrix velocity of calcite versus quartz, and the higher elastic moduli created by the effective cement bridges connecting grains.
Somatically acquired hypomethylation of IGF2 in breast and colorectal cancer

The imprinted insulin-like growth factor 2 (IGF2) gene is expressed predominantly from the paternal allele. Loss of imprinting (LOI) associated with hypomethylation at the promoter proximal sequence (DMR0) of the IGF2 gene was proposed as a predisposing constitutive risk biomarker for colorectal cancer. We used pyrosequencing to assess whether IGF2 DMR0 methylation is either present constitutively prior to cancer or whether it is acquired tissue-specifically after the onset of cancer. DNA samples from tumour tissues and matched non-tumour tissues from 22 breast and 42 colorectal cancer patients as well as peripheral blood samples obtained from colorectal cancer patients [SEARCH (n=case 192, controls 96)], breast cancer patients [ABC (n=case 364, controls 96)] and the European Prospective Investigation of Cancer [EPIC-Norfolk (n=breast 228, colorectal 225, controls 895)] were analysed. The EPIC samples were collected 2–5 years prior to diagnosis of breast or colorectal cancer. IGF2 DMR0 methylation levels in tumours were lower than matched non-tumour tissue. Hypomethylation of DMR0 was detected in breast (33%) and colorectal (80%) tumour tissues with a higher frequency than LOI indicating that methylation levels are a better indicator of cancer than LOI. In the EPIC population, the prevalence of IGF2 DMR0 hypomethylation was 9.5% and this correlated with increased age not cancer risk. Thus, IGF2 DMR0 hypomethylation occurs as an acquired tissue-specific somatic event rather than a constitutive innate epimutation. These results indicate that IGF2 DMR0 hypomethylation has diagnostic potential for colon cancer rather than value as a surrogate biomarker for constitutive LOI.
Nature and onset age of neotectonic regime in the northern core of Isparta Angle, SW Turkey

The Isparta Angle (IA) is a reverse Λ-shaped morphotectonic structure located to the north of Antalya Gulf in the Eastern Mediterranean Sea. It resulted from the northward curvature of the originally E–W-trending Tauride orogenic belt owing to the nappe emplacements and related clockwise and anti-clockwise rotations in a time period of Early Paleocene to Early Pliocene. The IA is included in the southwest Anatolian tensional neotectonic domain and characterized by a series of grabens and horsts bounded by active normal faults of dissimilar length and trend. The evolutionary history of the graben-horst system is episodic. It is evidenced by two graben fills. These are older and modern (younger) graben fills separated by an intervening angular unconformity. The modern graben fill is nearly flat-lying (non-deformed) whereas older graben fill was deformed into a series of anticlines and synclines with ENE-trending curvi-linear axes by a short-term compressive tectonic regime operated in NNW–SSE direction during Late Pliocene. The diagnostic structures taking a part in the development of grabens and shaping the northern section of the IA are the margin-boundary normal faults. They occur in numerous single and several fault zones displaying a basin ward facing step-like land shape. Most of fault segments, particularly the master faults, are active and have a capacity of creating destructive earthquakes with a magnitude (up to Mw = 7.0). This is evidenced by both the historical and instrumental period earthquakes. Both the focal mechanism solution of earthquakes and the stereographic plots of slip-plane data, measured on the active margin-boundary faults of various grabens comprising the IA, on the Schmidt lower hemisphere net obviously reveal that the IA is under the influence of the tensional neotectonic regime, not a compressive tectonic regime, i.e. the sinistral strike-slip shearing along the Pliny arc has not propagated yet onshore, and its commencement age is Early Quaternary.
Caries Management Aided by Fluorescence-Based Devices

Fluorescence-based intraoral cameras are increasingly gaining more interest in the modern dental practice, as an aid for the early detection of carious lesions. Such devices can have different operating systems, such as infrared lasers, quantitative light fluorescence (QLF), or LED lights, but they all rely on the fluorescent properties of tooth structures. Healthy enamel and enamel affected by demineralization have different light-scattering properties, a fact that allows for distinction under excitation with light of a known wavelength. The central problem in the treatment of dental decay is that operational care is still considered the predominant management plan for caries control in the general practice. Devices that use fluorescence have the potential to improve the detection and management of carious lesions significantly. Currently, there are several intraoral devices that employ fluorescence on the market, but more validation studies would be required to uphold the interest of the newly developed devices and to justify their reliability in clinical practice. Dental professionals cannot yet solely rely on one single-fluorescence device for incipient caries diagnosis, but they already present themselves as useful adjunctive tools to traditional examination methods.
Widespread tropical atmospheric drying from 1979 to 1995

A daily gridded data base of tropical precipitable water (PW) from 1979–95 shows 3% average drying from 1979–87 to 1989–95. Spatial patterns of the change are consistent with strengthening of the thermally direct overturning circulation. Moistening in most of the Inter‐Tropical Convergence Zone (ITCZ), the South Pacific Convergence Zone (SPCZ), and the Americas is more than offset by drying in oceanic subtropical highs and desert land areas.
Airborne gravity gradiometry: Terrain corrections and elevation error

Terrain corrections for airborne gravity gradiometry data are calculated from a digital elevation model (DEM) grid. The relative proximity of the terrain to the gravity gradiometer and the relative magnitude of the density contrast often result in a terrain correction that is larger than the geologic signal of interest in resource exploration. Residual errors in the terrain correction can lead to errors in data interpretation. Such errors may emerge from a DEM that is too coarsely sampled, errors in the density assumed in the calculations, elevation errors in the DEM, or navigation errors in the aircraft position. Simple mathematical terrains lead to the heuristic proposition that terrain-correction errors from elevation errors in the DEM are linear in the elevation error but follow an inverse power law in the ground clearance of the aircraft. Simulations of the effect of elevation error on terrain-correction error over four measured DEMs support this proposition. This power-law relation may be used in selecting an optimum survey flying height over a known terrain, given a desired terrain-correction error.