Miracle-dz/UniFAR-FTUs huggingface dataset:
3-D vector velocity estimation with row-column addressed arrays

The concept of 2-D row-column (RC) addressed arrays for 3-D imaging have shown to be an interesting alternative to 2-D matrix array, due to the reduced channel count. However, the properties for RC arrays to estimate blood velocities have never been reported, which is of great importance for a clinical implementation of this type of array. The aim of this study is, thus, to develop a technique for estimating 3-D vector flow with a RC array using the transverse oscillation (TO) method. The properties are explored both in a simulation study and with a prototype probe for experimental use. In both setups, a 124 channel 2-D RC array with integrated apodization, pitch = 270 μm and a center frequency of 3.0 MHz was used. The performance of the estimator was tested on a simulated vessel (Ø = 12 mm) with a parabolic flow profile and a peak velocity of 1 m/s. Measurements were made in a flowrig (Ø = 12 mm) containing a laminar parabolic flow and a peak velocity of 0.54 m/s. Data was sampled and stored on the experimental ultrasound scanner SARUS. Simulations yields relative mean biases at (-1.1%, -1.5%, -1.0%) with mean standard deviations of σ̃ were (8.5%, 9.0%, 1.4%) % for (vx; vy; vz) from a 3-D velocity vector in a 15° rotated vessel with a 75° beam-to-flow angle. In the experimental setup with a 90° beam-to-flow angle, the relative mean biases were (-2.6%, -1.3%, 1.4%) with a relative standard deviation of (5.0%, 5.2%, 1.0%) for the respective transverse, lateral and axial velocity component.
Gene therapy for cystic fibrosis

Background: Although cystic fibrosis (CF) seems a good candidate for gene therapy (GT), 15 years of intense investigations and a number of clinical trials have not yet produced a viable clinical GT strategy. Objective: To review the strategies used to optimize the current GT vectors, to overcome the extra- and cellular barriers to efficient gene delivery to the CF airways, and the poor long-term persistence of gene expression. Methods: We describe a selected set of patents, which were published in the last 5 years (2003 – 2008), with the aim of covering the issues related to GT and the airways; however, in some cases, they are intended for a broader use than CFGT. World Intellectual Property Organization (WIPO), the European network of patent databases, and the US Patent Office were queried. Results/conclusions: Novel biodegradable and biocompatible non-viral GT vectors have been characterized and used for gene transfer into the airways, along with physical methods to enhance their concentration at the level of airway epithelium. Less immunogenic and more efficient adeno-associated viral vectors are being studied, whereas integrating lentiviral viruses are currently investigated for their potential use to give prolonged gene expression. Methods for overcoming the mucus barrier and for increasing accessibility to the basolateral receptors have been described. Although a wealth of GT vectors has been produced, their fabrication, storage and administration are still critical issues, and these shortcomings are tackling translation of laboratory non-viral and viral vectors to the clinic. Thus, in the near future, we expect new developments in GT vector technology, above all of delivery, expression and safety. These improvements, along with better comprenhension of CF lung disease pathophysiology, will aid CFGT to achieve clinical benefits in CF patients.
Urine Examination and Renal Function in Adult Patients Attending Outpatient Clinics in Kumasi: Cross-Sectional Study

Background: Early identification and treatment of kidney diseases in adults are important in prevention of chronic kidney diseases. Objective: To determine the prevalence of abnormal urine dipstick findings, abnormal urine microscopy and chronic kidney diseases (CKD) among patients reporting at KomfoAnokye Teaching Hospital (KATH), Kumasi, Ghana. Design: Cross-sectional study Setting: Directorate of Medicine and Polyclinic outpatient clinics of KATH. Methods: A total of 424 patients, 20 years and over reporting for the first time to KATH were recruited, 414 were included in the analysis and 10 were excluded. 76 had neither diabetes mellitus (DM) nor systemic hypertension 92 had only DM, 106 had only hypertension and 140 had both. A questionnaire was filled and anthropometric measurements were taken. Serum creatinine was determined from venous blood samples and urine dipsticks and microscopy were done. The estimated glomerular filtration rate (eGFR) was calculated using the Cockcroft and Gault equation. CKD was defined and classified by The National Kidney Foundation’s Kidney Diseases Outcomes Quality Initiative guidelines. Results: The prevalence of proteinuria was 16%, glycosuria was 16%, abnormal urine microscopy 6%, haematuria 1% and CKD 39%. There were no cases of Stage 5 CKD. The mean (sd) creatinine was 98.61 (27.30) μmol/L, mean urea was 4.41 (1.71) mmol/L and mean eGFR was 118.5 (57.5)ml/min/1.73 m2. There were significantly more males than females and more hypertensives than normotensives with CKD. Conclusion: The prevalence of proteinuria and CKD in patients attending clinics in Kumasi, Ghana was high. There is the need for more and regular screening of patients especially those with hypertension and DM.
Organic Solvent and Laundry Detergent Stable Crude Protease from Nile Tilapia (Oreochromis niloticus) Viscera

The objective of this study was to explore the characteristic activity of crude protease extracted from Nile tilapia viscera. The optimal temperature and pH of the crude protease from Nile tilapia viscera were 60°C and 8.0, respectively. The enzyme was stable to heat treatment up to 45°C and over a pH range of 7–11 for 30–120 min. The protease was effectively inhibited by phenylmethylsulfonyl fluoride (PMSF) and soybean trypsin inhibitor (SBTI). It was activated by Ca2+ and Fe2+, while inhibited in order by Hg2+ > Fe3+ > Cu2+ > Mn2+. The protease showed great stability toward Tween 20, Tween 80, and Triton X-100 and moderate stability toward sodium dodecyl sulfate (SDS) and hydrogen peroxide (H2O2). Nevertheless, it showed excellent stability and compatibility with various solid and liquid laundry detergents at temperatures from 30 to 50°C. The protease showed not only an improved activity but also a satisfied stability in 25% (v/v) organic solvents for 7 days at 37°C. At higher concentrations (50–75%), the protease activity was decreased by hydrophilic solvents, except dimethyl sulfoxide (DMSO), whereas it was enhanced by hydrophobic solvents. Thus, the crude protease is an excellent candidate as a biocatalyst for detergents, foods, pharmaceuticals, and environmental applications.
Metagenomics: Access to Unculturable Microbes in the Environment

More than 99% of the microbes that exist in the environment can not be cultivated easily. Thus, most of the microbes in the environment have not been described and accessed for biotechnology or basic research. "Metagenomics," which is the culture-independent genomic analysis of the microbial community, attempts to overcome these difficulties. This technology has the potential for providing insight into the functional dimensions of environmental genomic datasets and will help to achieve a major goal of environmental microbiology, the complexities of microbial community function and interaction among these microbes. This article gives an overview of the current knowledge of metagenomic technologies and presents examples of studies that have used these techniques. Furthermore, future technologies related to understanding the metagenome are discussed.
A Partial Budget Analysis for Phosphorus-Based Nutrient Management Plans for Connecticut Dairy Farms

Th is study estimated changes in costs of manure handling, costs of the fertilizer replacement value of manure, and expected changes in net revenues associated with the implementation of manure nutrient management plans (NMPs) based on the agronomic critical concentration for P using a partial budget analysis. Th e net revenue from manure management practices traditionally used by farmers in a baseline year was compared with the expected net revenue from practices recommended in NMPs for four dairy farms over 4 or 5 yr in Connecticut. Yields were not measured across the 2862 fi eld-years. Compared with the baseline year, the average annual estimated change in net revenue associated with manure applications based on the NMPs was a negative $2,900 for one large farm and a positive $17,600 for the other large farm, while the net revenue change was a positive $200 and $1,400 for the two medium-sized farms. In years aft er the baseline the average annual estimated change in net revenue for manure management practices for the NMPs compared with the practices reported by farmers was a negative $2,200 for one large farm and a positive $19,300 for the other large farm; the net revenue change was a positive $2,500 and $1,300 for the medium-sized farms. Th e net revenue changes from the NMPs were determined largely by the existing soil test P and K values. Th e complexity of implementing the NMPs made it diffi cult to obtain the expected net revenue changes.
On the occurrence of annual layers in Dome Fuji ice core early Holocene ice

Abstract. Whereas ice cores from high-accumulation sites in coastal Antarctica clearly demonstrate annual layering, it is debated whether a seasonal signal is also preserved in ice cores from lower-accumulation sites further inland and particularly on the East Antarctic Plateau. In this study, we examine 5 m of early Holocene ice from the Dome Fuji (DF) ice core at a high temporal resolution by continuous flow analysis. The ice was continuously analysed for concentrations of dust, sodium, ammonium, liquid conductivity, and water isotopic composition. Furthermore, a dielectric profiling was performed on the solid ice. In most of the analysed ice, the multi-parameter impurity data set appears to resolve the seasonal variability although the identification of annual layers is not always unambiguous. The study thus provides information on the snow accumulation process in central East Antarctica. A layer counting based on the same principles as those previously applied to the NGRIP (North Greenland Ice core Project) and the Antarctic EPICA (European Project for Ice Coring in Antarctica) Dronning Maud Land (EDML) ice cores leads to a mean annual layer thickness for the DF ice of 3.0 ± 0.3 cm that compares well to existing estimates. The measured DF section is linked to the EDML ice core through a characteristic pattern of three significant acidity peaks that are present in both cores. The corresponding section of the EDML ice core has recently been dated by annual layer counting and the number of years identified independently in the two cores agree within error estimates. We therefore conclude that, to first order, the annual signal is preserved in this section of the DF core. This case study demonstrates the feasibility of determining annually deposited strata on the central East Antarctic Plateau. It also opens the possibility of resolving annual layers in the Eemian section of Antarctic ice cores where the accumulation is estimated to have been greater than in the Holocene.
Behavioural effects of minor sex pheromone components in Brazilian apple leafroller Bonagota cranaodes (Lep., Tortricidae)

Abstract: The behavioural response of Brazilian apple leafroller males, Bonagota cranaodes (Meyrick), to natural and synthetic sex pheromone was studied in a wind tunnel. Calling females elicited upwind flights followed by landing and wingfanning at the source in 72% of the males tested. Female gland extracts, with the main compound (E, Z)3,5dodecadienyl acetate released at 100 pg/min, attracted 57% of the males to the source. Few males (1%) were attracted to the main compound alone, released at the same rate. Even a synthetic blend of all five gland compounds eliciting an antennal response, formulated according to their proportion in female gland extracts, was barely attractive (7%). Comparison of this synthetic blend and female gland extracts indicates a behavioural role of other gland compounds. Male attraction was significantly increased (34%) in response to a 100 : 5 : 5 : 5‐blend of the main compound and three minor gland compounds, (Z)‐5‐dodecenyl acetate, (E, Z)‐3,5‐tetradecadienyl acetate, and (Z)‐9‐hexadecenyl acetate.
Managing heterogeneity: the importance of grazing and environmental variation on post-fire succession in heathlands

Summary 1. Semi-natural habitats have been shaped by human disturbance regimes for centuries. Spatially and temporally heterogeneous land-use practices, such as cutting, burning, grazing and turf-cutting, have resulted in complex mosaic landscapes that are of high priority for conservation in Europe. Contemporary conservation subjects these systems to management regimes that are generally less diverse, in terms of disturbances and finescale temporal and spatial variability, than traditional land use, but the ecological consequences of these simplifications are unclear. 2. We investigated the interactive effects of fire and grazing on plant species composition and diversity along local environmental (moisture) gradients in coastal heathlands. A replicated series of post-fire successions ( n = 12) was initiated in three heathland habitats and the areas subjected to two grazing regimes. Floristic and environmental data were recorded in permanent plots over a 5-year period. Community data were analysed using multivariate ordination techniques (principal components analysis, partial redundancy analyses, and principal response curves) and generalized linear models. 3. Fire induced strong successional trends in the species composition of the heathlands. These trends differed among heathland habitats, and with grazing. Strong interactions between fire, habitat and grazing implied that the effect of grazing on the successional dynamics differed among habitats. Species diversity decreased in the first year after fire but increased beyond the pre-fire levels during succession. This trend was not affected by local environment or grazing, although there were main effect differences in diversity between environments and grazing regimes. 4. Synthesis and applications . Our results demonstrate that the two management practices do not have simple additive effects within the semi-natural system studied, as grazing created ecological opportunities for additional sets of species, increased variability among habitats, and added complexity to the post-fire successional dynamics. In order to preserve diversity, conservation management should thus aim to preserve the level of complexity of the traditional management regimes, both in terms of the actual disturbances (e.g. fire and grazing) as well as the spatial scales at which they are applied. Further, the considerable change in these effects along the local environmental gradient brings into question the efficiency of general management prescriptions, and indicates that local environmental variability should be taken into account in the conservation of semi-natural habitats.
Effects of Food Plants of Host Herbivores on Development of a Midgut-Resident Tachinid Parasitoid, Compsilura concinnata (Diptera: Tachinidae), and Two Hemocoel-Resident Parasitoids

ABSTRACT The tachinid fly Compsilura concinnata (Meigen) parasitizes insect herbivores throughout the larval period and develops in the midgut. Because the fly larva is directly exposed to the host's gut contents, including nutrients and toxic allelochemicals in the plants eaten by the host, it may be more susceptible to variation in the chemistry of the host's food plants. To evaluate this potential disadvantage of midgut parasitism, we compared the influence of foods of the lepidopteran host Mythimna separata (Walker) on the development of endoparasitoids between C. concinnata and two other species, the tachinid Exorista japonica Townsend and the braconid Cotesia kariyai (Watanabe), whose larvae develop in the host's hemocoel. When the parasitized hosts consumed one of four kinds of plants, all three parasitoid species showed a higher survival, a larger body size, and faster development on two natural food plants (maize and sorghum) than on two alternative foods (kidney bean and Japanese radish). Our results suggest that the development of C. concinnata during midgut parasitism was affected by the host's food species, but that the effects did not differ from those for endoparasitoids with hemocoel parasitism.
A complex chromosomal rearrangement with a translocation 4;10;14 in a fertile male carrier: ascertainment through an offspring with partial trisomy 14q24→1q22 and partial monosomy 4q27→q28

Complex chromosomal rearrangements (CCRs) are usually associated with infertility or subfertility in male carriers. If fertility is maintained, there is a high risk of abnormal pregnancy outcome. Few male carriers have been identified by children presenting with mental retardation/congenital malformations (MR/CM) or by spontaneous abortions of the spouses. We report a de novo CCR with five breakpoints involving chromosomes 4, 10 and 14 in a male carrier who was ascertained through a son presenting with MR/CM due to an unbalanced karyotype with partial trisomy 14 and partial monosomy 4. The child has a healthy elder brother. In the family history no abortions were reported. No fertility treatment was necessary. Cytogenetic analysis from the affected son showed a reciprocal translocation t(4;10) with additional chromosomal material inserted between the translocation junctions in the derivative chromosome 10. The father showed the same derivative chromosome 10 but had additionally one aberrant chromosome 14. Further molecular cytogenetic analyses determined the inserted material in the aberrant chromosome 10 as derived from chromosome 14 and revealed a small translocation with material of chromosome 4 inserted into the derivative chromosome 14. Thus the phenotype of the son is supposed to be associated with a partial duplication 14q13→q24.1 and a partial monosomy 4q27→q28. Including our case we are aware of eleven CCR cases with fertile male carriers. In eight of these families normal offspring have been reported. We propose that exceptional CCRs in fertile male carriers might form comparatively simple pachytene configurations increasing the chance of healthy offspring.
Coarse-scale relationships between seabirds and zooplankton off south-eastern Tasmania

Observations were made of seabird and zooplankton distribution in the waters adjacent to south-eastern Tasmania to examine correspondence at coarse scales (tens of kilometres). The distribution of seabirds was related mainly to changes in the water depth (and distance from land) over the length of the transect, whereas the distribution of zooplankton related to temporal changes. Significantly different associations of seabird species occurred in Storm Bay (mainly species breeding within the bay), and over the shelf-edge (with many non-breeding species dominant). Zooplankton diversity varied during the study, being greatest at the beginning (May) and end (September) of the study. Little correspondence was found between the distribution of seabirds and zooplankton at the community level, but there were significant relationships for several species, such as diving petrels and gannets. The lack of an overall correspondence between seabirds and zooplankton may have been due to the patchiness of seabird and zooplankton distribution, limits to the requirements of seabirds to find maximum prey densities (instead only needing to find 'enough'), the lack of certainty about whether seabirds were foraging when observed, and behavioural interactions among seabirds.
CHARGE syndrome: candidate genes and pathogenesis

CHARGE syndrome is a complex malformation syndrome affecting several organ systems like the central nervous system, ear, eye and heart. Heterozygous loss of function mutations in CHD7, a conserved chromatin remodelling enzyme, are responsible to cause about two-thirds of CHARGE syndrome cases. CHD7 is present in large multi-subunit complexes regulating gene transcription in a time and cell type specific manner. In this work, it was shown by co-immunoprecipitation and Duolink proximity ligation assay that CHD7 interacts with the WAR complex members WDR5, ASH2L and RBBP5. Additional direct yeast two-hybrid experiments revealed that CHD7 is most likely associated to this complex via its direct interaction partner CHD8. The WAR complex is one “core” complex of the methyltransferase KMT2D. Mutations in KMT2D are the main cause of Kabuki syndrome, a developmental disorder, showing a remarkable phenotypic overlap to features present in CHARGE syndrome. The results of this work demonstrate a possible link of CHD7 and KMT2D to the same regulatory process of chromatin remodelling and chromatin modification, which might explain the phenotypic overlap of CHARGE syndrome and Kabuki syndrome. It was proposed that CHARGE syndrome belongs to the neurocristopathies. Recent studies demonstrated that CHD7 is required for the formation of multipotent neural crest cells. However, little is known about CHD7 target genes in the process of neural crest cell development. Within this work a genome-wide microarray analysis was performed with embryos (wild-type (Chd7+/+), heterozygous (Chd7Whi/+) and homozygous (Chd7Whi/Whi)) of the Whirligig mouse line which carries a nonsense mutation in the Chd7 gene. 98 genes were identified to be differentially expressed comparing homozygous (Chd7Whi/Whi) to wild-type (Chd7+/+) embryos. In fact, many of these genes are involved in the development of neural crest cells, for example, the specification of neural crest cells, epithelial-to-mesenchymal-transition and guidance of migrating neural crest cells. In this work it was demonstrated that the regulatory effect of Chd7 on Sema3a, a secreted signalling molecule known to have chemorepulsive properties for axons and to guide migrating neural crest cells, is conserved in mouse and Xenopus laevis. Further, a regulatory effect on neural crest cell migration in Xenopus laevis was exposed for Sema3a and Sema3d. In this work three non-synonymous mutations were identified in CHD7 negative CHARGE patients within the SEMA3A gene and the SEMA3D gene, respectively. SEMA3A mutations are known to be involved in the pathogenesis of Kallmann syndrome, a genetic disorder, which represents the mild phenotypic end of CHARGE syndrome. It is assumed that SEMA3A and SEMA3D act as modifiers contributing to a more severe phenotype in CHARGE patients if they are mutated. This would explain the high inter- and intra-familial variability observed in CHARGE syndrome. In general, the results discovered in this work help to better understand the pathogenic mechanism behind CHARGE syndrome.