Miracle-dz/UniFAR-FTUs huggingface dataset:
Advances in modelling groundwater behaviour in Chalk catchments

Abstract Groundwater in Chalk catchments is a major resource that also helps support internationally important habitats and ecosystems. Its dual porosity and dual permeability properties, coupled with large-scale structural features (such as hard rock layers and marls), produce a highly complex hydrogeological system. Recent impacts from groundwater flooding as well as vulnerability to drought have raised questions over the ability of traditional approaches to model these aquifers. Current work on near-surface hydrological processes has highlighted the importance of the soil and weathered zone for controlling recharge rates. In addition, karst-like features, sedimentary deposits and valley bottom processes govern stream–aquifer interaction and present a challenge in their representation in any modelling system. Methods that have, and are being, developed to incorporate these features, and their use in modelling Chalk catchments, are described. These are required in order to address major challenges, such as groundwater flooding and drought impacts, both of which could become more frequent and intense as a result of climate change.
Evaluation of Expression and Glycosylation Status of UGT1A10 in Supersomes and Intestinal Epithelial Cells with a Novel Specific UGT1A10 Monoclonal Antibody

UDP-Glucuronosyltransferases (UGTs) are major phase II drug-metabolizing enzymes. Each member of the UGT family exhibits a unique but occasionally overlapping substrate specificity and tissue-specific expression pattern. Earlier studies have reported that human UGT1A10 is expressed in the gastrointestinal tract at the mRNA level, but the evaluation at the protein level, especially tissue or cellular localization, has lagged behind because of the lack of a specific antibody. In this study, we prepared a monoclonal antibody to UGT1A10 to elucidate the tissue/cellular distribution and interindividual variability of UGT1A10 protein expression. Western blot analysis revealed that the prepared antibody does not cross-react with any other human UGTs. Using this specific antibody, we observed that UGT1A10 protein is expressed in the small intestine but not in the liver or kidney. Immunohistochemical analysis revealed the expression of UGT1A10 protein in epithelial cells of the crypts and villi of the duodenum. In the small intestine microsomes from six individuals, the UGT1A10 protein levels exhibited 16-fold variability. Dopamine 3- and 4-glucuronidation, which is mainly catalyzed by UGT1A10 and by other UGT isoforms marginally, exhibited 50- to 65-fold variability, and they were not correlated with the UGT1A10 protein levels. Interestingly, the enzymatic activities of recombinant UGT1A10 in insect cells that were normalized to the UGT1A10 protein level were markedly lower than those in pooled human small intestine microsomes. Thus, the UGT1A10 antibody we generated made it possible to investigate the tissue/cellular distribution and interindividual variability of UGT1A10 protein expression for understanding the pharmacological and toxicological role of UGT1A10.
A Probabilistic Functional Network of Yeast Genes

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Blood Impedance Characterization from Pulsatile Measurements

This paper describes an in vivo measurement technique to calculate dielectric properties of blood excluding the contributions from surrounding tissues, based on analysis of the pulsatile component bioimpedance spectroscopy data. A tetrapolar electrode system applied on the fingers is simulated by a pspice equivalent circuit, and current is injected with frequency ranging from 5 kHz to 100 MHz. The finger is modeled as three parts: arterial blood, surrounding tissues and incremental infused arterial blood during systole. The pulsatile curve is fitted to a Cole-Cole model by Levenberg-Marquardt (LM) nonlinear curve fitting. Using the pulsatile impedance data, electrical properties of blood and surrounding tissues can be separated successfully. Parameter accuracies are illustrated according to various noise levels and sampling rates
GBAGC: A General Bayesian Framework for Attributed Graph Clustering

Graph clustering, also known as community detection, is a long-standing problem in data mining. In recent years, with the proliferation of rich attribute information available for objects in real-world graphs, how to leverage not only structural but also attribute information for clustering attributed graphs becomes a new challenge. Most existing works took a distance-based approach. They proposed various distance measures to fuse structural and attribute information and then applied standard techniques for graph clustering based on these distance measures. In this article, we take an alternative view and propose a novel Bayesian framework for attributed graph clustering. Our framework provides a general and principled solution to modeling both the structural and the attribute aspects of a graph. It avoids the artificial design of a distance measure in existing methods and, furthermore, can seamlessly handle graphs with different types of edges and vertex attributes. We develop an efficient variational method for graph clustering under this framework and derive two concrete algorithms for clustering unweighted and weighted attributed graphs. Experimental results on large real-world datasets show that our algorithms significantly outperform the state-of-the-art distance-based method, in terms of both effectiveness and efficiency.
Dopamine D2 Long Receptor-Deficient Mice Display Alterations in Striatum-Dependent Functions

The dopamine D2 receptor (D2) system has been implicated in several neurological and psychiatric disorders, such as schizophrenia and Parkinson's disease. There are two isoforms of the D2 receptor: the long form (D2L) and the short form (D2S). The two isoforms are generated by alternative splicing of the same gene and differ only by 29 amino acids in their protein structures. Little is known about the distinct functions of either D2 isoform, primarily because selective pharmacological agents are not available. We generated D2L receptor-deficient (D2L−/−) mice by making a subtle mutation in the D2 gene. D2L−/− mice (which still express functional D2S) displayed reduced levels of locomotion and rearing behavior. Interestingly, haloperidol produced significantly less catalepsy and inhibition of locomotor activity in D2L−/− mice. These findings suggest that D2L and D2S may contribute differentially to the regulation of certain motor functions and to the induction of the extrapyramidal side effects associated with the use of typical antipsychotic drugs (e.g., haloperidol). Quinpirole induced a similar initial suppression of locomotor activity in both D2L−/− and wild-type mice. In addition, the D2S receptor in the mutant mice functioned approximately equally well as did D2L as an impulse-modulating autoreceptor. This suggests that the functions of these two isoforms are not dependent on the formation of receptor heterodimers. Our findings may provide novel information for potentially developing improved antipsychotic drugs.
Can bi‐cubic surfaces be class A?

'Class A surface’ is a term in the automotive design industry, describing spline surfaces with aesthetic, non‐oscillating highlight lines. Tensor‐product B‐splines of degree bi‐3 (bicubic) are routinely used to generate smooth design surfaces and are often the de facto standard for downstream processing. To bridge the gap, this paper explores and gives a concrete suggestion, how to achieve good highlight line distributions for irregular bi‐3 tensor‐product patch layout by allowing, along some seams, a slight mismatch of normals below the industry‐accepted tolerance of one tenth of a degree. Near the irregularities, the solution can be viewed as transforming a higher‐degree, high‐quality formally smooth surface into a bi‐3 spline surface with few pieces, sacrificing formal smoothness but qualitatively retaining the shape.
The Putative Cofactor TIF1α Is a Protein Kinase That Is Hyperphosphorylated upon Interaction with Liganded Nuclear Receptors*

Ligand-induced gene activation by nuclear receptors (NRs) is a complex process requiring dissociation of corepressors and recruitment of coactivators. The putative transcriptional intermediary factor TIF1α has been previously characterized as a nuclear protein that interacts directly with the AF-2 ligand-dependent activating domain present in the ligand-binding domain of numerous steroid and nonsteroid receptors, including the estrogen (ERα) and retinoid X (RXRα) receptors. We report here that TIF1α is both a phosphoprotein and a protein kinase. TIF1α coexpressed in COS-1 cells with RXRα or ERα is phosphorylated and becomes hyperphosphorylated upon ligand treatment. This hyperphosphorylation requires the binding of TIF1α to transcriptionally active NRs since it is prevented by mutations either in the core (α-helix 12 of the ligand-binding domain) of the AF-2 activating domains of RXRα and ERα or in the NR box of TIF1α that are known to prevent TIF1α-NR interactions. Thus, TIF1α is a phosphoprotein that undergoes ligand-dependent hyperphosphorylation as a consequence of nuclear receptor binding. We further show that purified recombinant TIF1α possesses intrinsic kinase activity and that, in addition to autophosphorylation, TIF1α selectively phosphorylates the transcription factors TFIIEα, TAFII28, and TAFII55 in vitro. These latter results raise the possibility that TIF1α may act, at least in part, by phosphorylating and modifying the activity of components of the transcriptional machinery.
A mixed nodal-mesh formulation of the PEEC method based on efficient graph algorithms

In this paper a new mixed nodal-mesh formulation of the PEEC method is proposed. Based on the hypothesis that charges reside only on the surface of conductors and that current density is solenoidal inside them, a novel scheme is developed fully exploiting the physical properties of charges and currents. It comes out that the presented approach allows to reduce the number of unknowns while preserving the accuracy. An elegant and efficient algorithm, based on graph theory, is proposed to automatically search independent loops on three dimensional rectangular grids such as those arising in volumetric PEEC formulation. The method is validated through numerical results that confirm the accuracy of the proposed formulation from DC-to-daylight and its capability to provide memory saving.
Structure of the Culm Basin : rapid mapping of the Tiverton Sheet and the latest Variscan inversion in Devon

The Silesian (Upper Carboniferous) sedimentary rocks of the Culm Basin, to the west of Tiverton, belong to the Crackington and Bude Formations. These comprise turbidite and debrite sandstone, interbedded with mudstone. In the field the formations are differentiated on the basis of thickness and weathering characteristics of the sandstone packages. In the study area although bedrock is commonly obscured by overlying superficial deposits, the character of these deposits can be used as an indicator of bedrock geology. Using both bedrock and superficial analytical techniques, the Crackington / Bude boundary has been mapped in the study area. Tracing of large scale structure has been helped by the use of shaded relief digital terrain models, however in areas of moorland the distinctive featuring is not present and there are no indicators of the underlying bedrock structure. Geophysical data, in particular a recent gravity survey, provide considerable information on the structure of the Culm Basin. It is clear that the east-west trend of the Tiverton Trough, depicted by a negative gravity anomaly over the Permo-Triassic infill, continues westwards in the Silesian sedimentary rocks. Further west of the Tiverton Trough an area of relatively high gravity covers the area of Witheridge and Rackenford moors. North of this is a negative gravity anomaly whose northern boundary lies close to the crop of the basal Crackington Formation and whose southern margin follows the Crackington / Bude boundary. The strong east-west linear nature of the gravity anomalies indicates that the structure controlling the northern boundary of the Tiverton Trough was probably active during Variscan inversion. The gravity high over Witheridge is thought to be related to the presence of dense, earlier Palaeozoic rocks that form a structural high underlying the Silesian; given its linear nature and its alignment with the northern boundaries of both the Tiverton and Crediton troughs.
Hairpin filters with tunable transmission zeros

In the previous work, it was found that filter designed with 0/spl deg/ feed structure could have two extra transmission zeros in the stopband. In this paper, a method for tuning the frequencies of these two transmission zeros using impedance transformers is proposed. These zeros can be tuned to reject unwanted signals near the passband, such as image signals, This new approach has been experimentally verified with three second-order Butterworth filters.
Hyperspectral proximal sensing of the botanical composition and nutrient content of New Zealand pastures : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Earth Science

The potential of hyperspectral proximal sensing to quantify sward characteristics important in making critical decisions on the management of sheep and dairy pastures in New Zealand has been investigated. Hyperspectral data were acquired using an ASD FieldSpec ® Pro FR spectroradiometer attached to the Canopy Pasture Probe (CAPP). The CAPP was developed to enable the collection of in situ reflectance data from New Zealand pasture canopies independent of ambient light conditions. A matt white ceramic tile was selected as a reflectance standard to be used with the CAPP, after testing a variety of materials. Pasture reflectance factor spectra between 350-2500 nm (with spectral resolutions of 3 nm between 350-1000 nm and 10 nm between 1000-2500 nm) and pasture samples were collected from six hill country and lowland areas, across all seasons (August 2006 to September 2007) in a number of regions in the North Island of New Zealand. After pre-processing (e.g. spectral averaging, de-stepping, elimination of noisy wavelengths, smoothing) the spectral data collected from sites were correlated against pasture botanical composition (expressed as proportions of grass, legume and weed) and pasture nutrients (nitrogen, phosphorus, potassium, calcium, magnesium, sodium and sulphur) expressed in percentage of dry matter (%) and amount (kg ha -1 ) using partial least squares regressions (PLSR). The accuracy and precision of the calibrations were tested using either the full cross-validation leave-one-out method or testing datasets. Regressions were carried out using the reflectance factor data per se and after mathematical transformation, including first derivative, absorbance and continuum-removed spectra. Overall best results were obtained using the first derivative data. The quality of predictions varied greatly with the pasture attribute, site and season. Some reasonable results were achieved for the prediction of pasture grass and legume proportions when analysing samples collected during autumn (grass: R 2 > 0.81 and SD/RMSEP 2.3 and legume: R 2 > 0.80 and SD/RMSEP 2.2), but predicting pasture weed content was poor for all sites and seasons (R 2 ≤ 0.44 and SD/RMSEP ≤ 1.2). The inaccurate predictions might be explained by the fact that the diversity found in the field
DFT study of electronic and magnetic properties of bare and substitutionally doped ZnO nanoribbons

First-principles calculations were carried out on electronic and magnetic properties of zinc oxide nanoribbons doped with 3d transitional metals with both zigzag and armchair edges. Bare armchair ZnO nanoribbons (aZnONRs) are nonmagnetic semiconductors whereas bare zigzag ZnO nanoribbons (zZnONRs) are metallic magnets. However, when zigzag edges are passivated with hydrogen, degeneracy between the up and down spin was found, which turns ribbons into nonmagnetic ones. The magnetization of the 3d-TM-impurity-doped aZnONRs and zZnONRs is configuration dependent. The band gap and carrier concentration of aZnONRs can be tuned by 3d-TM doping.
Absence of B‐ and T‐Cell Markers on Acute Lymphoblastic Leukaemic Cells and Persistence of the T‐Cell Marker on Mitogen‐Transformed T‐Lymphocytes

Summary. Lymphocytes from six patients with acute lymphoblastic leukaemia (ALL) were studied in vitro for thymus (T‐cell) and bone marrow‐derived (B‐cell) markers. Leukaemic lymphoblasts did not form rosettes with sheep erythrocytes (T‐cell marker) or bear surface immunoglobulin determinants by indirect immuno‐fluorescent staining (B‐cell marker). The failure of lymphoblasts to form rosettes was apparently not due to the fact that lymphoblasts were in various stages of the cell cycle, as mitogen‐transformed T‐cells and T‐cells in mitosis retained their capacity to form rosettes with sheep erythrocytes. In contrast, leukaemic B‐cells, obtained from a patient with chronic lymphocytic leukaemia and recognized by intracellular immunoglobulin crystals, did not form rosettes nor did a small number of mitogen‐transformed leukaemic cells. These studies suggest that lymphoblasts from some patients with the haematological picture of ALL do not have surface markers for either T‐ or B‐cells.
HLA‐DR antigen expression on keratinocytes in highly inflamed parts of psoriatic lesions

We have investigated the immunoperoxidase staining pattern in the epidermis and dermal infiltrates of highly inflamed portions of psoriatic lesions, selecting for biopsy early pinpoint lesions or margins of active plaque lesions. We found positive intercellular staining for HLA‐DR antigens in localized areas of the epidermis in about half of the patients tested. In contrast, OKT6 antigen was found only on the dendritic cells in the epidermis and dermis in all cases. These findings support the hypothesis that an active cellular immune reaction involving the epidermis, possibly associated with the expression of HLA‐DR antigens on keratinocytes, occurs in the highly inflamed areas of psoriatic lesions, particularly in early pinpoint lesions or at the edges of spreading plaque lesions.
Identifying Overlapped Objects for Video Indexing and Modeling in Multimedia Database Systems

The identification of the overlapped objects is a great challenge in object tracking and video data indexing. For this purpose, a backtrack-chain-updation split algorithm is proposed to assist an unsupervised video segmentation method called the "simultaneous partition and class parameter estimation" (SPCPE) algorithm to identify the overlapped objects in the video sequence. The backtrack-chain-updation split algorithm can identify the split segment (object) and use the information in the current frame to update the previous frames in a backtrack-chain manner. The split algorithm provides more accurate temporal and spatial information of the semantic objects so that the semantic objects can be indexed and modeled by multimedia input strings and the multimedia augmented transition network (MATN) model. The MATN model is based on the ATN model that has been used in artificial intelligence (AI) areas for natural language understanding systems, and its inputs are modeled by the multimedia input strings. In this paper, we will show that the SPCPE algorithm together with the backtrack-chain-updation split algorithm can significantly enhance the efficiency of spatio-temporal video indexing by improving the accuracy of multimedia database queries related to semantic objects.
Cerebral Blood Volume (CBV) in Humans during Normo- and Hypocapnia: Influence of Nitrous Oxide (N2O)

Background It is generally argued that variations in cerebral blood flow create concomitant changes in the cerebral blood volume (CBV). Because nitrous oxide (N2O) inhalation both increases cerebral blood flow and may increase intracranial pressure, it is reasonable to assume that N2O acts as a general vasodilatator in cerebral vessels both on the arterial and on the venous side. The aim of the current study was to evaluate the effect of N2O on three-dimensional regional and global CBV in humans during normocapnia and hypocapnia. Methods Nine volunteers were studied under each of four conditions: normocapnia, hypocapnia, normocapnia + 40–50% N2O, and hypocapnia + 40–50% N2O. CBV was measured after 99mTc-labeling of blood with radioactive quantitative registration via single photon emission computer-aided tomography scanning. Results Global CBV during normocapnia and inhalation of 50% O2 was 4.25 ± 0.57% of the brain volume (4.17 ± 0.56 ml/100 g, mean ± SD) with no change during inhalation of 40–50% N2O in O2. Decreasing carbon dioxide (CO2) by 1.5 kPa (11 mmHg) without N2O inhalation and by 1.4 kPa (11 mmHg) with N2O inhalation reduced CBV significantly (F = 57, P < 0.0001), by 0.27 ± 0.10% of the brain volume per kilopascal (0.26 ± 0.10 ml · 100 g−1 · kPa−1) without N2O inhalation and by 0.35 ± 0.22% of the brain volume per kilopascal (0.34 ± 0.22 ml · 100 g−1 · kPa−1) during N2O inhalation (no significant difference). The amount of carbon dioxide significantly altered the regional distribution of CBV (F = 47, P < 0.0001), corresponding to a regional difference in &Dgr;CBV when CO2 is changed. N2O inhalation did not significantly change the distribution of regional CBV (F = 2.4, P = 0.051) or &Dgr;CBV/&Dgr;CO2 in these nine subjects. Conclusions Nitrous oxide inhalation had no effect either on CBV or on the normal CBV–CO2 response in humans.
3D human action recognition using Gaussian processes dynamical models

An efficient method to automatically recognize basic human actions is proposed to improve the communication between a human and a computer. Human actions are considered as patterns generated by complex non-linear dynamical models. A non-linear dynamical model is used to represent human actions. Gaussian process dynamical models are used to capture the spatial and temporal behaviors of actions. To make the process more efficient a 7-dimensional feature is extracted for each action. Although the extracted feature vector is compact compared to a high-dimensional temporal pattern, it can efficiently discriminate among different actions. The tests run on CMU MoCap database with SVM show promising results.