Miracle-dz/UniFAR-FTUs huggingface dataset:
The Geosciences in Europe’s Urban Sustainability: Lessons from Glasgow and Beyond (CUSP) Geochemistry and related studies of Clyde Estuary sediments

Geochemical and related studies have been made of near-surface sediments from the River Clyde estuary and adjoining areas, extending from Glasgow to the N, and W as far as the Holy Loch on the W coast of Scotland, UK. Multibeam echosounder, sidescan sonar and shallow seismic data, taken with core information, indicate that a shallow layer of modern sediment, often less than a metre thick, rests on earlier glacial and post-glacial sediments. The offshore Quaternary history can be aligned with onshore sequences, with the recognition of buried drumlins, settlement of muds from quieter water, probably behind an ice dam, and later tidal delta deposits. The geochemistry of contaminants within the cores also indicates shallow contaminated sediments, often resting on pristine pre-industrial deposits at depths less than 1 m. The distribution of different contaminants with depth in the sediment, such as Pb (and Pb isotopes), organics and radionuclides, allow chronologies of contamination from different sources to be suggested. Dating was also attempted using microfossils, radiocarbon and Pb, but with limited success. Some of the spatial distribution of contaminants in the surface sediments can be related to grain-size variations. Contaminants are highest, both in absolute terms and in enrichment relative to the natural background, in the urban and inner estuary and in the Holy Loch, reflecting the concentration of industrial activity.
Ordered rearrangement of immunoglobulin heavy chain variable region segments.

The immunoglobulin heavy chain variable region is encoded as three separate libraries of elements in germ‐line DNA: VH, D and JH. To examine the order and regulation of their joining, we have developed assays that distinguish their various combinations and have used the assays to study tumor cell analogs of B‐lymphoid cells as well as normal B‐lymphoid cells. Abelson murine leukemia virus (A‐MuLV) transformed fetal liver cells ‐ the most primitive B‐lymphoid cell analog available for analysis ‐ generally had DJH rearrangements at both JH loci. These lines continued DNA rearrangement in culture, in most cases by joining a VH gene segment to an existing DJH complex with the concomitant deletion of intervening DNA sequences. None of these lines or their progeny showed evidence of VHD or DD rearrangements. Heavy chain‐producing tumor lines, representing more mature stages of the B‐cell pathway, and normal B‐lymphocytes had either two VHDJH rearrangements or a VHDJH plus a DJH rearrangement at their two heavy chain loci; they also showed no evidence of VHD or DD rearrangements. These results support an ordered mechanism of variable gene assembly during B‐cell differentiation in which D‐to‐JH rearrangements generally occur first and on both chromosomes followed by VH‐to‐DJH rearrangements, with both types of joining processes occurring by intrachromosomal deletion. The high percentage of JH alleles remaining in the DJH configuration in heavy chain‐producing lines and, especially, in normal B‐lymphocytes supports a regulated mechanism of heavy chain allelic exclusion in which a VHDJH rearrangement, if productive, prevents an additional VH‐to‐DJH rearrangement.
Type 3 inositol 1,4,5‐trisphosphate receptor modulates cell death

Mechanisms accounting for the cellular entry of calcium that mediates cellular proliferation and apoptosis have been obscure. Previously we reported selective augmentation of type 3 inositol (1,4,5) trisphosphate receptors (IP3R3) in lymphocytes undergoing programmed cell death, which was prevented by antisense constructs to IP3R3. We now report increases in mRNA and protein levels for IP3R3 associated with cell death in several apoptotic paradigms in diverse tissues. Elevations of IP3R3 occur during developmental apoptosis in early postnatal cerebellar granule cells, dorsal root ganglia, embryonic hair follicles, and intestinal villi. Neurotoxic damage elicited by the glutamate agonist kainate is also associated with IP3R3 augmentation. In chick dorsal root ganglia neurons undergoing apoptosis due to deprivation of nerve growth factor, levels of IP3R3 are selectively increased and cell death is selectively prevented by antisense oligonucleotides to IP3R3. Thus, IP3R3 appears to participate actively in cell death in a diversity of tissues. —Blackshaw, S. , Sawa, A. , Sharp, A. H. , Ross, C. A. , Snyder, S. H. , Khan, A. A. Type 3 inositol 1,4,5‐trisphosphate receptor modulates cell death. FASEB J. 14, 1375–1379 (2000)
Ancestral origins and invasion pathways in a globally invasive bird correlate with climate and influences from bird trade

Invasive species present a major threat to global biodiversity. Understanding genetic patterns and evolutionary processes that reinforce successful establishment is paramount for elucidating mechanisms underlying biological invasions. Among birds, the ring‐necked parakeet (Psittacula krameri) is one of the most successful invasive species, established in over 35 countries. However, little is known about the evolutionary genetic origins of this species and what population genetic signatures tell us about patterns of invasion. We reveal the ancestral origins of populations across the invasive range and explore the potential influence of climate and propagule pressure from the pet trade on observed genetic patterns. Ring‐necked parakeet samples representing the ancestral native range (n = 96) were collected from museum specimens, and modern samples from the invasive range (n = 855) were gathered from across Europe, Mauritius and Seychelles, and sequenced for two mitochondrial DNA markers comprising 868 bp of cytochrome b and control region, and genotyped at 10 microsatellite loci. Invasive populations comprise birds that originate predominantly from Pakistan and northern areas of India. Haplotypes associated with more northerly distribution limits in the ancestral native range were more prevalent in invasive populations in Europe, and the predominance of Asian haplotypes in Europe is consistent with the higher number of Asian birds transported by the pet trade outside the native range. Successful establishment of invasive species is likely to be underpinned by a combination of environmental and anthropogenic influences.
Quantification of confounding factors in MRI-based dose calculations as applied to prostate IMRT

Magnetic resonance (MR)-only radiotherapy treatment planning requires pseudo-CT (pCT) images to enable MR-based dose calculations. To verify the accuracy of MR-based dose calculations, institutions interested in introducing MR-only planning will have to compare pCT-based and computer tomography (CT)-based dose calculations. However, interpreting such comparison studies may be challenging, since potential differences arise from a range of confounding factors which are not necessarily specific to MR-only planning. Therefore, the aim of this study is to identify and quantify the contribution of factors confounding dosimetric accuracy estimation in comparison studies between CT and pCT. The following factors were distinguished: set-up and positioning differences between imaging sessions, MR-related geometric inaccuracy, pCT generation, use of specific calibration curves to convert pCT into electron density information, and registration errors. The study comprised fourteen prostate cancer patients who underwent CT/MRI-based treatment planning. To enable pCT generation, a commercial solution (MRCAT, Philips Healthcare, Vantaa, Finland) was adopted. IMRT plans were calculated on CT (gold standard) and pCTs. Dose difference maps in a high dose region (CTV) and in the body volume were evaluated, and the contribution to dose errors of possible confounding factors was individually quantified. We found that the largest confounding factor leading to dose difference was the use of different calibration curves to convert pCT and CT into electron density (0.7%). The second largest factor was the pCT generation which resulted in pCT stratified into a fixed number of tissue classes (0.16%). Inter-scan differences due to patient repositioning, MR-related geometric inaccuracy, and registration errors did not significantly contribute to dose differences (0.01%). The proposed approach successfully identified and quantified the factors confounding accurate MRI-based dose calculation in the prostate. This study will be valuable for institutions interested in introducing MR-only dose planning in their clinical practice.
Relationship between RPE and choriocapillaris in age-related macular degeneration.

PURPOSE The purpose of this study was to examine the relationships between choriocapillaris (CC) and retinal pigment epithelial changes in age-related macular degeneration (AMD). Morphologic changes in the retinal pigment epithelium (RPE)/choriocapillaris complex were quantified in dry and wet forms of AMD, and the results were compared with those in aged control eyes without maculopathy. METHODS Postmortem choroids from three aged control subjects, five subjects with geographic atrophy (GA), and three subjects with wet AMD were analyzed using a semiquantitative computer-assisted morphometric technique developed to measure the percentages of retinal pigment epithelial and CC areas in choroidal wholemounts incubated for alkaline phosphatase activity. The tissues were subsequently embedded in methacrylate and were sectioned so that structural changes could be examined. RESULTS There was a linear relationship between the loss of RPE and CC in GA. A 50% reduction in vascular area was found in regions of complete retinal pigment epithelial atrophy. Extreme constriction of remaining viable capillaries was found in areas devoid of RPE. Adjacent to active choroidal neovascularization (CNV) in wet AMD, CC dropout was evident in the absence of retinal pigment epithelial atrophy, resulting in a 50% decrease in vascular area. Lumenal diameters of the remaining capillaries in wet AMD eyes were similar to those in control eyes. CONCLUSIONS The primary insult in GA appears to be at the level of the RPE, and there is an intimate relationship between retinal pigment epithelial atrophy and secondary CC degeneration. CC degeneration occurs in the presence of viable RPE in wet AMD. The RPE in regions of vascular dropout are presumably hypoxic, which may result in an increase in VEGF production by the RPE and stimulation of CNV.
A dynamically-tunable graphene-based fano metasurface

A planar graphene metasurface with rectangular holes, which is capable of supporting a dynamically tunable Fano resonance at Terahertz (THz) frequencies, is proposed. The rectangular hole is patterned asymmetrically within the metasurface's unit cell to “brighten” an originally-dark quadrupolar surface plasmon mode. Fano resonance is achieved via the destructive interference of this mode with a dipolar surface plasmon. The spectral location and line shape of the Fano resonance can be dynamically tuned via a gate voltage applied to the metasurface to change graphene's optical properties. The dynamic tunability of the Fano resonance suggests the applicability of the proposed metasurface in designing THz wave modulators and band-pass filters.
Taxonomy and epidemiology of Mucor irregularis, agent of chronic cutaneous mucormycosis

Mucormycosis usually presents as a progressive infection with significant angio-invasion. Mucormycosis due to Mucor irregularis (formerly Rhizomucor variabilis var. variabilis), however, is exceptional in causing chronic cutaneous infection in immunocompetent humans, ultimately leading to severe morbidity if left untreated. More than 90 % of the cases known to date were reported from Asia, mainly from China. The nearest neighbour of M. irregularis is the saprobic species M. hiemalis. The aim of this study was to evaluate the taxonomic position, epidemiology, and intra- and inter-species diversity of M. irregularis based on 21 strains (clinical n = 17) by multilocus analysis using ITS, LSU, RPB1 and RPB2 genes, compared to results of cluster analysis with amplified fragment length polymorphism (AFLP) data. By combining MLST and AFLP analyses, M. irregularis was found to be monophyletic with high bootstrap support, and consisted of five subgroups, which were not concordant in all partitions. It was thus confirmed that M. irregularis is a single species at 96.1–100 % ITS similarity and low recombination rates between populations. Some geographic structuring was noted with some localised populations, which may be explained by limited air-dispersal. The natural habitat of the species is likely to be in soil and decomposing plant material.
Voiceless speech recognition using dynamic visual speech features

This paper describes a voiceless speech recognition technique that utilizes dynamic visual features to represent the facial movements during phonation. The dynamic features extracted from the mouth video are used to classify utterances without using the acoustic data. The audio signals of consonants are more confusing than vowels and the facial movements involved in pronunciation of consonants are more discernible. Thus, this paper focuses on identifying consonants using visual information. This paper adopts a visual speech model that categorizes utterances into sequences of smallest visually distinguishable units known as visemes. The viseme model used is based on the viseme model of Moving Picture Experts Group 4 (MPEG-4) standard. The facial movements are segmented from the video data using motion history images (MHI). MHI is a spatio-temporal template (grayscale image) generated from the video data using accumulative image subtraction technique. The proposed approach combines discrete stationary wavelet transform (SWT) and Zernike moments to extract rotation invariant features from the MHI. A feed forward multilayer perceptron (MLP) neural network is used to classify the features based on the patterns of visible facial movements. The preliminary experimental results indicate that the proposed technique is suitable for recognition of English consonants.
Involvement of Epigenetics and EMT-Related miRNA in Arsenic-Induced Neoplastic Transformation and Their Potential Clinical Use

Exposure to toxicants leads to cumulative molecular changes that overtime increase a subject's risk of developing urothelial carcinoma. To assess the impact of arsenic exposure at a time progressive manner, we developed and characterized a cell culture model and tested a panel of miRNAs in urine samples from arsenic-exposed subjects, urothelial carcinoma patients, and controls. To prepare an in vitro model, we chronically exposed an immortalized normal human bladder cell line (HUC1) to arsenic. Growth of the HUC1 cells was increased in a time-dependent manner after arsenic treatment and cellular morphology was changed. In a soft agar assay, colonies were observed only in arsenic-treated cells, and the number of colonies gradually increased with longer periods of treatment. Similarly, invaded cells in an invasion assay were observed only in arsenic-treated cells. Withdrawal of arsenic treatment for 2.5 months did not reverse the tumorigenic properties of arsenic-treated cells. Western blot analysis demonstrated decreased PTEN and increased AKT and mTOR in arsenic-treated HUC1 cells. Levels of miR-200a, miR-200b, and miR-200c were downregulated in arsenic-exposed HUC1 cells by quantitative RT-PCR. Furthermore, in human urine, miR-200c and miR-205 were inversely associated with arsenic exposure (P = 0.005 and 0.009, respectively). Expression of miR-205 discriminated cancer cases from controls with high sensitivity and specificity (AUC = 0.845). Our study suggests that exposure to arsenic rapidly induces a multifaceted dedifferentiation program and miR-205 has potential to be used as a marker of arsenic exposure as well as a maker of early urothelial carcinoma detection. Cancer Prev Res; 8(3); 208–21. ©2015 AACR.
Role of zinc in pediatric diarrhea

Zinc supplementation is a critical new intervention for treating diarrheal episodes in children. Recent studies suggest that administration of zinc along with new low osmolarity oral rehydration solutions / salts (ORS), can reduce the duration and severity of diarrheal episodes for up to three months. The World Health Organization (WHO) and UNICEF recommend daily 20 mg zinc supplements for 10 – 14 days for children with acute diarrhea, and 10 mg per day for infants under six months old, to curtail the severity of the episode and prevent further occurrences in the ensuing -two to three months, thereby decreasing the morbidity considerably. This article reviews the available evidence on the efficacy and safety of zinc supplementation in pediatric diarrhea and convincingly concludes that zinc supplementation has a beneficial impact on the disease outcome.
Effect of a peptide in cosmetic formulations for hair volume control

The capacity of hair to absorb water causes changes in its physical and cosmetic properties under different environmental conditions. Hence, the control of hair volume in variable relative humidity settings is an important topic in cosmetics. The behaviour of two types of hair, Caucasian and Asian, was studied regarding their volume change in different relative humidity conditions. The ability of a peptide as a hair volume treatment was evaluated in two climate control formulations.
Preparation of Papers for the WCE 2009 (1-3 July, 2009)

—Motion tracking and object recognition often use cameras that are mounted in motion platforms like pan-tilt units, linear tables and even robots. Tracking can be automated by visually servoing the platform’s degrees-of-freedom (DOF) thus keeping the camera’s point-of-view directed at the target. Tracking quick moving targets often demands faster bandwidth platforms. However biology suggests a redundant approach where DOF, like the eye and head, cooperate to direct vision systems and overcome joint limits. This paper illustrates the eﬀectiveness of this concept using a robot-mounted camera.
Using Cycles and Quasi-Cycles to Disambiguate Dictionary Glosses

We present a novel graph-based algorithm for the automated disambiguation of glosses in lexical knowledge resources. A dictionary graph is built starting from senses (vertices) and explicit or implicit relations in the dictionary (edges). The approach is based on the identification of edge sequences which constitute cycles in the dictionary graph (possibly with one edge reversed) and relate a source to a target word sense. Experiments are performed on the disambiguation of ambiguous words in the glosses of WordNet and two machine-readable dictionaries.
Multiple shifts between violet and ultraviolet vision in a family of passerine birds with associated changes in plumage coloration

Colour vision in diurnal birds falls into two discrete classes, signified by the spectral sensitivity of the violet- (VS) or ultraviolet-sensitive (UVS) short wavelength-sensitive type 1 (SWS1) single cone. Shifts between sensitivity classes are rare; three or four are believed to have happened in the course of avian evolution, one forming UVS higher passerines. Such shifts probably affect the expression of shortwave-dominated plumage signals. We have used genomic DNA sequencing to determine VS or UVS affinity in fairy-wrens and allies, Maluridae, a large passerine family basal to the known UVS taxa. We have also spectrophotometrically analysed male plumage coloration as perceived by the VS and UVS vision systems. Contrary to any other investigated avian genus, Malurus (fairy-wrens) contains species with amino acid residues typical of either VS or UVS cone opsins. Three bowerbird species (Ptilonorhynchidae) sequenced for outgroup comparison carry VS opsin genes. Phylogenetic reconstructions render one UVS gain followed by one or more losses as the most plausible evolutionary scenario. The evolution of avian ultraviolet sensitivity is hence more complex, as a single shift no longer explains its distribution in Passeriformes. Character correlation analysis proposes that UVS vision is associated with shortwave-reflecting plumage, which is widespread in Maluridae.
Prenatal Nicotine Exposure Alters Central Cardiorespiratory Responses to Hypoxia in Rats: Implications for Sudden Infant Death Syndrome

Maternal cigarette smoking and prenatal nicotine exposure are the highest risk factors for sudden infant death syndrome (SIDS). During hypoxia, respiratory frequency and heart rate transiently increase and subsequently decrease. These biphasic cardiorespiratory responses normally serve to prolong survival during hypoxia by reducing the metabolic demands of cardiac and respiratory muscles. However, exaggerated responses to hypoxia may be life threatening and have been implicated in SIDS. Heart rate is primarily determined by the activity of brainstem preganglionic cardioinhibitory vagal neurons (CVNs) in the nucleus ambiguus. We developed an in vitro rat brainstem slice preparation that maintains rhythmic inspiratory-related activity and contains fluorescently labeled CVNs. Synaptic inputs to CVNs were examined using patch-clamp electrophysiological techniques. Hypoxia evoked a biphasic change in the frequency of both GABAergic and glycinergic IPSCs in CVNs, comprised of an initial increase followed by a decrease in IPSC frequency. Prenatal exposure to nicotine changed the GABAergic response to hypoxia from a biphasic response to a precipitous decrease in spontaneous GABAergic IPSC frequency. This study establishes a likely neurochemical mechanism for the heart rate response to hypoxia and a link between prenatal nicotine exposure and an exaggerated bradycardia during hypoxia that may contribute to SIDS.
Privacy-Assured Aggregation Protocol for Smart Metering: A Proactive Fault-Tolerant Approach

Smart meters are integral to demand response in emerging smart grids, by reporting the electricity consumption of users to serve application needs. But reporting real-time usage information for individual households raises privacy concerns. Existing techniques to guarantee differential privacy (DP) of smart meter users either are not fault tolerant or achieve (possibly partial) fault tolerance at high communication overheads. In this paper, we propose a fault-tolerant protocol for smart metering that can handle general communication failures while ensuring DP with significantly improved efficiency and lower errors compared with the state of the art. Our protocol handles fail-stop faults proactively by using a novel design of future ciphertexts, and distributes trust among the smart meters by sharing secret keys among them. We prove the DP properties of our protocol and analyze its advantages in fault tolerance, accuracy, and communication efficiency relative to competing techniques. We illustrate our analysis by simulations driven by real-world traces of electricity consumption.