Miracle-dz/UniFAR-FTUs huggingface dataset:
Biodiversity Information Organization using Taxonomy (BIOT)

Biological resources are the basis of much of this Nations prosperity. The wise stewardship of these riches affects current and future generations and, therefore, must be rooted in decisions based on the best information available. Because of the rapid growth of all content on the Internet, there is a corresponding increase in online biological information of all types. However, the sheer volume of data, and its widely varying quality and physical distribution make it impossible for decision makers to make critical decisions without the benefit of the existing body of information. This project aims to investigate and develop intelligent knowledge management tools and deploy them in this important domain. In particular, we will investigate the use of a taxonomy as a reference ontology to provide a conceptual framework to allow intelligent agents to browse biodiversity information in a variety of formats widely distributed on the World Wide Web.
Developmental programming of the metabolic syndrome by maternal nutritional imbalance: how strong is the evidence from experimental models in mammals?

The incidence of the metabolic syndrome, a cluster of abnormalities focusing on insulin resistance and associated with high risk for cardiovascular disease and diabetes, is reaching epidemic proportions. Prevalent in both developed and developing countries, the metabolic syndrome has largely been attributed to altered dietary and lifestyle factors that favour the development of central obesity. However, population‐based studies have suggested that predisposition to the metabolic syndrome may be acquired very early in development through inappropriate fetal or neonatal nutrition. Further evidence for developmental programming of the metabolic syndrome has now been suggested by animal studies in which the fetal environment has been manipulated through altered maternal dietary intake or modification of uterine artery blood flow. This review examines these studies and assesses whether the metabolic syndrome can be reliably induced by the interventions made. The validity of the different species, diets, feeding regimes and end‐point measures used is also discussed.
The actin filament content of hair cells of the bird cochlea is nearly constant even though the length, width, and number of stereocilia vary depending on the hair cell location

By direct counts off scanning electron micrographs, we determined the number of stereocilia per hair cell of the chicken cochlea as a function of the position of the hair cell on the cochlea. Micrographs of thin cross sections of stereociliary bundles located at known positions on the cochlea were enlarged and the total number of actin filaments per stereocilium was counted and recorded. By comparing the counts of filament number with measurements of actin filament bundle width of the same stereocilium, we were able to relate actin filament bundle width to filament number with an error margin (r2) of 16%. Combining this data with data already published or in the process of publication from our laboratory on the length and width of stereocilia, we were able to calculate the total length of actin filaments present in stereociliary bundles of hair cells located at a variety of positions on the cochlea. We found that stereociliary bundles of hair cells contain 80,000-98,000 micron of actin filament, i.e., the concentration of actin is constant in all hair cells with a range of values that is less than our error in measurement and/or biological variation, the greatest variation being in relating the diameters of the stereocilia to filament number. We also calculated the membrane surface needed to cover the stereocilia of hair cells located throughout the cochlea. The values (172-192 micron 2) are also constant. The implications of our observation that the total amount of actin is constant even though the length, width, and number of stereocilia per hair cell vary are discussed.
Tandem Repeats Are Involved in G1 Domain Inhibition of Versican Expression and Secretion and the G3 Domain Enhances Glycosaminoglycan Modification and Product Secretion via the Complement-binding Protein-like Motif*

The large aggregating chondroitin sulfate proteoglycans, including aggrecan, versican (PG-M), neurocan, and brevican, are characterized by N-terminal and C-terminal globular (or selectin-like) domains known as the G1 and G3 domains, respectively. For this study, we generated a series of expression constructs containing various combinations of chicken versican/PG-M domains and a leading peptide of link protein in order to examine the roles of the G1 and G3 domains in versican function. In transfection studies, we observed that the presence of the G1 domain was sufficient to inhibit product secretion, while the G3 domain enhanced this process. We also demonstrated that the G1 domain inhibited the attachment of glycosaminoglycan chains to the core proteins, while the G3 domain enhanced this process. Further studies revealed that inhibition of secretion by G1 was mediated by its two tandem repeats, while G3's promotion of glycosaminoglycan chain attachment was apparently dependent on G3's complement-binding protein (CBP)-like motif. The modulatory effects of these two molecular domains may contribute to versican's biological activities.
Learning from Chemical Visualizations: Comparing generation and selection

Dynamic visualizations can make unseen phenomena such as chemical reactions visible but students need guidance to benefit from them. This study explores the value of generating drawings versus selecting among alternatives to guide students to learn chemical reactions from a dynamic visualization of hydrogen combustion as part of an online inquiry unit. In prior research, generation has been more successful than selection in helping students distinguish among ideas to learn complex topics. However, selecting among perplexing alternatives may motivate learners to distinguish among ideas they might otherwise neglect. To test the value of selection for helping students distinguish ideas, this study contrasted complex selection (involving normative as well as non-normative ideas identified in prior research) from typical selection (involving images from the visualization). Results showed that all conditions improved student understanding and that typical selection was less effective than generation while complex selection was as successful as generation. In both generation and complex selection students revisited the visualization while learning, whereas revisiting was rare in typical selection. These results support the idea that distinguishing among common non-normative ideas is more valuable than distinguishing among images from the visualization. In addition, for students with low prior knowledge, both generation and complex selection had some advantages. Overall, the results suggest that students learning from complex visualizations could benefit from a combination of complex selection and generation.
Sex, sun, sea, and STIs: sexually transmitted infections acquired on holiday

“The Dane in Spain was mainly on the Dane. ”1 These words were spoken by the late Dr Robbie Morton, drawing on three decades' experience in venereology, about the sexual behaviour of holidaymakers and their risk of acquiring sexually transmitted infections (STIs) while abroad. Despite Morton's years of clinical expertise his opinion would not survive the rigours of evidence based guidelines and at best would be graded as level 4, if at all. So is his assumption that sexual encounters while on holiday tend to be between people of the same nationality correct? What are the implications of international mixing on the risk of acquiring sexually transmitted infections? How should we manage people at risk before and after their holiday? I searched Medline in November 2003, using the key words “sexually transmitted infection”, “abroad”, “tourist”, “holiday”. I reviewed websites of the Health Protection Agency, the World Health Organization, the Department of Health, the Foreign Office, and the Association of British Travel Agents as these could be expected to provide information on travel abroad. Clinical information is from Sexually Transmitted Diseases . 2 More than 30 million UK residents travel abroad each year.3 Sexual activity is known to vary by season; increased sexual intercourse and unsafe sex occur around the Christmas period and the summer vacation.4 Holidays are increasingly being taken abroad and in far flung locations, and the number of UK residents travelling abroad has increased by 27% since 1997.5 Holidays provide an opportunity for increased sexual mixing whether taken at home or abroad (fig 1, fig 2). Few recent data exist on sexual behaviour while on holiday abroad, and even fewer for people holidaying in the United Kingdom. Studies in the early 1990s showed notable risk behaviour in international travellers who attended for a “tropical check. ” …
Network flow based cut redistribution and insertion for advanced 1D layout design

End Cutting 1D layout design is a promising candidate for sub-10nm process nodes. Given a 1D layout with horizontal wires, cut redistribution technique is used for sliding the line-end cuts in order to align them vertically or resolve spacing conflicts. The aligned cuts can then be merged into a single shot of cuts. In this paper, we proposed a network flow based method for efficient cut redistribution and insertion. Normally, a pair of movable cuts could have three possible relations, left-of, right-of and merge-into. We observe that if the left-right-merge orderings of cuts are fixed, the cut redistribution can be formulated as a network flow problem, which can be solved efficiently. We also find that inserting cuts can resolve the spacing conflicts in some circumstances. This cut insertion strategy is introduced in our proposed method to reduce the spacing conflicts. Moreover, the complementary e-beam lithography for printing the cuts is also considered in this paper. Experimental results show that compared with a previous ILP-based method, our method can achieve a 200X speedup and competitive solution quality.
Use of One-Point Coverage Representations, Product Space Conditional Event Algebra, and Second-Order Probability Theory for Constructing and Using Probability-Compatible Inference Rules in Data-Fusion Problems

Abstract : This paper covers issues relating to the establishment of a sound and conditional probability-compatible rationale for generating linguistic-based inference rules concerning a population. By extending previous preliminary results, the authors detail, in a fully rigorous manner and within the confines of traditional probability theory, that a comprehensive technique can be derived that converts linguistic-based conditional information, couched only in fuzzy-logic terms, into naturally corresponding conditional probabilities. In turn, they demonstrate how such typically underconstrained conditional probabilities can be combined for suitable conclusions and decision making, via a new use of second-order probability logic. This research is part of the ongoing SSC San Diego In-house Laboratory Independent Research FY 01 project CRANOF (a Complexity-Reducing Algorithm for Near-Optimal Fusion).
Lightning Data Observed With Lightning Location System in Portugal

This paper presents an investigation into cloud-to-ground lightning activity over the continental territory of Portugal with data collected by the National Lightning Location System. The lightning location system in Portugal is first presented. Analyses about geographical, seasonal, and polarity distribution of cloud-to-ground lightning activity and cumulative probability of peak current are carried out. An overall ground flash density map is constructed from the database, which contains the information of more than five years and almost four million records. This map is compared with the thunderstorm days map, produced by the Portuguese Institute of Meteorology, and with the orographic map of Portugal. Finally, conclusions are duly drawn.
A new hybrid spring brake orthosis for controlling hip and knee flexion in the swing phase

It is proposed that active contraction of muscles might be artificially replaced by a spring brake orthosis (SBO) to provide near-natural knee and hip swing phase trajectories for gait in spinal cord injured subjects. The SBO is a new gait restoration system in which stored spring elastic energy and potential energy of limb segments are utilized to aid gait. It is also shown that hip flexion can be produced without the need for withdrawal reflex, hip flexor stimulus or any mechanical actuator at the hip. A hip flexion angle of 21 degrees was achieved by a nonimpaired subject wearing a prototype orthosis.
Extracellular compartments in tendon morphogenesis: collagen fibril, bundle, and macroaggregate formation

The formation of collagen fibrils, fibril bundles, and tissue-specific collagen macroaggregates by chick embryo tendon fibroblasts was studied using conventional and high voltage electron microscopy. During chick tendon morphogenesis, there are at least three extracellular compartments responsible for three levels of matrix organization: collagen fibrils, bundles, and collagen macroaggregates. Our observations indicate that the initial extracellular events in collagen fibrillogenesis occur within narrow cytoplasmic recesses, presumably under close cellular regulation. Collagen fibrils are formed within these deep, narrow recesses, which are continuous with the extracellular space. Where these narrow recesses fuse with the cell surface, it becomes highly convoluted with folds and processes that envelope forming fibril bundles. The bundles laterally associate and coalesce, forming aggregates within a third cell-defined extracellular compartment. Our interpretation is that this third compartment forms as cell processes retract and cytoplasm is withdrawn between bundles. These studies define a hierarchical organization within the tendon, extending from fibril assembly to fascicle formation. Correlation of different levels of extracellular compartmentalization with tissue architecture provides insight into the cellular controls involved in collagen fibril and higher order assembly and a better understanding of how collagen fibrils are collected into structural groups, positioned, and woven into functional tissue-specific collagen macroaggregates.
Transient myopia after visual work.

Abstract After viewing at near distances for several hours observers may become temporarily myopic. This effect, known as transient myopia after visual work, was studied by measuring contrast sensitivity to a sinusoidally modulated grating pattern. After 3 hours of editing text at a visual display terminal, a significant decrease in sensitivity was found in five subjects out of seven. The results show interpersonal differences in the strength and the time course of work-induced myopia. Measurement of transient myopia by means of contrast sensitivity has the advantage of being rapid enough that even short-term effects can be followed. The decrease in sensitivity can be shown to be a purely optical effect of the eye.
Microscopic Description of Entanglements in Polyethylene Networks and Melts: Strong, Weak, Pairwise, and Collective Attributes

We present atomistic molecular dynamics simulations of two Polyethylene systems where all entanglements are trapped: a perfect network, and a melt with grafted chain ends. We examine microscopically at what level topological constraints can be considered as a collective entanglement effect, as in tube model theories, or as certain pairwise uncrossability interactions, as in slip-link models. A pairwise parameter, which varies between these limiting cases, shows that, for the systems studied, the character of the entanglement environment is more pairwise than collective. We employ a novel methodology, which analyzes entanglement constraints into a complete set of pairwise interactions, similar to slip links. Entanglement confinement is assembled by a plethora of links, with a spectrum of confinement strengths, from strong to weak. The strength of interactions is quantified through a link “persistence”, which is the fraction of time for which the links are active. By weighting links according to their stren.
Spline-based modelling of trends in the force of HIV infection, with application to the UNAIDS Estimation and Projection Package

Objective We previously developed a flexible specification of the UNAIDS Estimation and Projection Package (EPP) that relied on splines to generate time-varying values for the force of infection parameter. Here, we test the feasibility of this approach for concentrated HIV/AIDS epidemics with very sparse data and compare two methods for making short-term future projections with the spline-based model. Methods Penalised B-splines are used to model the average infection risk over time within the EPP 2011 modelling framework, which includes antiretroviral treatment effects and CD4 cell count progression, and is fit to sentinel surveillance prevalence data with a Bayesian algorithm. We compare two approaches for future projections: (1) an informative prior related to equilibrium prevalence and (2) a random walk formulation. Results The spline-based model produced plausible fits across a range of epidemics, which included 87 subpopulations from 14 countries with concentrated epidemics and 75 subpopulations from 33 countries with generalised epidemics. The equilibrium prior and random walk approaches to future projections yielded similar prevalence estimates, and both performed well in tests of out-of-sample predictive validity for prevalence. In contrast, in some cases the two approaches varied substantially in estimates of incidence, with the random walk formulation avoiding extreme changes in incidence. Conclusions A spline-based approach to allowing the force of infection parameter to vary over time within EPP 2011 is robust across a diverse array of epidemics, including concentrated ones with limited surveillance data. Future work on the EPP model should consider the impact that different modelling approaches have on estimates of HIV incidence.
“Animal Intelligence”

IN a review of my monograph on “Animal Intelligence,” in a recent number of NATURE, Mr. Lloyd Morgan credits me with upholding the theory that we have sensations caused by outgoing currents which innervate muscles, and with depending on that theory in some of my own statements about the nature of animals' consciousness. A careless and ambiguous sentence of mine was responsible for this. I believe with Mr. Morgan that the feelings which go with innervations of the muscles are due to currents coming back from the muscles or joints and tendons, and do not think that any of my conclusions in any way involve an acceptance of the other theory. Such sensations due to return currents (together with the images built up from them) were just what I meant by the phrase which he quotes, “the consciousness accompanying a muscular innervation apart from that feeling of the act which comes from seeing oneself move, &#38;c. ” It was because I presupposed general agreement in accepting the return-current theory that I was so careless as to leave the obvious ambiguity.
Mass Spectrometry as a Diagnostic and a Cancer Biomarker Discovery Tool

Serum proteomic profiling, by using surfaced-enhanced laser desorption/ionization-time-of-flight mass spectrometry, is one of the most promising new approaches for cancer diagnostics. Exceptional sensitivities and specificities have been reported for some cancer types such as prostate, ovarian, breast, and bladder cancers. These sensitivities/specificities are far superior to those obtained by using classical cancer biomarkers. In this review, I concentrate more on questions that cast doubt on the results reported and propose experiments to investigate these questions in detail, before the technique is used at the clinic. It is clear that the method needs to be externally and thoroughly validated before clinical implementation is warranted.
Everyday robotic action: lessons from human action control

Robots are increasingly capable of performing everyday human activities such as cooking, cleaning, and doing the laundry. This requires the real-time planning and execution of complex, temporally extended sequential actions under high degrees of uncertainty, which provides many challenges to traditional approaches to robot action control. We argue that important lessons in this respect can be learned from research on human action control. We provide a brief overview of available psychological insights into this issue and focus on four principles that we think could be particularly beneficial for robot control: the integration of symbolic and subsymbolic planning of action sequences, the integration of feedforward and feedback control, the clustering of complex actions into subcomponents, and the contextualization of action-control structures through goal representations.
Model-Based Interpretation of High-Resolution SAR Images of Buildings

High-resolution (HR) synthetic aperture radar (SAR) images of urban areas reveal a large variety of details that, although potentially bringing a lot of information, are often very difficult to interpret. Until now, most of the research activity in this field has been devoted to the attempt to retrieve geometric information on buildings in terms of their positions and sizes, by using simplified geometrical models. However, this approach does not allow us to fully exploit the large amount of information present in HR SAR images. In order to improve information retrieval from such images, and, hence, their interpretation, in this paper, we propose to employ a more refined model that accounts for both geometrical (including fine details) and electromagnetic properties of the building. A meaningful case study is presented to show that the main features appearing on the SAR image of a building can be interpreted by using our geometric and electromagnetic model. In addition, a first example of retrieval of the complex dielectric constant of building materials from a SAR image is presented.
Thiamin deficiency in a colony of cats

Twenty-eight cats belonging to a cat rescue society developed clinical signs consistent with thiamin deficiency after being fed a proprietary canned food containing inadequate amounts of the vitamin. Five of the cats died but the others recovered after appropriate therapy. The diagnosis was based on clinical signs, histopathological findings, food analysis and response to treatment.
On the relay-fallback tradeoff in millimeter wave wireless system

Millimeter wave (mmWave) communications systems are promising candidate to support extremely high data rate services in future wireless networks. MmWave communications exhibit high penetration loss (blockage) and require directional transmissions to compensate for severe channel attenuations and for high noise powers. When blockage occurs, there are at least two simple prominent options: 1) switching to the conventional microwave frequencies (fallback option) and 2) using an alternative non-blocked path (relay option). However, currently it is not clear under which conditions and network parameters one option is better than the other. To investigate the performance of the two options, this paper proposes a novel blockage model that allows deriving maximum achievable throughput and delay performance of both options. A simple criterion to decide which option should be taken under which network condition is provided. By a comprehensive performance analysis, it is shown that the right option depends on the payload size, beam training overhead, and blockage probability. For a network with light traffic and low probability of blockage in the direct link, the fallback option is throughput- and delay-optimal. For a network with heavy traffic demands and semistatic topology (low beam-training overhead), the relay option is preferable.