Miracle-dz/UniFAR-FTUs huggingface dataset:
Uricase protein sequences: conserved during vertebrate evolution but absent in humans

Uricase is a peroxisomal liver enzyme that catalyzes the oxidation of uric acid to allantoin during purine catabolism. It is present in vertebrates in most species of fish, amphibians, and mammals but its enzymatic activity is absent in hominoids. We have used Western blot analysis in a comparative study to establish a homology among uricases from different species of vertebrates. Using antibodies against denatured rat liver uricase, we have been able to detect for the first time cross‐reactivity with the uricase of species ranging in the evolutionary scale from fish to primates (macaque). Our results suggest that these uricases have a common evolutionary origin. Our conclusion is also supported by the fact that uricase from different species exhibits identical tissue, subcellular localization, and similarity of molecular weights. This study was extended to include human liver samples. Using the same approach but with a more sensitive detection system (alkaline phosphatase instead of peroxidase), we did not detect polypeptide species related to rat uricase in human fetal or adult liver samples, which indicates that during hominoid evolution, the mutational event responsible for the loss of uricase activity in humans precluded formation of a translatable uricase mRNA. — Varela‐Echavarria, A. ; Montes de Oca‐Luna, R. ; Barrera‐Saldana, H. A. Uricase protein sequences: conserved during vertebrate evolution but absent in humans. FASEB J. 2: 3092‐3096; 1988.
Output bipartite consensus of heterogeneous linear multi-agent systems under switching topologies

This paper considers bipartite consensus of linear multi-agent systems over signed directed graphs, where both collaboration and competition coexist. The agent dynamics are distinct and can all have different dimensions. The communication graph can be time-varying and need not to be connected at each time. A distributed control law is proposed which enables the group to split into two disjoint subgroups, and the outputs of all agents within each subgroup achieve consensus, but the two subgroups move oppositely towards each other. Rigorous analysis and a simulation example are provided.
Vocal control pathways through the anterior forebrain of a parrot (Melopsittacus undulatus)

A feature of the telencephalic vocal control system in the budgerigar (Melopsittacus undulatus) that has been hypothesized to represent a profound difference in organization from the oscine vocal system is its reported lack of an inherent circuit through the anterior forebrain. The present study reports anatomical connections that indicate the existence of an anterior forebrain circuit comparable in important ways to the “recursive” pathway of oscine songbirds. Results from anterograde and retrograde tracing experiments with biocytin and fluorescently labeled dextran amines indicate that the central nucleus of the anterior archistriatum (AAc) is the source of ascending projections upon the oval nuclei of the anterior neostriatum and ventral hyperstriatum (NAo and HVo, respectively). Efferent projections from the latter nuclei terminate in the lateral neostriatum afferent to AAc, thereby forming a short recurrent pathway through the pallium. Previously reported projections from HVo and NAo upon the magnocellular nucleus of the lobus parolfactorius (LPOm), and from LPOm onto the magnocellular nucleus of the dorsal thalamus (DMm; G.F. Striedter [1994] J. Comp. Neurol. 343:35–56), are confirmed. A specific projection from DMm onto NAom is also demonstrated; therefore, a recurrent pathway through the basal forebrain also exists in the budgerigar vocal system that is similar to the anterior forebrain circuit of oscine songbirds. Parallels between these circuits and mammalian basal ganglia‐thalamo‐cortical circuits are discussed. It is hypothesized that vocal control nuclei of the avian anterior neostriatum may perform a function similar to the primate supplemental motor area. J. Comp. Neurol. 377:179–206, 1997. © 1997 Wiley‐Liss, Inc.
A tumor-targeting cRGD-EGFR siRNA conjugate and its anti-tumor effect on glioblastoma in vitro and in vivo

Abstract The epidermal growth factor receptor (EGFR) is an important anti-tumor target. The development of novel molecular-targeted anti-tumor drugs that can target the interior of tumor cells and specifically silence EGFR expression is valuable and promising. In this work, a promising anti-tumor conjugate comprising methoxy-modified EGFR siRNA and cyclic arginine-glycine-aspartic acid (cRGD) peptides, which selectively bind to αvβ3 integrins, was synthesized and examined. To prepare cRGD-EGFR siRNA (cRGD-siEGFR), cRGD was covalently conjugated to the 5′-end of an siRNA sense strand using a thiol-maleimide linker. The cellular uptake and cytotoxicity of cRGD-siEGFR in vitro were tested using an αvβ3-positive U87MG cell line. In vivo bio-distribution, anti-tumor activity, immunogenicity and toxicity were investigated in a nude mouse tumor model through repeated i.v. administration of cRGD-siEGFR (7 times over a 48 h interval). Analyses of in vitro data showed that cRGD-siEGFR silenced EGFR expression effectively, with high tumor targeting ability. Administration of cRGD-siEGFR to tumor-bearing nude mice led to significant inhibition of tumor growth, obvious reduction of EGFR expression and down-regulation of EGFR mRNA and protein in tumor tissue. Furthermore, serum biochemistry and pathological section evaluation did not indicate any serious toxicity of cRGD-siEGFR in vivo. cRGD-siEGFR is likely a promising candidate with high targeting ability, substantial anti-tumor effects and low toxicity in vitro and in vivo.
Marginal Noise Reduction in Historical Handwritten Documents -- A Survey

This paper presents a survey on different approaches for removing the marginal noise from document images, and anlaysing the research challenges of those methods relating to handwritten historical datasets. In this survey, historical documents collected from Australian Archives and Libraries are introduced and the associated layout complexities of those document images are also described. Benchmarking other historical databases related to this work is also discussed. This survey discusses the difficulties and suitability of the state-of-the-art methods to remove marginal noise as well as preserving the text content from handwritten historical documents. This survey helps researchers to identify appropriate methods according to the associated marginal noise and also illustrates their drawbacks in order to make suggestions for developing approaches, which are more general and robust for any datasets.
Primary stenting versus primary balloon angioplasty for treating acute myocardial infarction.

BACKGROUND Balloon angioplasty following myocardial infarction (MI) reduces death, non-fatal MI and stroke compared to thrombolytic reperfusion. However up to 50% of patients experience restenosis and 3% to 5% recurrent myocardial infarction. Therefore, primary stenting may offer additional benefits compared to balloon angioplasty in patients with acute myocardial infarction. OBJECTIVES To examine whether primary stenting compared to primary balloon angioplasty reduces clinical outcomes in patients with acute myocardial infarction. SEARCH STRATEGY We searched MEDLINE, EMBASE, Pascal, Index medicus and The Cochrane Controlled Trials Register (The Cochrane Library) from 1979 to March 2002. SELECTION CRITERIA Randomised controlled trials of primary stenting or balloon angioplasty prior to the invasive procedure; intervention in native coronary arteries within 24 hours after onset of symptoms of myocardial infarction; report of death or reinfarction; and follow-up of at least 1 month. Trials were excluded when randomisation occurred after an invasive procedure and if they exclusively included patients with cardiogenic shock. DATA COLLECTION AND ANALYSIS Two reviewers independently selected and extracted data from identified trials. Outcomes included mortality, reinfarction, coronary artery bypass grafting, target vessel revascularization, need for vascular repair or blood transfusion. Peto odds ratios were calculated. To explore the stability of the overall treatment effect various sensitivity analyses were performed. MAIN RESULTS We included nine trials of 4433 participants. Odds ratios for mortality after stenting compared to balloon angioplasty at 30 days, 6 and 12 months were 1.16 (95% CI 0.78 to 1.73), 1.27 (95% CI 0.89 to 1.83), and 1.06 (95% CI 0.77 to 1.45). At 30 days, 6 and 12 months odds ratios for reinfarction after stenting compared to balloon angioplasty were 0.52 (95% CI 0.31 to 0.87), 0.67 (95% CI 0.45 to 1.00), and 0.67 (95% CI 0.45-0.98) and odds ratio for target vessel revascularization after stenting compared to balloon angioplasty were 0.45 (95%CI 0.34 to 0.60), 0.42 (95% CI 0.35 to 0.51), and 0.47 (95% CI 0.38 to 0.57). The odds ratio for post-interventional bleeding complications after stenting compared to balloon angioplasty was 1.34 (95% CI 0.95 to 1.88; test of heterogeneity p > 0.1). AUTHORS' CONCLUSIONS There is no evidence to suggest that primary stenting reduces mortality when compared to balloon angioplasty. Stenting seems to be associated with a reduced risk of reinfarction and target vessel revascularization, but potential confounding due to unbalanced post-interventional antithrombotic/anticoagulant therapies can not be ruled out on basis of this review.
[Analysis of relationships among syndrome, therapeutic treatment, and Chinese herbal medicine in patients with coronary artery disease based on complex networks].

OBJECTIVE To analyze the relationships among syndrome, therapeutic method and Chinese herbal medicine in patients with coronary artery disease (CAD). METHODS Using cross-sectional survey, we collected the clinical information of hospitalized CAD patients through individualized Information Acquisition Platform of CAD. The relationships among syndrome, therapeutic treatment and Chinese herbs were excavated by means of complex networks based on theory of correspondence between prescription and syndrome. RESULTS The fundamental syndrome factors were blood stasis, qi deficiency, phlegm-turbid, yin deficiency, yang deficiency, qi stagnation, and blood deficiency. The therapeutic treatment mainly included activating blood circulation, clearing heat, invigorating qi, resolving turbid and phlegm, nourishing yin, warming yang qi, and dispersing obstruction. These methods constituted an association with major syndrome factors. The major syndrome factors constituted an association with the following Chinese herbal medicines: Huangqi (Radix Astragali Mongolici), Chenpi (Pericarpium Citri Reticulatae), Dihuang (Radix Rehmanniae), Chuanxiong (Rhizoma Chuanxiong), Baizhu (Rhizoma Atractylodis Macrocephalae), Taoren (Semen Persicae), Fuling (Poria), Gancao (Radix Glycyrrhizae), Banxia (Rhizoma Pinelliae), Zexie (Rhizoma Alismatis), Chishao (Radix Paeoniae Rubra), Danggui (Radix Angelicae Sinensis), Danshen (Radix Salviae Miltiorrhizae), Zhiqiao (Fructus Aurantii Submaturus.), Guizhi (Ramulus Cinnamomi) and Maidong (Radix Ophiopogonis Japonici). The efficacy of Chinese berbal medicines constituting association with syndrome factors mainly included alleviating pain, resolving turbid and phlegm, clearing heat, activating blood circulation, invigorating qi, cooling blood, promoting urination, resolving stagnation, removing toxic material, nourishing blood, regulating qi, quieting spirit, invigorating spleen, regulating menstruation, promoting defecation, moistening dryness, and resolving stasis. CONCLUSION The therapeutic methods for CAD are based on consistency in theory, method, formula and medicines. Therapeutic methods for clearing heat and removing toxical material should be further studied.
Hemodynamic imaging using an implantable self-reset image sensor

In this study, we examine hemodynamic imaging by using an implantable CMOS image sensor with self-reset pixels. The self-reset function prevents saturation and allows imaging under a high light intensity condition. Thus, effective signal-to-noise ratio (SNR) over the photon shot noise limit in a normal pixel can be achieved. We designed a prototype using a 0.35-pm process. The self-reset function is implemented using a Schmitt trigger inverter driven by a low voltage. A pixel that is relatively small (15 × 15 pm) and consumes low power is applied to an implantable image sensor. An effective SNR of the sensor is approximately 1.5 dB higher than the photon shot noise limit. We demonstrate hemodynamic imaging of a mouse brain by implanting the proposed sensor with a frame synchronized two-color illumination.
Short-range growth inhibitory signals from the epithelium can drive non-stereotypic branching in the pancreas

Many organs such as the vasculature, kidney, lungs, pancreas and several other glands form ramified networks of tubes that either maximize exchange surfaces between two compartments or minimize the volume of an organ dedicated to the production and local delivery of a cell-derived product. The structure of these tubular networks can be stereotyped, as in the lungs, or stochastic with large variations between individuals, as in the pancreas. The principles driving stereotyped branching have attracted much attention and several models have been proposed and refined. Here we focus on the pancreas, as a model of non-stereotyped branching. In many ramified tubular organs, an important role of the mesenchyme as a source of branching signals has been proposed, including in the pancreas. However, our previous work has shown that in the absence of mesenchyme, epithelial cells seeded in vitro in Matrigel form heavily branched organoids. Here we experimentally show that pancreatic organoids grow primarily at the tips. Furthermore, in contrast to classical ‘depletion of activator’ mechanisms, organoids growing in close vicinity seem not to affect each other’s growth before they get in contact. We recapitulate these observations in an in silico model of branching assuming a ‘local inhibitor’ is secreted by the epithelium. Remarkably this simple mechanism is sufficient to generate branched organoids similar to those observed in vitro, including their transition from filled spheres to a tree like structure. Quantifying the similarity between in silico and in vitro development through a normalized surface to volume ratio, our in silico model predicts that inhibition is likely to be cooperative and that the diffusing inhibitor decays within a length scale of 10–20 μm.
Nasopharyngeal colonization by Haemophilus influenzae in children living in an orphanage

Aim. To study colonization and transmission of Haemophilus influenzae in a cohort of children <2 years old living in the unique epidemiologic conditions of a closed community of an orphanage. Methods. Fifty-three children, ages 0 to 24 months, were followed for 1 year. All children >2 months were vaccinated against H. influenzae serotype b. Nasopharyngeal cultures were collected monthly or, in children <6 months of age, every 2 weeks. Antibiotic susceptibility, serotype, biotype and genotype (pulsed field gel electrophoresis) of each isolate were determined. As control, 39 H. influenzae isolates were recovered from various regions in France. Results. The mean monthly rate of carriage was 45% ranging from 17 to 70%. Most isolates belonged to biotype II (62%), 4 isolates to serotype f (3.6%) and none to serotype b, and 60% of the 111 isolates produced beta-lactamase. A complete concordance was found among biotype, serotype, pulsotype and antimicrobial susceptibility. On average children were sequentially colonized by 3 different isolates. The mean duration of carriage for a given isolate was ∼1.4 months. In younger children the mean age of primary colonization was 2 months. Contrasting with the high genetic heterogeneity of 39 control isolates, most isolates (82%) belonged to only 5 pulsotypes. Three main H. influenzae clones rapidly spread in the community and colonized children in waves. Conclusion. During early life nasopharyngeal colonization by H. influenzae is a dynamic phenomenon with sequential carriage of various clones spreading in the community.
Induction of a protective antibody response to foot and mouth disease virus in mice following oral or parenteral immunization with alfalfa transgenic plants expressing the viral structural protein VP1.

The utilization of transgenic plants expressing recombinant antigens to be used in the formulation of experimental immunogens has been recently communicated. We report here the development of transgenic plants of alfalfa expressing the structural protein VP1 of foot and mouth disease virus (FMDV). The presence of the transgenes in the plants was confirmed by PCR and their specific transcription was demonstrated by RT-PCR. Mice parenterally immunized using leaf extracts or receiving in their diet freshly harvested leaves from the transgenic plants developed a virus-specific immune response. Animals immunized by either method elicited a specific antibody response to a synthetic peptide representing amino acid residues 135-160 of VP1, to the structural protein VP1, and to intact FMDV particles. Additionally, the immunized mice were protected against experimental challenge with the virus. We believe this is the first report demonstrating the induction of a protective systemic antibody response in animals fed transgenic plants expressing a viral antigen. These results support the feasibility of producing edible vaccines in transgenic forage plants, such as alfalfa, commonly used in the diet of domestic animals even for those antigens for which a systemic immune response is required.
Comparison of the incidence of schizophrenia in rural Dumfries and Galloway and urban Camberwell

Background Being born or living in urban areas is associated with high rates of schizophrenia. However, few studies have compared the incidence in urban/rural areas using the same methodology. Aims To compare service-based incidence rates for schizophrenia in rural Dumfries and Galloway in south-west Scotland with urban Camberwell in south-east London. Method Using Research Diagnostic Criteria diagnoses from the OPCRIT computer algorithm, we compared the incidence of schizophrenia over 12 years (1979–1984 and 1992–1997) using indirect standardisation techniques and Poisson regression modelling. Results The incidence was 61% higher in urban Camberwell than in rural Dumfries and Galloway (standardised incidence ratio (SIR)= 1.61; 95% Cl=1.42–1.81). There was no difference in incidence when we compared the White population in Camberwell with Dumfries and Galloway (SIR=1.12; 95% CI=0.86–1.43). Conclusions The incidence of schizophrenia in urban Camberwell was higher than that in rural Dumfries and Galloway; the high incidence of non-Whites in Camberwell largely explains the urban/rural difference.
Evaluation of ERBB2 Gene Status and Chromosome 17 Anomalies in Male Breast Cancer

Male breast cancer (MBC) is an uncommon neoplasm that shares several biologic characteristics with its female counterpart. In the latter, abnormalities in the expression and/or copy number of the ERBB2 gene are present in 10% to 30% of invasive carcinoma and behave as poor prognostic markers. ERBB2 abnormalities have also been reported in MBC, yet at lower frequency, but their prognostic significance remains controversial. Furthermore, no study has addressed the impact of chromosome 17 abnormalities in MBC survival. In this study, the ERBB2-gene status (overexpression and amplification) and chromosome 17 numerical abnormalities were investigated in a series of 50 archival cases of MBC. The results, together with patient's age, histologic grade, pathologic stage, and estrogen receptor status were correlated with overall survival. ERBB2-protein overexpression was present in 7 cases (14%), ERBB2-gene amplification in 4 (8%), and aneuploidy of chromosome 17 in 12 cases (33.3%). The pathologic stage, ERBB2 overexpression and ERBB2 amplification were significantly correlated with overall survival (P=0.002, 0.016, and 0.009, respectively). No correlation was observed between chromosome 17 aneuploidy and overall survival. Therefore, despite their low incidence in MBC, expression abnormalities of ERBB2 behave, together with the pathologic stage of the tumor, as predictors of overall survival, akin to what has been reported for its female counterpart.
Imagined practices and the future of personal mobility

We report from a project on the futures of personal mobility in the UK, in the context of sustainable mobility and the need to reduce greenhouse gas emissions from transport. This paper looks at how people, behaviour and mobility are imagined in visioning documents (forecasts, pathways, etc.) in the future up to 2050, a timeline with great emission reduction targets. We use the lens of two innovations, electric vehicles and car clubs, to consider how potential adopters/users are imagined and constructed. We find that people are imagined primarily as consumers, using the rational actor paradigm. The analysis highlights a tension and seeming dissonance between the imagined public as rational actors and more complex real behaviour. Choice-based approaches limit imagined behaviour (change) to modal choice, or even choice of vehicle purchase, thereby limiting discourse on behaviour change, rather than opening it up. Imagined future mobility in most visions is business-as-usual, with privately owned car transport dominating personal mobility, and technological innovation supplying vehicles with reduced emissions; the link between transport and economic growth is invoked to support continued high transport demand. Car club visions show less car ownership, but retain high mobility and an economic growth perspective. Our findings support the idea that some future mobility visioning is used to support the status quo, rather than explore a variety of futures, by portraying a near business-as-usual option as the only future.
Sulfate-Reducing Bacterium Desulfovibrio desulfuricans ND132 as a Model for Understanding Bacterial Mercury Methylation

ABSTRACT We propose the use of Desulfovibrio desulfuricans ND132 as a model species for understanding the mechanism of microbial Hg methylation. Strain ND132 is an anaerobic dissimilatory sulfate-reducing bacterium (DSRB), isolated from estuarine mid-Chesapeake Bay sediments. It was chosen for study because of its exceptionally high rates of Hg methylation in culture and its metabolic similarity to the lost strain D. desulfuricans LS, the only organism for which methylation pathways have been partially defined. Strain ND132 is an incomplete oxidizer of short-chain fatty acids. It is capable of respiratory growth using fumarate as an electron acceptor, supporting growth without sulfide production. We used enriched stable Hg isotopes to show that ND132 simultaneously produces and degrades methylmercury (MeHg) during growth but does not produce elemental Hg. MeHg produced by cells is mainly excreted, and no MeHg is produced in spent medium. Mass balances for Hg and MeHg during the growth of cultures, including the distribution between filterable and particulate phases, illustrate how medium chemistry and growth phase dramatically affect Hg solubility and availability for methylation. The available information on Hg methylation among strains in the genus Desulfovibrio is summarized, and we present methylation rates for several previously untested species. About 50% of Desulfovibrio strains tested to date have the ability to produce MeHg. Importantly, the ability to produce MeHg is constitutive and does not confer Hg resistance. A 16S rRNA-based alignment of the genus Desulfovibrio allows the very preliminary assessment that there may be some evolutionary basis for the ability to produce MeHg within this genus.