Miracle-dz/UniFAR-FTUs huggingface dataset:
Regional Circulatory Adjustments to Moderate and Severe Chronic Anemia in Conscious Dogs at Rest and during Exercise

The successive changes in regional blood flows and resistances due to moderate and severe anemia were studied serially in nine conscious dogs after they recovered from implantation of ultrasonic Doppler transducers or electromagnetic flow probes on the left circumflex coronary, the mesenteric, the renal, and the iliac arteries and pressure gauges or catheters in the aorta. Anemia was induced by progressive phlebotomy and volume replacement over a period of 2−4 weeks. In moderate anemia (average hematocrit 22%) heart rate increased from 73 beats/min to 105 beats/min, and mean arterial pressure fell from 98 mm Hg to 94 mm Hg. Flow increased to the coronary bed by 75% and to the iliac bed by 45%, but flow to the mesenteric bed was not significantly affected and renal flow fell by 9%. Coronary and iliac resistances fell by 45% and 32%, respectively, but mesenteric and renal resistances were not significantly affected. In severe anemia (hematocrit 14%) heart rate increased to 129 beats/min, and mean arterial pressure was at control levels; coronary flow increased by 227%, iliac flow by 102%, mesenteric flow by 29%, and renal flow by 20%. Resistance decreased in the coronary bed by 69%, in the iliac bed by 52%, in the mesenteric bed by 23%, and in the renal bed by 19%. Exercise during severe anemia increased heart rate to 224 beats/min, mean arterial pressure to 114 mm Hg, coronary flow by 34%, and iliac flow by 215%; it reduced mesenteric flow by 59% and renal flow by 48%. Thus, blood flow increased and resistance decreased to all beds studied, indicating that in the resting conscious dog compensatory reduction of visceral flow is not a feature of the cardiovascular response to severe anemia at rest, although a redistribution of regional blood flow does occur. However, the added stress of exercise during severe anemia results in substantial reductions in mesenteric and renal blood flows.
Mph1 requires mismatch repair-independent and -dependent functions of MutSα to regulate crossover formation during homologous recombination repair

In budding yeast the DNA helicase Mph1 prevents genome rearrangements during ectopic homologous recombination (HR) by suppressing the formation of crossovers (COs). Here we show that during ectopic HR repair, the anti-CO function of Mph1 is intricately associated with the mismatch repair (MMR) factor, MutSα. In particular, during HR repair using a completely homologous substrate, we reveal an MMR-independent function of MutSα in generating COs that is specifically antagonized by Mph1, but not Sgs1. In contrast, both Mph1 and MutSα are required to efficiently suppress COs in the presence of a homeologous substrate. Mph1 acts redundantly with Sgs1 in this respect since mph1Δ sgs1Δ double mutant cells pheno-copy MutSα mutants and completely fail to discriminate homologous and homeologous sequences during HR repair. However, this defect of mph1Δ sgs1Δ cells is not due to an inability to carry out MMR but rather is accompanied by elevated levels of gene conversion (GC) and bi-directional GC tracts specifically in non-crossover products. Models describing how Mph1, MutSα and Sgs1 act in concert to suppress genome rearrangements during ectopic HR repair are discussed.
Gamma Radiation Effects in Vertically Aligned Carbon Nanotubes

This paper describes an experimental study of gamma radiation effects in low-density arrays of vertically aligned carbon nanotubes. These arrays are characterized by excellent anti-reflective and absorbing properties for wavelengths from UV to IR, which makes them an interesting option for stray light control in optical space applications. Gamma irradiation equivalent to an estimated surface lifetime exposition in geostationary orbit does not affect the reflectivity of the structures. First high-energy proton irradiation studies indicate that the reflectivity of the carbon nanotubes forests remains unchanged.
Inhibition of experimental neointimal hyperplasia and thrombosis depends on the type of vascular injury and the site of drug administration.

BACKGROUND Heparin inhibits vascular smooth muscle cell proliferation in tissue culture and limits neointimal hyperplasia after experimental arterial injury but has been ineffective in reducing clinical restenosis. We examined how this discrepancy might reflect suboptimal drug-tissue interactions and/or differences in the vascular response to injury. METHODS AND RESULTS Intravenous infusion was compared with local administration of heparin to injured rabbit iliac arteries either from drug-impregnated polymeric controlled release matrices in the perivascular space or from drug-releasing endovascular stents. Occlusive thrombosis, seen in 42% of control stent-bearing arteries, and partial thrombosis were virtually eliminated by heparin delivery from any route. Intimal area 14 days after balloon withdrawal denudation alone was reduced to an equal extent by continuous systemic heparin or by perivascular heparin for the first 3 days. In contrast, endovascular stents produced more exuberant neointimal hyperplasia, the inhibition of which required continuous rather than only early heparin administration. Neither perivascular delivery limited to the first 3 days nor stent-based delivery reduced neointimal hyperplasia as effectively. CONCLUSIONS The antiproliferative and antithrombotic effects of heparin differ markedly, depending on the type of arterial injury and the mode of drug administration. Different forms of injury may require different therapies, and complications of arterial intervention such as excessive neointimal hyperplasia and thrombosis may demand alternate therapeutic regimens. Duration, dose, and site of delivery rather than frank resistance to therapy may explain why experimentally effective antiproliferative and antithrombotic agents fail clinically.
Androgen-dependent expression of the gastrin-releasing peptide receptor in human prostate tumor xenografts.

UNLABELLED Human prostate cancers (PC) overexpress gastrin-releasing peptide (GRP) receptors. This observation suggests that GRP receptors may be used as new visualization and treatment modalities for these tumors. Radiolabeled GRP receptor-targeting analogs of GRP and bombesin (BN) have successfully been developed for these purposes. Expression of GRP receptors in human prostate tumors is, however, primarily evaluated in early stages of tumor development and information on expression in the more progressive prostate tumors is uncertain. To evaluate GRP receptor expression in all stages of PC, we investigated GRP receptor expression using a panel of 12 established human PC xenograft models representing the different stages of human PC and the effect of antiandrogen treatment (castration). METHODS Human PC xenografts were grown in male nude mice, and GRP receptor density in the tumors was evaluated using displacement receptor autoradiography with the universal BN receptor analog (125)I-[D-Tyr(6),beta-Ala(11),Phe(13),Nle(14)]BN(6-14) and the BN analog (111)In-[DTPA-Pro(1),Tyr(4)]BN (DTPA is diethylenetriaminepentaacetic acid) before and after castration. RESULTS Autoradiography showed high-density GRP receptor expression in the androgen-dependent tumors (3/12 models), whereas only very low receptor expression was found in the androgen-responsive and -independent tumors (9/12 models). Castration resulted in GRP receptor downregulation (11%-36% of initial values) in the 3 androgen-dependent tumors. CONCLUSION High GRP receptor density was only observed in androgen-dependent PC xenografts, indicating high GRP receptor expression in the early, androgen-dependent, stages of prostate tumor development and not in later stages. In addition, castration strongly reduced GRP receptor expression in androgen-dependent tumors, indicating that GRP receptor expression in human PC is androgen-regulated.
Specificity prediction of adenylation domains in nonribosomal peptide synthetases (NRPS) using transductive support vector machines (TSVMs)

We present a new support vector machine (SVM)-based approach to predict the substrate specificity of subtypes of a given protein sequence family. We demonstrate the usefulness of this method on the example of aryl acid-activating and amino acid-activating adenylation domains (A domains) of nonribosomal peptide synthetases (NRPS). The residues of gramicidin synthetase A that are 8 Å around the substrate amino acid and corresponding positions of other adenylation domain sequences with 397 known and unknown specificities were extracted and used to encode this physico-chemical fingerprint into normalized real-valued feature vectors based on the physico-chemical properties of the amino acids. The SVM software package SVMlight was used for training and classification, with transductive SVMs to take advantage of the information inherent in unlabeled data. Specificities for very similar substrates that frequently show cross-specificities were pooled to the so-called composite specificities and predictive models were built for them. The reliability of the models was confirmed in cross-validations and in comparison with a currently used sequence-comparison-based method. When comparing the predictions for 1230 NRPS A domains that are currently detectable in UniProt, the new method was able to give a specificity prediction in an additional 18% of the cases compared with the old method. For 70% of the sequences both methods agreed, for <6% they did not, mainly on low-confidence predictions by the existing method. None of the predictive methods could infer any specificity for 2.4% of the sequences, suggesting completely new types of specificity.
Analysis of Search and Browsing Behavior of Young Users on the Web

The Internet is increasingly used by young children for all kinds of purposes. Nonetheless, there are not many resources especially designed for children on the Internet and most of the content online is designed for grown-up users. This situation is problematic if we consider the large differences between young users and adults since their topic interests, computer skills, and language capabilities evolve rapidly during childhood. There is little research aimed at exploring and measuring the difficulties that children encounter on the Internet when searching for information and browsing for content. In the first part of this work, we employed query logs from a commercial search engine to quantify the difficulties children of different ages encounter on the Internet and to characterize the topics that they search for. We employed query metrics (e.g., the fraction of queries posed in natural language), session metrics (e.g., the fraction of abandoned sessions), and click activity (e.g., the fraction of ad clicks). The search logs were also used to retrace stages of child development. Concretely, we looked for changes in interests (e.g., the distribution of topics searched) and language development (e.g., the readability of the content accessed and the vocabulary size). In the second part of this work, we employed toolbar logs from a commercial search engine to characterize the browsing behavior of young users, particularly to understand the activities on the Internet that trigger search. We quantified the proportion of browsing and search activity in the toolbar sessions and we estimated the likelihood of a user to carry out search on the Web vertical and multimedia verticals (i.e., videos and images) given that the previous event is another search event or a browsing event. We observed that these metrics clearly demonstrate an increased level of confusion and unsuccessful search sessions among children. We also found a clear relation between the reading level of the clicked pages and characteristics of the users such as age and educational attainment. In terms of browsing behavior, children were found to start their activities on the Internet with a search engine (instead of directly browsing content) more often than adults. We also observed a significantly larger amount of browsing activity for the case of teenager users. Interestingly we also found that if children visit knowledge-related Web sites (i.e., information-dense pages such as Wikipedia articles), they subsequently do more Web searches than adults. Additionally, children and especially teenagers were found to have a greater tendency to engage in multimedia search, which calls to improve the aggregation of multimedia results into the current search result pages.
Learning Sub-structures of Document Semantic Graphs for Document Summarization

paper we present a method for summarizing document by creating a semantic graph of the original document and identifying the substructure of such a graph that can be used to extract sentences for a document summary. We start with deep syntactic analysis of the text and, for each sentence, extract logical form triples, subject-predicate-object. We then apply cross-sentence pronoun resolution, co-reference resolution, and semantic normalization to refine the set of triples and merge them into a semantic graph. This procedure is applied to both documents and corresponding summary extracts. We train linear Support Vector Machine on the logical form triples to learn how to extract triples that belong to sentences in document summaries. The classifier is then used for automatic creation of document summaries of test data. Our experiments with the DUC 2002 data show that increasing the set of attributes to include semantic properties and topological graph properties of logical triples yields statistically significant improvement of the micro-average F1 measure for the extracted summaries. We also observe that attributes describing various aspects of semantic graph are weighted highly by SVM in the learned model.
Thrombomodulatory Effect of Anti-B2-Glycoprotein I Antibodies on Crystalline Annexin A5 on Phospholipid Bilayers, as Observed by Atomic Force Microscopy

Antibodies against β2-glycoprotein I are a subset of very heterogeneous family of antiphospholipid antibodies. It is well recognised that anti-β2-glycoprotein I antibodies are the main pathogenic players in the autoimmune disease known as antiphospholipid syndrome. Many mechanisms have been proposed through which these autoantibodies could cause microplacental, arterial or venous thrombosis. One of the suggested mechanisms is an antiphospholipid antibody-mediated disruption of annexin A5 protective crystalline shield on negatively charged phospholipid membranes. In current report the study of β2-glycoprotein I, anti-β2-glycoprotein I antibodies and annexin A5 interactions was performed on in vitro model of planar solid-supported phospholipid bilayers and visualized by atomic force microscopy. Planar phospholipid bilayers comprised 30 % L-α-phosphatidylserine and 70 % L-α-phosphatidylcholine. For the study of interactions 10 mg/l annexin A5, 0.15 g/l β2-glycoprotein I, 10 g/l of IgG fraction from healthy blood donor, 10 g/l of IgG fraction from a patient with anti-β2-glycoprotein I antibodies and 0.4 g/l of isolated IgG anti-β2-glycoprotein I antibodies from the same patients in Hepes buffered saline with 1.5 mM Ca2+ were used. We confirmed the clustering of β2-glycoprotein I on planar phospholipid bilayers. We also found that in the presence of annexin A5, β2-glycoprotein I does not bind to planar phospholipid bilayers. However, when adding the anti-β2-glycoprotein I antibodies, the growth of β2-glycoprotein I-anti-β2-glycoprotein I antibodies complexes in the presence of incompletely crystallized annexin A5 on planar phospholipid bilayers was observed. Results confirm the possible thrombomodulatory activity of anti-β2-glycoprotein antibodies through their effect on crystalline annexin A5. In addition, the hypothesis that the presence of possibly pathologic antigen-antibody pair itself is not sufficient to start the pathological process is confirmed and visualized for the first time.
High Working Memory Load Impairs Language Processing during a Simulated Piloting Task: An ERP and Pupillometry Study

Given the important amount of visual and auditory linguistic information that pilots have to process, operating an aircraft generates a high working-memory load (WML). In this context, the ability to focus attention on relevant information and to remain responsive to concurrent stimuli might be altered. Consequently, understanding the effects of WML on the processing of both linguistic targets and distractors is of particular interest in the study of pilot performance. In the present work, participants performed a simplified piloting task in which they had to follow one of three colored aircraft, according to specific written instructions (i.e., the written word for the color corresponding to the color of one of the aircraft) and to ignore either congruent or incongruent concurrent auditory distractors (i.e., a spoken name of color). The WML was manipulated with an n-back sub-task. Participants were instructed to apply the current written instruction in the low WML condition, and the 2-back written instruction in the high WML condition. Electrophysiological results revealed a major effect of WML at behavioral (i.e., decline of piloting performance), electrophysiological, and autonomic levels (i.e., greater pupil diameter). Increased WML consumed resources that could not be allocated to the processing of the linguistic stimuli, as indexed by lower P300/P600 amplitudes. Also, significantly, lower P600 responses were measured in incongruent vs. congruent trials in the low WML condition, showing a higher difficulty reorienting attention toward the written instruction, but this effect was canceled in the high WML condition. This suppression of interference in the high load condition is in line with the engagement/distraction trade-off model. We propose that P300/P600 components could be reliable indicators of WML and that they allow an estimation of its impact on the processing of linguistic stimuli.
A Collaborative Filtering Algorithm Employing Genetic Clustering to Ameliorate the Scalability Issue

Collaborative filtering technologies are facing two major challenges: scalability and recommendation quality, which are two goals in conflict. Nowadays more studies are focusing on the quality issue but less on the scalability one. We introduce a genetic clustering algorithm to partition the source data, guaranteeing that the intra-similarity is high but the inter-similarity is low. The clustering process is off-line running. Our empirical results show that the genetic clustering based collaborative filtering recommender system outperforms the memory-based one in scalability, and outperforms the k-means clustering based one and the memory-based one in recommendation quality
A Unique Arabinose 5-Phosphate Isomerase Found within a Genomic Island Associated with the Uropathogenicity of Escherichia coli CFT073

ABSTRACT Previous studies showed that deletion of genes c3405 to c3410 from PAI-metV, a genomic island from Escherichia coli CFT073, results in a strain that fails to compete with wild-type CFT073 after a transurethral cochallenge in mice and is deficient in the ability to independently colonize the mouse kidney. Our analysis of c3405 to c3410 suggests that these genes constitute an operon with a role in the internalization and utilization of an unknown carbohydrate. This operon is not found in E. coli K-12 but is present in a small number of pathogenic E. coli and Shigella boydii strains. One of the genes, c3406, encodes a protein with significant homology to the sugar isomerase domain of arabinose 5-phosphate isomerases but lacking the tandem cystathionine beta-synthase domains found in the other arabinose 5-phosphate isomerases of E. coli. We prepared recombinant c3406 protein, found it to possess arabinose 5-phosphate isomerase activity, and characterized this activity in detail. We also constructed a c3406 deletion mutant of E. coli CFT073 and demonstrated that this deletion mutant was still able to compete with wild-type CFT073 in a transurethral cochallenge in mice and could colonize the mouse kidney. These results demonstrate that the presence of c3406 is not essential for a pathogenic phenotype.
A vitamin B12 conjugate of exendin‐4 improves glucose tolerance without associated nausea or hypophagia in rodents

While pharmacological glucagon‐like peptide‐1 receptor (GLP‐1R) agonists are FDA‐approved for treating type 2 diabetes mellitus (T2DM) and obesity, a major side effect is nausea/malaise. We recently developed a conjugate of vitamin B12 (B12) bound to the GLP‐1R agonist exendin‐4 (Ex4), which displays enhanced proteolytic stability and retention of GLP‐1R agonism. Here, we evaluate whether the conjugate (B12‐Ex4) can improve glucose tolerance without producing anorexia and malaise.
Global geospatial data from Earth observation: status and issues

ABSTRACT Data covering the whole of the surface of the Earth in a homogeneous and reliable manner has been accumulating over many years. This type of data became available from meteorological satellites from the 1960s and from Earth-observing satellites at a small scale from the early 1970s but has gradually accumulated at larger scales up to the present day when we now have data covering many environmental themes at large scales. These data have been used to generate information which is presented in the form of global data sets. This paper will give a brief introduction to the development of Earth observation and to the organisations and sensors which collect data and produce global geospatial data sets. Means of accessing global data sets will set out the types of data available that will be covered. Digital elevation models are discussed in a separate section because of their importance in georeferencing image data as well as their application to analysis of thematic data. The paper will also examine issues of availability, accuracy, validation and reliability and will look at future challenges.
The mitochondrial Hsp70 chaperone Ssq1 facilitates Fe/S cluster transfer from Isu1 to Grx5 by complex formation

The monothiol glutaredoxin Grx5 is defined as a core member of mitochondrial Fe/S protein biogenesis. Grx5 undergoes a highly specific protein interaction with the dedicated Hsp70 chaperone Ssq1. The simultaneous presence of the scaffold protein Isu1 and Grx5 on Ssq1 facilitates the transfer of newly synthesized Fe/S clusters from Isu1 to Grx5.
The reliability, validity and sensitivity to change of the Chinese version of SF-36 in oriental patients with rheumatoid arthritis.

OBJECTIVE To assess the reliability, validity and sensitivity to change of a Chinese version of the 36-item Short-Form Health Survey (SF-36) in Chinese-speaking patients with rheumatoid arthritis (RA) in Singapore. METHODS The psychometric properties of the Chinese Hong Kong standard version of the SF-36 were assessed in 401 RA patients. The construct validity of the Chinese SF-36 was assessed by comparison with the American College of Rheumatology (ACR) functional status, a validated Chinese Health Assessment Questionnaire (C-HAQ) and markers of RA activity and severity. RESULTS The overall Cronbach's coefficient alpha was 0.921, reflecting excellent internal consistency. The instrument showed reasonable test-retest reliability except in the social functioning (SF) subscale. There was a significant ceiling effect in the role physical (RP), SF and role emotional (RE) subscales and a floor effect in the RP and RE subscales. Physical function (PF) and SF were strongly correlated with C-HAQ and patient's assessment of RA activity [Pearson's correlation coefficient (r) ranging from -0.41 to -0.53] and moderately correlated with ACR functional status (r = -0.35 and -0.3, respectively). Weak correlations were also found between the Chinese SF-36 and markers of RA activity, deformed joint count and radiographic damage. PF and SF were the subscales most responsive to change in quality of life (QOL). CONCLUSION The Chinese SF-36 showed reasonable reliability, criterion validity and responsiveness with limitations in certain subscales. Overall, the physical domains and PF in particular may be the most ideal psychometric measures of QOL in RA.