Miracle-dz/UniFAR-FTUs huggingface dataset:
Mechanisms Controlling Anaemia in Trypanosoma congolense Infected Mice

Background Trypanosoma congolense are extracellular protozoan parasites of the blood stream of artiodactyls and are one of the main constraints on cattle production in Africa. In cattle, anaemia is the key feature of disease and persists after parasitaemia has declined to low or undetectable levels, but treatment to clear the parasites usually resolves the anaemia. Methodology/Principal Findings The progress of anaemia after Trypanosoma congolense infection was followed in three mouse strains. Anaemia developed rapidly in all three strains until the peak of the first wave of parasitaemia. This was followed by a second phase, characterized by slower progress to severe anaemia in C57BL/6, by slow recovery in surviving A/J and a rapid recovery in BALB/c. There was no association between parasitaemia and severity of anaemia. Furthermore, functional T lymphocytes are not required for the induction of anaemia, since suppression of T cell activity with Cyclosporin A had neither an effect on the course of infection nor on anaemia. Expression of genes involved in erythropoiesis and iron metabolism was followed in spleen, liver and kidney tissues in the three strains of mice using microarrays. There was no evidence for a response to erythropoietin, consistent with anaemia of chronic disease, which is erythropoietin insensitive. However, the expression of transcription factors and genes involved in erythropoiesis and haemolysis did correlate with the expression of the inflammatory cytokines Il6 and Ifng. Conclusions/Significance The innate immune response appears to be the major contributor to the inflammation associated with anaemia since suppression of T cells with CsA had no observable effect. Several transcription factors regulating haematopoiesis, Tal1, Gata1, Zfpm1 and Klf1 were expressed at consistently lower levels in C57BL/6 mice suggesting that these mice have a lower haematopoietic capacity and therefore less ability to recover from haemolysis induced anaemia after infection.
On the Performance of an Implicit–Explicit Runge--Kutta Method in Models of Cardiac Electrical Activity

Mathematicalmodels of electric activity in cardiac tissue are becoming increasingly powerful tools in the study of cardiac arrhythmias. Considered here are mathematical models based on ordinary differential equations (ODEs) that describe the ionic currents at the myocardial cell level. Generating an efficient numerical solution of these ODEs is a challenging task, and, in fact, the physiological accuracy of tissue-scale models is often limited by the efficiency of the numerical solution process. In this paper, we examine the efficiency of the numerical solution of four cardiac electrophysiological models using implicit-explicit Runge-Kutta (IMEX-RK) splitting methods. We find that variable step-size implementations of IMEX-RK methods (ARK3 and ARK5) that take advantage of Jacobian structure clearly outperform the methods commonly used in practice.
Visual tracking via geometric particle filtering on the affine group with optimal importance functions

We propose a geometric method for visual tracking, in which the 2-D affine motion of a given object template is estimated in a video sequence by means of coordinate-invariant particle filtering on the 2-D affine group Aff(2). Tracking performance is further enhanced through a geometrically defined optimal importance function, obtained explicitly via Taylor expansion of a principal component analysis based measurement function on Aff(2). The efficiency of our approach to tracking is demonstrated via comparative experiments.
Methods for injury surveillance in international cricket

Background: The varying methods of cricket injury surveillance have made direct comparison of published studies in this field impossible. Methods: A consensus regarding definitions and methods to calculate injury rates in cricket was sought between researchers in this field. This was arrived at through a variety of face to face meetings, email communication, and draft reviews between researchers from six of the major cricket playing nations. Results: It is recommended that a cricket injury is defined as any injury or other medical condition that either (a) prevents a player from being fully available for selection for a major match or (b) during a major match, causes a player to be unable to bat, bowl, or keep wicket when required by either the rules or the team’s captain. Recommended definitions for injury incidence (for matches, training sessions, and seasons) and injury prevalence are also provided. It is proposed that match injury incidence is calculated using a denominator based on a standard time estimated for player exposure in matches, for the purposes of simplicity. This will allow all injury surveillance systems, including those with limited resources, to make calculations according to a standard definition. Conclusion: The consensus statement presented provides a standard which, if followed, allows meaningful comparison of injury surveillance data from different countries and time periods, which will assist in the possible identification of risk factors for injury in cricket.
Evolving Lose-Checkers players using genetic programming

We present the application of genetic programming (GP) to the zero-sum, deterministic, full-knowledge board game of Lose Checkers. Our system implements strongly typed GP trees, explicitly defined introns, local mutations, and multi-tree individuals. Explicitly defined introns in the genome allow for information selected out of the population to be kept as a reservoir for possible future use. Multi-tree individuals are implemented by a method inspired by structural genes in living organisms, whereby we take a single tree describing a state evaluator and split it.
Polio Patients in Northern Italy, a 50 Year Follow-up

Background: Poliomyelitis was before the immunization an important medical problem. Nowadays polio prior patients (PP) suffer from polio sequelae or have developed post-polio-syndrome (PPS) with increasing paresis, pain and fatigue. Objectives: To analyze the medical situation 50 years after acute polio. The degree of paresis was compared between the recovery 1952-1961 and 2012.The prevalence of patients fulfilling the criteria for PPS was estimated Method: The study was performed in Italy. Included were PP with rehabilitation after acute polio 1952-1961 and in 2012. During the years PP underwent yearly evaluation. A thorough neurological examination was performed in 2012. A telephone interview with questions concerning pain, paresis, fatigue, walking aids and concomitant diseases was performed in 2012. The patients were divided in two groups, if they fulfilled the criteria for PPS or not. Results: Included were 67(94%) patients receiving rehabilitation after acute poliomyelitis and 2012. 78% were walkers, half of the PPS used wheelchair. Eight out of ten suffered from pain. Four out of ten fulfilled the PPS criteria. Pain was slightly more common in PPS. Conclusion: Female gender, fatigue and wheelchair dependency were significantly more common in PPS while pain was common in both groups.
Study of the Radical Species Induced by Electron-Beam Irradiation in Vacuum on Biomedical UHMWPE

Ultra high molecular weight polyethylene (UHMWPE) is a component of mobile prostheses. The irradiation performed to sterilize and cross-link the polymer limits its life because of the free radicals originated during this process. In this work, a UHMWPE was electron-beam irradiated under high vacuum and annealed. Mechanical tests were performed on the UHMWPE samples before and after the annealing treatment. The results were compared with a study of radical species type and amount and the crystalline degree changes. Experimental results show that the annealing treatment prevents degrading reactions, favors intermolecular and/or intramolecular chemical rearrangements, and improves wear resistance without compromising the typical elasto-plastic mechanical behavior.
The Dust and Gas Content of a Disk around the Young Star HR 4796A

Abstract We have used the James Clerk Maxwell Telescope in Hawaii to search at submillimeter wavelengths for continuum emission from dust, and spectral line emission from carbon monoxide (CO) gas, in the neighborhood of HR 4796A. This young star has a dusty disk with a central cavity, where planets may have formed. We detect the dust component at a wavelength of 850 μm, and the inferred mass of solid material is ≥0.25 M ⊕ . An upper limit for the CO J =3–2 rotational line implies less than 1–7 M ⊕ (≤0.003–0.02 Jupiter masses) of molecular H 2 gas in the system. Thus, it is no longer possible to form new Jupiter-like gaseous giant planets around HR 4796A. If planet formation explains the observed dust cavity and lack of gas, then it must have occurred before the current stellar age of ∼10 Myr. A search was also made for CO J =3–2 emission around four other stars with dust excesses revealed by infrared measurements with the Infrared Astronomical Satellite (IRAS). Two were detected, both of them young sources with optical emission lines indicative of ongoing accretion of disk material onto the star. The gas mass lower limits are approximately 30 and 200 Earth masses, at least an order of magnitude higher than that for HR 4796A, illustrating the diversity of disk properties at ages of up to 10 Myr.
The protective role of transferrin in Müller glial cells after iron-induced toxicity

Purpose Transferrin (Tf) expression is enhanced by aging and inflammation in humans. We investigated the role of transferrin in glial protection. Methods We generated transgenic mice (Tg) carrying the complete human transferrin gene on a C57Bl/6J genetic background. We studied human (hTf) and mouse (mTf) transferrin localization in Tg and wild-type (WT) C57Bl/6J mice using immunochemistry with specific antibodies. Müller glial (MG) cells were cultured from explants and characterized using cellular retinaldehyde binding protein (CRALBP) and vimentin antibodies. They were further subcultured for study. We incubated cells with FeCl3-nitrilotriacetate to test for the iron-induced stress response; viability was determined by direct counting and measurement of lactate dehydrogenase (LDH) activity. Tf expression was determined by reverse transcriptase-quantitative PCR with human- or mouse-specific probes. hTf and mTf in the medium were assayed by ELISA or radioimmunoassay (RIA), respectively. Results mTf was mainly localized in retinal pigment epithelium and ganglion cell layers in retina sections of both mouse lines. hTf was abundant in MG cells. The distribution of mTf and hTf mRNA was consistent with these findings. mTf and hTf were secreted into the medium of MG cell primary cultures. Cells from Tg mice secreted hTf at a particularly high level. However, both WT and Tg cell cultures lose their ability to secrete Tf after a few passages. Tg MG cells secreting hTf were more resistant to iron-induced stress toxicity than those no longer secreted hTf. Similarly, exogenous human apo-Tf, but not human holo-Tf, conferred resistance to iron-induced stress on MG cells from WT mice. Conclusions hTf localization in MG cells from Tg mice was reminiscent of that reported for aged human retina and age-related macular degeneration, both conditions associated with iron deposition. The role of hTf in protection against toxicity in Tg MG cells probably involves an adaptive mechanism developed in neural retina to control iron-induced stress.
Comparing Three Different Modularity Methods

Modularity has many advantages but few methods exist to partition a product into modules, and no knowledge on which method to use and when. This study compares the heuristic method, the design structure matrix, and modular function deployment. The methods are applied on four commercial products. The disturbing result is that, given the same inputs, all methods partition the products differently. Some consider functionality and interface simplicity whereas others focus on strategic factors. A method developed for single products is poorly suited to modularizing product families. The methods find almost no common module boundaries that would be ideal regardless of the method used. This result is not due to poor application of the methods: the repeatability of each method was analyzed. It varied from 68% to nearly perfect. Modular function deployment was the least repeatable whereas the computerized design structure matrix the most repeatable. The heuristic approach fell in between.Copyright © 2003 by ASME
Hydration of the RNA duplex r(CGCAAAUUUGCG)2 determined by NMR.

The so-called spine of hydration in the minor groove of AnTn tracts in DNA is thought to stabilise the structure, and kinetically bound water detected in the minor groove of such DNA species by NMR has been attributed to a narrow minor groove [Liepinsh, E. , Leupin, W. and Otting, G. (1994) Nucleic Acids Res. 22, 2249-2254]. We report here an NMR study of hydration of an RNA dodecamer which has a wide, shallow minor groove. Complete assignments of exchangeable protons, and a large number of non-exchangeable protons in r(CGCAAAUUUGCG)2 have been obtained. In addition, ribose C2'-OH resonances have been detected, which are probably involved in hydrogen bonds. Hydration at different sites in the dodecamer has been measured using ROESY and NOESY experiments at 11.75 and 14.1 T. Base protons in both the major and minor grooves are in contact with water, with effective correlation times for the interaction of approximately 0.5 ns, indicating weak hydration, in contrast to the hydration of adenine C2H in the homologous DNA sequence. NOEs to H1' in the minor groove are consistent with hydration water present that is not observed in the analogous DNA sequence. Hydration kinetics in nucleic acids may be determined by chemical factors such as hydrogen-bonding more than by simple conformational factors such as groove width.
Antimicrobial Susceptibility of Clinically Relevant Gram-Positive Anaerobic Cocci Collected over a Three-Year Period in the Netherlands

ABSTRACT The susceptibility of 14 species of 115 Gram-positive anaerobic cocci (GPAC) was determined for 14 antibiotics. To assure correct identification, strains were genotypically identified by fluorescence in situ hybridization and sequencing. Susceptibility differences (MIC50 and MIC90) for penicillin G, clindamycin, tigecycline, levofloxacin, amoxicillin-clavulanic acid, cefoxitin, ertapenem, meropenem, metronidazole, and doxycycline were found for the three clinically most relevant GPAC species: Finegoldia magna, Parvimonas micra, and Peptoniphilus harei.
Antimicrobial resistance in clinical Escherichia coli isolates from poultry and livestock, China

Poultry and livestock are the most important reservoirs for pathogenic Escherichia coli and use of antimicrobials in animal farming is considered the most important factor promoting the emergence, selection and dissemination of antimicrobial-resistant microorganisms. The aim of our study was to investigate antimicrobial resistance in E. coli isolated from food animals in Jiangsu, China. The disc diffusion method was used to determine susceptibility to 18 antimicrobial agents in 862 clinical isolates collected from chickens, ducks, pigs, and cows between 2004 and 2012. Overall, 94% of the isolates showed resistance to at least one drug with 83% being resistance to at least three different classes of antimicrobials. The isolates from the different species were most commonly resistant to tetracycline, nalidixic acid, sulfamethoxazole, trimethoprim/sulfamethoxazole and ampicillin, and showed increasing resistance to amikacin, aztreonam, ceftazidime, cefotaxime, chloramphenicol, ciprofloxacin. They were least resistant to amoxicillin/clavulanic acid (3.4%) and ertapenem (0.2%). MDR was most common in isolates from ducks (44/44, 100%), followed by chickens (568/644, 88.2%), pigs (93/113, 82.3%) and cows (13/61, 21.3%). Our finding that clinical E. coli isolates from poultry and livestock are commonly resistant to multiple antibiotics should alert public health and veterinary authorities to limit and rationalize antimicrobial use in China.
Medication Adherence Improvement By Using Administration Timing Simplification Protocol (ATSP) in Cardiovascular Disease Patients

Aims: In chronic diseases, keeping adherence to medication is very difficult. The objective of this study was to evaluate the impact of administration timing simplification protocol (ATSP) on medication adherence and clinical parameters of cardiovascular diseases. Methods: 210 out-patients with cardiovascular disease, who were taking two or more pills of any type of medication per day for more than one year, were enrolled and randomized. The intervention group followed the simplified administration schedule of ATSP with two main strategies: 1) moving medication from “pc” (30 minute after meal) to “stat. pc” (immediately after meal); and 2) moving medication time from “at evening” to “at morning. ” In contrast, the control group maintained the same medication schedule. Both patient groups were equally educated about the names and effects of the medication. Results: The intervention group had more pills than the control group with marginal statistical significance (5.1 ± 2.3 vs 4.6 ± 1.8, p = 0.05). The total frequency of administration was significantly higher in the intervention group than that of the control group (2.9 ± 1.0 vs 2.6 ± 0.9, p = 0.03) at the baseline. In the intervention group, the frequency was significantly decreased to 1.5 ± 0.6 times per day after following ATSP application (p < 0.01). In both patient groups, knowledge about the medication was significantly improved by education. However, medication adherence was only improved in the intervention group. Interestingly, total cholesterol was significantly decreased in the intervention group (p < 0.01). The decrease in serum cholesterol concentration was significantly correlated with the improvement in medication adherence evaluated with Morisky Medication Adherence Scale (MMAS)-8 items (r = 0.507, p < 0.01). Conclusion: ATSP was shown to be an effective strategy to improve medication adherence in chronic cardiovascular disease patients.
An Information Theoretic Approach to Speaker Diarization of Meeting Data

A speaker diarization system based on an information theoretic framework is described. The problem is formulated according to the information bottleneck (IB) principle. Unlike other approaches where the distance between speaker segments is arbitrarily introduced, the IB method seeks the partition that maximizes the mutual information between observations and variables relevant for the problem while minimizing the distortion between observations. This solves the problem of choosing the distance between speech segments, which becomes the Jensen-Shannon divergence as it arises from the IB objective function optimization. We discuss issues related to speaker diarization using this information theoretic framework such as the criteria for inferring the number of speakers, the tradeoff between quality and compression achieved by the diarization system, and the algorithms for optimizing the objective function. Furthermore, we benchmark the proposed system against a state-of-the-art system on the NIST RT06 (rich transcription) data set for speaker diarization of meetings. The IB-based system achieves a diarization error rate of 23.2% compared to 23.6% for the baseline system. This approach being mainly based on nonparametric clustering, it runs significantly faster than the baseline HMM/GMM based system, resulting in faster-than-real-time diarization.
Percutaneous Laser Ablation of Fetal Congenital Cystic Adenomatoid Malformation: Too Little, Too Late?

Objective: Congenital cystic adenomatoid malformation, type III (CCAM III) lesions are large, bulky tumors which can cause mediastinal shift, prevent normal pulmonary growth, and compress the esophagus, thus leading to complications of nonimmune hydrops, pulmonary hypoplasia and polyhydramnios. Because the mortality rate of untreated fetuses with CCAM and hydrops is high, early delivery or intrauterine resection of the enlarged pulmonary lobe (lobectomy) is indicated; however, open fetal resection of CCAM at less than 30 weeks is associated with perioperative mortality that approaches 40%, as well as the usual maternal and fetal morbidity of open fetal surgery. As an alternative, percutaneous laser ablation of a CCAM III lesion with hydrops was attempted. Methods: A 30-year-old G3 P1011 with CCAM III in the left fetal hemithorax developed mediastinal shift, hydrops and polyhydramnios at 23 weeks’ gestation. After pregnancy termination and open fetal resection were declined, an 18-gauge needle was placed into the fetal tumor percutaneously under real-time ultrasonographic guidance, using sterile technique with light sedation. A cleaved 400-μm Nd:YAG laser fiber was passed through the needle lumen, and using a power setting of 15 W, a total of 2,943 J of laser energy was delivered in pulses of 1.0 s at 0.2-second intervals over two sessions one week apart. Results: Although tumor size decreased, the hydrops worsened and fetal death occurred. Conclusions: The fetus with CCAM complicated by hydrops is already so compromised by the advanced state of the disease that insufficient time is available for necrotic tissue reabsorption after minimally invasive therapy with laser energy. Until earlier markers for intervention are determined, percutaneous laser debulking of CCAM is unlikely to be successful.
Neural Activity Changes Associated with Impulsive Responding in the Sustained Attention to Response Task

Humans can anticipate and prepare for uncertainties to achieve a goal. However, it is difficult to maintain this effort over a prolonged period of time. Inappropriate behavior is impulsively (or mindlessly) activated by an external trigger, which can result in serious consequences such as traffic crashes. Thus, we examined the neural mechanisms underlying such impulsive responding using functional magnetic resonance imaging (fMRI). Twenty-two participants performed a block-designed sustained attention to response task (SART), where each task block was composed of consecutive Go trials followed by a NoGo trial at the end. This task configuration enabled us to measure compromised preparation for NoGo trials during Go responses using reduced Go reaction times. Accordingly, parametric modulation analysis was conducted on fMRI data using block-based mean Go reaction times as an online marker of impulsive responding in the SART. We found that activity in the right dorsolateral prefrontal cortex (DLPFC) and the bilateral intraparietal sulcus (IPS) was positively modulated with mean Go reaction times. In addition, activity in the medial prefrontal cortex (MPFC) and the posterior cingulate cortex (PCC) was negatively modulated with mean Go reaction times, albeit statistically weakly. Taken together, spontaneously reduced activity in the right DLPFC and the IPS and spontaneously elevated activity in the MPFC and the PCC were associated with impulsive responding in the SART. These results suggest that such a spontaneous transition of brain activity pattern results in impulsive responding in monotonous situations, which in turn, might cause human errors in actual work environments.
Phylogenetic Relationships and Coaggregation Ability of Freshwater Biofilm Bacteria

ABSTRACT Nineteen numerically dominant heterotrophic bacteria from a freshwater biofilm were identified by 16S ribosomal DNA gene sequencing, and their coaggregation partnerships were determined. Phylogenetic trees showed that both distantly related and closely related strains coaggregated at intergeneric, intrageneric, and intraspecies levels. One strain, Blastomonas natatoria 2.1, coaggregated with all 18 other strains and may function as a bridging organism in biofilm development.