Miracle-dz/UniFAR-FTUs huggingface dataset:
Physiological characterization of anaerobic ammonium oxidizing bacterium 'Candidatus Jettenia caeni'.

To date, six candidate genera of anaerobic ammonium-oxidizing (anammox) bacteria have been identified, and numerous studies have been conducted to understand their ecophysiology. In this study, we examined the physiological characteristics of an anammox bacterium in the genus 'Candidatus Jettenia'. Planctomycete KSU-1 was found to be a mesophilic (20-42.5°C) and neutrophilic (pH 6.5-8.5) bacterium with a maximum growth rate of 0.0020 h(-1) . Planctomycete KSU-1 cells showed typical physiological and structural features of anammox bacteria; i.e. (29) N2 gas production by coupling of (15) NH4 (+) and (14) NO2 (-) , accumulation of hydrazine with the consumption of hydroxylamine and the presence of anammoxosome. In addition, the cells were capable of respiratory ammonification with oxidation of acetate. Notably, the cells contained menaquinone-7 as a dominant respiratory quinone. Proteomic analysis was performed to examine underlying core metabolisms, and high expressions of hydrazine synthase, hydrazine dehydrogenase, hydroxylamine dehydrogenase, nitrite/nitrate oxidoreductase and carbon monoxide dehydrogenase/acetyl-CoA synthase were detected. These proteins require iron or copper as a metal cofactor, and both were dominant in planctomycete KSU-1 cells. On the basis of these experimental results, we proposed the name 'Ca. Jettenia caeni' sp. nov. for the bacterial clade of the planctomycete KSU-1.
A Potential Role for U2AF-SAP 155 Interactions in Recruiting U2 snRNP to the Branch Site

ABSTRACT Base pairing between U2 snRNA and the branchpoint sequence (BPS) is essential for pre-mRNA splicing. Because the metazoan BPS is short and highly degenerate, this interaction alone is insufficient for specific binding of U2 snRNP. The splicing factor U2AF binds to the pyrimidine tract at the 3′ splice site in the earliest spliceosomal complex, E, and is essential for U2 snRNP binding in the spliceosomal complex A. We show that the U2 snRNP protein SAP 155 UV cross-links to pre-mRNA on both sides of the BPS in the A complex. SAP 155’s downstream cross-linking site is immediately adjacent to the U2AF binding site, and the two proteins interact directly in protein-protein interaction assays. Using UV cross-linking, together with functional analyses of pre-mRNAs containing duplicated BPSs, we show a direct correlation between BPS selection and UV cross-linking of SAP 155 on both sides of the BPS. Together, our data are consistent with a model in which U2AF binds to the pyrimidine tract in the E complex and then interacts with SAP 155 to recruit U2 snRNP to the BPS.
Multifractal behavior of linear polymers in disordered media.

The scaling behavior of linear polymers in disordered media modeled by self-avoiding random walks (SAWs) on the backbone of two- and three-dimensional percolation clusters at their critical concentrations p(c) is studied. All possible SAW configurations of N steps on a single backbone configuration are enumerated exactly. We find that the moments of order q of the total number of SAWs obtained by averaging over many backbone configurations display multifractal behavior; i.e., different moments are dominated by different subsets of the backbone. This leads to generalized coordination numbers mu(q) and enhancement exponents gamma(q), which depend on q. Our numerical results suggest that the relation mu(1)=p(c)mu between the first moment mu(1) and its regular lattice counterpart mu is valid.
Molecular study on human tuberculosis in three geographically distinct and time delineated populations from ancient Egypt

We describe the molecular identification of human tuberculosis (TB) from vertebral bone tissue samples from three different populations of ancient Egypt. The specimens were obtained from the predynastic to early dynastic necropolis of Abydos (7 individuals, c. 3500–2650 B.C.), from a Middle Kingdom to Second Intermediate Period tomb of the necropolis of Thebes-West (37, c. 2100–1550 B.C.) and from five further Theban tombs used in the New Kingdom and the Late Period (39, c. 1450–500 B.C.). A total of 18 cases tested positive for the presence of ancient DNA (aDNA) of the M. tuberculosis complex. Out of the 9 cases with typical macromorphological signs of tuberculous spondylitis, 6 were positive for mycobacterial aDNA (66·7%). Of 24 cases with non-specific pathological alterations, 5 provided a positive result (20·8%). In 50 cases of normally appearing vertebral bones 7 tested positive (14·0%). There were only minor differences in the frequencies between the three populations. These data strongly support the notion that tuberculosis was present and prevalent in ancient Egypt since very early periods of this civilization. The unexpectedly high rate of mycobacterial aDNA in normal bone samples is presumably due to a pre- to perimortal systemic spread of the bacteria and indicates a generalized infection by M. tuberculosis.
Biofilm Analysis of Retrieved Dental Implants after Different Peri-Implantitis Treatments

The aim of the current study was to analyse the planktonic growth of Streptococcus mutans on the surfaces of three implants retrieved after three different peri-implantitis treatments. Three implants from a male patient with high levels of bone loss were treated by mechanical debridement, chemical decontamination, and implantoplasty. After 4 months of follow-up, the implants were removed. The growth and biofilm formation were measured by spectrophotometry (OD630 nm) and scanning electron microscopy (SEM), after 48 hours of incubation. Results showed an average of Streptococcus mutans planktonic growth over the implants of 0.21 nm (mechanical debridement), 0.16 nm (chemical decontamination), and 0.15 nm (implantoplasty). Data were analysed by ANOVA and Tukey's test (p < 0.05 for chemical decontamination and implantoplasty). Implantoplasty and chemical decontamination showed the lowest levels of planktonic growth, indicating a possible influence of the modification procedures on the titanium surface on the initial biofilm attachment.
Aeromonas salmonicida from salmonids and cyprinids--serological and cultural identification.

Summary In a two years period 357 samples of diseased fresh water fish from hatcheries in Northwest Germany were examined. Ten different species of salmonids and cyprinids were investigated. Most were rainbow trout (Salmo gairdneri Richardson) and carp (Cyprinus carpio L.). Pathological and bacteriological findings are reported. In cultural examination for Aeromonas salmonicida, 9% of rainbow trout (Salmo gairdneri Richardson) and 7% of carp (Cyprinus carpio L.) gave positive results. Bacterial isolates were characterized by their morphological and biochemical properties and their antibiotic resistance pattern was studied. Specimens (185) were examined for Aeromonas salmonicida-antigen by means of the indirect fluorescent antibody technique, which is described in detail. The sensitivity of the test was more than twice that of cultural examination. Aeromonas salmonicida-isolates from goldfish (Carassius auratus L.) and shubunkin (Carassius sp.) differed from all the others in their biochemical and cultural pattern; the classification of this group is discussed. Zusammenfassung Aeromonas salmonicida isoliert von Salmoniden und Cypriniden — serologische und kulturelle Identifizierung In einem Zeitraum von zwei Jahren wurden 357 Proben erkrankter Suswasserfische aus Fischzuchten in Nordwestdeutschland untersucht. Zehn verschiedene Salmoniden- und Cyprinidenarten, hauptsachlich Regenbogenforellen (Salmo gairdneri Richardson) und Karpfen (Cyprinus carpio L.) wurden untersucht. Pathologische und bakteriologische Untersuchungsbefunde wurden erhoben. Die kulturelle Untersuchung auf Aeromonas salmonicida war bei 9% der Regenbogenforellen (Salmo gairdneri L.) und 7% der Karpfen (Cyprinus carpio L.) positiv. Die Isolate wurden aufgrund ihrer morphologischen und biochemischen Eigenschaften charakterisiert und ihr antibiotisches Resistenzverhalten wurde ermittelt. 185 Proben wurden mit Hilfe der indirekten Immunfluoreszenz auf Aeromonas salmonicida-Antigene untersucht. Die Methode wird ausfuhrlich beschrieben. Verglichen mit der kulturellen Untersuchung ergab sich mit dieser Methode eine mehr als doppelt so hohe Rate positiver Ergebnisse. Aeromonas-salmonicida-Isolate von Goldfisch (Carassius auratus L.) und Shubunkin (Carassius sp.) unterschieden sich vor allen anderen in ihren biochemischen und kulturellen Eigenschaften, eine Klassifikation dieser Gruppe wird diskutiert.
An analysis of safety information registration interface on the iaa system - a first step toward universal accessibility

a 4-2-1 Nukuikita-machi, Koganei, Tokyo, 184-8795, Japan ABSTRACT Universal accessibility is a challenging issue, one in which many factors have to be considered. The IAA system (that origin is "I Am Alive"), which was introduced for managing the registration and retrieval of victim safety information in the event of a disaster, is evaluated from a universal accessibility point-of-view. Experiments were conducted on five user groups: adult, child, elderly, visually impaired, and hearing impaired. The child and elderly groups had difficulties in conducting a task using the system's interface. An analysis of these two groups showed that the elderly group failed to hear the message, while the child group failed to understand it.
Coping With Loss

Ed Colin Murray Parkes, Andrew Markus BMJ Books, £14.95, pp168 ISBN 072791068X Rating: ! [Graphic][1] ! [Graphic][2] ! [Graphic][3] Doctors have largely replaced the village curate as the confidante of their patients' sorrows. Feelings of loss and the resulting distress—be it through bereavement or the break up of relationships —are therefore encountered more frequently by doctors. But how well equipped are we to deal with such patients, and how do we know when we have reached the ceiling of our competence? How do we cope with the continuous emotional pain of others and the pressures … [1]: /embed/inline-graphic-1.gif [2]: /embed/inline-graphic-2.gif [3]: /embed/inline-graphic-3.gif
Acclimation conditions modify physiological response of the diatom Thalassiosira pseudonana to elevated CO2 concentrations in a nitrate‐limited chemostat

Diatoms are responsible for a large proportion of global carbon fixation, with the possibility that they may fix more carbon under future levels of high CO2. To determine how increased CO2 concentrations impact the physiology of the diatom Thalassiosira pseudonana Hasle et Heimdal, nitrate‐limited chemostats were used to acclimate cells to a recent past (333 ± 6 μatm) and two projected future concentrations (476 ± 18 μatm, 816 ± 35 μatm) of CO2. Samples were harvested under steady‐state growth conditions after either an abrupt (15–16 generations) or a longer acclimation process (33–57 generations) to increased CO2 concentrations. The use of un‐bubbled chemostat cultures allowed us to calculate the uptake ratio of dissolved inorganic carbon relative to dissolved inorganic nitrogen (DIC:DIN), which was strongly correlated with fCO2 in the shorter acclimations but not in the longer acclimations. Both CO2 treatment and acclimation time significantly affected the DIC:DIN uptake ratio. Chlorophyll a per cell decreased under elevated CO2 and the rates of photosynthesis and respiration decreased significantly under higher levels of CO2. These results suggest that T. pseudonana shifts carbon and energy fluxes in response to high CO2 and that acclimation time has a strong effect on the physiological response.
Changes in Hippocampal Neuronal Activity During and After Unilateral Selective Hippocampal Ischemia In Vivo

The hippocampal formation is one of the brain regions most sensitive to ischemic damage. However, there are no studies about changes in hippocampal neuronal activity during and after a selective unilateral hippocampal ischemia. We developed a novel unilateral cerebrovascular ischemia model in mice that selectively shuts down blood supply to the ipsilateral hippocampal formation. Using a modified version of the photothrombotic method, we stereotaxically targeted the initial ascending part of the longitudinal hippocampal artery in urethane anesthetized and rose bengal-injected mice. To block blood flow in the targeted artery, we photoactivated the rose bengal by illuminating the longitudinal hippocampal artery through an optical fiber inserted into the brain. In vivo field potential recordings in the CA1 region of the hippocampus before, during and after the induction of ischemia demonstrated a high-frequency discharge (HFD) reaching frequencies of >300 Hz and lasting 7–24 s during the illumination consistent with a massive synchronous neuronal activity. The HFD was invariably followed by a DC voltage shift and a decreased activity at both low (30–57 Hz)- and high (63–119 Hz)-gamma frequencies. This decrease in gamma activity lasted for the entire duration of the recordings (∼160 min) following ischemia. The contralateral hippocampus displayed HFDs but with different frequency spectra and without DC voltage shifts or long-lasting decreases in gamma oscillations. Our findings reveal for the first time the acute effects of unilateral hippocampal ischemia on ensemble hippocampal neuronal activities.
Cometary glycine detected in samples returned by Stardust

Abstract— Our previous analysis of cometary samples returned to Earth by NASA's Stardust spacecraft showed several amines and amino acids, but the origin of these compounds could not be firmly established. Here, we present the stable carbon isotopic ratios of glycine and ε‐amino‐n‐caproic acid (EACA), the two most abundant amino acids identified in Stardust‐returned foil samples measured by gas chromatography‐mass spectrometry coupled with isotope ratio mass spectrometry. The δ13C value for glycine of +29 ± 6‰ strongly suggests an extraterrestrial origin for glycine, while the δ13C value for EACA of −25 ± 2‰ indicates terrestrial contamination by Nylon‐6 during curation. This represents the first detection of a cometary amino acid.
The Analysis and Research of a High-Stability and High-Accuracy VLDO

A very low dropout voltage linear regulator (VLDO) with high precision and stability is presented in this paper. With ESR compensation, internal pole-zero compensation and feed-forward compensation can be used for this proposed schematic. In addition, the VLDO loop op-amp, PMOS adjustment module and resistance feedback module are analyzed. Finally the VLDO has been implemented in CSMC 0.5um CMOS process.
Knowledge-aided informed dynamic scheduling for LDPC decoding

Low-density parity-check (LDPC) codes offer excellent performance at competitive levels of complexity. Short block length LDPC codes avoid the large processing latency incurred by the large block lengths classically considered for this class of codes, making them a potential candidate for next generation wireless communications systems. In this paper, a novel informed dynamic scheduling (IDS) approach for decoding LDPC codes is developed based on the use of the current message reliabilities and the residuals of the potential updates to select the messages passed in the graph during iterative Sum Product decoding. An alternative measure of the iteration of the IDS schemes is also proposed which highlights the high cost of those algorithms in terms of processing complexity and motivates the development of the proposed approach. The proposed Rel. -RBP decoding algorithm offers very fast convergence at reduced complexity and gains in error rate performance when compared to the previous schemes.
SVM Combined with FCM and PCA for Financial Diagnosis

Financial diagnosis is an important and widely studied topic in the last three decades. Recently, the support vector machine (SVM) has been applied to the problem of financial diagnosis. Fuzzy c-means clustering (FCM) is among considerable techniques for data reduction. In addition, principal component analysis (PCA) is a powerful technique for feather extraction. This paper proposes using fuzzy c-means clustering algorithm, principle component analysis to make SVM more effective. The algorithm proposed in this paper, FCM-PCA-SVM composed of three subnetworks: fuzzy classifier, layer of feather extraction with principal component analysis and support vector machine. Empirical results using Chinese listed companies show that the hybrid model is very promising for financial diagnosis in terms of predictive accuracy.
Transplasma membrane redox activity of monocytes/macrophages

Abstract Oxidation of low density lipoprotein in the arterial intima has been implicated in atherogenesis. Numerous studies have shown that various cells of the arterial wall, including macrophages, are able to oxidatively modify LDL in vitro. Although the exact mechanism of macrophage-mediated LDL oxidation in vitro remains unclear, it is generally accepted that it occurs via a transition metal-dependent process. Recently, it has been demonstrated that macrophages are able to reduce extracellular copper and iron, and the contribution to this reduction of a transplasma membrane electron transport (TPMET) system of the cells has been suggested.1 In the present paper, we investigate the presence of a TPMET system in monocytes/ macrophages and ways to manipulate its activity. The establishment of ways to change the expression or activity of the TPMET system in these cells could provide convenient tool to further investigate the possible correlation between cellular transmembrane electron transport and the ability of cells to oxidise LDL.
A new sturcture AlGaN/GaN HEMT

In several decades, the world has witnessed various dramatic changes since applying of semiconductor. The performance requirements of semiconductor products are continue increasing while the technology is improving. In order to satisfy the requirements, the researches of new material and device structure is necessary. This paper shows a new structure of GaN HEMT. An AlGaN/GaN HEMT consists of AlGaN/GaN Heterojunction, drain electrode, source electrode and gate electrode. Though the researchers have reported a large number of HEMT structures since M. Asif Khan and his colleagues repot the first AlGaN/GaN HEMT in 1993, there is none of the structures, which three electrodes are in different surfaces of device. This paper describes a new structure called different-surface-gate structure, which drain and source electrodes are on the other surface while the gate electrode is on the top surface (AlGaN surface) of the device as normal HEMTs. This paper will establish two models by TCAD simulation software. One is the model of different-surface-gate AlGaN/GaN HEMT and the other one is normal structure AlGaN/GaN HEMT, which is the control model. After building the models, the compare of the models will show the saturation current of the different-surface-gate model is 120% as large as it of the other model.
Heuristic Function Negotiation for Markov Decision Process and Its Application in UAV Simulation

The traditional reinforcement learning (RL) methods can solve Markov Decision Processes (MDPs) online, but these learning methods cannot effectively use a priori knowledge to guide the learning process. The exploration of the optimal policy is time-consuming and does not employ the information about specific issues. To tackle the problem, this paper proposes heuristic function negotiation (HFN) as an online learning framework. The HFN framework extends MDPs and introduces heuristic functions. HFN changes the state-action dual layer structure of traditional RL to the triple layer structure, in which multiple heuristic functions can be set to meet the needs required to solve the problem. The HFN framework can use different algorithms to let the functions negotiate to determine the appropriate action, and adjust the impact of each function according to the rewards. The HFN framework introduces domain knowledge by setting heuristic functions and thus speeds up the problem solving of MDPs. Furthermore, user preferences can be reflected in the learning process, which improves the flexibility of RL. The experiments show that, by setting reasonable heuristic functions, the learning results of the HFN framework are more efficient than traditional RL. We also apply HFN to the air combat simulation of unmanned aerial vehicles (UAVs), which shows that different function settings lead to different combat behaviors. key words: Markov decision processes, heuristic function, reinforcement learning, UAV
Information-giving practice: an audit of patients attending a GUM clinic.

AIM Patients are known to have difficulty assimilating information about diagnosis and treatment given verbally during consultations with healthcare professionals. Written information in the form of leaflets is often used to reinforce the message. The aim of this study was to audit the written and verbal information given to patients. METHOD Questionnaires were given to patients attending the clinic for repeat treatments for genital warts. RESULTS Female patients generally seemed more satisfied with the information they received than male patients. Overall, patients were more satisfied with verbal information than written information. CONCLUSION Recommendations for changes to information-giving practice are described and plans for future audits to help improve the quality and content of information are outlined.
Evidence for two distinct perceptual alterations in irritable bowel syndrome

Background and aims—Visceral hyperalgesia has been implicated as a factor contributing to symptom generation in irritable bowel syndrome (IBS). However, previous studies using intestinal balloon distension have used psychophysical procedures which do not provide adequate and unbiased measures of visceral sensitivity. Methods—Three psychophysical tasks were examined in 45 patients with IBS (positive Rome criteria) and 14 controls using rectal balloon distension with a computerised distension device. Discomfort threshold and tolerance were assessed during an ascending series of phasic pressure stimuli and during an interactive threshold tracking procedure. In addition, stimulus response functions were generated from intensity and unpleasantness ratings of the rectal distensions. Results—Discomfort threshold and tolerance for the ascending stimuli were significantly lower for the patients with IBS compared with the controls. In contrast, discomfort thresholds during the tracking procedure and stimulus response curves for the ascending series were not different between the groups. A factor analysis of the psychophysical data was consistent with the presence of two distinct and unrelated perceptual alterations related to rectal distension: hypervigilance for visceral stimuli, manifested as lowered response criteria for using the descriptor “discomfort”; and rectal hypersensitivity, manifested as a lower discomfort threshold and left shift of the stimulus response curves. Conclusions—Patients with IBS as a group have a greater propensity to label visceral sensations negatively and show a lower tolerance for rectal balloon distension. A subgroup of patients also have baseline rectal hypersensitivity, assessed by unbiased measures of discomfort threshold and stimulus intensity judgements.