Miracle-dz/UniFAR-FTUs huggingface dataset:
16S rRNA Phylogeny of Sponge-Associated Cyanobacteria

ABSTRACT Phylogenetic analyses of 16S rRNA sequences of sponge-associated cyanobacteria showed them to be polyphyletic, implying that they derived from multiple independent symbiotic events. Most of the symbiont sequences were affiliated to a group of Synechococcus and Prochlorococcus species. However, other symbionts were related to different groups, such as the Oscillatoriales.
The Physiological Effects of Dietary Boron

Boron may be an essential nutrient for animals and humans. Dietary boron influences the activity of many metabolic enzymes, as well as the metabolism of steroid hormones and several micronutrients, including calcium, magnesium, and vitamin D. Boron supplementation in rats and chicks has been shown to increase bone strength. Boron may also play a role in improving arthritis, plasma lipid profiles, and brain function. Additional research is necessary to further clarify boron's influence in human and animal physiology, as well as determine a dietary requirement for humans. Referee: Dr. Susan Meacham, Associate Professor and Department Head, University of Nevada, Las Vegas, College of Health Sciences, Room 329, Rod Lee Bigelow Building, 4505 Maryland Parkway, Las Vegas, NV 89154-3019
Collaborative Learning via the Internet

Certain researchers suggest that a teaching method which encapsulates collaboration and interaction would likely work well within the framework of Internet based distance education courses. In order to verify how interaction and collaboration work between students in distance education courses, we observed and researched two undergraduate university courses offered via the Internet. All communications were text based and in asynchronous mode relying upon e-mail, group discussions and hypertext navigation to facilitate the collaborative work process. This exploratory study has enabled us to identify some problematic elements which can hamper collaboration between distance education students. For example, even though most of the distance education students enjoyed communicating with one another, with the professor and with the teaching assistant, the collaborative learning assignments were not always a successful endeavour. To begin with, some students complained of technical difficulties which greatly hampered communication, interaction and collaboration with distant partners. Other students, who had a good technical knowledge of the Internet, had trouble developing a working relationship with out of province or overseas partners. Another interesting observation was the fact that some autonomous, highly independent students preferred working alone. They felt that the collaborative tasks placed undue constraints on their personal work schedule. From these results, we developed recommendations for ensuring the success of collaborative assignments for future Internet courses.
Grammatical Error Correction Using Integer Linear Programming

We propose a joint inference algorithm for grammatical error correction. Different from most previous work where different error types are corrected independently, our proposed inference process considers all possible errors in a uni ed framework. We use integer linear programming (ILP) to model the inference process, which can easily incorporate both the power of existing error classi ers and prior knowledge on grammatical error correction. Experimental results on the Helping Our Own shared task show that our method is competitive with state-of-the-art systems.
Practices for rehabilitating bauxite‐mined areas and an integrative approach to monitor soil quality

Mining activities cause severe impacts to soil, the restoration of which requires specific management, and proper evaluation and monitoring. In this research, our objectives were to study recovery strategies and integrate indicators for monitoring the reclamation of an agricultural soil after bauxite mining. Distinct fertilizations (nonfertilized control [CT], poultry litter [PL], chemical fertilization [CF], and PL + CF combined) and intercrops (bare soil with no intercrops [NI], grass [G], legume [L], and G + L combined) treatments were used as recovery strategies to restore soil capacity to sustain a coffee plantation. We selected 27 quality indicators to compare the premining condition, postmining (reconfigured topsoil), and 19 months after the application of fertilization/intercrops treatments. We used univariate statistics to select soil quality indicators and multivariate analyses to group the selected indicators into organic, chemical, physical, and microbiological properties. From each group, one representative attribute was selected, and its averaged weight was summarized into a soil quality index (SQI). In postmining, the estimated SQI was approximately 65% lower than in premining. The SQI recalculated 19 months after the application of fertilization (PL or PL + CF) and intercrops (G, L, or G + L) was 23% higher than in postmining and showed strong correlation with coffee bean yield (at 27 months). Coffee bean yield was highest in plots with L or G + L receiving PL or PL + CF. We conclude that organic amendments and intercrops are suitable approaches to recover soil following bauxite mining, and soil indicators can be integrated to properly monitor the land reclamation progress.
Effects of Acute Hyperglucagonemia on Hepatic and Intestinal Lipoprotein Production and Clearance in Healthy Humans

OBJECTIVE The metabolism of hepatic- and intestinally derived lipoproteins is regulated in a complex fashion by nutrients, hormones, and neurologic and other factors. Recent studies in animal models suggest an important role for glucagon acting via the glucagon receptor in regulating hepatic triglyceride (TG) secretion. Here we examined the direct effects of glucagon on regulation of hepatic and intestinal lipoprotein metabolism in humans. RESEARCH DESIGN AND METHODS Eight healthy men underwent two studies each, in random order, 4–6 weeks apart in which de novo lipogenesis, kinetics of larger VLDL1 TG, and kinetics of VLDL1 and smaller VLDL2 apolipoprotein (apo)B100 and B48 were studied using established stable isotope enrichment methods. Subjects were studied in the constant fed state under conditions of a pancreatic clamp (with infusion of somatostatin, insulin, and growth hormone) at either basal glucagon (BG study, 64.5 ± 2.1 pg/mL) or hyperglucagonemia (high glucagon [HG] study, 183.2 ± 5.1 pg/mL). RESULTS There were no significant differences in plasma concentration of VLDL1 or VLDL2 TG, apoB100 or apoB48 between BG and HG studies. There was, however, lower (P < 0.05) VLDL1 apoB100 fractional catabolic rate (−39%) and production rate (−30%) in HG versus BG, but no difference in de novo lipogenesis or TG turnover, and glucagon had no effect on intestinal (B48-containing) lipoprotein metabolism. CONCLUSIONS Glucagon acutely regulates hepatic but not intestinal lipoprotein particle metabolism in humans both by decreasing hepatic lipoprotein particle production as well as by inhibiting particle clearance, with no net effect on particle concentration.
Attenuation of Nephrotoxic Acute Renal Failure in the Dog with Angiotensin‐Converting Enzyme Inhibitor (SQ‐20,881)

Angiotensin-converting enzyme inhibitor was used in dogs with uranyl nitrate-induced acute renal failure to evaluate (1) a possible protective effect of angiotensin blockade and (2) the role of angiotensin II in the generation of renal failure in this model. Angiotensin-converting enzyme inhibitor treatment attenuated the fall in glomerular filtration rate and renal blood flow during the first 6 hours after injection of the nephrotoxic agent. A protective effect of similar magnitude was observed whether angiotensin-converting enzyme inhibitor treatment preceded, or shortly followed, the administration of uranyl nitrate. This indicates that angiotensin-converting enzyme inhibitor delivery to its intrarenal site of action remains effective after administration of the nephrotoxin. In addition, protection of glomerular filtration rate correlated with sodium and renal solute excretion. However, combined treatment with angiotensin-converting enzyme inhibitor and furosemide enhanced solute excretion but did not further improve the protection of renal function. Finally, the protective effects of angiotensin-converting enzyme inhibitor on renal function and hemodynamics were abolished by intravenous indomethacin. In conclusion, early, continuous blockade of angiotensin II protects partially against the initiation of acute renal failure. These findings support a major pathogenic role for angiotensin II in the generation phase of acute renal failure in this model. Furthermore, they suggest that an imbalance between vasoconstrictive (angiotensin II) and vasodilating factors (prostaglandins) may be operative in the early phase of uranyl nitrate-induced acute renal failure in the dog.
Global and regional evaluation of a global model simulated AODs with AERONET and MODIS observations

Aerosol optical properties vary widely globally due to their short residence time and the large variability in their composition and size resulting from varying sources. In this study, we make use of the three‐dimensional global atmospheric chemistry transport model MOZART (Model for OZone And Related chemical Tracers), to simulate Aerosol Optical Depths (AODs) and compare with observations from MODIS (Moderate Resolution Imaging Spectroradiometer, level‐3) on board the Terra satellite and AERONET (AErosol RObotic NETwork level‐2), at regional and global scale for the period 2000–2007. The AOD values at a reference wavelength 550 nm are reported for all the data sets. Model and observations show intense aerosol burden over the parts of the world where developing countries are located. On a regional scale, varying features are noted for different regions depending upon topography, regional emissions and weather conditions. MOZART captures the general features observed in AERONET and MODIS fairly well; however, in biomass burning dominated regions (Central South America, South Africa, and North Australia) it underestimates the observed AOD. In industrial regions (North Europe and Mediterranean) MOZART overestimates the observations and over dust dominant regions (Saharan Africa, Middle East, and East Asia), the model AODs are comparable to AERONET and MODIS observations. In general, MOZART simulated AOD show similar seasonal and regional variability as observed in AERONET and MODIS. Our results are similar to the most commonly used models, i.e. GOCART (the GOddard Chemistry, Aerosol, Radiation, and Transport) and GEOS‐4 (Goddard Earth Observing System‐version 4).
Spectral EEG During Short‐Term Discontinuation of Antiepileptic Medication in Partial Epilepsy

Summary: The effect of short‐term discontinuation of antiepileptic drugs (AEDs) on spectral analysis of EEG background activity (spectral EEG) was studied in patients undergoing preoperative evaluation for epilepsy surgery. We also wished to clarify whether AED discontinuation would provide lateralizing evidence in spectral EEGs of patients with temporal lobe epilepsy (TLE). Spectral EEGs were performed in 15 patients receiving their regular medication regimen and again after a 1‐week period during AED withdrawal. A subgroup of 9 patients who had previously undergone temporal lobectomies (TLE group) was studied separately. In this group, we evaluated the effect of preceding seizures on spectral EEG derived from temporal neocortical areas. In all patients, spectral EEG changes were detected even after a short‐term AED withdrawal. The total amount of absolute delta activity was reduced and occipital peak frequency and relative alpha activity were increased as compared with baseline values. In TLE patients with habitual seizures occurring <20 h before the spectral EEG recording, lateralization was correctly identified by the greater amount of absolute delta activity ipsilateral to the epileptogenic focus. Epileptic seizures are accompanied by subtle focal slowing in spectral EEG for a much longer period than has been assumed. In addition, postictal spectral EEG over the temporal lobes may have lateralizing value. Further studies in larger numbers of patients are needed to evaluate the role of spectral EEG in the preoperative evaluation of patients for temporal lobe surgery.
Prediction of Ice‐Free Conditions for a Perennially Ice‐Covered Antarctic Lake

Although perennially ice‐covered Antarctic lakes have experienced variable ice thicknesses over the past several decades, future ice thickness trends and associated aquatic biological responses under projected global warming remain unknown. Heat stored in the water column in chemically stratified Antarctic lakes that have middepth temperature maxima can significantly influence the ice thickness trends via upward heat flux to the ice/water interface. We modeled the ice thickness of the west lobe of Lake Bonney, Antarctica, based on possible future climate scenarios utilizing a 1D thermodynamic model that accounts for surface radiative fluxes as well as the heat flux associated with the temperature evolution of the water column. Model results predict that the ice cover of Lake Bonney will shift from perennial to seasonal within one to four decades, a change that will drastically influence ecosystem processes within the lake.
Women on patrol: an analysis of differences in officer arrest behavior

Purpose – The current research seeks to examine whether officer gender influences the decision to arrest, and whether correlates of officer decision making vary across gender.Design/methodology/approach – Data on police‐public encounters were systematically collected by performing social observations of police officers. Multivariate models were estimated to examine the correlates of arrest for all encounters, encounters involving male officers, and encounters involving female officers. Results were compared and contrasted across officer gender.Findings – Gender has little direct impact on the arrest decision; however, some variation exists depending on citizens' race, gender and demeanor. The most noteworthy differences were observed based upon whether officer actions are conducted in the presence of other members of the organization, and where these other members are in the organizational hierarchy. Female officers were significantly more likely to arrest when observed by supervisors, yet less likely to .
Patient-specific electronic decision support reduces prescription of excessive doses

Objectives Prescription of excessive doses is the most common prescription error, provoking dose-dependent adverse drug reactions. Clinical decision support systems (CDSS) can prevent prescription errors especially when mainly clinically relevant warnings are issued. We have built and evaluated a CDSS providing upper dose limits personalised to individual patient characteristics thus guaranteeing for specific warnings. Methods For 170 compounds, detailed information on upper dose limits (according to the drug label) was compiled. A comprehensive software-algorithm extracted relevant patient information from the electronic chart (eg, age, renal function, comedication). The CDSS was integrated into the local prescribing platform for outpatients and patients at discharge, providing immediate dosage feedback. Its impact was evaluated in a 90-day intervention study (phase 1: baseline; phase 2: intervention). Outcome measures were frequency of excessive doses before and after intervention considering potential induction of new medication errors. Moreover, predictors for alert adherence were analysed. Results In phase 1, 552 of 12 197 (4.5%) prescriptions exceeded upper dose limits. In phase 2, initially 559 warnings were triggered (4.8%, p=0.37). Physicians were responsive to one in four warnings mostly adjusting dosages. Thus, the final prescription rate of excessive doses was reduced to 3.6%, with 20% less excessive doses compared with baseline (p<0.001). No new manifest prescription errors were induced. Physicians' alert adherence correlated with patients' age, prescribed drug class, and reason for the alert. Conclusion During the 90-day study, implementation of a highly specific algorithm-based CDSS substantially improved prescribing quality with a high acceptance rate compared with previous studies.
Groundwaters at Risk: Wetland Loss Changes Sources, Lengthens Pathways, and Decelerates Rejuvenation of Groundwater Resources

Wetland loss alters the hydrology of wetlandscapes in poorly understood ways. To quantify the effects of wetland loss on subsurface hydrology, a physically based hydrologic model that simulates the timing and pathways of subsurface hydrologic connections was coupled with wetland inventories over a 50‐year period during which substantial wetland loss occurred. The model revealed, based on vertical variations in saturated hydraulic conductivities, wetland loss of different degrees led to a contraction of catchment contributing areas to local surface waters but an expansion of contributing areas to the regional surface water body. This shift in groundwater contributing areas reflected (1) a decrease in baseflow contribution to the local surface water bodies, and (2) an increase in the transit time and length of subsurface hydrologic connections with an associated increase in the magnitude and age of baseflow discharging to the regional surface water body. The model also showed regions with thick permeable aquifers were particularly sensitive to the loss of wetlands. Our ability to predict these changes in hydrology of the watershed provides important support for designing science‐based policies to promote sustainable water resource management.
Applications of Dynamic Clamp to Cardiac Arrhythmia Research: Role in Drug Target Discovery and Safety Pharmacology Testing

Dynamic clamp, a hybrid-computational-experimental technique that has been used to elucidate ionic mechanisms underlying cardiac electrophysiology, is emerging as a promising tool in the discovery of potential anti-arrhythmic targets and in pharmacological safety testing. Through the injection of computationally simulated conductances into isolated cardiomyocytes in a real-time continuous loop, dynamic clamp has greatly expanded the capabilities of patch clamp outside traditional static voltage and current protocols. Recent applications include fine manipulation of injected artificial conductances to identify promising drug targets in the prevention of arrhythmia and the direct testing of model-based hypotheses. Furthermore, dynamic clamp has been used to enhance existing experimental models by addressing their intrinsic limitations, which increased predictive power in identifying pro-arrhythmic pharmacological compounds. Here, we review the recent advances of the dynamic clamp technique in cardiac electrophysiology with a focus on its future role in the development of safety testing and discovery of anti-arrhythmic drugs.
Mutation Rates of TGFBR2 and ACVR2 Coding Microsatellites in Human Cells with Defective DNA Mismatch Repair

Microsatellite instability promotes colonic tumorigenesis through generating frameshift mutations at coding microsatellites of tumor suppressor genes, such as TGFBR2 and ACVR2. As a consequence, signaling through these TGFβ family receptors is abrogated in DNA Mismatch repair (MMR)-deficient tumors. How these mutations occur in real time and mutational rates of these human coding sequences have not previously been studied. We utilized cell lines with different MMR deficiencies (hMLH1−/−, hMSH6−/−, hMSH3−/−, and MMR-proficient) to determine mutation rates. Plasmids were constructed in which exon 3 of TGFBR2 and exon 10 of ACVR2 were cloned +1 bp out of frame, immediately after the translation initiation codon of an enhanced GFP (EGFP) gene, allowing a −1 bp frameshift mutation to drive EGFP expression. Mutation-resistant plasmids were constructed by interrupting the coding microsatellite sequences, preventing frameshift mutation. Stable cell lines were established containing portions of TGFBR2 and ACVR2, and nonfluorescent cells were sorted, cultured for 7–35 days, and harvested for flow cytometric mutation detection and DNA sequencing at specific time points. DNA sequencing revealed a −1 bp frameshift mutation (A9 in TGFBR2 and A7 in ACVR2) in the fluorescent cells. Two distinct fluorescent populations, M1 (dim, representing heteroduplexes) and M2 (bright, representing full mutants) were identified, with the M2 fraction accumulating over time. hMLH1 deficiency revealed 11 (5.91×10−4) and 15 (2.18×10−4) times higher mutation rates for the TGFBR2 and ACVR2 microsatellites compared to hMSH6 deficiency, respectively. The mutation rate of the TGFBR2 microsatellite was ∼3 times higher in both hMLH1 and hMSH6 deficiencies than the ACVR2 microsatellite. The −1 bp frameshift mutation rates of TGFBR2 and ACVR2 microsatellite sequences are dependent upon the human MMR background.
Linear regression analysis of template aging in iris biometrics

The aim of this work is to determine how vulnerable different iris coding methods are in relation to biometric template aging phenomenon. This is considered to be particularly important when the time lapse between gallery and probe samples extends significantly, to more than a few years. Our experiments employ iris aging analysis conducted using three different iris recognition algorithms and a database of 583 samples from 58 irises collected up to nine years apart. To determine the degradation rates of similarity scores with extending time lapse and also in relation to multiple image quality and geometrical factors of sample images, a linear regression analysis was performed. 29 regression models have been tested with both the time parameter and geometrical factors being statistically significant in every model. Quality measures that showed statistically significant influence on the predicted variable were, depending on the method, image sharpness and local contrast or their mutual relations. To our best knowledge, this is the first paper describing aging analysis using multiple regression models with data covering such a wide time period. Results presented suggest that template aging effect occurs in iris biometrics to a statistically significant extent. Image quality and geometrical factors may contribute to the degradation of similarity score. However, the estimate of time parameter showed statistical significance and similar value in each of the tested models. This reveals that the aging phenomenon may as well be unrelated to quality and geometrical measures of the image.