Miracle-dz/UniFAR-FTUs huggingface dataset:
In Situ Expression of nifD in Geobacteraceae in Subsurface Sediments

ABSTRACT In order to determine whether the metabolic state of Geobacteraceae involved in bioremediation of subsurface sediments might be inferred from levels of mRNA for key genes, in situ expression of nifD, a highly conserved gene involved in nitrogen fixation, was investigated. When Geobacter sulfurreducens was grown without a source of fixed nitrogen in chemostats with acetate provided as the limiting electron donor and Fe(III) as the electron acceptor, levels of nifD transcripts were 4 to 5 orders of magnitude higher than in chemostat cultures provided with ammonium. In contrast, the number of transcripts of recA and the 16S rRNA gene were slightly lower in the absence of ammonium. The addition of acetate to organic- and nitrogen-poor subsurface sediments stimulated the growth of Geobacteraceae and Fe(III) reduction, as well as the expression of nifD in Geobacteraceae. Levels of nifD transcripts in Geobacteraceae decreased more than 100-fold within 2 days after the addition of 100 μM ammonium, while levels of recA and total bacterial 16S rRNA in Geobacteraceae remained relatively constant. Ammonium amendments had no effect on rates of Fe(III) reduction in acetate-amended sediments or toluene degradation in petroleum-contaminated sediments, suggesting that other factors, such as the rate that Geobacteraceae could access Fe(III) oxides, limited Fe(III) reduction. These results demonstrate that it is possible to monitor one aspect of the in situ metabolic state of Geobacteraceae species in subsurface sediments via analysis of mRNA levels, which is the first step toward a more global analysis of in situ gene expression related to nutrient status and stress response during bioremediation by Geobacteraceae.
D-brane interactions in type IIB plane wave background

The cylinder diagrams that determine the static interactions between pairs of Dp-branes in the type IIB plane wave background are evaluated. The resulting expressions are elegant generalizations of the flat-space formulae that depend on the value of the Ramond-Ramond flux of the background in a non-trivial manner. If each of the interacting D-branes separately preserves half the supersymmetries, the closed-string and open-string descriptions consistently transform into each other under a modular transformation. These results are derived for configurations of euclidean signature D(p+1)-instantons but also generalize to lorentzian signature Dp-branes.
Cryopreservation of human hematopoietic cells with membrane stabilizers and bioantioxidants as additives in the conventional freezing medium.

Cord blood (CB) and fetal liver (FL) cells are two alternative sources of human hematopoietic stem cells. Optimization of cryopreservation protocols is an important aspect in the banking of these tissues. Out of the multiple factors responsible for cryodamage of cells, membrane leakage and oxygen free-radical generation have been shown to contribute substantially toward the process. We have studied the effect of certain additives, like membrane stabilizers and bioantioxidants, to the conventional freezing medium on viability, nucleated cell recovery, and clonogenic potential of frozen cells. Our results show that trehalose, a membrane stabilizer, when used in combination with 10% dimethyl sulfoxide (DMSO) affords better cryoprotection as evidenced by significantly increased colony formation as compared to 10% DMSO alone. The cryoprotection afforded by trehalose persists at least for 1.5 years and there is no bias toward protection of a particular lineage. We also found that this increased cryoprotective effect of trehalose is seen both at -196 degrees C and -80 degrees C storage temperatures. Addition of taurine, an amino acid, another membrane stabilizer, and a natural cryoprotectant to the traditional freezing medium also results in beneficial effect. Of the three bioantioxidants tested, i.e., ascorbic acid, alpha-tocopherol acetate, and catalase, catalase shows maximum cryoprotective effect both at -196 degrees C and at -80 degrees C. Because the mode of cryoprotective action of catalase and trehalose are totally different, we tried a combination of these two compounds along with 10% DMSO. At -196 degrees C the protection afforded by the combination was significantly better than that afforded by individual components. At -80 degrees C, however, the combination did not give any added protection as compared to the individual single additives, although it was significantly better than 10% DMSO alone. These results indicate that the addition of membrane stabilizers and antioxidants to the conventional freezing medium may help to improve post thaw recovery of hematopoietic cells.
Research as Spiritual Covenant

Conducting research with Native American communities poses special challenges from misunderstandings that may arise from the interface of differing cultural worldviews held by the scientific and the Native communities. Although the community-based participatory research approach shows promise for conducting research that can maximize benefits and minimize the risks of harm to Native American people, there is little information related to the practical implementation of culturally appropriate research practices when working with Native American communities. Drawing on the authors’ research with three Native American communities in the Northwest, this article describes culturally appropriate processes for engaging Native American communities. The first section identifies and describes the principles that provide the foundation for the authors’ research activity as a spiritual covenant and guides the authors’ research with the three communities. The second section describes the project phase matrix that was used to organize the approaches employed in this work.
Recurrent Reinforcement Learning: A Hybrid Approach

Successful applications of reinforcement learning in real-world problems often require dealing with partially observable states. It is in general very challenging to construct and infer hidden states as they often depend on the agent's entire interaction history and may require substantial domain knowledge. In this work, we investigate a deep-learning approach to learning the representation of states in partially observable tasks, with minimal prior knowledge of the domain. In particular, we propose a new family of hybrid models that combines the strength of both supervised learning (SL) and reinforcement learning (RL), trained in a joint fashion: The SL component can be a recurrent neural networks (RNN) or its long short-term memory (LSTM) version, which is equipped with the desired property of being able to capture long-term dependency on history, thus providing an effective way of learning the representation of hidden states. The RL component is a deep Q-network (DQN) that learns to optimize the control for maximizing long-term rewards. Extensive experiments in a direct mailing campaign problem demonstrate the effectiveness and advantages of the proposed approach, which performs the best among a set of previous state-of-the-art methods.
Experimental investigation of effects of mach number on the flow instability in a supersonic inlet

An extensive wind tunnel tests were conducted on an axisymmetric supersonic inlet at Mach numbers from 1.8 to 2.2 and at different values of mass flow rates. Frequencies of the buzz were achieved from the pressure data as well as the high speed shadowgraph pictures. For each Mach number, two main frequencies for the buzz were obtained. The inlet at its design condition was stable, but when the mass flow rate was reduced, at first the shock wave started to oscillate with a small amplitude which is matched the Ferri criterion (little buzz). In this situation, both high- and low-frequency oscillations occurred; however, the high frequency one was dominant, but the oscillations seemed to be irregular. By further decreasing the inlet mass flow, the shock oscillations got a single low frequency and high amplitude, which in agreement with the Dailey criterion (big buzz). At a free stream Mach number of 2.2, the frequencies of these two kinds of instabilities are about 554 and 137 Hz, respectively. At this Mach number for moderate mass flow, an oscillation with high frequency/large amplitude and constant period was observed. The oscillation has the combined characteristics of the little buzz and the big buzz, which is named “added buzz” here. It is shown that at fairly constant mass flow, the frequency of the buzz is independent of the Mach number. It is further found that the buzz instability affects the external flow as well as the internal one with the same frequency.
Why Do Institutional Plan Sponsors Hire and Fire their Investment Managers

This paper examines the investment allocation decisions of pension plans, endowments, foundations, and other institutional plan sponsors. The experience and education of plan sponsors and the environment (both regulatory and agency) of the institutional market suggests that institutional investors rely less on past performance and use diffe rent criteria when evaluating performance compared to mutual fund investors. Institutional investors are expected to be less concerned with total returns and more considerate of benchmark-adjusted excess returns, and the consistency with which they are delivered, over longer time horizons. An examination of asset and account flows for actively-managed U.S. equity products is largely consistent with these expectations. The consistency with which managers deliver positive or negative active returns relative to the S&P500 over multiple horizons, without regard to the magnitude of these returns, plays a key role in determining the flow of assets among investment products. Style benchmarks play a larger role in determining account movements, which is found to employ more criteria than asset moves. However, total return is also considered, as the magnitudes of a one-year loss and 3 and 5-year total returns are found to be incremental factors in plan sponsors? allocation decisions. One explanation for this result is the principal-agent arrangement faced by plan sponsors. Although the sponsors may be more sophisticated than the typical retail investor, their clients, investors and the investment board, may not be. Plan sponsors may minimize job risk by hiring and firing managers based on excess returns with incremental allocations based on total returns, thereby satisfying both their mandate and their clients. It is also found that smaller and older products capture relatively greater flows.
Correlation between bone quality evaluated by cone-beam computerized tomography and implant primary stability.

PURPOSE To examine the relationship between bone quality, as evaluated by cone-beam computerized tomography (CBCT), and implant primary stability, as measured by resonance frequency analysis (RFA). MATERIALS AND METHODS A preliminary clinical study was conducted in which implant placements were scheduled for 20 patients. The CT scan was obtained after initial drilling, and implant stability was measured with the Osstell Mentor instrument before flap closure. With CBCT, CT numbers of surrounding bone were calculated and the thickness of compact bone was measured at the buccal, lingual, mesial, and distal surfaces of each implant. The correlations between CT numbers and implant stability quotients (ISQs) and between compact bone thickness and ISQs were tested with the Pearson correlation coefficient. RESULTS Overall, 61 implants were examined in 20 patients. The statistics showed that the CT numbers and the thickness of compact bone had strong correlations to ISQs (P < .025). CONCLUSION CT scanning was suggested to be effective for evaluating bone quality and predicting initial implant stability.
Bipolar versus monopolar technique for palliative transurethral prostate resection

Introduction The aim was to evaluate the postoperative morbidity and outcome of palliative endoscopic resections for relief of infravesical obstruction in prostate cancer patients with hormone deprivation therapy, and to investigate the added value of bipolar technology over conventional monopolar resections. Material and methods A retrospective study was performed on 70 patients with prostate cancer under hormone deprivation therapy undergoing 75 endoscopic procedures, by either monopolar or bipolar technology, between August 2005 and March 2009 at a single institution. The analysis used outpatient, inpatient, and operative records, and observations of electrolyte changes in the serum, postoperative morbidity, and the overall results of palliative endoscopic resections. Preoperative cancer stages and grades were compared with the pathological findings after surgery. Postoperative outcome and complications of conventional monopolar and bipolar technology were compared. Results Over a period of 44 months, 34 conventional monopolar resections were performed in 32 patients and 41 bipolar resections in 38 patients. Patients’ profiles regarding age, initial cancer stage and grade, resection weight, resection speed, catheterization time, and hospital stay were similar in both groups. No statistically significant difference was observed in sodium drop (p = 0.802), clot retention (p = 0.565), or urinary retention (p = 0.292). The overall success rate in relieving obstruction leading to spontaneous voiding was 77%. While 38% of the patients had a high grade tumour at diagnosis, 79% were found to be high grade after the endoscopic resection (p < 0.0001). Conclusions Palliative endoscopic transurethral resection is an acceptable and safe adjunctive surgical treatment for voiding disorders in prostate cancer patients. Bipolar technology offers no substantial benefit over conventional monopolar technology.
Detection of a ULVZ at the base of the mantle beneath the northwest Pacific

We used the Yellowknife seismic array (YKA) to measure the slowness of 1,371 P and Pdiff waves from earthquakes occurring in the circum‐Pacific region. The corresponding anomalies in P‐velocity show a sharp reduction of up to 6% across a patch of the lowermost mantle beneath the Northwest Pacific with lateral dimensions of several hundred kilometers. The location of this ultra low velocity zone (ULVZ) correlates with a long‐wavelength compositional boundary revealed by probabilistic mantle tomography. We interpret the ULVZ as partial melt created by paleo‐slab material that is being swept laterally from northwestern Pacific subduction zones towards the large, chemically distinct province beneath the south‐central Pacific.
Effect of the timing of treatment of port-wine stains with the flash-lamp-pumped pulsed-dye laser.

BACKGROUND Port-wine stains can be treated with a flash-lamp-pumped pulsed-dye laser, but it is uncertain whether this treatment is more effective if administered early in life, when the skin is thinner and the lesion is smaller. METHODS We prospectively studied 100 patients with a previously untreated port-wine stain of the head or neck. They were treated with the flash-lamp-pumped pulsed-dye laser and divided into four age groups (0 to 5, 6 to 11, 12 to 17, and 18 to 31 years). The outcome measure was lightening of the port-wine stain (reduction in the difference in color between the skin with the stain and contralateral healthy skin) as measured with a colorimeter after an average of five treatments (range, three to seven) of the entire lesion. RESULTS Of the 100 patients, 11 could not be included in the analysis because they had received fewer than three or more than seven treatments, had an erroneous base-line color measurement, or were lost to follow-up. The sizes, locations, and colors of the port-wine stains were similar among the groups. When all 89 patients were analyzed together, the average reduction in the difference in color between the skin with the port-wine stain and contralateral healthy skin was 40 percent. The differences between age groups in the average reduction in color differences were not significant (P= 0.26). By the end of the study, only 7 of 89 patients had completed laser therapy, and in no case was clearance complete. Treatment was discontinued in all seven because the last three treatments did not lead to further lightening. CONCLUSIONS We found no evidence that treatment of port-wine stains with the flash-lamp-pumped pulsed-dye laser in early childhood is more effective than treatment at a later age.
Polarization in Bistatic Radar Probing of Planetary Surfaces: Application to Mars Express Data

Spacecraft-to-ground bistatic radar provides a straightforward method for surveying planetary surfaces on scales of importance to landers and rovers. Centimeter wavelengths, currently in use for deep-space telecommunications, interact with surface structure of similar to somewhat larger scales. For the quasi-specular component of scattering and for surfaces uniformly illuminated by monochromatic signals from an orbiting or flyby vehicle, the echo Doppler dispersion is proportional to the root mean square (rms) surface slope. When the specular condition occurs within 10°-20° of the Brewster angle, the surface dielectric constant can be derived from relative echo power measured simultaneously in orthogonal polarizations and the Fresnel reflection laws. Cross spectra, computed from outputs of the orthogonally polarized receivers, may be used to calculate a complete description of the polarization properties of the scattered fields. Application to planetary studies requires accurate amplitude and phase calibration of the polarization channels, including correction for any leakage between the two receiving paths, such as from imperfectly isolated antenna feeds. We illustrate these techniques using Mars Express results from “Stealth” (Medusae Fossae), a region on Mars that has not previously been detected by Earth-based radar, and from a long profile including Acidalia Planitia. Single-location Stealth observations support previous conclusions that the surface is rough and porous (dielectric constant ≈ 1.4). But the longest experiment (in which the specular point was followed for an hour) yields relatively high dielectric constants (2.8), suggesting that the model is incomplete. The surface of Acidalia Planitia has low dielectric constants ( ≈2.6) over 60-90 W at 50 N and higher values (≈3.6) as the specular point moves south and crosses the equator.
Biomechanical and antibacterial properties of Tobramycin loaded hydroxyapatite coated fixation pins.

The present study investigates the use of nanoporous, biomimetic hydroxyapatite (HA) coatings deposited on TiO₂ coated fixation pins as functional implant surfaces for the local release of Tobramycin in order to prevent bacterial colonization. The impact of HA-coating thickness, coating morphology and biomechanical forces during insertion into synthetic bone on the drug loading and release properties are analyzed. The coatings are shown to exhibit bactericidal effects against Staphylococcus aureus in agar medium for a duration of 6 days after loading by adsorption with Tobramycin for only 5 min at elevated temperature and pressure. Furthermore, high performance liquid chromatography analysis shows a drug release in phosphate buffered saline for 8 days with antibiotic concentration remaining above the minimal inhibitory concentration for S. aureus during the entire release period. Biomechanical insertion tests into synthetic bone and conventional scratch testing demonstrate adhesive strength at the HA/TiO₂ interface. Biocompatibility is verified by cell viability tests. Outgrowth endothelial cells, as well as primary osteoblasts, are viable and firmly attached to both HA and TiO₂ surfaces. The results presented are encouraging and support the concept of functional HA coatings as local drug delivery vehicles for biomedical applications to treat as well as to prevent post-surgical infections.
Altered mRNA Editing and Expression of Ionotropic Glutamate Receptors after Kainic Acid Exposure in Cyclooxygenase-2 Deficient Mice

Kainic acid (KA) binds to the AMPA/KA receptors and induces seizures that result in inflammation, oxidative damage and neuronal death. We previously showed that cyclooxygenase-2 deficient (COX-2−/−) mice are more vulnerable to KA-induced excitotoxicity. Here, we investigated whether the increased susceptibility of COX-2−/− mice to KA is associated with altered mRNA expression and editing of glutamate receptors. The expression of AMPA GluR2, GluR3 and KA GluR6 was increased in vehicle-injected COX-2−/− mice compared to wild type (WT) mice in hippocampus and cortex, whereas gene expression of NMDA receptors was decreased. KA treatment decreased the expression of AMPA, KA and NMDA receptors in the hippocampus, with a significant effect in COX-2−/− mice. Furthermore, we analyzed RNA editing levels and found that the level of GluR3 R/G editing site was selectively increased in the hippocampus and decreased in the cortex in COX-2−/− compared with WT mice. After KA, GluR4 R/G editing site, flip form, was increased in the hippocampus of COX-2−/− mice. Treatment of WT mice with the COX-2 inhibitor celecoxib for two weeks decreased the expression of AMPA/KA and NMDAR subunits after KA, as observed in COX-2−/− mice. After KA exposure, COX-2−/− mice showed increased mRNA expression of markers of inflammation and oxidative stress, such as cytokines (TNF-α, IL-1β and IL-6), inducible nitric oxide synthase (iNOS), microglia (CD11b) and astrocyte (GFAP). Thus, COX-2 gene deletion can exacerbate the inflammatory response to KA. We suggest that COX-2 plays a role in attenuating glutamate excitotoxicity by modulating RNA editing of AMPA/KA and mRNA expression of all ionotropic glutamate receptor subunits and, in turn, neuronal excitability. These changes may contribute to the increased vulnerability of COX-2−/− mice to KA. The overstimulation of glutamate receptors as a consequence of COX-2 gene deletion suggests a functional coupling between COX-2 and the glutamatergic system.
Users' guides to the medical literature: XIX. Applying clinical trial results. A. How to use an article measuring the effect of an intervention on surrogate end points. Evidence-Based Medicine Working Group.

CLINICAL SCENARIO You are a physician seeing a 62-yearold woman with postmenopausal osteoporosis. Her bone mineral density, as measured by dual-energy x-ray absorptiometry, is 2.5 SDs below the mean value in premenopausal women. Although she does not have back pain, a spinal radiograph shows an old vertebral fracture. Thepatienthasnotyet experiencedproblems as a result of her vertebral fracture, but she is disturbed by the prospect that she may end up like her mother whose osteoporotic fractures have resulted in severe, long-term back pain. The patient has reflux esophagitis and a past endoscopy revealed nonspecific gastritis. A specialist had prescribed alendronate, which the patient had to stop taking after several weeks because of dyspepsia. She searched the Web and discovered a new drug, raloxifene, and wonders whether this drug might be an alternative. You know that this drug has been licensed for the prevention of postmenopausal osteoporosis. You promise to examine the literature and to get back to her. THE SEARCH Using MEDLINE you identify a study of raloxifene for the treatment of osteoporosis demonstrating an effect on bone mineral density. You are wondering whether this warrants administration to lower your patient’s risk of osteoporotic fracture.