Miracle-dz/UniFAR-FTUs huggingface dataset:
Strictly aerobic and anaerobic bacteria associated with sinking particulate matter and zooplankton fecal pellets

Particulate material collected in sediment traps at 80 m depth in coastal northwestern Mediterranean waters, and fresh fecal pellets of copepods harvested in the surrounding water, were examined for the presence and activity of ammonia-oxidizing and methanogenic bacteria. Results provide the first evidence for the coexistence of living and active cells of methanogenic and nitrifying bacteria in either fresh zooplankton fecal pellets or large settling particles containing numerous large size fecal pellets. In addition, the presence of these 2 bacterial types in both copepods and the fecal pellets produced by them suggests that the bacteria probably originate from the digestive tract of zooplankton, most likely as ingested species for nitrifiers and enteric species for methanogens.
A Numerical Study of Convective‐Scale Structures in the Outer Cores of Sheared Tropical Cyclones: 1. Updraft Traits in Different Vertical Wind Shear Magnitudes

This study investigates the outer‐core convective‐scale updraft features of numerically simulated tropical cyclones under vertical wind shear of different magnitudes. Updrafts in the outer core were weighted in favor of downshear formation, and the increase in the shear value led to more short‐lived updrafts. The tops of detected updrafts tended to cluster at either 4‐ to 6‐km or 12‐ to 14‐km height. Downshear‐left updrafts mostly moved radially inward, and updrafts on the left side of the shear vector moved more rapidly azimuthally. Longer‐lived updrafts gained greater vertical mass fluxes during their life cycles, with those in strongly sheared tropical cyclones having larger vertical mass fluxes for the same updraft life span. The height of stronger vertical velocity in convective bursts decreased as shear increased, whereas larger vertical velocity within nonconvective‐burst cells held between 3 and 4 km. The values of several environmental parameters (such as the supercell composite parameter and the energy‐helicity index) associated with updrafts in the downshear‐left quadrant were larger than those in the downshear‐right quadrant for the weakly sheared tropical cyclone, whereas they became much larger in the downshear‐right quadrant for highly sheared vortices. There were no relationships between the parameters and updraft mean mass fluxes, so the use of these parameters for predicting the likelihood of updraft strength in tropical cyclones requires caution.
A comparison of the in vitro antimicrobial activity of liposomes containing meropenem and gentamicin

The antimicrobial activity of eight cationic, two neutral and three anionic liposome compositions containing meropenem and gentamicin was tested in vitro in broth and serum medium. The cationic formulations showed better antibacterial efficacy against both Gram-positive and Gram-negative bacteria than the anionic and neutral ones, regardless of the encapsulated drug. The most effective formulations were the cationic PC/DOPE/DOTAP 3:4:3 and PC/Chol/DOTAP 3:4:3, as the MICs with meropenem were 2 to 4 times lower than those of the free drug.
Detection of multiple annexin autoantibodies in a patient with recurrent miscarriages, fulminant stroke and seronegative antiphospholipid syndrome

Anti-phospholipid syndrome (APS) is one of the main causes for recurrent miscarriages. The diagnosis of APS is based on the occurrence of clinical symptoms such as thrombotic events or obstetric complications as well as the detection of antiphospholipid antibodies directed against β2-glycoprotein I and cardiolipin, or a positive lupus anticoagulant assay. However, there is a subpopulation of patients with clinical symptoms of APS, but the lack of serological markers (seronegative APS). In addition, a large proportion of patients with unexplained recurrent miscarriages exist. These cases may be attributed, at least in part, to a seronegative APS. The presence of autoantibodies against annexins is potentially associated with APS. Here we used immunoassays and immunoblots to detect autoantibodies directed against annexin A1-5, and A8, respectively, in a patient with a seronegative APS and a history of six recurrent pregnancy losses and fulminant stroke. We found strong IgM isotype antibody reactivity directed against annexin A2 and annexin A8, and moderate to weak IgM isotype antibody reactivity directed against annexin A1, A3, and A5. Further studies will evaluate the diagnostic value of IgM isotype antibodies against annexin A1-A5, and A8 for seronegative APS and recurrent miscarriages.
Regional reference total electron content model over Japan based on neural network mapping techniques

A regional reference model of total electron content (TEC) was constructed using data from the GPS Earth Observation Network (GEONET), which consists of more than 1000 Global Positioning System (GPS) satellite receivers distributed over Japan. The data covered almost one solar activity period from April 1997 to June 2007. First, TECs were determined for 32 grid points, expanding from 27 to 45° N in latitude and from 127 to 145° E in longitude at 15-min intervals. Secondly, the time-latitude variation averaged over three days was determined by using the surface harmonic functional expansion. The coefficients of the expansion were then modeled by using a neural network technique with input parameters of the season (day of the year) and solar activity (F10.7 index and sunspot number). Thus, two-dimensional TEC maps (time vs. latitude) can be obtained for any given set of solar activity and day of the year.
A NEW APPROACH FOR INTEREXAMINER RELIABILITY DATA ANALYSIS ON DENTAL CARIES CALIBRATION

Objectives a) to evaluate the interexaminer reliability in caries detection considering different diagnostic thresholds and b) to indicate, by using Kappa statistics, the best way of measuring interexaminer agreement during the calibration process in dental caries surveys. Methods Eleven dentists participated in the initial training, which was divided into theoretical discussions and practical activities, and calibration exercises, performed at baseline, 3 and 6 months after the initial training. For the examinations of 6-7-year-old schoolchildren, the World Health Organization (WHO) recommendations were followed and different diagnostic thresholds were used: WHO (decayed/missing/filled teeth – DMFT index) and WHO + IL (initial lesion) diagnostic thresholds. The interexaminer reliability was calculated by Kappa statistics, according to WHO and WHO+IL thresholds considering: a) the entire dentition; b) upper/lower jaws; c) sextants; d) each tooth individually. Results Interexaminer reliability was high for both diagnostic thresholds; nevertheless, it decreased in all calibration sections when considering teeth individually. Conclusion The interexaminer reliability was possible during the period of 6 months, under both caries diagnosis thresholds. However, great disagreement was observed for posterior teeth, especially using the WHO+IL criteria. Analysis considering dental elements individually was the best way of detecting interexaminer disagreement during the calibration sections.
Hierarchical Compound Poisson Factorization

Non-negative matrix factorization models based on a hierarchical Gamma-Poisson structure capture user and item behavior effectively in extremely sparse data sets, making them the ideal choice for collaborative filtering applications. Hierarchical Poisson factorization (HPF) in particular has proved successful for scalable recommendation systems with extreme sparsity. HPF, however, suffers from a tight coupling of sparsity model (absence of a rating) and response model (the value of the rating), which limits the expressiveness of the latter. Here, we introduce hierarchical compound Poisson factorization (HCPF) that has the favorable Gamma-Poisson structure and scalability of HPF to high-dimensional extremely sparse matrices. More importantly, HCPF decouples the sparsity model from the response model, allowing us to choose the most suitable distribution for the response. HCPF can capture binary, non-negative discrete, non-negative continuous, and zero-inflated continuous responses. We compare HCPF with HPF on nine discrete and three continuous data sets and conclude that HCPF captures the relationship between sparsity and response better than HPF.
Soft Robotic Grippers for Biological Sampling on Deep Reefs

Abstract This article presents the development of an underwater gripper that utilizes soft robotics technology to delicately manipulate and sample fragile species on the deep reef. Existing solutions for deep sea robotic manipulation have historically been driven by the oil industry, resulting in destructive interactions with undersea life. Soft material robotics relies on compliant materials that are inherently impedance matched to natural environments and to soft or fragile organisms. We demonstrate design principles for soft robot end effectors, bench-top characterization of their grasping performance, and conclude by describing in situ testing at mesophotic depths. The result is the first use of soft robotics in the deep sea for the nondestructive sampling of benthic fauna.
An Evaluation Exercise for Word Alignment

This paper presents the task definition, resources, participating systems, and comparative results for the shared task on word alignment, which was organized as part of the HLT/NAACL 2003 Workshop on Building and Using Parallel Texts. The shared task included Romanian-English and English-French sub-tasks, and drew the participation of seven teams from around the world.
Association between the pre-mir-218 polymorphism and cancer risk in the Chinese population: a meta-analysis.

BACKGROUND Several recent studies have explored associations between pre-mir-218 polymorphism (rs11134527) and cancer risk. However, published data are still inconclusive. To obtain a more precise estimation of the relationship in the Chinese population, we carried out a meta-analysis for the first time. MATERIALS AND METHODS Through retrieval from the PubMed, Medline, Embase, Web of Science databases, China National Knowledge Infrastructure and the Chinese BioMedical Literature Database, a total of four studies were analyzed with 3,561 cases and 3,628 controls for SNP pre-mir-218 rs11134527. We calculated odds ratios (ORs) and 95% confidence intervals (95%CIs) to explore the strength of associations. RESULTS The results showed that the rs11134527 polymorphism was associated with decreased cancer risk in GG versus AA and GG versus AA+AG models tested ( GG vs AA: OR=0.82, 95%CI: 0.71-0.94; GG vs AA+AG: OR=0.84, 95%CI: 0.74-0.96), and significantly decreased cervical cancer risk was observed in GG versus AA and GG versus AA+AG models (GG vs AA: OR=0.79, 95%CI: 0.66-0.94; GG vs AA+AG: OR=0.80, 95%CI: 0.68-0.94). However, no significant association between the rs11134527 polymorphism and hepatocellular carcinoma risk was observed in all comparison models tested (AG vs AA: OR=0.94, 95%CI: 0.79-1.11; GG vs AA: OR=0.88, 95%CI: 0.70-1.10; GG+AG vs AA: OR=0.92, 95%CI: 0.79-1.08; GG vs AA+AG: OR=0.91, 95%CI: 0.75-1.11). CONCLUSION The findings suggest that pre-miR-218 rs11134527 polymorphism may have some relation to cancer development in Chinese. However, well-designed studies with larger sample size and more detailed data are needed to confirm these conclusions.
Molecular Imaging of Temporal Dynamics and Spatial Heterogeneity of Hypoxia-Inducible Factor-1 Signal Transduction Activity in Tumors in Living Mice

Tumor hypoxia is a spatially and temporally heterogeneous phenomenon, which results from several tumor and host tissue-specific processes. To study the dynamics and spatial heterogeneity of hypoxia-inducible factor-1 (HIF-1)-specific transcriptional activity in tumors, we used repetitive noninvasive positron emission tomography (PET) imaging of hypoxia-induced HIF-1 transcriptional activity in tumors in living mice. This approach uses a novel retroviral vector bearing a HIF-1–inducible “sensor” reporter gene (HSV1-tk/GFP fusion) and a constitutively expressed “beacon” reporter gene (DsRed2/XPRT). C6 glioma cells transduced with this multireporter system revealed dose-dependent patterns in temporal dynamics of HIF-1 transcriptional activity induced by either CoCl2 or decreased atmospheric oxygen concentration. Multicellular spheroids of C6 reporter cells developed a hypoxic core when >350 μm in diameter. 18F-2′-fluoro-2′deoxy-1β-D-arabionofuranosyl-5-ethyl-uracil (FEAU) PET revealed spatial heterogeneity of HIF-1 transcriptional activity in reporter xenografts in mice as a function of size or ischemia-reperfusion injury. With increasing tumor diameter (>3 mm), a marked increase in HIF-1 transcriptional activity was observed in the core regions of tumors. Even a moderate ischemia-reperfusion injury in small C6 tumors caused a rapid induction of HIF-1 transcriptional activity, which persisted for a long time because of the inability of C6 tumors to rapidly compensate acute changes in tumor microcirculation.
Overexpression of a secretory leukocyte protease inhibitor in human gastric cancer

Complementary DNA microarrays have identified aberrantly expressed genes in patients with gastric cancer. One that encodes secretory leukocyte protease inhibitor (SLPI) is among the aberrantly expressed genes and is associated with metastasis in gastric cancers. We evaluated the potential of SLPI expression as a helpful biomarker for detection of gastric cancer. Tumor tissue and matching noncancerous mucosa were obtained from 60 patients immediately after gastric resection. SLPI expression levels were determined by Northern and Western blot tests and quantitative‐reverse transcriptase‐polymerase chain reaction (Q‐RT‐PCR). Paraffin‐fixed tumor tissues were used for immunohistochemistry study in 119 patients. A consistent result was obtained between all examinations except plasma SLPI. SLPI mRNA transcripts and protein were overexpressed in gastric cancer cells, and the depth of wall invasion was significantly greater in serosa‐invading (T3 and T4) cancers compared to the serosa‐free (T1 and T2) cancers. These enhanced expressions were significantly associated with lymph node metastasis, and were significantly higher in stages III and IV, and higher than those in stages I and II. Five‐year survival of patients with lower expression of the SLPI gene was significantly better than among patients with a higher expression. To better understand the function of SLPI in human gastric cancer cells, isogenic SLPI overexpressing cell lines (AZ521) were prepared. The migratory and invasive abilities were increased 4.4‐fold to 6.9‐fold, or 3.0‐fold to 4.1‐fold, respectively, in SLPI‐overexpressing cell lines. The results point to SLPI as a potential prognostic marker for gastric cancer and its function in cell invasion. © 2008 Wiley‐Liss, Inc.
Impact of nanostructured thin ZnO film in ultraviolet protection

Nanoscale ZnO is one of the best choices for ultraviolet (UV) protection, not only because of its antimicrobial properties but also due to its potential application for UV preservation. However, the behavior of nanostructured thin ZnO films and long-term effects of UV-radiation exposure have not been studied yet. In this study, we investigated the UV-protection ability of sol gel-derived thin ZnO films after different exposure times. Scanning electron microscopy, atomic force microscopy, and UV-visible optical spectroscopy were carried out to study the structure and optical properties of the ZnO films as a function of the UV-irradiation time. The results obtained showed that the prepared thin ZnO films were somewhat transparent under the visible wavelength region and protective against UV radiation. The UV-protection factor was 50+ for the prepared samples, indicating that they were excellent UV protectors. The deposited thin ZnO films demonstrated promising antibacterial potential and significant light absorbance in the UV range. The experimental results suggest that the synthesized samples have potential for applications in the health care field.
Cerebral Blood Flow in Patients With Chronic Heart Failure Before and After Heart Transplantation

Background and Purpose— Arterial blood pressure and cardiac output are often reduced in patients with chronic heart failure (CHF). Counterregulatory mechanisms with increased neurohormonal activation and changes in the distribution of cardiac output are assumed to secure vital organ perfusion. However, clinical examination of patients with CHF frequently reveals neurological symptoms with dizziness and memory problems, suggesting altered brain perfusion. In this study we determined whether cerebral blood flow (CBF) is reduced in patients with New York Heart Association (NYHA) functional class III and IV (n=12) compared with healthy control subjects (n=12). Furthermore, we examined whether heart transplantation (n=5) could restore CBF. Methods— CBF was estimated by single-photon emission computed tomography and 133Xe as tracer, and middle cerebral artery velocity was measured by transcranial Doppler ultrasound. Results— In the CHF patients, CBF was 36±1 mL/min per 100 g, corresponding to a 31% reduction compared with the control group (52±5 mL/min per 100 g) (P <0.05). After heart transplantation, CBF increased from 35±3 mL/min per 100 g before transplantation to 50±3 mL/min per 100 g within the first postoperative month (P <0.05). Conclusions— We conclude that CBF is substantially, but reversibly, reduced in patients with NYHA class III/IV heart failure. This phenomenon suggests that redistribution of cardiac output inadequately secures brain perfusion in patients with severe CHF.
CRYOTHERAPY: A NEW TECHNIQUE TO OBTAIN GRAPEVINE PLANTS FREE OF VIRUSES

Through in vitro tissue culture techniques it is possible to propagate high quality nursery plants faster. Cryotherapy is a promising tool, based on in vitro culture techniques, for achieving in a short time, high frequency of regenerating plants free of viruses. The objective of this review is to present and analyze the results of research conducted in cryotherapy methods based on cryopreservation protocols for recovery of cultivars free of micro-organisms with potential agronomic interest. The main methods employed in cryotherapy are encapsulation-dehydration, vitrification, encapsulation-vitrification and droplet vitrification, which are based on the immersion of preconditioned shoot tips in liquid nitrogen, followed by their recovery in vitro on to culture media for regeneration of healthy plantlets. Improvements to cryotherapy protocols used for grapevine are still needed, since there are variations in response according to the genotype. The published research mostly relates to Vitis vinifera and the few studies applied to other species show that the protocols need to be improved. This specificity goes beyond species, with different responses among cultivars, limiting the broader application of the technology. On the other hand, traditional methods used for virus removal from infected plant materials also have limitations and therefore investment in research for the development and application of cryopreservation techniques is highly justified, considering its efficiency and low-cost, once the protocols are developed. High frequency of virus-free plants among regenerants within a short time frame is the most desirable aspect of cryotherapy. Therefore, these advantages make the technique a promising tool for institutions mandated to the development of high-health planting materials with high genetic and agronomic potential for viticulture.
Monotonicity, Thinning, and Discrete Versions of the Entropy Power Inequality

We consider the entropy of sums of independent discrete random variables, in analogy with Shannon's Entropy Power Inequality, where equality holds for normals. In our case, infinite divisibility suggests that equality should hold for Poisson variables. We show that some natural analogues of the EPI do not in fact hold, but propose an alternative formulation which does always hold. The key to many proofs of Shannon's EPI is the behavior of entropy on scaling of continuous random variables. We believe that Rényi's operation of thinning discrete random variables plays a similar role to scaling, and give a sharp bound on how the entropy of ultra log-concave random variables behaves on thinning. In the spirit of the monotonicity results established by Artstein, Ball, Barthe, and Naor, we prove a stronger version of concavity of entropy, which implies a strengthened form of our discrete EPI.
DigitalCommons@UNO DigitalCommons@UNO

: Mechanistic insights into the reaction of an estrogen o -quinone with deoxyguanosine has been further investigated using high level density functional calculations in addition to the use of 4-hyroxycatecholestrone (4-OHE 1 ) regioselectivity labeled with deuterium at the C1-position. Calculations using the M06-2X functional with large basis sets indicate the tautomeric form of an estrogen-DNA adduct present when glycosidic bonds cleavage occurs is comprised of an aromatic A ring structure. This tautomeric form was further verified by use of deuterium labelling of the catechol precursor use to form the estrogen o -quinone. Regioselective deuterium labelling at the C1-position of the estrogen A ring allows discrimination between two tautomeric forms of a reaction intermediate either of which could be present during glycosidic bond cleavage. HPLC-MS analysis indicates a reactive intermediate with a m / z of 552.22 consistent with a tautomeric form containing no deuterium. This intermediate is consistent with a reaction mechanism that involves: (1) proton assisted Michael addition; (2) re-aromatization of the estrogen A ring; and (3) glycosidic bond cleavage to form the known estrogen-DNA adduct, 4-OHE 1 -1-N7Gua.
Estimation of Apparent Survival, Detectability, and Density of Three Federally Threatened Mussel Species in a Small Watershed

ABSTRACT Almost half of the mussel species in North America are imperiled, and eight species found in the eastern Gulf Coastal Plain drainages were recently federally listed. Information regarding the status of known populations of these species is either limited or outdated. Three sites in the Choctawhatchee River watershed (southeast Alabama), where federally threatened mussel species were known to occur, were sampled for mussels eight times each over 4 mo. Three federally threatened species, Fusconaia burkei, Hamiota australis, and Pleurobema strodeanum, and one common species, Elliptio pullata, were individually tagged and released using a robust mark-recapture sampling design. Each species-site combination having sufficient sample sizes was analyzed using a set of six candidate mark-recapture models chosen a priori, and estimates of apparent survival, detectability, and density were derived using the computer program MARK to average models. A total of 820 mussels, 427 of which are listed as federally threatened or endangered, were tagged over eight sampling occasions at three sites. Apparent survival of E. pullata varied among sampling occasions (0.96–0.99), while threatened species tended to have nearly constant survival. Detectability increased with mussel length for E. pullata at all sites (0.07–0.82), but with the exception of P. strodeanum at 8M1, length did not affect detectability of threatened species (0.11–0.52). Densities of threatened species (0.05–1.0 individuals/m2) were typically lower than those of E. pullata (0.15–1.78 individuals/m2) at each site. These data offer insights into the current status of known populations of threatened species at three sites in the Choctawhatchee watershed and will serve as a baseline against which the future status of these populations can be measured. These data also demonstrate the potential viability of using these methods for long-term monitoring of these populations.