Miracle-dz/UniFAR-FTUs huggingface dataset:
Evolutionary flexibility in routes to mat formation by Pseudomonas

Many bacteria form mats at the air-liquid interface of static microcosms. These structures typically involve the secretion of exopolysaccharide(s), the production of which is often controlled by the secondary messenger c-di-GMP. Mechanisms of mat formation have been particularly well characterized in Pseudomonas fluorescens SBW25; mutations that lead to an increase in c-di-GMP production by diguanylate cyclases (WspR, AwsR, or MwsR) result in the secretion of cellulose, and mat formation. Here, we characterize and compare mat formation in two close relatives of SBW25: Pseudomonas simiae PICF7 and Pseudomonas fluorescens A506. We find that PICF7 – the strain more closely related to SBW25 – can form mats through mutations affecting the activity of the same three diguanylate cyclases as SBW25. However, instead of cellulose, these mutations activate the production of the Pel exopolysaccharide. We also provide evidence for at least two further – as yet uncharacterized – routes to PICF7 mat formation. P. fluorescens A506, while retaining the same mutational routes to mat formation as SBW25 and PICF7, forms mats by a semi-heritable mechanism that likely culminates in Pga and/or Psl production. Overall, our results demonstrate a high level of evolutionary flexibility in the molecular and structural routes to mat formation, even among close relatives.
Coastal profile evolution at Duck, North Carolina: A cautionary note

The Hurst exponents of 10.8-year-long time series of cumulative bed level observed between the shoreline and ∼8-m water depth on an ocean beach are shown to be consistent with bed-level time series described by a sinusoid with a 10.8-year period plus white noise. Thus, for these observations, Hurst exponents cannot distinguish self-organized morphological evolution from the hypothesis that nearshore morphology on monthly to decadal timescales is a forced response to small-scale physical processes driven by waves and currents.
Computational Modelling of Nephron Progenitor Cell Movement and Aggregation During Kidney Organogenesis

During early kidney organogenesis, nephron progenitor (NP) cells move from the tip to the corner region of the ureteric bud (UB) branches in order to form the pretubular aggregate, the early structure giving rise to nephron formation. Chemotaxis and cell-cell adhesion differences are believed to drive cell patterning during this critical period of organogenesis, but the spatiotemporal organization of this process is incompletely understood. We applied a Cellular Potts model to explore to how these processes contribute to directed cell movement and aggregation. Model parameters were estimated based on �tting to experimental data obtained in ex vivo kidney explant and dissociation-reaggregation organoid culture studies. Our simulations indicated that optimal enrichment and aggregation of NP cells in the UB corner niche requires chemoattractant secretion from both the UB epithelial cells and the NP cells themselves, as well as differences in cell-cell adhesion energies. Furthermore, NP cells were observed, both experimentally and by modelling, to move at higher speed in the UB corner as compared to the tip region where they originated. The existence of different cell speed domains along the UB was con�rmed using self-organizing map analysis. In summary, we demonstrated the suitability of a Cellular Potts Model approach to simulate cell movement and patterning during early nephrogenesis. Further re�nement of the model should allow us to recapitulate the effects of developmental changes of cell phenotypes and molecular crosstalk during organ development.
The Value of Nonconsumptive Wildlife Recreation in the United States

Public interest in wildlife and wildliferelated activities extends well beyond the traditional hunting and fishing activities. In 1980, approximately 29 million individuals (16 years and older) took trips primarily to observe wildlife while 83 million (49 percent of population 16 years and older) observed specifically wildlife in both residential and nonresidential settings (USFWS 1982). Moreover, there are at least 18 national conservation or wildlife-related organizations with memberships ranging from 5,000 in the American Birding Association to 4.2 million in the National Wildlife Federation. The extent of participation in these activities reflects a substantial demand for the products of wildlife management and yet, with few notable exceptions (Cicchetti 1973; Bishop 1978; Hay and McConnell 1979, 1984), the relationship between management programs and nonconsumptive wildlife recreation has not been investigated. Just as economic studies have contributed greatly to managers' knowledge of the value of wildlife resources for fishing and hunting (Brown, Singh, and Castle 1965; Hammack and Brown 1974; Gum and Martin 1975; Bishop and Heberlein 1979; McConnell and Strand 1981; Kealy and Bishop 1986), so they can inform on the value and extent of nonconsumptive uses of wildlife, and the sensitivity of those uses to changes in management programs. In this paper we provide information for the wildlife management community and the public trustees by developing a model to estimate first, the probability of participation and second, the number of hours people observe, photograph, and feed wildlife away from the home conditional on participation. The model is used to show how participation in these activities may be changed with changes in habitat. In addition, we use it to calculate a lower bound estimate for the total benefits from nonconsumptive wildlife recreation trips in 1980. The data used for estimation are from the 1980 National Survey of Fishing, Hunting, and Wildlife-Associated Recreation (USFWS 1982).
Testing global ocean carbon cycle models using measurements of atmospheric O2 and CO2 concentration

We present a method for testing the performance of global ocean carbon cycle models using measurements of atmospheric O2 and CO2 concentration. We combine these measurements to define a tracer, atmospheric potential oxygen (APO ≈ O2 + CO2), which is conservative with respect to terrestrial photosynthesis and respiration. We then compare observations of APO to the simulations of an atmospheric transport model which uses ocean‐model air‐sea fluxes and fossil fuel combustion estimates as lower boundary conditions. We present observations of the annual‐average concentrations of CO2, O2, and APO at 10 stations in a north‐south transect. The observations of APO show a significant interhemispheric gradient decreasing towards the north. We use air‐sea CO2, O2, and N2 fluxes from the Princeton ocean biogeochemistry model, the Hamburg model of the ocean carbon cycle, and the Lawrence Livermore ocean biogeochemistry model to drive the TM2 atmospheric transport model. The latitudinal variations in annual‐average APO predicted by the combined models are distinctly different from the observations. All three models significantly underestimate the interhemispheric difference in APO, suggesting that they underestimate the net southward transport of the sum of O2 and CO2 in the oceans. Uncertainties in the model‐observation comparisons include uncertainties associated with the atmospheric measurements, the atmospheric transport model, and the physical and biological components of the ocean models. Potential deficiencies in the physical components of the ocean models, which have previously been suggested as causes for anomalously large heat fluxes out of the Southern Ocean, may contribute to the discrepancies with the APO observations. These deficiencies include the inadequate parameterization of subgrid‐scale isopycnal eddy mixing, a lack of subgrid‐scale vertical convection, too much Antarctic sea‐ice formation, and an overestimation of vertical diffusivities in the main thermocline.
Finer resolution observation and monitoring of global land cover: first mapping results with Landsat TM and ETM+ data

We have produced the first 30 m resolution global land-cover maps using Landsat Thematic Mapper (TM) and Enhanced Thematic Mapper Plus (ETM+) data. We have classified over 6600 scenes of Landsat TM data after 2006, and over 2300 scenes of Landsat TM and ETM+ data before 2006, all selected from the green season. These images cover most of the world's land surface except Antarctica and Greenland. Most of these images came from the United States Geological Survey in level L1T (orthorectified). Four classifiers that were freely available were employed, including the conventional maximum likelihood classifier (MLC), J4.8 decision tree classifier, Random Forest (RF) classifier and support vector machine (SVM) classifier. A total of 91,433 training samples were collected by traversing each scene and finding the most representative and homogeneous samples. A total of 38,664 test samples were collected at preset, fixed locations based on a globally systematic unaligned sampling strategy. Two software tools, Global Analyst and Global Mapper developed by extending the functionality of Google Earth, were used in developing the training and test sample databases by referencing the Moderate Resolution Imaging Spectroradiometer enhanced vegetation index (MODIS EVI) time series for 2010 and high resolution images from Google Earth. A unique land-cover classification system was developed that can be crosswalked to the existing United Nations Food and Agriculture Organization (FAO) land-cover classification system as well as the International Geosphere-Biosphere Programme (IGBP) system. Using the four classification algorithms, we obtained the initial set of global land-cover maps. The SVM produced the highest overall classification accuracy (OCA) of 64.9% assessed with our test samples, with RF (59.8%), J4.8 (57.9%), and MLC (53.9%) ranked from the second to the fourth. We also estimated the OCAs using a subset of our test samples (8629) each of which represented a homogeneous area greater than 500 m × 500 m. Using this subset, we found the OCA for the SVM to be 71.5%. As a consistent source for estimating the coverage of global land-cover types in the world, estimation from the test samples shows that only 6.90% of the world is planted for agricultural production. The total area of cropland is 11.51% if unplanted croplands are included. The forests, grasslands, and shrublands cover 28.35%, 13.37%, and 11.49% of the world, respectively. The impervious surface covers only 0.66% of the world. Inland waterbodies, barren lands, and snow and ice cover 3.56%, 16.51%, and 12.81% of the world, respectively.
Erzincan’a (Türkiye) özgü endemik bitki taksonlarının IUCN tehdit kategorileri

Arastirmada Erzincan’a ozgu 49 taksona ait populasyon gozlemlerine yer verildi. Gozlem sonuclarina gore Turkiye Bitkileri Kirmizi Kitabi’nda yer alan 31 taksona ait IUCN kategorisi guncellendi. Soz konusu eserin yayin tarihinden sonra bilim dunyasina tanitilan Erzincan’a ozgu 18 takson icin de yeni kategoriler onerildi. Sonuclara gore taksonlardan 22 19 tanesinin Kritik Tehlikede (CR), 8 tanesinin Tehlikede (EN), 5 tanesinin Zarar Gorebilir (VU) kategorisindedir. 14 taksonun ise simdilik risk altinda olmadigi degerlendirildi. CR ve EN kategorisindeki taksonlarin dagilimlarina gore il genelindeki bitkiler acisindan korumada oncelikli alanlar belirlendi.
Austral thermospheric wind circulation and interplanetary magnetic field orientation

Ground-based high-resolution spectral measurements of the OI ¹D emission at 15,867 K (630 nm; 1 K = 1 cm−1) from thermospheric altitudes at the geographic south pole are used to determine the relationship between the southern hemisphere high-latitude thermospheric wind circulation and the interplanetary magnetic field (IMF) during the austral winter of 1989. A clear dependence is shown between the thermospheric wind direction and magnitude and the IMF. In the midnight sector, the zonal wind magnitude is dependent on By, and the meridional component on Bz. The magnetic local times of the largest polar cap electric fields are also inferred for either sign of By. In addition, it is shown that the field angle Φ of the IMF in the Y–Z plane is also useful for ordering the neutral wind data. These ground-based wind measurements also reflect the polarity and magnitude of the IMF, at least near the observing station's magnetic midnight.
Gender and Racial Disparities in Driving Cessation Among Older Adults

Objectives: To longitudinally examine gender and racial disparities in driving cessation among older adults. Methods: Data came from the Advanced Cognitive Training for Independent and Vital Elderly (ACTIVE) Study (N = 1,789). Logistic generalized estimating equations (GEE) were used to identify predictors of driving cessation; stratified analysis and interaction terms were used to determine whether factors differed by gender and race. Results: Two hundred and five (11.5%) participants stopped driving over the study period. Education was associated with increased risk of cessation for men (adjusted odds ratio [AOR] =1.40, 95% confidence interval [CI] =1.10 to 1.78), but decreased risk for women (AOR = 0.90, 95% CI = 0.82-0.98). Being married was associated with lower risk of cessation for men (AOR = 0.18, 95% CI = 0.06-0.56) but was unrelated to cessation for women (AOR = 1.00, 95% CI = 0.56-1.80). Results were consistent with the hypothesis that racial disparities in cessation widen with increasing age. Discussion: Factors predictive of driving cessation vary by gender. Racial disparities in cessation are wider at older ages. Transportation policies and programs should account for social determinants and aim to address social disparities in driving mobility among older adults.
Ground-roll Separation By Sparsity And Morphological Diversity Promotion

In land based seismic surveys, the seismic data are usually contaminated by low-frequency, high-amplitude groundroll noise, which overlay important reflector information in both the t-x and f-k domains and severely degrade the quality of the information obtained from the seismic record. Standard techniques of ground-roll removal commonly alter reflector information. Based on the morphological component analysis (MCA) technique, this paper proposes to separate seismic signals into reflector and ground-roll parts, exploiting both the sparsity and the waveform diversity mechanism. The basic idea of this method is the use of two appropriate dictionaries, one for the representation of the reflection information and the other for the ground-roll component. Both dictionaries are chosen such that they lead to sparse representation over one type of the signal content (reflector or ground-roll). To further improve the wavefield separation quality, a modified-MCA (MMCA) algorithm is proposed meanwhile. We successfully tested this method on a real data set with complex ground-roll and reflector structures.
INTRAOPERATIVE THREE DIMENSIONAL FLUOROSCOPIC CHOLANGIOGRAPHY

Background: In liver surgery, biliary complications represent a major clinical problem. Intraoperative assessment of the architecture of the biliary vessel tree improves intraoperative decision making and possibly reduces lesions to intraor extrahepatic bile ducts. Methods: Isocentric C-arm fluoroscopy acquires a defined set of images in 60 to 120 seconds during a 190° orbital rotation. Water soluble contrast media is injected into the bile ducts. The biliary vessels are displayed by real-time rotational projections or multiplanar reconstruction. The technique was evaluated initially by experiments in a preserved human liver. Intraoperative data acquisition was performed in five patients with centrally located liver malignancies. Results: Complete data acquisition was possible in three patients. Each single intraoperatively acquired data-set depicted precise anatomical details of the architecture of the biliary vessel tree. Conclusions: Intraoperative biliary imaging can be improved by the application of intraoperative three dimensional cholangiography. For the development of navigation in hepatobiliary procedures this technique will be an important tool by defining landmarks of the liver in a three dimensional space.
Mouse spleen lymphoblasts generated in vitro. Recovery in high yield and purity after floatation in dense bovine plasma albumin solutions

Mouse spleen lymphoblasts, stimulated to divide in vitro, acquired a low cell density and could be separated by isopycnic techniques. Cultured cells were suspended in BPA columns, rho = 1.080, and spun to equilibrium. The method was simple, fast, accomodated large numbers of cells, and was reproducible. It provided lymphoblasts in high yield and purity (at least 80% of the low density cells were blasts). It allowed for the recovery of proliferating cells in their first cell cycle, and did not alter the subsequent ability of cells to proliferate when recultured in vitro. Certain properties of mouse spleen lymphoblasts were analyzed in detail. Lymphoblasts induced by LPS, FCS, con A (tetravalent and succinylated), and MLC were very similar except in the absolute numbers that were induced. The blasts exhibited the classic cytologic features of enlarged nucleoli and abundant cytoplasmic polyribosomes (basophilia). As a population, they were enlarged in size relative to nondividing cells, but this seemed to apply primarily to cells in the S and G2+ M phase of the cell cycle rather than G1. The cell cycle distribution of lymphoblasts was analyzed by flow microfluorometry. By analyzing low density cells obtained at varying intervals after mitogen stimulation, FMF indicated that lymphoblasts enter the S phase of their first cell cycle beginning at 20-24 h after stimulation.
A targeted genetic screen identifies crucial players in the specification of the Drosophila abdominal Capaergic neurons AUTHORS

SUMMARY The central nervous system contains a wide variety of neuronal subclasses generated by neural progenitors. The achievement of a unique neural fate is the consequence of a sequence of early and increasingly restricted regulatory events, which culminates in the expression of a specific genetic combinatorial code that confers individual characteristics to the differentiated cell. How the earlier regulatory events influence postmitotic cell fate decisions is beginning to be understood in the Drosophila NB 5-6 lineage. However it remains unknown to what extent these events operate in other lineages. To better understand this issue, we have used a very highly specific marker that identifies a small subset of abdominal cells expressing the Drosophila neuropeptide Capa: the ABCA neurons. Our data support the birth of the ABCA neurons from NB5-3 in a cas temporal window in the abdominal segments A2-A4. Moreover, we show that the ABCA neuron has an ABCA sibling cell which dies by apoptosis. Surprisingly, both cells are also generated in the abdominal segments A5-A7, although they undergo apoptosis before expressing Capa. In addition, we have performed a targeted genetic screen to identify players involved in ABCA specification. We have found that the ABCA fate requires zfh2, grain, Grunge and hedgehog genes. Finally we show that the NB 5-3 generates other subtype of Capa-expressing cells (SECAs) in the third suboesophageal segment, which are born during a pdm/cas temporal window, and have different genetic requirements for their specification.
High (cid:1) -Lactamase Levels Change the Pharmacodynamics of (cid:1) -Lactam Antibiotics in Pseudomonas aeruginosa Bioﬁlms

Resistance to (cid:1) -lactam antibiotics is a frequent problem in Pseudomonas aeruginosa lung infection of cystic ﬁbrosis (CF) patients. This resistance is mainly due to the hyperproduction of chromosomally encoded (cid:1) -lactamase and bioﬁlm formation. The purpose of this study was to investigate the role of (cid:1) -lactamase in the pharmacokinetics (PK) and pharmacodynamics (PD) of ceftazidime and imipenem on P. aeruginosa bioﬁlms. P. aeruginosa PAO1 and its corresponding (cid:1) -lactamase-overproducing mutant, PA (cid:2) DDh2Dh3, were used in this study. Bioﬁlms of these two strains in ﬂow chambers, microtiter plates, and on alginate beads were treated with different concentrations of ceftazidime and imipenem. The kinetics of antibiotics on the bioﬁlms was investigated in vitro by time-kill methods. Time-dependent killing of ceftazidime was observed in PAO1 bioﬁlms, but con-centration-dependent killing activity of ceftazidime was observed for (cid:1) -lactamase-overproducing bioﬁlms of P. aeruginosa in all three models. Ceftazidime showed time-dependent killing on planktonic PAO1 and PA (cid:2) DDh2Dh3. This difference is probably due to the special distribution and accumulation in the bioﬁlm matrix of (cid:1) -lactamase, which can hydrolyze the (cid:1) -lactam antibiotics. The PK/PD indices of the AUC/MBIC and C max /MBIC (AUC is the area under concentration-time curve, MBIC is the minimal bioﬁlm-inhibitory concentration, and C max is the maximum concentration of drug in serum) are probably the best parameters to describe the effect of ceftazidime in (cid:1) -lactamase-overproducing P. aeruginosa bioﬁlms. Meanwhile, imipenem showed time-dependent killing on both PAO1 and PA (cid:2) DDh2Dh3 bioﬁlms. An inoculum effect of (cid:1) -lactams was found for both planktonic and bioﬁlm P. aeruginosa cells. The inoculum effect of ceftazidime for the (cid:1) -lactamase-overproducing mutant PA (cid:2) DDh2Dh3 bioﬁlms was more obvious than for PAO1 bioﬁlms, with a requirement of higher antibiotic concentration and a longer period of treatment.
Therapeutic Administration of 131I for Differentiated Thyroid Cancer: Radiation Dose to Ovaries and Outcome of Pregnancies

Radiation is known to be mutagenic. The present study updates a 10-y-old study regarding pregnancy outcome and the health of offspring of women previously exposed to radioiodine (131I) during thyroid carcinoma treatment, by doubling the number of pregnancies that occurred after exposure. Methods: Data on 2,673 pregnancies were obtained by interviewing female patients who were treated for thyroid carcinoma but had not received significant external radiation to the ovaries. Results: The incidence of miscarriages was 10% before any treatment for thyroid cancer; this percentage increased after surgery for thyroid cancer, both before (20%) and after (19%) 131I treatment, with no variation according to the cumulative dose. In contrast to previously reported data, miscarriages were not significantly more frequent in women treated with radioiodine during the year before conception, not even in women who had received more than 370 MBq during that year. The incidences of stillbirths, preterm births, low birth weight, congenital malformations, and death during the first year of life were not significantly different before and after 131I therapy. The incidences of thyroid and nonthyroid cancers were similar in children born either before or after the mother's exposure to radioiodine. Conclusion: There is no evidence that exposure to radioiodine affects the outcomes of subsequent pregnancies and offspring. The question as to whether the incidences of malformations and thyroid and nonthyroid cancers are related to gonadal irradiation remains to be established. The doubling dose is still being heatedly debated, and the value of 1 Gy as the doubling dose in humans should be reevaluated.
Apoptotic Signaling through CD95 (Fas/Apo-1) Activates an Acidic Sphlngomyellnase

From the "Department of Experimental Medicine and Biochemical Sciences, University of Romg "Tor Vergata" and the ~Departraent of Experimental Medicine, University of Rome "La Sapienza" 00161 Rome, Italy; the SDe~rtmem of Experimental Medicine, Uniuersity of L'Aquila, 67100 L'Aquila, Italy; and IIDepartsent of Human Immunology, DNAX Research Institute of Molecular and Cellular Biology, In~, Palo Alg California 94304