Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of the Peptidoglycan Hydrolase Complement of Lactobacillus casei and Characterization of the Major γ-D-Glutamyl-L-Lysyl-Endopeptidase

Peptidoglycan (PG) is the major component of Gram positive bacteria cell wall and is essential for bacterial integrity and shape. Bacteria synthesize PG hydrolases (PGHs) which are able to cleave bonds in their own PG and play major roles in PG remodelling required for bacterial growth and division. Our aim was to identify the main PGHs in Lactobacillus casei BL23, a lactic acid bacterium with probiotic properties. The PGH complement was first identified in silico by amino acid sequence similarity searches of the BL23 genome sequence. Thirteen PGHs were detected with different predicted hydrolytic specificities. Transcription of the genes was confirmed by RT-PCR. A proteomic analysis combining the use of SDS-PAGE and LC-MS/MS revealed the main seven PGHs synthesized during growth of L. casei BL23. Among these PGHs, LCABL_02770 (renamed Lc-p75) was identified as the major one. This protein is the homolog of p75 (Msp1) major secreted protein of Lactobacillus rhamnosus GG, which was shown to promote survival and growth of intestinal epithelial cells. We identified its hydrolytic specificity on PG and showed that it is a γ-D-glutamyl-L-lysyl-endopeptidase. It has a marked specificity towards PG tetrapeptide chains versus tripeptide chains and for oligomers rather than monomers. Immunofluorescence experiments demonstrated that Lc-p75 localizes at cell septa in agreement with its role in daughter cell separation. It is also secreted under an active form as detected in zymogram. Comparison of the muropeptide profiles of wild type and Lc-p75-negative mutant revealed a decrease of the amount of disaccharide-dipeptide in the mutant PG in agreement with Lc-p75 activity. As a conclusion, Lc-p75 is the major L. casei BL23 PGH with endopeptidase specificity and a key role in daughter cell separation. Further studies will aim at investigating the role of Lc-p75 in the anti-inflammatory potential of L. casei BL23.
Detailed aeromagnetic investigation of the Arctic Basin

Over 150,000 line-kilometers of low-level (152 m) aeromagnetic data were recorded in the western Arctic Basin by the U.S. Navy during four field seasons (1975–1978); data from the first 2 years were presented by Vogt et al. (1979a), while the data from the last two years are described in this paper. These data (1977–1978) cover a swath from the north slope of Alaska to the north geographic pole. Flight lines were spaced between 10 and 24 km. The east-west oriented aeromagnetic profiles across the Canada Basin and the Beaufort Sea suggest that Alaska was moving away from the Queen Elizabeth Islands of the Canadian Arctic from 153 m.y. B.P. (anomaly M-25 time) to 127 m.y. B.P. (M-12), at an opening rate of 2.6 cm/yr. An extinct spreading center is defined by a positive free-air gravity anomaly, with the relic spreading axis generally paralleling the 150°W meridian. We are unable to recognize a coherent pattern of lineated anomalies over the Alpha Ridge; therefore its origin remains uncertain. A series of seafloor spreading type anomalies have been tentatively identified in the Fletcher (Makarov) Basin. Spreading began in the Upper Cretaceous (anomaly 34; 80 m.y. B.P.) and continued until mid-Eocene (anomaly 21; 53 m.y. B.P.); total opening rate was about 1.7 cm/yr. During the opening of the Fletcher Basin, rifting began in Baffin Bay and the Norwegian and Labrador seas and the Eurasian Basin. Our results suggest a tectonic coupling between these areas at this time, with the Nares Strait acting as a transform fault and serving as a connector with the Baffin Bay/Labrador Sea spreading centers.
Early Cambrian eclogites in SW Mongolia: evidence that the Palaeo‐Asian Ocean suture extends further east than expected

Newly discovered eclogites, Early Cambrian carbonates and chloritoid‐bearing metapelites form the Tsakhir Uul accretionary wedge, which was thrust during the Early Cambrian over the Mesoproterozoic Dzabkhan‐Baydrag continent. The rock association of the wedge forms a tectonic window emerging through the hangingwall Khantaishir ophiolite unit, which preserves a typical Tethyan‐type ophiolitic sequence. The eclogites correspond geochemically to T‐MORB modified by fluid circulation. They are composed of garnet, omphacite, amphibole, rutile ±muscovite ±quartz ±epidote and exhibit well‐equilibrated matrix textures. Jadeite content of the omphacite reaches up to 45 mol. %, the Si content of muscovite is between 3.40 and 3.45 p.f. u. , amphibole is winchite to barroisite, but reaches tschermakitic composition at some rims, and garnet composition is grs0.24–0.36, alm0.43–0.56, py0.05–0.18, sps0.00–0.18, . The peak assemblage, together with the composition of garnet rims, omphacite, amphibole and muscovite, correspond in a pseudosection to 20−22.5 kbar and 590−610 °C. The tschermakitic rim of amphibole is interpreted as partial reequilibration on decompression below 16 kbar and ∼600−630 °C. Two muscovite separates from the eclogite yielded an Ar–Ar plateau age of 543.1 ± 3.9 Ma (1σ) and a mean age of 547.9 ± 2.6 Ma (1σ), whereas muscovite from an interbedded garnet‐chloritoid micaschist yielded an Ar–Ar plateau age of 536.9 ± 2.7 Ma (1σ); these ages are interpreted as cooling ages. The P–T data, geochemistry of eclogites and cooling ages suggest an affinity between the Tsakhir Uul wedge and the Gorny Altai and the north Mongolian blueschist belt, which are believed typical for subduction of warm oceanic lithosphere and closure of small oceanic basins. Thus, the discovery of the Tsakhir Uul eclogites represents an important finding suggesting extension of the Early Cambrian subduction system of the Central Asian Orogenic Belt far to the east in a region where it was not expected.
El Niño–Southern Oscillation Sea Level Pressure Anomalies in the Western Pacific: Why Are They There?*

AbstractAlthough sea level pressure (SLP) anomalies in the western Pacific have long been recognized as an integral part of the classic Southern Oscillation pattern associated with El Nino–Southern Oscillation (ENSO), there is an unresolved question regarding the dynamics that maintain these anomalies. Traditional studies of the ENSO response in the tropics assume a single deep baroclinic mode associated with the tropospheric temperature anomalies. However, the SLP anomalies in the western Pacific are spatially separated from the baroclinic signal in the NCEP–NCAR reanalysis, CMIP5 models, and an intermediate complexity model [a quasi-equilibrium tropical circulation model (QTCM)]. Separation of ENSO SLP anomalies in the tropical Pacific into baroclinic and barotropic components indicates that the barotropic component contributes throughout the tropics and constitutes the primary contribution in the western Pacific. To demonstrate the roles of baroclinic and barotropic modes in ENSO teleconnections within.
The serine-threonine kinase LKB1 is essential for survival under energetic stress in zebrafish

Mutations in the serine-threonine kinase (LKB1) lead to a gastrointestinal hamartomatous polyposis disorder with increased predisposition to cancer (Peutz–Jeghers syndrome). LKB1 has many targets, including the AMP-activated protein kinase (AMPK) that is phosphorylated under low-energy conditions. AMPK phosphorylation in turn, affects several processes, including inhibition of the target of rapamycin (TOR) pathway, and leads to proliferation inhibition. To gain insight into how LKB1 mediates its effects during development, we generated zebrafish mutants in the single LKB1 ortholog. We show that in zebrafish lkb1 is dispensable for embryonic survival but becomes essential under conditions of energetic stress. After yolk absorption, lkb1 mutants rapidly exhaust their energy resources and die prematurely from starvation. Notably, intestinal epithelial cells were polarized properly in the lkb1 mutants. We show that attenuation of metabolic rate in lkb1 mutants, either by application of the TOR inhibitor rapamycin or by crossing with von Hippel–Lindau (vhl) mutant fish (in which constitutive hypoxia signaling results in reduced metabolic rate), suppresses key aspects of the lkb1 phenotype. Thus, we demonstrate a critical role for LKB1 in regulating energy homeostasis at the whole-organism level in a vertebrate. Zebrafish models of Lkb1 inactivation could provide a platform for chemical genetic screens to identify compounds that target accelerated metabolism, a key feature of tumor cells.
Ensemble‐based assimilation of discharge into rainfall‐runoff models: A comparison of approaches to mapping observational information to state space

The optimization of hydrologic models using the ensemble Kalman filter has received increasing attention during the last decade. The application of this algorithm is straightforward when the relationship between the state variables and the observations is linear, in other words, when the observations can be directly mapped onto the state space. However, when this relationship is nonlinear, a number of methods can be derived in order to perform this transfer. Up till now, it has not been demonstrated which of these methods is recommended for discharge assimilation with the ensemble Kalman filter. The objective of this paper is to analyze these methods for conceptual rainfall‐runoff models in a small‐scale catchment. The study has been performed in the Bellebeek catchment (86.36 km2) in Belgium, using two time series models and one conceptual rainfall‐runoff model. A first analysis of the algorithms has been performed using the one time step ahead discharge predictions. The results indicate that linearization of the storage‐discharge relationship (the observation system) should be avoided if discharge data are assimilated using the ensemble Kalman filter. Further, assimilating discharge data into conceptual rainfall‐runoff models for small catchments does not work well when a unit hydrograph is used for runoff routing. This can be explained by the stronger impact of the model error (caused by errors in the forcings, model structure, and parameters), accumulated over the duration of the unit hydrograph, as compared to the impact of erroneous initial conditions. A second analysis using longer lead times has led to the conclusion that, for the type of catchment and model used in this study, the accuracy of the meteorological forcings is more important than an accurate estimation of the model initial conditions through data assimilation.
Discussion Paper Series

This paper brings together the key research findings of some 20 projects conducted in New Zealand on the economic impacts of immigration from 2005 to 2010. Besides providing a synthesis of this research, knowledge gaps that could be addressed in future research are also identified. The report concludes that immigration has made a positive contribution to economic outcomes in New Zealand and that fears for negative economic impacts such as net fiscal costs, lower wages, and increasing unemployment find very little support in the available empirical evidence. Moreover, the economic integration of immigrants is broadly successful. Once migrants are in New Zealand for more than 10–15 years, their labour market outcomes are predominantly determined by the same success factors as those for the New Zealand born. Migration increases trade and tourism, both inbound and outbound. The net fiscal impact of immigration is positive. Findings on impacts on housing and on technological change are less conclusive. Simulations over a 15-year period with a CGE model suggest that even without additional technological change, additional immigration raises gross domestic product (GDP) per capita, albeit only modestly. Conversely, without net immigration, GDP per capita would be less. The CGE model simulations also suggest that changes in immigration policy and changes in the New Zealand economy over the last quarter century now yield greater economic benefits from immigration than in the past. Future research should focus on: the path of adjustment of the economy over time, following a change in the level of immigration; physical and human capital investment in the economy triggered by immigration; the economic consequences of greater diversity; and differences in impacts between temporary and long-term migration. JEL code: D58, F22, J15, J18, J61
Field measurement of basal forces generated by erosive debris flows

It has been proposed that debris flows cut bedrock valleys in steeplands worldwide, but field measurements needed to constrain mechanistic models of this process remain sparse due to the difficulty of instrumenting natural flows. Here we present and analyze measurements made using an automated sensor network, erosion bolts, and a 15.24 cm by 15.24 cm force plate installed in the bedrock channel floor of a steep catchment. These measurements allow us to quantify the distribution of basal forces from natural debris‐flow events that incised bedrock. Over the 4 year monitoring period, 11 debris‐flow events scoured the bedrock channel floor. No clear water flows were observed. Measurements of erosion bolts at the beginning and end of the study indicated that the bedrock channel floor was lowered by 36 to 64 mm. The basal force during these erosive debris‐flow events had a large‐magnitude (up to 21 kN, which was approximately 50 times larger than the concurrent time‐averaged mean force), high‐frequency (greater than 1 Hz) fluctuating component. We interpret these fluctuations as flow particles impacting the bed. The resulting variability in force magnitude increased linearly with the time‐averaged mean basal force. Probability density functions of basal normal forces were consistent with a generalized Pareto distribution, rather than the exponential distribution that is commonly found in experimental and simulated monodispersed granular flows and which has a lower probability of large forces. When the bed sediment thickness covering the force plate was greater than ∼ 20 times the median bed sediment grain size, no significant fluctuations about the time‐averaged mean force were measured, indicating that a thin layer of sediment (∼ 5 cm in the monitored cases) can effectively shield the subjacent bed from erosive impacts. Coarse‐grained granular surges and water‐rich, intersurge flow had very similar basal force distributions despite differences in appearance and bulk‐flow density. These results demonstrate that debris flows can have strong control on rates of steepland evolution and contribute to a foundation needed for modeling debris‐flow incision stochastically.
Assessing Ecological Resilience of Eastern Indonesian Coral Reefs

Eastern Indonesian reefs are located on the CTI region, that understanding their ecological resiliencies are therefore very important for management of the region. Coral reef resilience was assessed using a resilience index on the 2009 Coremap data. Resilience index used in the assessment was developed by the author but published elsewhere. The study included 7 districts in eastern Indonesia: Pangkep (Pangkajene Kepulauan), Selayar, Buton, Wakatobi, Sikka, Raja Ampat and Biak. The results showed that coral reefs at Wakatobi had the highest average resilience indices, while Sikka had the lowest one. High resilience index at Wakatobi coincided with high number of coral functional groups (life forms) and coral cover. Low average resilience index at Sikka coincided with high algae and other fauna covers. Raja Ampat had coral reefs with a fair resilience index which is similar to coral reefs at Pangkep and Selayar.
Les facteurs déterminants de la stratégie des groupes français en matière de communication sur les activités de R&D

This study is interested in the relationship between firm's characteristics (R&D intensity, industry, American or British stock market listing, R&D accounting method used, and size) and its strategy of communication on its R&D activities. We have analyzed annual reports of firms belonging to the SBF 250 index in order to determine the disclosure level of each company on R&D. The study confirmed the impact of Anglo-Saxon market listing (or of the size of the firm) and of the belonging to certain high-tech sectors on the communication related to the R&D. It also showed the lack of linkage between this communication and the R&D intensity, which is explained by the primacy of the preservation of industrial secrets on a full disclosure policy.
Evoluzione del paesaggio costiero tra Parthenope e Neapolis

Il paesaggio costiero fra Parthenope e Neapolis e stato ridisegnato dopo i recenti risultati ottenuti dagli studi archeologici, geo-archeologici e stratigrafici effettuati durante i lavori per il completamento delle stazioni della nuova metropolitana di Napoli. In particolare e stata identificata l’antica linea di costa, nonche le sue variazioni nel tempo, e la posizione del porto della citta greco-romana nell’insenatura presente fra Piazza Bovio e Piazza Municipio. Gli scavi nel sito di Municipio hanno messo in luce una successione di sedimenti di riempimento dell’antico bacino portuale che fu attivo dal tardo iv – inizio iii secolo a.C. fino all’inizio del v secolo d.C. Grazie alla scoperta di tre relitti di navi romane e di varie strutture portuali, fra cui un molo e dei pali, nonche di numerosi oggetti sui diversi fondali stratigraficamente sovrapposti, e stato possibile ricostruire la storia della frequentazione di questa parte del porto di Neapolis.
Addressing in-work poverty

The existence of ‘in-work’ poverty has only been officially recognised in the last couple of years. Yet the steady upward trend and number of children involved mean that it should be given high priority. The report includes an in-depth analysis of the progress that has been made on in-work poverty among children since the start of the government’s poverty programme in the late 1990s.
Development, factor structure and application of the Dog Obesity Risk and Appetite (DORA) questionnaire

Background. Dogs are compelling models in which to study obesity since the condition shares many characteristics between humans and dogs. Differences in eating behaviour are recognised to contribute to obesity susceptibility in other species but this has not been systematically studied in dogs. Aim. To develop and validate an owner-reported measure of canine eating behaviour and owner or dog related factors which can alter the development of obesity. Further, to then test variation in food-motivation in dogs and its association with obesity and owner management. Methods. Owner interviews, a literature review and existing human appetite scales were used to identify relevant topics and generate items for the questionnaire. Following a pilot phase, a 75 item online questionnaire was distributed via social media. Responses from 302 dog/owner dyads were analysed and factor structure and descriptive statistics calculated. Results were compared with descriptions of dog behaviour and management from a subset of respondents during semi-structured interviews. The optimum questions were disseminated as a 34 item final questionnaire completed by 213 owners, with a subset of respondents repeating the questionnaire 3 weeks later to assess test–retest reliability. Results. Analysis of responses to the final questionnaire relating to 213 dog/owner dyads showed a coherent factor structure and good test–retest reliability. There were three dog factors (food responsiveness and satiety, lack of selectivity, Interest in food), four owner factors (owner motivation to control dog weight, owner intervention to control dog weight, restriction of human food, exercise taken) and two dog health factors (signs of gastrointestinal disease, current poor health). Eating behaviour differed between individuals and between breed groups. High scores on dog factors (high food-motivation) and low scores on owner factors (less rigorous control of diet/exercise) were associated with obesity. Owners of more highly food-motivated dogs exerted more control over their dogs’ food intake than those of less food-motivated dogs. Conclusions. The DORA questionnaire is a reliable and informative owner-reported measure of canine eating behaviour and health and management factors which can be associated with obesity development. The tool will be applicable to study of the canine obesity model and to clinical veterinarians. Results revealed eating behaviour to be similarly associated with obesity as exercise and owners giving titbits.
On the long‐term stability of Gulf Stream transport based on 20 years of direct measurements

In contrast to recent claims of a Gulf Stream slowdown, two decades of directly measured velocity across the current show no evidence of a decrease. Using a well‐constrained definition of Gulf Stream width, the linear least square fit yields a mean surface layer transport of 1.35 × 105 m2 s−1 with a 0.13% negative trend per year. Assuming geostrophy, this corresponds to a mean cross‐stream sea level difference of 1.17 m, with sea level decreasing 0.03 m over the 20 year period. This is not significant at the 95% confidence level, and it is a factor of 2–4 less than that alleged from accelerated sea level rise along the U.S. Coast north of Cape Hatteras. Part of the disparity can be traced to the spatial complexity of altimetric sea level trends over the same period.
Strain accumulation in Owens Valley, California, 1974 to 1988

Strain accumulation observed over the 1974 to 1988 interval in a 25 by 100 km aperture trilateration network spanning Owens Valley is adequately described by a strain rate that is uniform in space and time. The tensor strain-rate components referred to a coordinate system with the 2 axis directed N18°W (parallel to the trend of the valley) and the 1 axis N72°E are ∈˙11′ = 0.042 ± 0.014 μstrain/yr, ∈˙12′ = -0.058 ± 0.007 μstrain/yr, and ∈˙22′ = 0.002 ± 0.014 μstrain/yr; quoted uncertainties are standard deviations and extension is reckoned positive. Across the 25-km breadth of the network, this amounts to 1.0 ± 0.3 mm/yr extension normal to the axis of the valley, 2.9 ± 0.4 mm/yr right-lateral shear across the axis, and no extension parallel to the axis. If the measured strain accumulation is attributed to slip on the deeper section of the Owens Valley fault with the uppermost 10 km of the fault locked, the observed right-lateral deformation would imply about 7 mm/yr right-lateral slip on the buried fault, much greater than the geologic estimate of 2 ± 0.5 mm/yr right-lateral secular slip (Beanland and Clark, 1994). Nor is the observed uplift profile across the valley consistent with continuing normal slip on just the deep segment of the Owens Valley fault; normal slip at depth on the Sierra frontal fault also seems to be required. The observed deformation across Owens Valley apparently implies processes more complicated than those represented by the conventional model of strain accumulation along a throughgoing fault.
Regional sources and sinks of dust on Mars: Viking observations of Cerberus, Solis Planum and Syrtis Major

A study of seasonal variations of albedo features in the Cerberus, Solis Planum, and Syrtis Major regions was based on Viking Orbiter data obtained over more than one complete Martian year. Contour maps of Lambert albedo and single-point thermal inertia were constructed from the Infrared Thermal Mapper (IRTM) experiment data, and Orbiter images were used to determine the pattern and variability of regional winds (inferred from wind streak orientations). Coupled with ground-based radar data, these data allow the regional sediment transport direction, surface properties (texture, morphology, and roughness), and the implications of the observed seasonal and longer term dust redistribution to be investigated. Results are outlined.