Miracle-dz/UniFAR-FTUs huggingface dataset:
Encoding and retrieval in a model of the hippocampal CA1 microcircuit

It has been proposed that the hippocampal theta rhythm (4–7 Hz) can contribute to memory formation by separating encoding (storage) and retrieval of memories into different functional half‐cycles (Hasselmo et al. ( 2002 ) Neural Comput 14:793–817). We investigate, via computer simulations, the biophysical mechanisms by which storage and recall of spatio‐temporal input patterns are achieved by the CA1 microcircuitry. A model of the CA1 microcircuit is presented that uses biophysical representations of the major cell types, including pyramidal (P) cells and four types of inhibitory interneurons: basket (B) cells, axo‐axonic (AA) cells, bistratified (BS) cells and oriens lacunosum‐moleculare (OLM) cells. Inputs to the network come from the entorhinal cortex (EC), the CA3 Schaffer collaterals and medial septum. The EC input provides the sensory information, whereas all other inputs provide context and timing information. Septal input provides timing information for phasing storage and recall. Storage is accomplished via a local STDP mediated hetero‐association of the EC input pattern and the incoming CA3 input pattern on the CA1 pyramidal cell target synapses. The model simulates the timing of firing of different hippocampal cell types relative to the theta rhythm in anesthetized animals and proposes experimentally confirmed functional roles for the different classes of inhibitory interneurons in the storage and recall cycles (Klausberger et al., ( 2003 , 2004 ) Nature 421:844–848, Nat Neurosci 7:41–47). Measures of recall performance of new and previously stored input patterns in the presence or absence of various inhibitory interneurons are employed to quantitatively test the performance of our model. Finally, the mean recall quality of the CA1 microcircuit is tested as the number of stored patterns is increased. © 2009 Wiley‐Liss, Inc.
Orographic effects on snow deposition patterns in mountainous terrain

Orographic lifting of air masses and other topographically modified flows induce cloud and precipitation formation at larger scales and preferential deposition of precipitation at smaller scales. In this study, we examine orographic effects on small‐scale snowfall patterns in Alpine terrain. A polarimetric X‐band radar was deployed in the area of Davos (Switzerland) to determine the spatial variability of precipitation. In order to relate measured precipitation fields to flow dynamics, we model flow fields with the atmospheric prediction model “Advanced Regional Prediction System. ” Additionally, we compare radar reflectivity fields with snow accumulation at the surface as modeled by Alpine3D. We investigate the small‐scale precipitation dynamics for one heavy snowfall event in March 2011 at a high resolution of 75 m. The analysis of the vertical and horizontal distribution of radar reflectivity at horizontal polarization and differential reflectivity shows polarimetric signatures of orographic snowfall enhancement near the summit region. Increasing radar reflectivity at horizontal polarization over the windward slopes toward the crest and downwind decreasing reflectivity over the leeward slopes is observed. The temporal variation of the location of maximum concentration of snow particles is partly attributed to the effect of preferential deposition of snowfall: For situations with strong horizontal winds, the concentration maximum is shifted from the ridge crest toward the leeward slopes. Qualitatively, we discuss the relative role of cloud microphysics such as the seeder‐feeder mechanism versus atmospheric particle transport in generating the observed snow deposition at the ground.
Adaptive index models for marker-based risk stratification.

We use the term "index predictor" to denote a score that consists of K binary rules such as "age > 60" or "blood pressure > 120 mm Hg. " The index predictor is the sum of these binary scores, yielding a value from 0 to K. Such indices as often used in clinical studies to stratify population risk: They are usually derived from subject area considerations. In this paper, we propose a fast data-driven procedure for automatically constructing such indices for linear, logistic, and Cox regression models. We also extend the procedure to create indices for detecting treatment-marker interactions. The methods are illustrated on a study with protein biomarkers as well as a large microarray gene expression study.
Tuning of p K a values activates substrates in flavin-dependent aromatic hydroxylases

Hydroxylation of substituted phenols by flavin-dependent monooxygenases is the first step of their biotransformation in various microorganisms. The reaction is thought to proceed via electrophilic aromatic substitution, catalyzed by enzymatic deprotonation of substrate, in single-component hydroxylases thatuseflavinasacofactor(groupA). However,two-component hydroxylases
Multiple-View Geometry Under the Linfinity-Norm

This paper presents a new framework for solving geometric structure and motion problems based on Linfinity-norm. Instead of using the common sum-of-squares cost-function, that is, the L2-norm, the model-fitting errors are measured using the L-norm. Unlike traditional methods based on L2, our framework allows for efficient computation of global estimates. We show that a variety of structure and motion problems, for example, triangulation, camera resectioning and homography estimation can be recast as quasi-convex optimization problems within this framework. These problems can be efficiently solved using Second-Order Cone Programming (SOCP) which is a standard technique in convex optimization. The methods have been implemented in Matlab and the resulting toolbox has been made publicly available. The algorithms have been validated on real data in different settings on problems with small and large dimensions and with excellent performance.
Geostatistics versus inverse distance squares in ore reserves estimation: comparative case study in copper ore body in Cyprus

The ‘Phoenix’ copper ore body is located in Cyprus Island. Its reserves were initially estimated by inverse distance square (IDS) algorithm. Ore extraction begun in 1996 and ever since the owner company keeps a detailed file of blast hole samples analyses. These data are used to for a continuous check of the validity of estimation. Even tough sampling was systematic and dense, the results of these checks revealed small discrepancies between the ore body model and reality and therefore it was decided to employ geostatistics to possibly improve the estimation quality even more. The two resulting models were compared to reality inside the exploited area and showed that no substantial improvement occurred due to the employment of geostatistics. The above is in agreement to recent theoretical results which state that, when the sampling density is greater than a critical value, geostatistics and deterministic interpolation methods give similar estimations. The ‘Phoenix’ copper ore body is located in Cyprus Island. Its reserves were initially estimated by IDS algorithm. Ore extraction begun in 1996 and ever since the owner company keeps a detailed file of blast hole samples analyses. These data are used to for a continuous check of the validity of estimation. Even tough sampling was systematic and dense, the results of these checks revealed small discrepancies between the ore body model and reality and therefore it was decided to employ geostatistics to possibly improve the estimation quality even more. The two resulting models were compared to reality inside the exploited area and showed that no substantial improvement occurred due to the employment of geostatistics. The above is in agreement to recent theoretical results which state that, when the sampling density is greater than a critical value, geostatistics and deterministic interpolation methods give similar estimations.
Natural and experimental constraints on formation of the continental crust based on niobium–tantalum fractionation

Fractionation between Nb and Ta, elements generally regarded as geochemical ‘identical twins’, is a key to deciphering the formation of the continental crust (CC). Here we show that Nb/Ta of rutile grains in eclogitic rocks from the Chinese Continental Scientific Drilling (CCSD) project are remarkably heterogeneous but overall subchondritic at core depths of 100–700 m, and are less variable and mainly suprachondritic at core depths of 700–3025 m, indicating clear Nb/Ta fractionation across a subducted slab. To understand the potential mechanism of Nb/Ta fractionation within the subducted plate, we analysed by laser ablation ICPMS a thermal migration experiment in which a wet andesite was placed in a large thermal gradient (300°C/cm with ends ranging from 950–350°C) at 0.5Gpa. Results show that Nb, Ta and Ti, driven by the thermal gradient, preferentially migrate by diffusion through supercritical fluids into the cooler end of the experiment (at ∼650–350°C). Due to contrasting Nb and Ta thermal migration patterns, dramatic fractionation between Nb, Ta, and Ti took place in the cooler end. Experimental results are consistent with the measured Nb, Ta in rutile from CCSD drillhole samples. We consider that major fractionation between Nb, Ta must occur before rutile appears, most likely during the prograde blueschist to amphibole–eclogite transformation, when Ti is also mobile. Before rutile appears, partitioning between Ti‐rich dominant minerals such as amphiboles and fluids in the hotter region where dehydration preferentially occurs, produces Nb–Ta–Ti‐rich fluids with subchondritic Nb/Ta, and dehydration residues with suprachondritic Nb/Ta. Meanwhile, owing to evolution of the thermal gradient within the subducting slab, thermal migration of Nb, Ta, and Ti in aqueous fluids result in Nb, Ta, and Ti enrichment in the cooler region and depletion in the hotter region. As a result of high‐pressure metamorphism, hydrous rutile‐rich eclogites with overall subchondritic Nb/Ta form in the cooler region, whereas relatively anhydrous rutile‐poor eclogites with suprachondritic Nb/Ta form in the hotter region. Subsequently, partial melting of hydrous rutile‐rich eclogites with initial subchondritic Nb/Ta at deeper levels transfers overall subchondritic Nb/Ta coupled with Nb, Ta, and Ti depletion characteristics to the CC, leaving dry rutile‐poor eclogites with suprachondritic Nb/Ta and rutile‐rich residual eclogites with overall, heterogeneous subchondritic Nb/Ta as a complementary reservoir to the CC.
Source complexity of the 1987 Whittier Narrows, California, earthquake from the inversion of strong motion records

Strong motion records for the Whittier Narrows earthquake are inverted to obtain the history of slip. Both constant rupture velocity models and variable rupture velocity models are considered. The results show a complex rupture process within a relatively small source volume, with at least four separate concentrations of slip. Two sources are associated with the hypocenter, the larger having a slip of 55-90 cm, depending on the rupture model. These sources have a radius of approximately 2-3 km and are ringed by a region of reduced slip. The aftershocks fall within this low slip annulus. Other sources with slips from 40 to 70 cm each ring the central source region and the aftershock pattern. All the sources are predominantly thrust, although some minor right-lateral strike-slip motion is seen. The overall dimensions of the Whittier earthquake from the strong notion inversions is 10 km long (along the strike) and 6 km wide (down the dip). The preferred dip is 30{degree} and the preferred average rupture velocity is 2.5 km/s. Moment estimates range from 7.4 to 10.0 {times} 10{sup 24} dyn cm, depending on the rupture model.
Quality control on a 3D vibroseis crew

Since the early 90's, 3D land acquisition techniques have all evolved towards an increase in productivity and improved monitoring of quality. For this purpose, dedicated software running on UNIX platforms are now commonly used to help staff in their daily activities. This paper presents some of the tools which are now proposed on a 3D vibroseis crew. We emphasise the link between acquisition and processing and see the benefits of generating during the acquisition phase a database with attributes of all support data available while recording. This information can help processors and interpreters in seismic data analysis.
uORF and Phosphate-Regulated Expression of Rice OsNLA1 Controls 1 Phosphate Transport and Reproduction

Rice ( Oryza sativa ) OsNLA1 has been proposed to play a crucial role in regulating phosphate (Pi) acquisition in roots, similar to that of Arabidopsis AtNLA. However, 28 unlike AtNLA , OsNLA1 is not a target of miR827, a Pi starvation-induced miRNA. It is, 29 therefore, of interest to know whether the expression of OsNLA1 depends on Pi 30 supply and how it is regulated. In this study, we provide evidence that OsNLA1 31 controls Pi acquisition by directing the degradation of several OsPHT1 Pi transporters 32 (i.e., OsPT1/2/4/7/8/12). We further show that OsNLA1 has an additional function in 33 reproduction and uncover the mechanism of its expression regulation. Analysis of 34 mRNA levels, promoter-GUS (β-glucuronidase) activity and protoplast transient 35 expression showed that the expression of OsNLA1.1 , the most abundant transcript 36 variant, is upregulated in response to increasing Pi supply. The OsNLA1 promoter 37 region was found to contain an upstream open reading frame (uORF) that is required 38 for Pi-responsive expression regulation. OsNLA1 promoter activity was observed in 39 roots, ligules, leaves, sheaths, pollen grains, and surrounding the vascular tissues of 40 anthers, suggesting that OsNLA1 is important throughout the development of rice. 41 Disruption of OsNLA1 resulted in increased Pi uptake from roots as well as impaired 42 pollen development and reduced grain production. In summary, our study reveals 43 that Pi-induced OsNLA1 expression regulated by a unique mechanism functions in Pi 44 acquisition, Pi translocation, and reproductive success.
Development-led Archaeology in Northwest Europe

Many countries in northern Europe have seen a huge expansion in development-led archaeology over the past few decades. Legislation, frameworks for heritage management and codes of practice have developed along similar but different lines. The Valetta Convention has had considerable impact on spatial planning and new legislation on archaeological heritage management within EC countries as well as on the funding, nature and distribution of archaeological fieldwork. For the first time these 12 papers bring together data on developer-led archaeology in Britain, Ireland, France, the Low Countries, Germany and Denmark in order to review and evaluate key common issues relating to organisation, practice, legal frameworks and quality management.
Geochemical differences between the Cadomian granites of Mancellia and the St Malo migmatites, Armorican Massif, France

Data sets used to suggest geochemical similarity between the St Malo migmatites and Mancellian granites (Brown & D’Lemos 1991) are reinterpreted. The samples have complex distributions with outliers. Three non-parametric tests show significant statistical differences between the samples in A12O3, CaO, K2O, Cr, Ni, Sr, Y and Zr. If outliers are culled from the samples the differences become more extreme. The differences are also apparent on both principal component and multidimensional scaling plots. Geotectonic models based on a similar petrogenesis for the two rock units (D’Lemos et al. 1992) must be able to account for these differences.
Optical classification, existence temperatures, and coexistence of different polar stratospheric cloud types

Multispectral lidar measurements of polar stratospheric clouds (PSCs) from two winter campaigns in 1994/1995 and 1996'1997 at Sodankyla, Finland, have been evaluated together with temperature data from local radiosondes to find optical parameters for a PSC classification of different particle types and their existence temperatures. Precise depolarization measurements show that both solid and liquid particles exist below the NAT (nitric acid trihydrate) temperature. A comparison of temperatures at the PSC base and at the cloud top shows a good agreement with the NAT-existence temperature for solid type Ia clouds and a 3–4 K lower temperature for liquid type Ib clouds. The two particle families are therefore consistent with solid NAT particle formation and condensational growth of HNO3, H2O and H2SO4 liquid ternary solutions. The coexistence of solid and liquid particles has been observed by means of the temporal development of parallel and perpendicular polarized lidar signals. These time series of subsequent lidar measurements show stronger and faster fluctuations in the liquid particle mode compared to the solid particles and thus indicate a higher sensitivity toward temperature fluctuations for the liquid PSCs. While the optical properties of most observations are consistent with the definition of PSC type Ia (solid) and type Ib (liquid) clouds, a third type has been observed which does not fit into the current type Ia/Ib optical classification. This cloud type consists of solid particles but has a higher backscatter than type Ia PSC.
A Modification of Lomnitz's Law of Creep in Rocks

Summary C. Lomnitz has shown that creep of rocks under sustained stress increases logarithmically with time. Data for the variation of latitude and seismic waves indicate that for most of the Earth's shell a term in tα, with α about 0.17, is better. This rule is applied in the present paper to the subsidence of a harmonic surface inequality. The indications are that this type of creep will not account for isostatic adjustment within a geological period, and the presumption is that the adjustment is due to fracture or flow near the elastic limit.
Multifaulting in a tectonic syntaxis revealed by InSAR: The case of the Ziarat earthquake sequence (Pakistan)

On 28–29 October 2008, within 12 h, two similar Mw = 6.4 strike‐slip earthquakes struck Baluchistan (Pakistan), as part of a complex seismic sequence. Interferometric Synthetic Aperture Radar (InSAR) data reveal that the peak of surface displacement is near the Ziarat anticline, a large active fold affected by Quaternary strike‐slip faulting. All coseismic interferograms integrate the deformation due to both earthquakes. As their causative faults ruptured close to each other, the individual signals cannot be separated. According to their focal mechanisms, each earthquake may have activated a NE‐SW sinistral or a NW‐SE dextral fault segment, which leads to four possible scenarios of fault orientations. A nonlinear inversion of the InSAR data set allows rejecting two scenarios. The best slip distributions on the two fault segments for the two remaining scenarios are determined by linear inversion. Stress‐change modeling favors a scenario involving two abutting conjugate strike‐slip faults. Two other fault segments accommodated left‐lateral strike slip during the seismic sequence. The activated fault system includes multiple fault segments with different orientations and little surface expression. This may highlight, at a smaller scale, the distributed, possibly transient character of deformation within a broader right‐lateral shear zone. It suggests that the activated faults delineate a small tectonic block extruding and subtly rotating within the shear zone. It occurs in the vicinity of the local tectonic syntaxis where orogenic structures sharply turn around a vertical axis. These mechanisms could participate in the long‐term migration of active tectonic structures within this kinematically unstable tectonic syntaxis.
Decreased alertness reconfigures cognitive control networks 1 2

16 Humans’ remarkable capacity to flexibly adapt their behaviour based on rapid situational changes is termed 17 cognitive control. Intuitively, cognitive control is thought to be affected by the state of alertness, for example, 18 when drowsy we feel less capable of adequately implementing effortful cognitive tasks. Although scientific 19 investigations have focused on the effects of sleep deprivation and circadian time, little is known about how 20 natural daily fluctuations in alertness in the regular awake state affect cognitive control. Here we combined a 21 conflict task in the auditory domain with EEG neurodynamics to test how neural and behavioural markers of 22 conflict processing are affected by fluctuations in alertness. Using a novel computational method, we 23 segregated alert and drowsy trials from two testing sessions and observed that, although participants (both 24 sexes) were generally sluggish, the typical Conflict Effect reflected in slower responses to conflicting 25 information compared to non-conflicting information was still intact, as well as the moderating effect of 26 previous conflict (Conflict Adaptation). However, the typical neural markers of cognitive control -local 27 midfrontal theta-band power changesthat participants show during full alertness were no longer noticeable 28 when alertness decreased. Instead, when drowsy, we found an increase in long-range information sharing 29 (connectivity) between brain regions in the same frequency band. These results show the resilience of the 30 human cognitive control system when affected by internal fluctuations of alertness, and suggest neural 31 compensatory mechanisms at play in response to physiological pressure during diminished alertness. 32
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Candida albicans is an important human fungal pathogen in both immunocompetent and immunocompromised individuals. C. albicans regulation has been studied in many contexts, including morphological transitions, mating competence, bioﬁlm formation, stress resistance, and cell wall synthesis. Analysis of kinase- and phosphatase-deﬁcient mutants has made it clear that protein phosphorylation plays an important role in the regulation of these pathways. In this study, to further our understanding of phosphorylation in C. albicans regulation, we performed a deep analysis of the phosphoproteome in C. albicans . We identiﬁed 19,590 unique peptides that corresponded to 15,906 unique phosphosites on 2,896 proteins. The ratios of serine, threonine, and tyrosine phosphosites were 80.01%, 18.11%, and 1.81%, respectively. The majority of proteins (2,111) contained at least two detected phosphorylation sites. Consistent with ﬁndings in other fungi, cytoskeletal proteins were among the most highly phosphorylated proteins, and there were differences in Gene Ontology (GO) terms for proteins with serine and threonine versus tyrosine phosphorylation sites. This large-scale analysis identiﬁed phosphosites in protein components of Mediator, an important transcriptional coregulatory protein complex. A targeted analysis of the phosphosites in Mediator complex proteins conﬁrmed the large-scale studies, and further in vitro assays identiﬁed a subset of these phosphorylations that were catalyzed by Cdk8 (Ssn3), a kinase within the Mediator complex. These data represent the deepest single analysis of a fungal phosphoproteome and lay the groundwork for future analyses of the C. albicans phosphoproteome and speciﬁc phosphoproteins. (cid:3) incubated 1 h. After-wards, quenched the of (cid:3) l of 2% 3 vortexing incubation 5 min Reactions quenched the of 16 (cid:3) l of formic vortexing 5 min of incubation and light mixed, acidiﬁed 6 (cid:3) l TFA, LC-MS/MS. LC-MS/MS analysis m m of includes and LC-MS includes and Oxidized methionine and phosphorylated serine, threonine, and tyrosine, isotopically heavy labeled dimethylation at peptide amino termini, and lysines were searched as variable modiﬁcations. The resulting peptide spectral matches were ﬁltered to a (cid:5) 1% FDR, based on reverse hit. Probability of phosphorylation site localization was deter-minedbyPhosphoRS(38). QuantiﬁcationofLC-MS/MSspectrawasper-formedusingMassChroQ(50).