Miracle-dz/UniFAR-FTUs huggingface dataset:
Inducible CRISPRi-based operon silencing and selective in trans gene complementation in Borrelia burgdorferi

To accelerate genetic studies on the Lyme disease pathogen Borrelia burgdorferi, we developed an enhanced CRISPR interference (CRISPRi) approach for IPTG-inducible repression of specific B. burgdorferi genes. The entire system is encoded on a compact 11-kb shuttle vector plasmid that allows for inducible expression of both the sgRNA module and a non-toxic codon-optimized dCas9 protein. We validated this CRISPRi system by targeting the genes encoding for OspA and OspB, abundant surface lipoproteins co-expressed by a single operon, and FlaB, the major subunit forming the periplasmic flagella. As in other systems, sgRNAs complementary to the non-template strand were consistently effective in gene repression, with 4- to 994-fold reductions in targeted transcript levels and concomitant reductions of in proteins levels. Furthermore, we showed that ospAB knockdowns could be selectively complemented in trans for OspA expression via the insertion of synonymous or non-synonymous CRISPRi-resistant PAM mutant (PAM*) ospA alleles into a unique site within the plasmid. Together, this establishes CRISPRi PAM* as a robust new genetic tool to simplify the study of B. burgdorferi genes, bypassing the need for gene disruptions by allelic exchange and avoiding rare-codon toxicity from heterologous expression of dCas9. SIGNIFICANCE Borrelia burgdorferi, the causative agent of Lyme disease, is a tick-borne pathogen of global importance. Here, we expand the genetic toolbox for studying B. burgdorferi physiology and pathogenesis by establishing a single-plasmid-based CRISPRi system with optional in trans complementation for the functional study of essential and non-essential proteins.
Eigenimage Processing of Seismic Sections

This chapter briefly reviews the important theoretical aspects of eigenimage processing and demonstrates the unique properties of this approach using various examples such as the separation of up and downgoing waves, multiple attenuation, and residual static correction. In particular, we will compare the eigenimage technique to the well-known frequency-wave number f k , method, (Treitel et al., 1967), and discuss important differences which arise especially with respect to spacial aliasing and the separation of signal and noise.
Specifying land surface characteristics in general circulation models: Soil profile data set and derived water‐holding capacities

A standardized global data set of soil horizon thicknesses and textures (particle size distributions) has been compiled from the Food and Agriculture Organization of the United Nations/United Nations Educational, Scientific, and Cultural Organization (FAO/UNESCO) Soil Map of the World, Vols. 2–10 [1971–1981]. This data set was developed for use by the improved land-surface hydrology parameterization designed by Abramopoulos et al. [1988] for the Goddard Institute for Space Studies General Circulation Model II (GISS GCM). The data set specifies the top and bottom depths and the percent abundance of sand, silt, and clay of individual soil horizons in each of the 106 soil types cataloged for nine continental divisions. When combined with the World Soil Data File [Zobler, 1986], the result is a l°×l° global data set of variations in physical properties throughout the soil profile. These properties are important in the determination of water storage in individual soil horizons and exchange of water with the lower atmosphere within global climate models. We have used these data sets, in conjunction with the Matthews [1983] global vegetation data set and texture-based estimates of available soil moisture, to calculate the global distributions of soil profile thickness, potential storage of water in the soil profile, potential storage of water in the root zone, and potential storage of water derived from soil texture. Comparisons with the water-holding capacities used in the GISS Model II show that our derived values for potential storage of water are consistently larger than those previously used in the GISS GCM. Preliminary analyses suggest that incorporation of this data set into the GISS GCM has improved the model's performance by including more realistic variability in land surface properties.
Deformation transfer in viscous detachments: comparison of sandbox models to the South Pyrenean Triangle Zone

Abstract Results of scaled sandbox models, containing three viscous layers located at different geographic and stratigraphic levels simulating three evaporitic units in the South Pyrenean Triangle Zone, and interpreted field data are presented here to explain structural variation and kinematics in shortened areas containing multiple weak horizons acting as detachments. In the Southern Pyrenean Triangle Zone, the Beuda, Cardona and Barbastro thrust fronts have similar geometric features to those developed in the models, suggesting that they could have formed and evolved in a similar way. These deformation fronts are not always perpendicular to the regional shortening direction. Instead, their direction is governed by the initial pinch-out of the viscous horizonts. Model results show that triangle zones form when: (1) deformation is transferred to weak horizons located at higher stratigraphic levels, and (2) the deformation front reaches the pinch-out of the weak horizons. Model results also show that the rheology of the detachment horizonts controls the geometry of the deformation front. Weak detachments (Cardona Formation, and pure silicone in the models) promote folding and back-vergent structures, and thus formation of triangle zones at the deformation front, irrespective of the location of the thrust front relative to the pinch-out of the viscous detachment. However, over strong (more viscous) detachments (Barbastro and Beuda formations, and impure silicone in the models), folds that eventually evolve to thrusts are dominant. In such cases, backthrusts form only at the pinch-out of the detachment layer. In cases where no viscous detachment is present, no backthrusts form, and therefore the thrust front does not develop a triangle zone geometry. Instead, a foreland-vergent piggyback sequence of thrusts forms. Model results show that the stratigraphic level of a detachment governs size, geometry and spacing of the imbricates formed above it.
Ensemble classifier for protein fold pattern recognition

MOTIVATION Prediction of protein folding patterns is one level deeper than that of protein structural classes, and hence is much more complicated and difficult. To deal with such a challenging problem, the ensemble classifier was introduced. It was formed by a set of basic classifiers, with each trained in different parameter systems, such as predicted secondary structure, hydrophobicity, van der Waals volume, polarity, polarizability, as well as different dimensions of pseudo-amino acid composition, which were extracted from a training dataset. The operation engine for the constituent individual classifiers was OET-KNN (optimized evidence-theoretic k-nearest neighbors) rule. Their outcomes were combined through a weighted voting to give a final determination for classifying a query protein. The recognition was to find the true fold among the 27 possible patterns. RESULTS The overall success rate thus obtained was 62% for a testing dataset where most of the proteins have <25% sequence identity with the proteins used in training the classifier. Such a rate is 6-21% higher than the corresponding rates obtained by various existing NN (neural networks) and SVM (support vector machines) approaches, implying that the ensemble classifier is very promising and might become a useful vehicle in protein science, as well as proteomics and bioinformatics. AVAILABILITY The ensemble classifier, called PFP-Pred, is available as a web-server at http://202.120. 37.186/bioinf/fold/PFP-Pred.htm for public usage.
Ground return signal simulation and retrieval algorithm of spaceborne integrated path DIAL for CO2 measurements

Spaceborne integrated path differential absorption (IPDA) lidar is an active-detection system which is able to perform global CO2 measurement with high accuracy of 1ppmv at day and night over ground and clouds. To evaluate the detection performance of the system, simulation of the ground return signal and retrieval algorithm for CO2 concentration are presented in this paper. Ground return signals of spaceborne IPDA lidar under various ground surface reflectivity and atmospheric aerosol optical depths are simulated using given system parameters, standard atmosphere profiles and HITRAN database, which can be used as reference for determining system parameters. The simulated signals are further applied to the research on retrieval algorithm for CO2 concentration. The column-weighted dry air mixing ratio of CO2 denoted by XCO2 is obtained. As the deviations of XCO2 between the initial values for simulation and the results from retrieval algorithm are within the expected error ranges, it is proved that the simulation and retrieval algorithm are reliable.
Step‐pool stability: Testing the jammed state hypothesis

[1] We investigate the stability of step-pool channels by examining how the traditional approach to bed stability based on the critical Shields number is modified by particles jamming across the width of the channel. Experiments were conducted in a flume with slopes ranging between 3% and 18% and either smooth or rough walls. By varying the size of sediment and width of the flume we observed that the stability of the bed increases as the jamming ratio (channel width/D84step is the diameter at which 84% of the step stones are smaller) decreases for jamming ratios less than six. At low jamming ratios both grain-on-grain structuring and sediment entrainment phenomena affect the stability of the bed. Actual bed failure, however, depends upon the history of bed development and the chance arrangement of the stone structures in the bed. Thus, the experiments also demonstrate that the inherently stochastic nature of sediment transport affects not only the movement of individual grains but also the stability of the channel as a whole. Since stochastic processes affect the stability of the entire channel, there is no clearly defined separation between stable and unstable beds, rather, an overlapping field where both stable and unstable bed states can exist. This field was modeled using logistic regression to derive a probability of bed failure. A comparison of data from experiments with rough banks and smooth banks showed that rough banks significantly increase the stability of the bed.
Relativity Between COD and TOC in Municipal Wastewater

TOC can reflect organic polluttion of water body more completely than COD_(Cr),and it is easier to be measured and get accurate data of TOC.It helps to make monitoring automatically and instrumentally.The interrelationship research of COD_(Cr) and TOC in municipal wastewater was made, and the regression equation were also made, which proved that the Interrelationship of COD_(Cr) and TOC is good enough to be used in daily monitoring.
The embarrassed brain : towards a neurobiology of generalized socal anxiety disorder

There is circumstantial evidence for the involvement of serotonergic and dopaminergic systems in the pathophysiology of social anxiety disorder. In the present study, using SPECT imaging, we examined the 123 I-ß-(4-iodophenyl)-tropane binding potential for the serotonin and dopamine transporter in patients with a generalized social anxiety disorder and age- and sex- matched healthy controls. Methods: Twelve psychotropic medication-naïve patients with social anxiety disorder, generalized type (5 women and 7 men) and 12 sex- and age- matched healthy controls were studied. Volumes of interest were constructed on MRI-coregistered SPECT scans. Binding ratios were compared using the Mann-Whitney U test. Possible correlations between binding patterns and symptomatology were assessed using the Spearman rank correlation coefficient. Results: Significantly higher binding potentials were found for the serotonin transporter in the left and right thalamus of patients. Patients had also a significantly higher binding potential for the dopamine transporter in the striatum. Conclusion: The present study provided direct evidence for abnormalities in both the dopaminergic and the serotonergic systems in patients with generalized social anxiety disorder.
Evidence that floodwaters filled and overflowed Capri Chasma, Mars

Erosional features on a plateau in the Valles Marineris provide evidence that a lake filled Capri Chasma until it overflowed its eastern rim, carving two large spillover channels. The floodwaters surged into the adjacent lowlands of ancestral Ganges Chasma and eastern Eos Chasma. The channel floor elevation and depth of incision at Daga Vallis reveal that a 1200‐m‐deep lake water column was drained by the flooding. The width, depth, and steep energy slope (∼0.02) of Daga Vallis and the existence of several cataracts, including a 500‐m‐high dry falls, demonstrate the power of the floodwaters. We estimate a possible peak discharge rate of 1–6 × 108 m3·s−1. The catastrophic flows may have been triggered by the collapse of topographic barriers in eastern Coprates Chasma, providing a gateway for lake waters in the central Valles Marineris to pour eastward toward Capri Chasma and the lowlands beyond. These may have been among the earliest flows in Simud‐Tiu Valles, contributing discharge to a possible sea in the northern plains of Mars.
A constitutive scaling law and a unified comprehension for frictional slip failure, shear fracture of intact rock, and earthquake rupture

[1] It is widely recognized that some of the physical quantities inherent in a rupture are scale-dependent, and the scale dependence is one of the most no facts and features of rupture phenomena. The paper addresses how such scale-dependent shear rupture of a broad range from laboratory-scale frictional slip failure and shear fracture of intact rock to field-scale rupture as an earthquake source can be unified by a single constitutive law. Noting that the earthquake rupture is a mixed process between frictional slip failure and the shear fracture of intact rock, it is concluded that the constitutive law for the earthquake rupture be formulated as a unifying law that governs both frictional slip failure and shear fracture of intact rock. It is demonstrated that the slip-dependent constitutive law is such a unifying law, and a constitutive scaling law is derived from laboratory data on both frictional slip failure and shear fracture of intact rock. This constitutive scaling law enables one to provide a consistent and unified comprehension for scale-dependent physical quantities inherent in the rupture, over a broad range from small-scale frictional slip failure and shear fracture in the laboratory to large-scale earthquake rupture in the field.
An analysis of SO2 negotiations between Finland and the Soviet Union

This paper considers Finnish-Soviet environmental cooperation. It is shown that efficient cooperation on reducing sulphur emissions may entail financial transfers from Finland to the Soviet Union because marginal abatement costs are much lower there. Soviet emissions should be drastically reduced in Kola peninsula and Estonia. The analysis is based on a sulphur transportation model, on estimated regional abatement cost functions and on the 'revealed-preference' approach in estimating the damage costs from pollution.
Implicit reconstruction of patch dynamics from single‐date aerial photographs: mutuality and complementarity in pattern change

A new concept of implicit (hypothetical) reconstruction of patch pattern dynamics from single‐date photography is presented, based on gradients in the surface properties reflected by spatial variation in photographic brightness. Changes in the characteristics of patch patterns formed, follow generalized relationships of mutuality and complementarity between fragmentation and shape distribution. Utilizing two images from the beginning and the end of the fragmentation processes may provide a full implicit description of patch pattern dynamics.
Future chemistry teachers use of knowledge dimensions and high-order cognitive skills in pre-laboratory concept maps

This poster describes a pilot case study, which aim is to study how future chemistry teachers use knowledge dimensions and high-order cognitive skills (HOCS) in their pre-laboratory concept maps to support chemistry laboratory work. The research data consisted of 168 pre-laboratory concept maps that 29 students constructed as a part of their chemistry laboratory studies. Concept maps were analyzed by using a theory based content analysis through Anderson & Krathwohls’ learning taxonomy (2001). This study implicates that novice concept mapper students use all knowledge dimensions and applying, analyzing and evaluating HOCS to support the pre-laboratory work.
Multi-Cyclic and Isotopically Diverse Silicic Magma Generation in an Arc Volcano: Gorely Eruptive Center, Kamchatka, Russia

The Kamchatka Peninsula is home to some of the most frequent and prolific subduction-related volcanic activity in the world, with the largest number of caldera-forming eruptions per length of the volcanic arc. Among those, Gorely volcano has a topographically prominent Late Pleistocene caldera (13 km (cid:2) 12 km, estimated to have produced 4 100 km 3 of magma), which is now almost completely filled by a central cone.We report new 40 Ar/ 39 Ar ages and geochemical and isotopic data for newly recognized Mid-Pleistocene ignimbrite units of large but unknown volume sourced from the Gorely eruptive center, most of which were deposited in marginal glacial conditions.These ignimbrites have crystallinities of 9^24% and most are quartz-, amphibole-, and zircon-undersaturated. Additionally, we studied 32 eruptive units, including stratigraphically constrained Holocene tephra, and pre- and post-caldera lava sequences, to understand the petrogenetic and temporal evolution of this long-lived, multi-cyclic, arc volcano. Material erupted prior to the formation of the modern Gorely edifice, including the voluminous ignimbrites and eruptions of the ‘pra-Gorely’ stage, consist primarily of dacite and andesite, whereas sequences of the modern Gorely edifice are represented by basalt to basaltic andesite. MELTS and EC-AFC modeling shows that it is magma can be generated rapidly between cone-building phases of volcanic activity through a combination of fractional crystallization, assimilation of older country rocks, and shallow assimilation of hydrothermally altered but otherwise petrochemically similar older intracaldera tuffs and intrusions. These transient shallow silicic magma chambers empty nearly completely in ignimbrite-forming eruptions after 10 3 ^10 5 years of assembly, partially triggered by glacial surface dynamics.
Middle- to late-Holocene storminess in Brittany (NW France): Part II – The chronology of events and climate forcing

This study focuses on the recurring climate conditions required for the largest storms occurring in NW France (Brittany). It is based on the analysed records of storm events along Western Brittany coast (see Part I). In this manuscript (Part II), storm recurrence is explored along with forcing mechanisms. Periods of more frequent storm events over the two last centuries are analysed first in order to link these events with possible forcing mechanisms (North Atlantic Oscillation (NAO) and Atlantic Multidecadal Oscillation (AMO) modes) triggering the most destructive storms. Then, palaeostorm events are discussed at the Holocene scale, from 6000 yr BP to present, to verify the forcing mechanisms. Most recorded events appear to be linked with cooling episodes, mostly in winter, a transition to or from a negative winter NAO mode, a positive AMO mode. Extreme storms occur immediately prior to the ‘Medieval Warm Period’ (MWP). Maximum effects are reached prior to the onset of the MWP and during the Maunder and Dalton solar minima. Low storm activity occurred during the Spörer Minimum linked to an acceleration of the Atlantic Meridional Overturning Circulation (AMOC). Main storm triggers seem to correspond to a positive AMO mode with an unstable jetstream configuration driving a negative NAO. In this study, four specific weather configurations were defined to explain each type of recorded storminess. The strongest storms correspond to low AMO and decennial-negative NAO modes (e.g. ‘Little Ice Age’), or high AMO in association with dominant low NAO modes, as during the early Middle Age and present-day period. Fresh or warm oceans in association with a positive NAO mode are stormy but with very low sting storms frequency. Although in agreement with the orbital forcing and the Holocene glacial history, increasing storm frequency and intensity is most probably partly biased by continuous sea-level rise and resulting erosion.
An analysis of lithic artefacts from the ~60 ka layers of Sibudu Cave

Since 1998 detailed excavations have been conducted at Sibudu Cave over an area of 21 m 2 . A trial trench of 2 m 2 has been excavated to a depth of nearly 3 m. Luminescence dating of the sediments from Sibudu Cave indicates that it was occupied for several relatively brief periods during the Middle Stone Age. One of these occupations occurred about 60 000 years ago. The lithic artefacts from this occupation appear to be the product of a variety of flaking strategies, including tool-maintenance. Retouched artefacts mainly fall within the categories of points and scrapers and display little standardization of form. Artefacts from layers immediately below this assemblage have been assigned to the Howiesons Poort Industry. A short-lived change in raw material preference appears to coincide roughly with the transition from Howiesons Poort to post-Howiesons Poort technology. To cite this article: Cochrane, G. W. G. 2006. An analysis of lithic artefacts from the ~60 ka layers of Sibudu Cave. Southern African Humanities 18 (1): 69-88.
Subdivision of Texas Watersheds for Hydrologic Modeling

The purpose of this report is to present a set of findings and examples for subdivision of watersheds for hydrologic modeling. Three approaches were used to examine the impact of watershed subdivision on modeled hydrologic response: (1) An equal-area approach, (2) an ad-hoc approach wherein subdivisions were created at locations based on engineering judgment, and (3) a distributed-modeling approach. The three methods were implemented by different individuals with varied hydrologic experience, using their professional judgment under the direction of project researchers. Technology included Natural Resources Conservation Service (NRCS) curve number method for runoff volume, a variety of runoff-transformation methods, and use of measured rainfall-runoff responses. In general, subdivision had little or no impact on runoff volume. Estimates of peak discharge from study watersheds showed modest improvement in accuracy, but none beyond about 5-7 subdivisions. Time to peak estimates tended to degrade with subdivision, most likely because hydrologic routing introduced additional parameters requiring estimates. The distributed-modeling approach was extremely difficult to apply. In general, subdivision of watersheds is beneficial primarily when flow rates at locations internal to the watershed are required. The improvement in implied accuracy does not generally justify the subdivision process.