Miracle-dz/UniFAR-FTUs huggingface dataset:
A phenotypic screen with Trypanosoma brucei for discovering small molecules that target the SLiM‐binding pocket of proliferating cell nuclear antigen orthologs

Proliferating cell nuclear antigen (PCNA) is a homo‐trimeric protein complex that clamps around DNA to tether DNA polymerases to the template during replication and serves as a hub for many other interacting proteins. It regulates DNA metabolic processes and other vital cellar functions through the binding of proteins having short linear motifs (SLiMs) like the PIP‐box (PCNA‐interacting protein‐box) or the APIM (AlkB homolog 2 PCNA‐interacting motif) in the hydrophobic pocket where SLiMs bind. However, overproducing TbPCNA or human PCNA (hPCNA) in the pathogenic protist Trypanosoma brucei triggers a dominant‐negative phenotype of arrested proliferation. The mechanism for arresting T. brucei proliferation requires the overproduced PCNA orthologs to have functional intact SLiM‐binding pocket. Sight‐directed mutagenesis studies showed that T. brucei overproducing PCNA variants with disrupted SLiM‐binding pockets grew normally. We hypothesized that chemically disrupting the SLiM‐binding pocket would restore proliferation in T. brucei, overproducing PCNA orthologs. Testing this hypothesis is the proof‐of‐concept for a T. brucei‐based PCNA screening assay. The assay design is to discover bioactive small molecules that restore proliferation in T. brucei strains that overproduce PCNA orthologs, likely by disrupting interactions in the SLiM‐binding pocket. The pilot screen for this assay discovered two hit compounds that linked to predetermined PCNA targets. Compound #1, a known hPCNA inhibitor, had selective bioactivity to hPCNA overproduced in T. brucei, validating the assay. Compound #6 had promiscuous bioactivity for hPCNA and TbPCNA but is the first compound discovered with bioactivity for inhibiting TbPCNA.
A comparison of solar radiation budgets in the Mackenzie river basin from satellite measurements and a regional climate model

Abstract Using a new narrowband to broadband conversion algorithm developed specifically for the Mackenzie River basin (MRB), Advanced Very High Resolution Radiometer (AVHRR) data for the summer of 1994 have been analyzed to obtain the top‐of‐the‐atmosphere (TOA) fluxes and the net surface solar radiation in the MRB. The AVHRR dataset contains mid‐afternoon scenes from 21 June to 14 September 1994. In addition, the Scanner for Radiation Budget (ScaRaB) instrument, which flew on the METEOR‐3 satellite, provided good coverage during the summer of 1994 with typically five passes over the northern part of the basin and three to four passes over the southern part of the basin each day. We merged the TOA fluxes from AVHRR with those from ScaRaB and then interpolated the observations (within ± 1.5 hours) to get the monthly means for each one‐hour period during the daytime for June, July, August and September 1994. The monthly means of each one‐hour average are compared with output from the Canadian Regional Climate Model (CRCM). The comparison shows that the CRCM simulated the TOA reflected fluxes well over the MRB. However, the differences in the partitioning of the absorbed energy between the surface and the atmosphere are large, the CRCM overestimating the surface net solar radiation budgets by about 15%.
Tertiary channelling in the Duntroon Basin, Australia ? significance for hydrocarbon trap styles and plays

Consecutive major Tertiary channelling episodes localised at a major offset in the Duntroon Basin have generated large erosional structures sealed by thick transgressive marls. The controls on the trap development are the sequence of channelling events, and the nature of the channel fill as it relates to seal risk of the structures. These erosional structures, draped by sands and capping marls, offer excellent hydrocarbon trapping potential.
Standard Seawater Comparisons Updated

Abstract Salinity adjustments that may reconcile differences in results from different expeditions are presented. These corrections are based upon batch-to-batch differences in Standard Seawater (SSW) after comparison with KC1-derived standards. Earlier SSW comparisons have shown that the chlorinity/conductivity relationship is not the same for all batches. Salinometers were standardized in terms of conductivity, while SSW was formerly labeled in terms of chlorinity. Labeling of SSW in terms of conductivity, relative to a standard KC1 solution was expected to eliminate SSW batch-to-batch differences. New SSW comparisons, presented below, reveal that while conductivity-labeled SSW batch-to-batch differences have been reduced, significant differences between batches persist. The new results have been adjusted relative to the KC1 standard as defined by the Practical Salinity Scale, 1978. In the past, it had not been possible to make absolute corrections to expedition salinities to account for SSW systematic .
Characterization of acoustic–gravity waves in the upper thermosphere using Dynamics Explorer 2 Wind and Temperature Spectrometer (WATS) and Neutral Atmosphere Composition Spectrometer (NACS) data

[1] Data obtained by the Neutral Atmosphere Composition Spectrometer (NACS) and the Wind and Temperature Spectrometer (WATS) instruments on Dynamics Explorer 2 (DE 2) show examples of large wave-like events in composition, vertical wind, and temperature, particularly (perhaps almost exclusively) at high geomagnetic latitudes. These events are believed to arise due to atmospheric gravity waves (AGWs). If so, the various perturbation quantities of mass density, pressure, temperature, horizontal wind, and vertical wind should be related in a manner consistent with the AGW theory. An analysis of a subset of the WATS (vertical and horizontal wind and temperature) and NACS data (number density and, hence, mass density) and pressure (as a derived quantity, from number density and temperature) was performed to investigate whether such perturbations could be clearly shown to be due to AGWs by comparing quantitatively the various simultaneous data sets with AGW theory. Seven examples of wave-like events in the vertical wind were studied, together with the accompanying variations in mass density, pressure, temperature, and horizontal wind. The pressure (acoustic) component of the density variation was calculated and then subtracted from the total density variation, allowing the wave-induced vertical displacement amplitude to be found. This was compared to the vertical wind amplitude, via a spectral analysis, to yield estimates of the possible AGW frequency. The observed variation in the ratio of O/N2 number densities during the course of the oscillations was found to be consistent with the calculated altitude displacements. Phase lags in the number density perturbations between different species also appeared consistent with the AGW theory. Horizontal velocity perturbations in phase with the pressure perturbations were also seen. It is concluded that the oscillations are consistent with acoustic–gravity waves, where the pressure perturbation is nonnegligible. Phase relationships between the various observables can define the direction of wave travel to within 90° of azimuth, relative to the direction of spacecraft motion. For the seven cases detailed here, the derived (intrinsic) wave frequencies are close to, but slightly less than, the estimated local Brunt–Vaisala frequency, while the vertical displacement amplitudes were typically around ±25 km. All of the wave events studied in this work were located at high latitudes, poleward of the nominal location of the auroral oval.
Negative emotional reactivity to minority stress: measure development and testing

ABSTRACT The purpose of the present investigation was to develop and test a measure of negative emotional reactivity to racial/ethnic minoritized stress. In Study 1, we developed item content for a measure of negative emotional reactivity to racial/ethnic minoritized stress. We then evaluated item performance and produced a refined 15-item scale among a large sample of racial/ethnic minority adults (N = 1,343). Results supported a unidimensional construct and high levels of internal consistency. The factor structure and internal consistency were replicated and extended to a sample of Latinx persons who smoke (N = 338) in Study 2. There was evidence of convergent validity of the Emotional Reactivity to Minoritized Stress (ERMS) total score in terms of theoretically consistent and statistically significant relations with indices of mental health problems, social determinants of health, and substance use processes. There was also evidence that the ERMS demonstrated divergent validity in that it was negatively associated with psychological well-being, health literacy, subjective social status in Study 1, and positive abstinence expectancies in Study 2. Overall, the present study establishes the reliability and validity of measuring individual differences in negative emotional reactivity to racial/ethnic minority stress with the ERMS and that such responsivity is associated with behavioral health problems.
Resveratrol prevents Drp1‐mediated mitochondrial fission in the diabetic kidney through the PDE4D/PKA pathway

To explore the role of PDE4D in diabetic nephropathy (DN) and investigate whether resveratrol protects against DN via inhibiting PDE4D. Diabetic db/db mouse and glomerular mesangial cell line (GMCs) were used to investigate the role of PDE4D and the protective effect of resveratrol on renal fibrosis under high glucose (HG) environment. Resveratrol alleviated the progress of DN via inhibiting mitochondrial fragmentation and restoring the expression of PDE4D, PKA, phosphorylated Drp1‐Ser637 and Drp1 in kidney of db/db mice. In HG‐exposed GMCs, resveratrol treatment decreased the expression of PDE4D, increased PKA level, and inhibited Drp1‐mediated mitochondrial fission. In contrast, PDE4D over‐expression blunted the inhibitory effects of resveratrol on Drp1 expression and mitochondrial fission. Moreover, PKA inhibitor H89 blunted the effects of resveratrol on phosphorylated Drp1‐Ser637 expression and mitochondrial fission in HG‐treated GMCs. Inhibition of mitochondrial fission with Drp1 inhibitor Mdivi‐1 alleviated mitochondrial dysfunction in GMCs under HG. These findings indicate PDE4D plays an important role in the process of DN. Resveratrol attenuates the development of DN by preventing mitochondrial fission through inhibiting PDE4D, which regulates the expression of phosphorylated Drp1‐Ser637 directly.
Plutonism and the origin of metamorphic core complexes

The formation of metamorphic core complexes may be triggered by plutonic activity during episodes of continental extension. Pulses of ductile deformation have taken place during short-lived thermal events initiated by the heat input from intruded plutons, sills, or dikes. Such intrusions may be the underlying cause for differential uplift of the footwall during tectonic denudation of metamorphic core complexes. Fast cooling inferred from 40 Ar/ 39 Ar apparent ages may have taken place after periods of magma arrival, and need not be the result of rapid erosional or tectonic denudation. Heterogeneity of 40 Ar/ 39 Ar apparent ages can be explained by rapid cooling of deforming mylonites formed at shallow crustal levels in the thermal aureoles of intruded sills (or sill swarms). Under such circumstances, apparently isothermal decompression paths may actually link pressure-temperature points set during periods of transient mineral growth during and after periods of igneous activity.
Discrete particle model for sheet flow sediment transport in the nearshore

Fully three-dimensional discrete particle computer simulations of high-concentration sheet flow transport in oscillatory flows quantify the effect of fluid acceleration on bed load transport in highly unsteady flows typical of nearshore marine environments. A simple impulse-momentum approach explains simulation results and forms the basis for adding an acceleration-related term to widely used energetics sediment transport formulae. Transport predicted by the acceleration term becomes increasingly significant as wave shape approaches the sawtooth profile characteristic of surf zone bores. Simulations integrate F = ma and a corresponding set of equations for the torques for each sphere. Normal and tangential forces between contacting particles are linear functions of the distance between sphere centers and the relative tangential displacement at the contact point, respectively; particle interactions are both inelastic and frictional. Pressure gradient forces generated by the passage of surface gravity waves drive fluid and particle motion in a stack of thin horizontal fluid layers that exchange momentum and exert fluid drag, added mass, and buoyancy forces on particles. Transport properties of the simulated granular-fluid assemblage are robust to large variations in material properties of the particles. Simulated transport rates agree with available experimental data for unsteady transport of coarse sands; the mode of bed load motion, dispersion of bed load particles, and particle segregation by size and density are qualitatively consistent with available particle-scale observations of bed load transport of natural particles.
A color-ratio-based image retrieval for e-catalog image databases

Most of the content-based image retrieval systems are based on RGB color space. Using the average amount of red, green, and blue is appropriate for natural images. But, for the case of e-catalog images, the number of colors for a given catalog image is only a few and the average color of an image is meaningless to customers. This paper presents a color comparison scheme based on the HSI color ratio to improve the accuracy of retrieval on e-catalog images. We have divided hue by 30 degrees, resulting in 12 colors. By considering saturation and intensity, and eliminating some duplicate combinations, we further divided each hue into 15 categories, thus resulting in 186 representative colors which is quite smaller than 1.7 million colors of 24 bit RGB case. The resulting 186-element HSI histogram is represented using presence bitmap vector(186 bit) and ratio vector(93 bytes). For the e-catalog images, most of the presence vector bits are 0 since there are only a few colors. We have implemented the prototype retrieval system and showed the usefulness of the proposed system by comparing measures such as precision and search speed with RGB histogram based schemes.
Reply to the Comments of Reviewer #1

The mass flux of air lifted within the updrafts of shallow convection was : is ::::::: usually : thought to be compensated outside the cloud through either large scale subsidence or stronger downdrafts in a thin shell surrounding the cloud. Subsiding shells were postulated based on large eddy simulation and are experimentally tested in this study for shallow convection over land. Isolated cumulus clouds were probed with a small research aircraft over flat land , mountains, ::: and ::::::::::: mountainous :::::: terrain, in different wind situations and at different levels of the clouds. The subsiding shell varies considerably between individual cloud 5 transects. A shell-like narrow downdraft region was present on at least one edge in 105 out of :::::: average :: of ::: the : 191 transects and on both edges in 29 transects. However, the average over all cloud transects shows ::: the :::::::: subsiding :::: shell :: as : a narrow downdraft region outside the cloud boundaries. The ensemble-mean subsiding shell is narrower on the upwind side of the cloud, while it is at least half a cloud diameter wide and more humid on the downwind side. At least half of the upward mass transport in the cloud is compensated within a distance of 20% of the cloud diameter. A :::::::: However, ::: this shell is not uniform. Distinct regions of 10 downdrafts and updrafts with high variability of the vertical wind are frequent and randomly distributed in the vicinity and also within the cloud. Based on these findings, a subsiding shell is , however, a valid concept to describe an ensemble of shallow cumulus clouds over land. ::: The ::::::: median :::::::: diameter :: of ::: the ::::: drafts ::::::: directly :: at :::: the ::::: cloud :::::::: boundary :: is :: at ::::: least : 4 ::::: times ::: as :::: large ::: as ::::: inside ::: the ::::: clouds :::: and :: in ::: the ::::::::::: environment. :::::::::: Downdrafts : at ::: the ::::: cloud :::::::: boundary ::: are ::::: twice :: as ::::::: frequent :: as :::::::: updrafts. :: In ::::::: contrast :: to ::: the ::::::: updrafts ::: the ::::: major :::: part :: of ::: the ::::::::: downdrafts :: is ::::::: situated :::::: outside ::: of ::: the ::::: cloud. :::: The :::::::: subsiding :::: shell :::::: results ::::: from ::: the ::::::::: distribution ::: of 15 :::: these ::: up:::: and :::::::::: downdrafts.
Geology of Petroleum in Kohat-Potwar Depression, Pakistan

The 36,000-km2 Kohat-Potwar depression in northern Pakistan has more than 5,000 m of marine deposition (Precambrian to Eocene, with a major break during Ordovician to Carboniferous). More than 10,000 m of Miocene to Pleistocene alluvial sediments overlies the marine sequence. The tectonic depression formed as a result of continent-to-continent collision at the northwestern margin of the Indian plate. Although the region has been under active petroleum exploration since the mid-nineteenth century, it has been tested by only 60 exploratory wells. Ten oil fields have been discovered; original recoverable reserves total 200 million bbl, of which 112 million bbl has been produced. The region has several attractive features for petroleum generation and accumulation i cluding source-reservoir-trap assemblages and thermal maturity regimes. Total ultimately recoverable hydrocarbon resource of the area is estimated at 2.4 billion bbl of oil equivalent. Many unexplored surface and subsurface prospects and stratigraphic leads are known. Parts of the region, particularly the Bannu depression and Kohat salt zone, can be regarded as frontier areas; based on the exposed geology and available seismic information, we believe these areas are promising. Recent discoveries of Dakhni field (1983) and Dhurnal field (1984), which were the first discoveries in the northern part of the platform zone of the Potwar plateau, and production from Paleozoic horizons have added new dimension to petroleum prospects of the area. The region needs careful reevaluation of available information, exploratory drilling on selected targets, and detailed exploration in its western part.
The early life history of swordfish (Xiphias gladius) in the western North Atlantic

Lengths and ages of sword-fish (Xiphias gladius) estimated from increments on otoliths of larvae collected in the Caribbean Sea, Florida Straits, and off the southeastern United States, indicated two growth phases. Larvae complete yolk and oil globule absorption 5 to 6 days after hatching (DAH). Larvae 11 mm eat exclusively neustonic fish larvae. This diet indicates that young larvae <11 mm occupy the near-surface pelagia, whereas, older and longer larvae are neustonic. Spawning dates for larvae collected in various regions of the western North Atlantic, along with the abundance and spatial distribution of the youngest larvae, indicate that spawning peaks in three seasons and in five regions. Swordfish spawn in the Caribbean Sea, or possibly to the east, in winter, and in the western Gulf of Mexico in spring. Elsewhere swordfish spawn year-round, but spawning peaks in the spring in the north-central Gulf of Mexico, in the summer off southern Florida, and in the spring and early summer off the southeastern United States. The western Gulf Stream frontal zone is the focus of spawning off the southeastern coast of the United States, whereas spawning in the Gulf of Mexico seems to be focused in the vicinity of the Gulf Loop Current. Larvae may use the Gulf of Mexico and the outer continental shelf off the east coast of the United States as nursery areas. Some larvae may be transported northward, but trans-Atlantic transport of larvae is unlikely.
Thirty years of elevation change on Antarctic Peninsula ice shelves from multimission satellite radar altimetry

[1] We use data acquired between 1978 and 2008 by four satellite radar altimeter missions (Seasat, ERS-1, ERS-2 and Envisat) to determine multidecadal elevation change rates (dhi/dt) for six major Antarctic Peninsula (AP) ice shelves. In areas covered by the Seasat orbit (to 72.16°S), regional-averaged 30-year trends were negative (surface lowering), with rates between −0.03 and −0.16 m a−1. Surface lowering preceded the start of near-continuous radar altimeter operations that began with ERS-1 in 1992. The average rate of lowering for the first 14 years of the period was typically smaller than the 30-year average; the exception was the southern Wilkins Ice Shelf, which experienced negligible lowering between 2000 and 2008, when a series of large calving events began. Analyses of the continuous ERS/Envisat time series (to 81.5°) for 1992–2008 reveal a period of strong negative dhi/dt on most ice shelves between 1992 and 1995. Based on prior studies of regional atmospheric and oceanic conditions, we hypothesize that the observed elevation changes on Larsen C Ice Shelf are driven primarily by firn compaction while the western AP ice shelves are responding to changes in both surface mass balance and basal melt rates. Our time series also show that large changes in dhi/dt can occur on interannual time scales, reinforcing the importance of long time series altimetry to separate long-term trends associated with climate change from interannual to interdecadal natural variability.
Geosynthetic/Soil Interface Friction Angles Using a Rotation Shear Device

A modified rotation shear device was used for measuring interface friction angles between soils and geosynthetics. The device was modified so that a geosynthetic specimen can be attached to the upper platen. A reliable method for cutting and attaching geosynthetic specimens to the device is described. The geosynthetic mounting system is simple, strong, and easy to remove. Interface friction angles and interface efficiencies for two ash samples and Boston Blue Clay with three geosynthetics are reported and compared. A range of strength increase is reported for a given soil with change from a smooth geomembrane to a textured geomembrane or nonwoven geotextile. Shear displacements up to 300 mm are quantified in the paper, showing that large, unidirectional displacements may accumulate in the rotation shear device.
Understanding the adoption of clusters by SMEs in Australia using innovation diffusion theory

SME clustering has attracted much attention to date as it encourages SMEs to achieve competitive advantage through co-operation. Although the Australian government advocates and actively promotes the formation of SME clusters, much academic commentary is dissatisfied with the theory on clusters, in particular its reliance on geographic proximity. The literature primarily addresses the benefits of industry clusters but overlooks the processes of how clusters are formed. This leaves some sections of the SME population underserved particularly those involved in horizontally integrated value chains. This thesis explores the formation process of a horizontal alliance and compares this to Rogers’ innovation-diffusion theory. Through a case study of an Australian carpet buying group, SMEs were surveyed to collect data on the characteristics of buying group growth over a 13 year period. Our results show that the S-shaped innovation diffusion pattern of Rogers’ theory accurately describes the growth of the buying group over this time. In particular, strong support was found for the opinion leadership theory. The use of Rogers’ theory led to a better understanding of the role of networks and ICTs in promoting information sharing. In particular, the research finds that the dominant theory of geographical proximity advanced by Porter (1998a) needs to be qualified in relation to horizontally integrated value chains where SMEs share a high degree of homogeneity.