Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction of Sp1 with the growth- and cell cycle-regulated transcription factor E2F

Within the region around 150 bp upstream of the initiation codon, which was previously shown to suffice for growth-regulated expression, the murine thymidine kinase gene carries a single binding site for transcription factor Sp1; about 10 bp downstream of this site, there is a binding motif for transcription factor E2F. The latter protein appears to be responsible for growth regulation of the promoter. Mutational inactivation of either the Sp1 or the E2F site almost completely abolishes promoter activity, suggesting that the two transcription factors interact directly in delivering an activation signal to the basic transcription machinery. This was verified by demonstrating with the use of glutathione S-transferase fusion proteins that E2F and Sp1 bind to each other in vitro. For this interaction, the C-terminal part of Sp1 and the N terminus of E2F1, a domain also present in E2F2 and E2F3 but absent in E2F4 and E2F5, were essential. Accordingly, E2F1 to E2F3 but not E2F4 and E2F5 were found to bind sp1 in vitro. Coimmunoprecipitation experiments showed that complexes exist in vivo, and it was estabilished that the distance between the binding sites for the two transcription factors was critical for optimal promoter activity. Finally, in vivo footprinting experiments indicated that both the sp1 and E2F binding sites are occupied throughout the cell cycle. Mutation of either binding motif abolished binding of both transcription factors in vivo, which may indicate cooperative binding of the two proteins to chromatin-organized DNA. Our data are in line with the hypothesis that E2F functions as a growth- and cell cycle regulated tethering factor between Sp1 and the basic transcription machinery.
The environment of early Mars and the missing carbonates

Abstract– A model is presented in which the aqueous conditions needed to generate phyllosilicate minerals in the absence of carbonates found in the ancient Noachian crust are maintained by an early CO2‐rich atmosphere, that, together with iron (II) oxidation, would prevent carbonate formation at the surface. After cessation of the internal magnetic dynamo, a CO2‐rich primordial atmosphere was stripped by interactions with the solar wind and surface conditions evolved from humid to arid, with ground waters partially dissolving subsurface carbonate and sulfide minerals to produce acid‐sulfate evaporitic deposits in areas with upwelling ground water. In a subsequent geochemical state (Late Noachian to Hesperian), surface and subsurface acidic solutions were neutralized in the subsurface through interaction with basaltic crust, allowing the precipitation of secondary carbonates. This model suggests that, in the early Noachian, the surface waters of Mars maintained acidity because of a drop in temperature. This would have favored increased dissolution of CO2 and a reduction in atmospheric pressure. In this scenario, physicochemical conditions precluded the formation of surface carbonates, but induced the precipitation of carbonates in the subsurface.
Endogenous PMN‐derived reactive oxygen intermediates provide feedback regulation on respiratory burst signal transduction

The role of polymorphonuclear leukocytes (PMN) in stemming systemic infection is executed mainly by the utilization of molecular O2 leading to the production of reactive oxygen intermediates (ROI). PMN‐derived ROI also serve as intra‐ and extracellular second messengers providing both positive and negative feedback on cellular autoregulation. We investigated the effect of endogenous ROI on two signal transducing pathways: the receptor (R)‐G‐protein‐phospholipase D (PLD) and receptor (R)‐G‐protein‐phospholipase C pathways responsible for the subsequent interleukin‐8 (IL‐8)‐induced PMN respiratory burst. Purified human PMN were primed with LPS adhered to plastic surfaces and stimulated with IL‐8 with or without the presence of each of five different selective ROI scavengers/antioxidants: DMSO, NaN3, L‐alanine, catalase, or superoxide dismutase. Total IL‐8 surface receptor expression was assessed by 125I‐IL‐8 125I‐labeled mAbs against IL‐8R type A and B binding assays; PLD activation was assessed by measuring formation of phosphatidyl ethanol (PEt) in the presence of ethanol; PLC activation was measured by quantitative conversion of [32P]ATP‐labeled phosphatidic acid (PA) into diacylglycerol (DAG); expression of Gα‐inhibitory subunit was assessed by SDS‐PAGE and immunoblotting with polyclonal Abs against this subunit. Production of O2 –, H2O2, HClO, and myeloperoxidase (MPO) in the experimental model was confirmed in a separate set of experiments. The overall impact of antioxidants on each component of the transducing tripartite complex was stimulatory; however, NaN3 and SOD exhibited the most ubiquitous effect with consistent upregulation by NaN3 of IL‐8R expression, whereas even trace amounts of externally added authentic MPO significantly down‐regulated the functional activity of both effector enzymes. These results demonstrate a multiple site‐specific targeting of the signal‐transducing complex by endogenous PMN‐derived ROI and an overall protective effect of ROI scavengers/antioxidants. J. Leukoc. Biol. 62: 268–276; 1997.
NDVI Variation and Its Responses to Climate Change on the Northern Loess Plateau of China from 1998 to 2012

This study analyzed temporal and spatial changes of normalized difference vegetation index (NDVI) on the northern Loess Plateau and their correlation with climatic factors from 1998 to 2012. The possible impacts of human activities on the NDVI changes were also explored. The results showed that (1) the annual maximum NDVI showed an upward trend. The significantly increased NDVI and decreasing severe desertification areas demonstrate that the vegetation condition improved in this area. (2) Over the past decades, climate tended to be warmer and drier. However, the mean temperature significantly decreased and precipitation slightly increased from 1998 to 2012, especially in spring and summer, which was one of the major reasons for the increase in the annual maximum NDVI. Compared to temperature, vegetation was more sensitive to precipitation changes in this area. The NDVI and annual precipitation changes were highly synchronous over the first half of the year, while a 1-month time lag existed between the two variables during the second half of the year. (3) Positive human activities, including the “Grain for Green” program and successful environmental treatments at coal mining bases, were some of the other factors that improved the vegetation condition.
Lactobacillus casei strain C1 attenuates vascular changes in spontaneously hypertensive rats

Hypertension can be caused by various factors while the predominant causes include increase in body fluid volume and resistance in the circulatory system that elevate the blood pressure. Consumption of probiotics has been proven to attenuate hypertension; however, the effect is much strain-dependent. In this study, a newly isolated Lactobacillus casei (Lb. casei) strain C1 was investigated for its antihypertensive properties in spontaneously hypertensive rats (SHR). Lactic acid bacteria (LAB) suspension of 11 log colony-forming unit (CFU) was given to SHR (SHR+LAB, n=8), and phosphate buffer saline (PBS) was given as a control in SHR (SHR, n=8) and in Wistar rats as sham (WIS, n=8). The treatment was given via oral gavage for 8 weeks. The results showed that the weekly systolic blood pressure (SBP), mean arterial pressure (MAP), diastolic blood pressure (DBP) and aortic reactivity function were remarkably improved after 8 weeks of bacterial administration in SHR+LAB. These effects were mostly attributed by restoration of wall tension and tensile stress following the bacterial treatment. Although not statistically significant, the level of malondialdehye (MDA) in SHR+LAB serum was found declining. Increased levels of glutathione (GSH) and nitric oxide (NO) in SHR+LAB serum suggested that the bacterium exerted vascular protection through antioxidative functions and relatively high NO level that induced vasodilation. Collectively, Lb. casei strain C1 is a promising alternative for hypertension improvement.
Combined constraints on global ocean primary production using observations and models

Primary production is at the base of the marine food web and plays a central role for global biogeochemical cycles. Yet global ocean primary production is known to only a factor of ~2, with previous estimates ranging from 38 to 65 Pg C yr−1 and no formal uncertainty analysis. Here, we present an improved global ocean biogeochemistry model that includes a mechanistic representation of photosynthesis and a new observational database of net primary production (NPP) in the ocean. We combine the model and observations to constrain particulate NPP in the ocean with statistical metrics. The PlankTOM5.3 model includes a new photosynthesis formulation with a dynamic representation of iron‐light colimitation, which leads to a considerable improvement of the interannual variability of surface chlorophyll. The database includes a consistent set of 50,050 measurements of 14C primary production. The model best reproduces observations when global NPP is 58 ± 7 Pg C yr−1, with a most probable value of 56 Pg C yr−1. The most probable value is robust to the model used. The uncertainty represents 95% confidence intervals. It considers all random errors in the model and observations, but not potential biases in the observations. We show that tropical regions (23°S–23°N) contribute half of the global NPP, while NPPs in the Northern and Southern Hemispheres are approximately equal in spite of the larger ocean area in the South.
The complex radio and X-ray structure in the nuclear regions of the active galaxy NGC 1365

ABSTRA C T We present a multiwavelength analysis of the prominent active galaxy NGC 1365, in particular looking at the radio and X-ray properties of the central regions of the galaxy. We analyse ROSAT (PSPC and HRI) observations of NGC 1365, and discuss recent ASCA results. In addition to a number of point sources in the vicinity of NGC 1365, we find a region of extended X-ray emission extending along the central bar of the galaxy, combined with an emission peak near the centre of the galaxy. This central X-ray emission is centred on the optical/radio nucleus, but is spatially extended. The X-ray spectrum can be well fitted by a thermal plasma model, with a temperature of kT a 0:6‐0:8 keV and a very low local absorbing column. The thermal spectrum is suggestive of starburst emission rather than emission from a central black hole. The ATCA radio observations show a number of hotspots, located in a ring around a weak radio nucleus. Synchrotron emission from electrons accelerated by supernovae and supernova remnants (SNRs) is the likely origin of these hotspots. The radio nucleus has a steep spectrum, indicative perhaps of an active galactic nucleus (AGN) or SNRs. The evidence for a jet emanating from the nucleus (as has been previously claimed) is at best marginal. The extent of the radio ring is comparable to that of the extended central X-ray source. We discuss the nature of the central activity in NGC 1365 in the light of these observations. The extended X-ray emission and the thermal spectra strongly suggest that at soft X-ray energies we are not seeing emission predominantly from a central black hole, although the presence of Fe K line emission at higher energies does suggest the presence of an AGN. Consequently, a black hole is probably not the dominant contributor to the energetics of the central regions of NGC 1365 at radio, optical or soft X-ray wavelengths. Activity associated with a starburst is likely the dominant explanation for the observed properties of NGC 1365.
Layer-Dependent Attentional Processing by Top-down Signals in a Visual Cortical Microcircuit Model

A vast amount of information about the external world continuously flows into the brain, whereas its capacity to process such information is limited. Attention enables the brain to allocate its resources of information processing to selected sensory inputs for reducing its computational load, and effects of attention have been extensively studied in visual information processing. However, how the microcircuit of the visual cortex processes attentional information from higher areas remains largely unknown. Here, we explore the complex interactions between visual inputs and an attentional signal in a computational model of the visual cortical microcircuit. Our model not only successfully accounts for previous experimental observations of attentional effects on visual neuronal responses, but also predicts contrasting differences in the attentional effects of top-down signals between cortical layers: attention to a preferred stimulus of a column enhances neuronal responses of layers 2/3 and 5, the output stations of cortical microcircuits, whereas attention suppresses neuronal responses of layer 4, the input station of cortical microcircuits. We demonstrate that the specific modulation pattern of layer-4 activity, which emerges from inter-laminar synaptic connections, is crucial for a rapid shift of attention to a currently unattended stimulus. Our results suggest that top-down signals act differently on different layers of the cortical microcircuit.
A brachial plexus variation characterized by the absence of the superior trunk

The brachial plexus is formed by the union of the ventral rami of the inferior four cervical (C5-C8) and first thoracic (T1) nerves (Figure 1). The C5 nerve usually receives a small contribution from the fourth-cervical nerve and the T1 nerve normally receives one from the second thoracic nerve. The brachial plexus supplies cutaneous and muscular innervation to the upper limb(s) and any injury at this level can lead to significant disability. The plexus extends from the inferior lateral portion of the neck downward and laterally over the first rib, posterior to the clavicle, and enters the axilla. Upon exit from the intervertebral foramina, the ventral rami of C5 and C6 cervical nerves unite to form the superior trunk. That of C7 nerve runs alone as the middle trunk and those of C8 and T1 nerves unite to form the inferior trunk; each of the trunks then bifurcates into anterior and posterior divisions as they pass beneath the clavicle. The anterior divisions of the superior and middle trunk form the lateral cord. The anterior division of the inferior trunk continues as the medial cord. The posterior divisions of all three trunks unite to form the posterior cord. From the cords arise the terminal branches of the brachial plexus including the musculocutaneous, median, ulnar, axillary, and radial nerves [1]. Anomalies of the cords and terminal branches of the brachial plexus are relatively common and have been well documented [2], however, anomalies of the roots and trunks are comparatively rare and have been reported in only a few cases. As the brachial plexus supplies cutaneous and muscular innervation to the upper limb, its anatomical variations have important clinical implications. Therefore, it is important for the anatomist, surgeon, anesthesiologist, and radiologist to be aware of anatomical variations that deviate from the classic anatomy.
Utterance partitioning with acoustic vector resampling for i-vector based speaker verification

I-vector has become a state-of-the-art technique for textindependent speaker verification. The major advantage of ivectors is that they can represent speaker-dependent information in a low-dimension Euclidean space, which opens up opportunity for using statistical techniques to suppress sessionand channel-variability. This paper investigates the effect of varying the conversation length and the number of training sessions per speakers on the discriminative ability of i-vectors. The paper demonstrates that the amount of speaker-dependent information that an i-vector can capture will become saturated when the utterance length exceeds a certain threshold. This finding motivates us to maximize the feature representation capability of i-vectors by partitioning a long conversation into a number of sub-utterances in order to produce more i-vectors per conversation. Results on NIST 2010 SRE suggest that (1) using more i-vectors per conversation enhances the capability of LDA and WCCN in suppressing session variability, especially when the number of conversations per training speaker is limited; and (2) increasing the number of i-vectors per target speaker helps the i-vector based SVMs to find better decision boundaries, thus making SVM scoring outperforms cosine distance scoring by 22% and 9% in terms of minimum normalized DCF and EER.
Species richness and diversity of a terrestrial insular environment: serpentine of the Barberton Greenstone Belt, South Africa

The serpentinite outcrops of the Barberton Greenstone Belt are considered to be amongst the oldest in the world and have been exposed for over 50 million years. Of the 30 large outcrops in eastern Mpumalanga, South Africa, seven were selected for detailed comparison of species richness and diversity with those of surrounding non-serpentine vegetation. Various non-parametric species richness estimators were calculated to predict the species richness of each site and these indicated that four serpentine outcrops have higher and three have lower species richness than the surrounding non-serpentine areas. The Shannon, Simpson’s and Fisher’s alpha indices of diversity were calculated for each site on and off serpentine and compared. The diversity values calculated show similar patterns to those of the species richness estimates. Significant differences in species composition between floras on and off serpentine were estimated using Sorenson’s Index of similarity. The serpentine outcrops of the Barberton Greenstone Belt show relatively high diversity when compared to some other serpentine outcrops around the world. Key words: Diversity indices, EstimateS, Modified-Whittaker plots, serpentine, species accumulation curves, species richness estimation.
An Evolutionary Strategy for Surrogate-Based Multiobjective Optimization

The paper presents a surrogate-based evolutionary strategy for multiobjective optimization. The evolutionary strategy uses distance based aggregate surrogate models in two ways: as a part of memetic search and as way to pre-select individuals in order to avoid evaluation of bad individuals. The model predicts the distance of individuals to the currently known Pareto set. The newly proposed algorithm is compared to other algorithms which use similar surrogate models on a set of benchmark functions.
Earliest Wuchiapingian (Lopingian, Late Permian) Brachiopods in Southern Hunan, South China: Implications for the Pre-Lopingian Crisis and Onset of Lopingian Recovery/Radiation

Abstract The uppermost 5–15 m of the Douling Formation in the southern Hunan area, South China, yields a diverse fauna comprised of ammonoids, bivalves, and brachiopods. The brachiopods reported in this paper consist of 51 species in 34 genera and are dominated by the Lopingian (Late Permian) species associated with a few species persisting from the underlying Maokouan (Late Guadalupian). This fauna is of earliest Wuchiapingian in age as precisely constrained by the associated conodont Clarkina postbitteri postbitteri and the Guadalupian-type ammonoid fauna of the Roadoceras-Doulingoceras Zone in the brachiopod horizon. The discovery of the Lopingian species-dominated brachiopod fauna in the earliest Wuchiapingian in southern Hunan suggests a much less pronounced effect of the pre-Lopingian crisis (end-Guadalupian mass extinction) than the end-Changhsingian mass extinction in terms of brachiopods, a contemporaneous onset of the Lopingian recovery/radiation during the pre-Lopingian crisis period, and taxonomic selectivity of the pre-Lopingian crisis in terms of different fossil groups. New taxa are Echinauris doulingensis n. sp. , Pararigbyella quadrilobata n. gen. and n. sp. and P. doulingensis n. gen. and n. sp.
Developmental anomalies with features of disorganization (Ds) and amniotic band sequence (ABS): A report of four cases

Disorganization (Ds) is a mouse mutant in which heterozygotes manifest defects in various organ systems including cranioschisis, hamartomas, limb abnormalities, body wall defects, eye defects, and craniopharyngeal defects. We report four patients with developmental anomalies that are seen in amniotic band sequence (ABS) with additional anomalies that could not be explained by amniotic bands alone. The anomalies seen in our patients included facial malformation and clefting, brain anomalies (encephalocele, agenesis of the corpus callosum, holoprosencephaly), eye anomalies (anophthalmia, microphthalmia, and microcornea), and extremity and digit anomalies (talipes equinovarus, absent/hypoplastic phalanges, amputation of an extremity, syndactyly, polydactyly, and anomalous attachment of an extremity). Other systems involved include genitourinary anomalies (hydronephrosis and abnormal testes, epidydimis and seminal vesicles), and skin appendages similar to those seen in Ds mice. Presence of amniotic bands in addition to malformations not attributed to amniotic bands, were seen in three of four patients. The four patients in this report have involvement of at least four organ systems including the skin appendages that have been reported in the Ds mouse and have clinical findings that overlap the spectrum of Ds and ABS. © 2009 Wiley‐Liss, Inc.
Iron oxides, divalent cations, silica, and the early earth phosphorus crisis

As a nutrient required for growth, phosphorus regulates the activity of life in the oceans. Iron oxides sorb phosphorus from seawater, and through the Archean and early Proterozoic Eons, massive quantities of iron oxides precipitated from the oceans, producing a record of seawater chemistry that is preserved as banded iron formations (BIFs) today. Here we show that Ca 2+ , Mg 2+ , and silica in seawater control phosphorus sorption onto iron oxides, influencing the record of seawater phosphorus preserved in BIFs. Using a model for seawater cation chemistry through time, combined with the phosphorus and silica content of BIFs, we estimate that seawater in the Archean and early Proterozoic Eons likely contained 0.04–0.13 µM phosphorus, on average. These phosphorus limiting conditions could have favored primary production through photoferrotrophy at the expense of oxygenic photosynthesis until upwelling waters shifted from phosphorus to iron limiting.
Robust Multimodal Graph Matching: Sparse Coding Meets Graph Matching

Graph matching is a challenging problem with very important applications in a wide range of fields, from image and video analysis to biological and biomedical problems. We propose a robust graph matching algorithm inspired in sparsity-related techniques. We cast the problem, resembling group or collaborative sparsity formulations, as a non-smooth convex optimization problem that can be efficiently solved using augmented Lagrangian techniques. The method can deal with weighted or unweighted graphs, as well as multimodal data, where different graphs represent different types of data. The proposed approach is also naturally integrated with collaborative graph inference techniques, solving general network inference problems where the observed variables, possibly coming from different modalities, are not in correspondence. The algorithm is tested and compared with state-of-the-art graph matching techniques in both synthetic and real graphs. We also present results on multimodal graphs and applications to collaborative inference of brain connectivity from alignment-free functional magnetic resonance imaging (fMRI) data. The code is publicly available.