Miracle-dz/UniFAR-FTUs huggingface dataset:
Novel Transcriptional Regulation of the Human CYP3A7Gene by Sp1 and Sp3 through Nuclear Factor κB-like Element

Abstract Human CYP3A7 and CYP3A4 are expressed in fetal and adult livers, respectively, although the 5′-flanking regions of the two genes show 90% homology. The purpose of this study was to clarify the mechanism(s) responsible for the transcriptional regulation of theCYP3A7 gene in human hepatoma HepG2 cells that showed fetal phenotypes. Transfection studies using a series of theCYP3A7 or CYP3A4 promoter-luciferase chimeric genes identified a nuclear factor κB (NF-κB)-like element between nucleotides −2326 and −2297 that conferred the transcriptional activation of the CYP3A7 gene. A 1-base pair mismatch within the corresponding region of the CYP3A4 gene was sufficient for a differential enhancer activity. A gel shift assay using nuclear extracts from HepG2 cells showed that Sp1 and Sp3 bound to the NF-κB-like element of the CYP3A7 but notCYP3A4 gene. Specific activation of the CYP3A7promoter by Sp1 and Sp3 was confirmed by a co-transfection of the p3A7NF-κB or p3A4NF-κB reporter gene with Sp1 or Sp3 expression plasmid into Drosophila cells, which lacked endogenous Sp family. Additionally, introduction of mutations into binding sites for hepatocyte nuclear factor 3β, upstream stimulatory factor 1, and a basic transcription element in the proximal promoter attenuated luciferase activity to 20% of the level seen with the intactCYP3A7 promoter. Thus, we conclude that the expression of the CYP3A7 gene in HepG2 cells is cooperatively regulated by Sp1, Sp3, hepatocyte nuclear factor 3β, and upstream stimulatory factor 1.
Improving 3D lattice boltzmann method stencil with asynchronous transfers on many-core processors

CPU-based many-core processors present an alternative to multicore CPU and GPU processors. In particular, the 93-Petaflops Sunway supercomputer, built from clustered many-core processors, has opened a new era for high performance computing that does not rely on GPU acceleration. However, memory bandwidth remains the main challenge for these architectures. This motivates our endeavor for optimizing one of the most data-intensive kind of stencil computations, namely the three-dimensional applications of the lattice Boltzmann method (LBM). We propose optimizations on many-cores processors by using local memory and asynchronous software-prefetching on a representative 3D LBM solver as an example. We achieve 33 % performance gain on the Kalray MPPA-256 many-core processor by actively streaming data from/to local memory, compared to the “passive” OpenCL programming model.
Evidence for presence of the founder Ia mtDNA haplotype of Phytophthora infestans in 19th century potato tubers from the Rothamsted archives

Late blight remained a significant disease for potato growers in Europe long after the famine of the 1840s. Of the four mitochondrial haplotypes of Phytophthora infestans, only the Ia mitochondrial DNA (mtDNA) haplotype has been identified previously in infected potato leaves from famine-era herbarium specimens collected in England, Ireland and Europe in the 19th century. Long-term soil fertility experiments were conducted on potato between 1876 and 1901 in Rothamsted to investigate effects of combinations of organic manures and mineral fertilizers on disease and yield. This report identifies for the first time the same Ia mtDNA haplotype of P. infestans in three diseased tubers from 1877 from the long-term Rothamsted trials, thus providing the earliest evidence of the presence of the founder Ia mtDNA haplotype of P. infestans in potato tubers in England. Soil amendments had a significant impact on disease and yield. A real-time PCR assay was used to detect and quantify P. infestans in tubers. The level of pathogen DNA was greatest in tubers from highest yielding plots that received combinations of inorganic nitrogenous and mineral fertilizers and least in tubers from plots with organic farmyard manures or non-nitrogenous mineral fertilizers. The Ia mtDNA haplotype was also confirmed from diseased potato leaves during the same time period. Thus, the founder Ia mtDNA haplotype survived in potato tubers after 1846 and was present over 30 years later in the UK.
Effects of Cryoprotectants and Post-storage Priming on Seed Germination of Sugi (Cryptomeria japonica

Abstract Among the ex situ methods for the preservation of forest tree germplasm, conventional seed banking is considered the most efficient method for the majority of species whilst cryopreservation has an important role in long-term conservation. The influence of cryoprotectants prior to liquid nitrogen (LN) storage and osmoconditioning priming treatments with polyethylene glycol (PEG) after LN storage were evaluated for germination (%), germination value (GV) and mean germination time (MGT) in seeds of Cryptomeria japonica. Sugi seeds were treated with two cryoprotectants (DMSO and PVS2) before immersion into LN and stored for three days. Although the C. japonica seeds survived liquid nitrogen treatment, their viability was reduced from 25% of intact seeds to 17% in LN. The seeds treated with 35% DMSO showed higher germination (28%) as compared with seeds directly-immersed in LN without cryoprotectant treatment. In contrast, PVS2 pretreated seeds decreased germination (13%). Two concentrations of PEG priming treatments were carried out. Osmoconditioning treatment in -0.4 MPa PEG solution after removal from LN enhanced the subsequent germination percentage and decreased MGT. PEG treatments at both -0.4 and -1.2MPa to PVS2 pretreated seeds before cryopreservation partially alleviated the negative effect of PVS2. DMSO pretreated seeds immersed into LN and treated with -0.4MPa PEG maintained the 28% of germination obtained in the control conditions and reduced the mean germination time (MGT). It can therefore be summarized that pretreatment with 35% DMSO was suitable for the cryopreservation of C. japonica seeds whilst the PEG priming treatment circumvented imbibitional damage after LN exposure.
The Impact of Workload on Operational Risk: Evidence from a Commercial Bank

Operational risk has been among the three most significant types of risks in the financial services industry, and its management is mandated by Basel II regulations. To inform better labor decisions, this paper studies how workload affects banks’ operational risk event occurrence. To achieve this goal, we use a unique data set from a commercial bank in China that contains 1,441 operational risk events over 16 months. We find that workload has a U-shaped impact on operational risk error rate. More specifically, the error rate of operational risk events decreases first, as workload increases, and then increases. Furthermore, when workload is low, employees tend to make performance-seeking risks; however, when workload is high, employees tend to exhibit quality degradation due to cognitive multitasking. Based on the causal relationship between workload and operational risk events from the empirical analysis, we discuss staffing policies among branches aimed at reducing operational risk losses. We find that employing a flexible staffing rule can significantly reduce the number of operational risk events by 3.2%–10% under different scenarios. In addition, this significant performance improvement can be achieved by adding even a little bit of flexibility to the process by allowing employees to either switch their business lines in the same branch or switch branches within the same business lines on a quarterly basis. This paper was accepted by Vishal Gaur, operations management.
Studying the Multi-frequency Angular Power Spectrum of the Cosmic Dawn 21-cm Signal

The light-cone (LC) anisotropy arises due to cosmic evolution of the cosmic dawn 21-cm signal along the line-of-sight (LoS) axis of the observation volume. The LC effect makes the signal statistically non-ergodic along the LoS axis. The multi-frequency angular power spectrum (MAPS) provides an unbiased alternative to the popular 3D power spectrum as it does not assume statistical ergodicity along every direction in the signal volume. Unlike the 3D power spectrum which mixes the cosmic evolution of the 21-cm signal along the LoS k modes, MAPS keeps the evolution information disentangled. Here we first study the impact of different underlying physical processes during cosmic dawn on the behaviour of the 21-cm MAPS using simulations of various different scenarios and models. We also make error predictions in 21-cm MAPS measurements considering only the system noise and cosmic variance for mock observations of HERA, NenuFAR and SKA-Low. We find that 100 h of HERA observations will be able to measure 21-cm MAPS at ≥3σ for ℓ ≲ 1000 with 0.1 MHz channel-width. The better sensitivity of SKA-Low allows reaching this sensitivity up to ℓ ≲ 3000. Note that due to the difference in the frequency coverage of the various experiements, the CD-EoR model considered for NenuFAR is different than those used for the HERA and SKA-Low predictions. Considering NenuFAR with the new model, measurements ≥2σ are possible only for ℓ ≲ 600 with 0.2 MHz channel-width and for a ten times longer observation time of tobs = 1000 h. However, for the range 300 ≲ ℓ ≲ 600 and tobs = 1000 h more than 3σ measurements are still possible for NenuFAR when combining consecutive frequency channels within a 5 MHz band.
Does a radio jet drive the massive multi-phase outflow in the ultra-luminous infrared galaxy IRAS 10565+2448?

We present new upgraded Giant Metrewave Radio Telescope (uGMRT) HI 21-cm observations of the ultra-luminous infrared galaxy IRAS 10565+2448, previously reported to show blueshifted, broad, and shallow HI absorption indicating an outflow. Our higher spatial resolution observations have localised this blueshifted outflow, which is $\sim$ 1.36 kpc southwest of the radio centre and has a blueshifted velocity of $\sim 148\,\rm km\,s^{-1}$ and a full width at half maximum (FWHM) of $\sim 581\,\rm km\,s^{-1}$. The spatial extent and kinematic properties of the HI outflow are consistent with the previously detected cold molecular outflows in IRAS 10565+2448, suggesting that they likely have the same driving mechanism and are tracing the same outflow. By combining the multi-phase gas observations, we estimate a total outflowing mass rate of at least $140\, \rm M_\odot \,yr^{-1}$ and a total energy loss rate of at least $8.9\times10^{42}\,\rm erg\,s^{-1}$, where the contribution from the ionised outflow is negligible, emphasising the importance of including both cold neutral and molecular gas when quantifying the impact of outflows. We present evidence of the presence of a radio jet and argue that this may play a role in driving the observed outflows. The modest radio luminosity $L_{\rm1.4GHz}$ $\sim1.3\times10^{23}\,{\rm W\,Hz^{-1}}$ of the jet in IRAS 10565+2448 implies that the jet contribution to driving outflows should not be ignored in low radio luminosity AGN.
Economic and Mathematical Model of Business Struggle with a Vertically Integrated Company in the Market

The paper contains an analysis of the market structure when the inferior process chain company supplies the superior company with input resources and at the same time is vertically integrated with one of the superior companies. The possible anticompetitive effects of such vertically integrated structures are analyzed as well as the influence of information flows between inferior and superior enterprises of the sector on drivers of innovation and national welfare. These issues are relevant, if important information, in particular, information technology, design and specific characteristics of the product is available to inferior and superior sector enterprises. This situation is typical for high-tech sectors in which the inferior and superior product information exchange needs ensuring compatibility of products and preventing the additional costs of adjustment and increased functionality. The problem of assessing the appropriateness of imposing a ban on various divisions of a vertically integrated company to exchange non-public information received by one of its divisions from external sources is important. In the case of such a restriction, the inferior organizational division of a vertically integrated company may use personal information of the superior competitor only within the powers of its supplier, and cannot make it public for its superior organizational division as an example. The aim of the research is to develop an economic and mathematical model of business struggle with a vertically integrated company in the market. The paper contains the hypotheses and supporting evidence.
Respostas dos besouros (INSECTA: COLEOPTERA) a pressões pastoris em campos naturais no sul do Brasil

Human population growth and exacerbated consumerism have raised the demands on food production and generated rural intensification, becoming one of the main drivers of biodiversity decline. Livestock management is intensifying and expanding, often at the cost of clearing forested areas. However, managing livestock in natural grasslands may be a strategy for the conservation of these ecosystems. Management methods determines the communities in grasslands, so that low pressure grazing seems promising for conservation. In general, environmental drivers tend to generate diversity patterns at large scales, while competition contributes to determining local coexistence. However, the assembly processes of communities may differ between regions. Thus, environmental filters and biotic interactions, especially, act dynamically and direct the community pattern. Species may persist when different, especially according to feeding groups, and compete within these groups when consumer niches overlap. In addition, individual morphological traits may facilitate or restrict a species ability to persist in an environment, while at the same time mediating ecosystem processes. Insects represent the largest component of biodiversity in terrestrial ecosystems, and have been considered sensitive to environmental conditions. Coleoptera is the insect order with the largest species richness, covering a wide range of functional groups, and are sensitive to environmental variations. The aim of this thesis was to test whether Coleoptera assemblages reflect differences in the pastoral pressures exerted by livestock. Grounddwelling beetle diversity showed a general pattern of positive relationship with grazing while grass-dwellers showed a negative relationship with grazing. Grass-dweller herbivores are quite sensitive to livestock effects, and decline with increasing grazing intensity, while grass-dweller predators appear to respond positively to scrubs rather than to grass vegetation. In addition, it seems that, potentially, beetles also respond with their morphological traits to differences in vegetation structure according to grazing intensity. Some of these results are unprecedented, especially considering the regional scale of the experiment. Low intensity grazing seems to be a good option to benefit biodiversity conservation. However, managing grasslands with a single technique would not provide grassland beetles conservation equally.
Development of approaches for immunotherapy by chimeric antigen receptor modified hematopoietic stem cell transfer

Cancer is an uncontrolled growth of the body’s own cells. While can cer rates increase with age, this disease afflicts both young and old. Traditional cance r therapy has had three major facets: 1) chemotherapy, which can non-specifically d mage healthy tissue, 2) radiation, which can make some types of cancer more likely in the fu ure, and 3) surgery, which can be physically traumatic and is not effective in removing unseen microtumors or circulating metastases. Immunotherapy, by its ver y nature, is drastically different. Immunotherapy seeks to employ cells or molecules from the immune system, in their original or a modified form, to augment, assist or replace missing elements of the native functioning immune system. Our immunotherapeutic approach has bee n to develop novel chimeric antigen receptors (CAR) and deliver the eng ineered transgene into hematopoietic stem cells (HSC). We have developed a novel singl e chain TCR (scTCR) in which the TCR V α and Vβ segments are joined by a flexible linker. In addition to our scTCR we developed a single chain antibody molecule ( scFv) to increase avidity to the tumor antigen and avoid the potential limitation of MHC restriction. Our lab has previously developed a signaling cassette based on the CD3 zeta chain, CD28 and p56Lck proteins which are prominent in the T-cell signaling pathway. T he single chain specificities are linked to the signaling cassette that w e have shown to function in T-cells. With specificity and signaling coupled, the chimeric antigen receptor can be transduced into hematopoietic stem cells (HSC) via a lentivirus vector. This adoptive immunotherapy can potentially eliminate malignant cells or suppleme nt traditional therapies by providing engineered specificity and a useful method to transfer and expand
New Role of Thermal Mapping in Winter Maintenance with Principal Components Analysis

Thermal mapping uses IR thermometry to measure road pavement temperature at a high resolution to identify and to map sections of the road network prone to ice occurrence. However, measurements are time-consuming and ultimately only provide a snapshot of road conditions at the time of the survey. As such, there is a need for surveys to be restricted to a series of specific climatic conditions during winter. Typically, five to six surveys are used, but it is questionable whether the full range of atmospheric conditions is adequately covered. This work investigates the role of statistics in adding value to thermal mapping data. Principal components analysis is used to interpolate between individual thermal mapping surveys to build a thermal map (or even a road surface temperature forecast), for a wider range of climatic conditions than that permitted by traditional surveys. The results indicate that when this approach is used, fewer thermal mapping surveys are actually required. Furthermore, comparisons with numerical models indicate that this approach could yield a suitable verification method for the spatial component of road weather forecasts—a key issue currently in winter road maintenance.
How does atmospheric elevated CO2 affect crop pests and their natural enemies? Case histories from China

Abstract Global atmospheric CO2 concentrations have risen rapidly since the Industrial Revolution and are considered as a primary factor in climate change. The effects of elevated CO2 on herbivore insects were found to be primarily through the CO2‐induced changes occurring in their host plants, which then possibly affect the intensity and frequency of pest outbreaks on crops. This paper reviews several ongoing research models using primary pests of crops (cotton bollworm, whitefly, aphids) and their natural enemies (ladybeetles, parasitoids) in China to examine insect responses to elevated CO2. It is generally indicated that elevated CO2 prolonged the development of cotton bollworm, Helicoverpa armigera, a chewing insect, by decreasing the foliar nitrogen of host plants. In contrast, the phloem‐sucking aphid and whitefly insects had species‐specific responses to elevated CO2 because of complex interactions that occur in the phloem sieve elements of plants. Some aphid species, such as cotton aphid, Aphis gossypii and wheat aphid, Sitobion avenae, were considered to represent the only feeding guild to respond positively to elevated CO2 conditions. Although whitefly, Bemisia tabaci, a major vector of Tomato yellow leaf curl virus, had neutral response to elevated CO2, the plants became less vulnerable to the virus infection under elevated CO2. The predator and parasitoid response to elevated CO2 were frequently idiosyncratic. These documents from Chinese scientists suggested that elevated CO2 initially affects the crop plant and then cascades to a higher trophic level through the food chain to encompass herbivores (pests), their natural enemies, pathogens and underground nematodes, which disrupt the natural balance observed previously in agricultural ecosystems.
Sperm DNA damage after scrotal insulation in rams

Human male fertility is in decline and one reason given for this is the increased incidence of sperm showing chromosomal or DNA damage. Previous work in laboratory and farm animals as well as humans has shown that elevated testicular temperatures increases the incidence of sperm with DNA damage. As part of a study into the effect of temperature on mutation rate in spermatozoa using rams as a model, measurements of sperm DNA damage were also recorded. Twelve mature Dorset x Romney rams, were trained to AV semen collection. Scrotal insulation harnesses were applied (plastic bag with cotton wool insulation inside a rubberised fabric protection cover) to two groups of 6 rams for either a 24 or 48 hour period at day 0. Semen was collected on days -4 and 0 as control samples for each ram before treatment and days 3, 7, 10, 14, 17, 21, 24, 28, 31, 35, 38, 43, 45 and 49 post treatment. Semen was diluted in RSD-1 + TNE and snap frozen in liquid nitrogen. Samples were thawed and assessed by the Sperm Chromatin Structure Assay (SCSA) on the flow cytometer. This measures sperm susceptibility to 'in situ' acid denaturation by staining with acridine orange fluorochrome, which fluoresces differentially when binding to double stranded DNA (green) or single stranded DNA (red). The data indicate an increase in the percentage of sperm that have DNA damage, appearing about 21 days post treatment and reaching a maximum at 35 days. The proportion of sperm with moderate to high levels of DNA damage was significantly (P<0.001) greater in the 48 hour treatment group and was still observed at 49 days while most of the 24 hour treated animals had recovered by this stage. Of particular interest was the shift of the entire sperm population, in DNA fragmentation index (ratio of red fluorescence:total (red + green) fluorescence), indicating increased susceptibility of DNA denaturation in all cells. This was accompanied by an increase in DNA stainability (increase of green fluorescence) which is interpreted as being due to an increase in the number of immature sperm cells with less compacted chromatin which results from abnormal or unprocessed protamines. The sperm damage seen after a relatively mild heat treatment indicates possible mechanisms for the adverse effects of modern life styles on male fertility.
Correlation of life-history traits with the molecular diversity of bird nuclear coding elements

Question: Is there a relationship between mutations in nuclear coding genes sites and lifehistory traits? Analyses of polymorphism data of Aves nuclear genes suggest that this is the case. Data: Obtained from Polymorphix and Popset of GenBank: 752 groups of polymorphism data from 104 Aves nuclear genes of 15 families, 53 genera, 297 species. Search method: We used Watterson’s estimator (θw), calculated separately from the nonsynonymous (θa) and synonymous (θs) sites of the various gene fragments. We performed correlation analysis of the proportion of average non-synonymous mutation sites in coding genes sites and four life-history traits (body mass, metabolic rate, generation time, and longevity). Conclusions: The proportion of non-synonymous sites is significantly negatively correlated with body mass. But the proportion of non-synonymous sites is not significantly correlated with generation time. A larger fraction of slightly deleterious mutations is fixed in species with either a bigger body mass or a low effective population size (Ne).