Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction of DevR with Multiple Binding Sites Synergistically Activates Divergent Transcription of narK2-Rv1738 Genes in Mycobacterium tuberculosis

ABSTRACT Under hypoxic conditions or upon exposure to low concentrations of nitric oxide, DevR transcriptional regulator mediates the activation of ∼50 genes that are believed to assist in dormancy development in Mycobacterium tuberculosis. Most of the strongly induced genes are characterized by the presence of one to four copies of a Dev box-like sequence at an upstream location. Among these are several gene pairs that are transcribed in opposite directions. This arrangement could provide for coordinated control of the adjacent genes under inducing conditions. In this work, we report the first detailed analysis of DevR-mediated hypoxic regulation of narK2-Rv1738 genes that are oppositely oriented in M. tuberculosis. Phosphorylated DevR interacts with intergenic sequences and protects ∼80 bp of DNA that contains three binding sites, designated Dev boxes D1, D2, and D3. The hypoxia-specific transcription start points of narK2 and Rv1738 were mapped, and it was noted that the −35 elements of both promoters overlapped with the proximally placed Dev box. DevR bound cooperatively to adjacently placed D2 and D3 boxes while binding to D1 was independent of DevR interaction with the D2 and D3 boxes. Mutational analysis and green fluorescent protein reporter assays established that the three Dev boxes function synergistically to mediate maximal transcriptional induction of both narK2 and Rv1738 in hypoxic cultures of M. tuberculosis. Analysis of narK2 promoter activity indicates that it is under negative regulation in addition to DevR-mediated positive regulation and also reveals differences between M. tuberculosis and Mycobacterium bovis BCG.
Spaceborne observation of columnar water vapor: SSMI observations and algorithm

An analysis of the transfer of microwave radiation with a frequency between 10 and 40 GHz through a cloud-free atmosphere is given, and the limitations of employing observations at 22.235 GHz for sensing the columnar water vapor (CWV) in the moist atmosphere (CWV > 40 kg m−2) are shown. It is because of this limitation that a new method for the retrieval of columnar water vapor is described. This method uses both the horizontally and vertically polarized brightness temperatures measured at 19.35 GHz by the special sensor microwave imager (SSMI) which was launched as part of the Defense Military Satellite Program. The water vapor derived from the SSMI observations is validated against radiosonde observations that are near coincident in time and space with an rms error of 6 kg m−2. This large rms is in part due to sensitivity of the retrieval method to the surface emission. Distributions of CWV over the oceans were obtained for a 3-month period starting September 1987. These results are compared to other water vapor retrievals for the same period using the same microwave radiance data; they show close agreement except over the warmest water in the equatorial tropics.
Sm-Nd dating of the giant Sullivan Pb-Zn-Ag deposit, British Columbia

We report here Sm and Nd isotope data for hydrothermal tourmalinites and sulfide ores from the giant Sullivan Pb-Zn-Ag deposit, which occurs in the lower part of the Mesoproterozoic Purcell (Belt) Supergroup. Whole-rock samples of quartz-tourmaline tourmalinite from the footwall alteration pipe yield a Sm-Nd isochron age of 1470 ± 59 Ma, recording synsedimentary B metasomatism of clastic sediments during early evolution of the Sullivan hydrothermal system. Data for variably altered (chloritized and/or albitized) tourmalinites from the hanging wall of the deposit, which are believed to have formed originally ca. 1470 Ma, define a younger 1076 ± 77 Ma isochron because of resetting of Sm and Nd isotopes during Grenvillian metamorphism. HCl leachates of bedded Pb-Zn ore yield a Sm-Nd isochron age of 1451 ± 46 Ma, which is consistent with syngenetic-exhalative mineralization ca. 1470 Ma; this age could also reflect a slightly younger, epigenetic hydrothermal event. Results obtained for the Sullivan deposit indicate that the Sm-Nd geochronometer has the potential to directly date mineralization and alteration in stratabound sulfide deposits that are not amenable to dating by other isotope methods.
Conditional Risk Premia and Correlations in Commodity Futures Markets

The article studies the conditional risk premia of commodity futures and the variation over time in their correlations with traditional asset classes. We find that investors in commodity futures markets earned significant risk premia over the period 1979004. We also reveal that the conditional correlations between commodity futures and equity returns fell over time, a sign that commodity futures have become better tools for strategic asset allocation. The correlations with equity returns also fell in periods of above average market volatility. We see this as welcome news to long institutional investors as they need the benefits of diversification most in periods of high market volatility.
Incentive Payment Design for Electricity Demand Response

In power systems, the interruptible load management (ILM) plays an important role in boosting demand responses, which can help a power system operator solve a variety of problems. A critical issue is the incentive paid to the consumers to participate in the ILM. It is widely recognized that integration of consumers' willingness to curtail load in the ILM is helpful to improve the allocation efficiency of the limited electricity resource. In order to design such ILMs, new methods for incentive payment of interruptible load, including the pay-as-you-go method and the pay-in-advance method, are presented, in which the consumers' type parameters are introduced to model the consumers' willingness to curtail load. It is shown that consumers with relatively large willingness to curtail load are encouraged to more actively participate in the ILM, and consumers are also encouraged to follow the load interruption dispatch in accordance with their true willingness to curtail load. Numerical examples are presented to validate the reasonableness and effectiveness of the proposed methods.
Biochemical and Kinetic Characterization of the Recombinant ADP-Forming Acetyl Coenzyme A Synthetase from the Amitochondriate Protozoan Entamoeba histolytica

ABSTRACT Entamoeba histolytica, an amitochondriate protozoan parasite that relies on glycolysis as a key pathway for ATP generation, has developed a unique extended PPi-dependent glycolytic pathway in which ADP-forming acetyl-coenzyme A (CoA) synthetase (ACD; acetate:CoA ligase [ADP-forming]; EC 6.2.1.13) converts acetyl-CoA to acetate to produce additional ATP and recycle CoA. We characterized the recombinant E. histolytica ACD and found that the enzyme is bidirectional, allowing it to potentially play a role in ATP production or in utilization of acetate. In the acetate-forming direction, acetyl-CoA was the preferred substrate and propionyl-CoA was used with lower efficiency. In the acetyl-CoA-forming direction, acetate was the preferred substrate, with a lower efficiency observed with propionate. The enzyme can utilize both ADP/ATP and GDP/GTP in the respective directions of the reaction. ATP and PPi were found to inhibit the acetate-forming direction of the reaction, with 50% inhibitory concentrations of 0.81 ± 0.17 mM (mean ± standard deviation) and 0.75 ± 0.20 mM, respectively, which are both in the range of their physiological concentrations. ATP and PPi displayed mixed inhibition versus each of the three substrates, acetyl-CoA, ADP, and phosphate. This is the first example of regulation of ACD enzymatic activity, and possible roles for this regulation are discussed.
The Lincoln Sill

The Lincoln sill extends from Squirrel Island, just off Boothbay Peninsula on the central part of the Maine coast, inland in a northerly direction for some 50 miles, with nearly continuous outcrops. The mineral composition of the sill is unusual, consisting of large dark-colored alkalic feldspars generally with euhedral to subhedral outlines set in a matrix of biotite, hornblende, and augite with minor feldspar and quartz. The sill is nearly vertical throughout most of its extent, and its structure is essentially concordant with regional trend lines. It has been suggested that the origin of the magma which produced this unusual rock type with the attendant unusual chemical composition is through hybridization. Late- or post-magma tic alterations, the intrusion of granitic material, and dynamic metamorphism superimposed on the original intrusive account for the rock in its present condition.
Far-field estimation of antennas above the earth using hemispherical source reconstruction

Far-field pattern of an antenna above the earth is different from the characteristics in free space. We propose an estimation method of antenna far-field above the earth from near-field data in free space. The method reconstructs current distribution on a surface of an antenna from near-field data in free space and estimates the far-field pattern above the earth using the reconstructed current distribution. It is shown that the use of the proposed method achieves the far-field estimation of an antenna above the earth from near-field data in free space by numerical simulation.
Quality‐of‐life, mood and executive functioning after childhood craniopharyngioma treated with surgery and proton beam therapy

Primary objective: Childhood craniopharyngioma, a benign tumour with a good survival rate, is associated with important neurocognitive and psychological morbidity, reducing quality‐of‐life (QoL). Method: This retrospective study analysed QoL, mood disorders, everyday executive functioning and disease's impact on family life in 29 patients (mean age at diagnosis 7 years 10 months (SD = 4.1); mean follow‐up period 6 years 2 months (SD = 4.5)) treated for childhood craniopharyngioma by surgery combined with radiotherapy using proton beam. Assessment included a semi‐structured interview and standardized scales evaluating self‐report of QoL (Kidscreen 52) and depression (MDI‐C) and proxy‐reports of QoL (Kidscreen 52), executive functioning (BRIEF) and disease's impact (Hoare and Russel Questionnaire). Results: Twenty‐three families answered the questionnaires completely. Overall QoL self‐report was within the normal range. QoL proxy‐report was lower than self‐report. Eleven patients reported depression; 24–38% had dysexecutive symptoms. A majority of families felt ‘very concerned’ by the disease. Depression and low parental educational level were associated with lower QoL and higher levels of executive dysfunction. Conclusion: Given the high morbidity of childhood craniopharyngioma, screening for psychosocial outcome, cognitive functioning, including executive functions, mood and QoL should be systematic and specific interventions should be developed and implemented.
Bounds and Capacity Theorems for Cognitive Interference Channels With State

A class of cognitive interference channels with state are investigated, in which a primary transmitter sends a message to two receivers (receivers 1 and 2) with assistance of a cognitive transmitter (that knows the primary transmitter's message), and the cognitive transmitter also sends a separate message to receiver 2. The channel is corrupted by an independent and identically distributed state sequence. The scenario, in which the state sequence is noncausally known at both the cognitive transmitter and receiver 2, is first studied. The capacity region is obtained for both the discrete memoryless and Gaussian channels. The second scenario, in which the state sequence is noncausally known only at the cognitive transmitter, is further studied. Inner and outer bounds on the capacity region are obtained for the discrete memoryless channel and its degraded version. The capacity region is characterized for the degraded semideterministic channel and for channels that satisfy a less noisy condition. The Gaussian channels are further studied, which are partitioned into two cases based on how the interference compares with the signal at receiver 1. For each case, inner and outer bounds on the capacity region are derived, and partial boundaries of the capacity region are characterized. The full capacity region is also characterized for channels that satisfy certain conditions. It is shown that certain Gaussian channels achieve the capacity of the same channels with state noncausally known at both the cognitive transmitter and receiver 2.
Evidence for tunneling in base-catalyzed isomerization of glyceraldehyde to dihydroxyacetone by hydride shift under formose conditions

Significance This paper describes experimental and computational evidence that the hydride shift that converts glyceraldehyde to dihydroxyacetone at basic pH with Ca2+ catalysis proceeds primarily by quantum tunneling. This answers the last question about the mechanism of the formose reaction, in which formaldehyde is converted to higher sugars under these conditions. This reaction has long been seen as an important clue to the formation of molecules needed for life under prebiotic conditions on Earth. Earlier work showed that the mechanism involved a hydride shift, not a deprotonation, and this work confirms those conclusions. It shows the critical role of tunneling, a quantum effect important in chemistry and biology, and in likely prebiotic reactions on Earth or elsewhere, one concern of astrobiology. Hydrogen atom transfer reactions between the aldose and ketose are key mechanistic features in formose chemistry by which formaldehyde is converted to higher sugars under credible prebiotic conditions. For one of these transformations, we have investigated whether hydrogen tunneling makes a significant contribution to the mechanism by examining the deuterium kinetic isotope effect associated with the hydrogen transfer during the isomerization of glyceraldehyde to the corresponding dihydroxyacetone. To do this, we developed a quantitative HPLC assay that allowed us to measure the apparent large intrinsic kinetic isotope effect. From the Arrhenius plot of the kinetic isotope effect, the ratio of the preexponential factors AH/AD was 0.28 and the difference in activation energies Ea(D) − Ea(H) was 9.1 kJ·mol−1. All these results imply a significant quantum-mechanical tunneling component in the isomerization mechanism. This is supported by multidimensional tunneling calculations using POLYRATE with small curvature tunneling.
A Square Root Unscented Kalman Filter for visual monoSLAM

This paper introduces a square root unscented Kalman filter (SRUKF) solution to the problem of performing visual simultaneous localization and mapping (SLAM) using a single camera. Several authors have proposed the conventional UKF for SLAM to improve the handling of non-linearities compared with the more widely used EKF, but at the expense increasing computational complexity from O(N2) to O(N3) in the map size, making it unattractive for video-rate application. Van der Merwe and Wan's general SRUKF delivers identical results to a general UKF along with computational savings, but remains O(N3) overall. This paper shows how the SRUKF for the SLAM problem can be re-posed with O(N2) complexity, matching that of the EKF. The paper also shows how the method of inverse depth feature initialization developed by Montiel et al. for the EKF can be reformulated to work with the SRUKF. Experimental results confirm that the SRUKF and the UKF produce identical estimates, and that the SRUKF is more consistent than the EKF. Although the complexity is the same, the SRUKF remains more expensive to compute.
Golgi-localized UDP-glucose transporter is required for cell wall integrity in rice

Cell wall-related nucleotide sugar transporters (NSTs) theoretically supply the cytosolic nucleotide sugars for glycosyltransferases (GTs) to carry out ploysaccharide synthesis and modification in the Golgi apparatus. However, the regulation of cell wall synthesis by NSTs remains undescribed. Recently, we have reported the functional characterization of Oryza sativa nucleotide sugar transport (Osnst1) mutant and its corresponding gene. OsNST1/BC14 is localized in the Golgi apparatus and transports UDP-glucose. This mutant provides us with a unique opportunity for evaluation of its abroad impacts on cell wall structure and components. We previously examined cell wall composition of bc14 and wild type plants. Here, the spatial distribution of these cell wall alterations was analyzed by immunolabeling approach. Analysis of the sugar yield in different cell wall fractions indicated that this mutation improves the extractability of cell wall components. Field emission scanning electron microscopy further showed that the orientation of microfibrils in bc14 is irregular when compared to that in wild type. Therefore, this UDP-glucose transporter, making substrates available for polysaccharide biosynthesis, plays a critical role in maintaining cell wall integrity.
Privacy Preserving Third Party Auditing in Multi Cloud Storage Environment

The on-demand, pay-per-use, and scalable services provided in cloud model guarantee to reduce capital as well as running expenditures for both hardware and software. In cloud environment, users can remotely store their data and access them from a shared pool of configurable computing resources, without local data storage burden. We discuss various methods related to the security and privacy capabilities in cloud paradigm especially data storage in multi cloud environment. We provide three models in form of multicloud architectures which allow categorizing the schemes and analyze them according to their security benefits. The different methods include, resource replication, split application system into tiers based on PIR methods, split both application logic and data into segments. In addition, since the integrity protection of data is a fearsome task in Cloud computing for users with limited computing resources, vulnerabilities in user data privacy are also possible in third party auditing. So we propose a safe cloud storage methodology which supports privacy-preserving third party auditing. And we study the outcomes to perform audits concurrently for multiple users in an efficient manner. Experimental results show that the third party auditing computation time is better than existing approach.
Association between Mammographic Breast Density and Breast Cancer Tumor Characteristics

Objective: Few studies have examined the association between breast density and breast cancer tumor characteristics. We examined the association between hormonal, proliferative, and histologic tumor characteristics and mammographic breast density in women with breast cancer. Methods: We conducted a cross-sectional analysis in 546 women diagnosed with invasive breast cancer to evaluate the associations between breast density and tumor size, lymph node status, lymphatic or vascular invasion, histologic grade, nuclear grade, tumor differentiation, mitotic index, tumor necrosis, Ki-67 proliferation, estrogen receptor, progesterone receptor, p53, p27, cyclin E, Bcl-2, and C-erb-B2 invasion. Breast density was classified as fatty (Breast Imaging Reporting and Data System code 1 or 2; n = 373) or dense (Breast Imaging Reporting and Data System code 3 or 4; n = 173) for the cancer-free breast. A single pathologist measured all tumor markers. We examined whether the relationships were modified by interval cancer or screen-detected cancer. Results: Women with a tumor size >1.0 cm were more likely to have dense breasts compared with women with a tumor size ≤1.0 cm after adjusting for confounders (odds ratio, 2.0; 95% confidence interval, 1.2-3.4 for tumor sizes 1.1-2.0 cm; odds ratio, 2.3; 95% confidence interval, 1.3-4.4 for tumor sizes 2.1-10 cm). Tumor size, lymph node status, and lymphatic or vascular invasion were positively associated with breast density among screen-detected cancers. Histologic grade and mitotic index were negatively associated with breast density in women diagnosed with an interval cancer. Conclusions: These results suggest that breast density is related to tumor size, lymph node status, and lymphatic or vascular invasion in screen-detected cancers. Additional studies are needed to address whether these associations are due to density masking the detection of some tumors, a biological relationship, or both.
Use of sulphur and carbon stable-isotope composition of fish scales and muscles to identify the origin of fish

Use of sulphur and carbon stable-isotope composition of fish scales and muscles to identify the origin of fish δ34S and δ13C analyses were used to determine the origin of trout specimens. The isotope record of their scales and muscles are compared with a database previously obtained from wild- and reared fish coming from Polish rivers and pond farms. The comparison made it possible to find out whether the trout were wild or reared.
User Group Oriented Temporal Dynamics Exploration

Temporal online content becomes the zeitgeist to reflect our interests and changes. Active users are essential participants and promoters behind it. Temporal dynamics becomes a viable way to investigate users. However, most current work only use global temporal trend and fail to distinguish such fine-grained patterns across groups. Different users have diverse interest and exhibit distinct behaviors, and temporal dynamics tend to be different. This paper proposes GrosToT (Group Specific Topics-over-Time), a unified probabilistic model to infer latent user groups and temporal topics at the same time. It models group-specific temporal topic variation from social content. By leveraging the comprehensive group-specific temporal patterns, GrosToT significantly outperforms state-of-the-art dynamics modeling methods. Our proposed approach shows advantage not only in temporal dynamics but also group content modeling. The dynamics over different groups vary, reflecting the groups' intention. GrosToT uncovers the interplay between group interest and temporal dynamics. Specifically, groups' attention to their medium-interested topics are event-driven, showing rich bursts; while its engagement in group's dominating topics are interest-driven, remaining stable over time.
On the Background Model For Non-linear Inversion of Seismic Data

This paper discusses the forward modelling based on scattering theory which forms the first step in the nonlinear inversion of seismic data. Since most of the present non-linear inversion techniques are still associated with high computational costs, we have focused our efforts on simplifying the forward model. In the method an inhomogeneous background model is exploited to reduce the contrasts sufficiently, and therefore to allow the linearisation. Using an inhomogeneous background model, on the other hand, complicates our problem significantly, as wavefields have to be calculated in an inhomogeneous medium. For this we use the WKBJ approximation. In the subsurface the possibility exists that the contrast is still too large for linearisation, resulting in inaccurately predicted wavefields. However, we demonstrate that by including a second (or a third) Neumann iteration into our modelling, this problem is resolved. In this paper, the 1D forward modelling results are presented, but the method is readily extendable to 2D and 3D configurations. We will discuss the earth model with both density and velocity contrast.