Miracle-dz/UniFAR-FTUs huggingface dataset:
RNA Polymerase I-Specific Subunit CAST/hPAF49 Has aRole in the Activation of Transcription by UpstreamBinding Factor

ABSTRACT Eukaryotic RNA polymerases are large complexes, 12 subunits of which are structurally or functionally homologous across the three polymerase classes. Each class has a set of specific subunits, likely targets of their cognate transcription factors. We have identified and characterized a human RNA polymerase I (Pol I)-specific subunit, previously identified as ASE-1 (antisense of ERCC1) and as CD3ε-associated signal transducer (CAST), and here termed CAST or human Pol I-associated factor of 49 kDa (hPAF49), after mouse orthologue PAF49. We provide evidence for growth-regulated Tyr phosphorylation of CAST/hPAF49, specifically in initiation-competent Pol Iβ complexes in HeLa cells, at a conserved residue also known to be important for signaling during T-cell activation. CAST/hPAF49 can interact with activator upstream binding factor (UBF) and, weakly, with selectivity factor 1 (SL1) at the rDNA (ribosomal DNA repeat sequence encoding the 18S, 5.8S, and 28S rRNA genes) promoter. CAST/hPAF49-specific antibodies and excess CAST/hPAF49 protein, which have no effect on basal Pol I transcription, inhibit UBF-activated transcription following functional SL1-Pol I-rDNA complex assembly and disrupt the interaction of UBF with CAST/hPAF49, suggesting that interaction of this Pol I-specific subunit with UBF is crucial for activation. Drawing on parallels between mammalian and Saccharomyces cerevisiae Pol I transcription machineries, we advance one model for CAST/hPAF49 function in which the network of interactions of Pol I-specific subunits with UBF facilitates conformational changes of the polymerase, leading to stabilization of the Pol I-template complex and, thereby, activation of transcription.
Direct Physiologic Evidence of a Heteromodal Convergence Region for Proper Naming in Human Left Anterior Temporal Lobe

Retrieving the names of friends, loved ones, and famous people is a fundamental human ability. This ability depends on the left anterior temporal lobe (ATL), where lesions can be associated with impaired naming of people regardless of modality (e.g., picture or voice). This finding has led to the idea that the left ATL is a modality-independent convergence region for proper naming. Hypotheses for how proper-name dispositions are organized within the left ATL include both a single modality-independent (heteromodal) convergence region and spatially discrete modality-dependent (unimodal) regions. Here we show direct electrophysiologic evidence that the left ATL is heteromodal for proper-name retrieval. Using intracranial recordings placed directly on the surface of the left ATL in human subjects, we demonstrate nearly identical responses to picture and voice stimuli of famous U.S. politicians during a naming task. Our results demonstrate convergent and robust large-scale neurophysiologic responses to picture and voice naming in the human left ATL. This finding supports the idea of heteromodal (i.e., transmodal) dispositions for proper naming in the left ATL.
Increased prolactin concentrations in a patient with bipolar disorder.

A 58-year-old woman in the depressive phase of bipolar disorder ( BPD)3 type 1 enrolled in a clinical study of the efficacy of a new form of electroconvulsive therapy (ECT) for her depression, because ECT has not been commonly used for the treatment for BPD or depression. BPD is any of several mood disorders characterized by alternating episodes of depression and mania or by episodes of depression alternating with mild nonpsychotic excitement. BPD type 1 is distinguished from type 2 according to the severity of increased mood symptoms (1). At study enrollment, the patient reported severe sadness, a lack of motivation, fatigue, general malaise, feelings of guilt, and an increased need for sleep, but she had no suicidal or homicidal thoughts. She had no history of galactorrhea. A physical examination revealed nothing outstanding except decreased tendon reflexes in the patellar and the achilles, and a small nodule on the closure site from a previous hysterectomy. A cranial computed axial tomography (CAT) scan was performed to assess for increased intracranial pressure before proceeding with ECT; no unusual findings were noted. Initial blood tests showed a serum sodium concentration of 135 mEq/L (135 mmol/L; reference interval, 135–145 mmol/L), a high triglyceride concentration [217 mg/dL (2.45 mmol/L); reference interval, <150 mg/dL (<1.69 mmol/L)], and a VLDL cholesterol concentration of 43 mg/dL [1.11 mmol/L; reference interval, <30 mg/dL (<0.78 mmol/L)]. The results of a urine drug screen for amphetamines, barbiturates, benzodiazepine, cannabinoids, cocaine, opiates, and phencyclidine were negative. As per the study protocol, a baseline blood sample was drawn 5 min before treatment, and at 5, 15, 30, 45 min after seizure termination. Prolactin (PRL) concentrations were assessed from these blood draws during the second and fourth treatments of the study by means of a 2-site sandwich immunochemiluminometric assay (Siemens ADVIA Centaur® System). These …
Three-dimensional electron microscopy reconstruction and cysteine-mediated crosslinking provide a model of the type III secretion system needle tip complex

Type III secretion systems are found in many Gram‐negative bacteria. They are activated by contact with eukaryotic cells and inject virulence proteins inside them. Host cell detection requires a protein complex located at the tip of the device's external injection needle. The Shigella tip complex (TC) is composed of IpaD, a hydrophilic protein, and IpaB, a hydrophobic protein, which later forms part of the injection pore in the host membrane. Here we used labelling and crosslinking methods to show that TCs from a ΔipaB strain contain five IpaD subunits while the TCs from wild‐type can also contain one IpaB and four IpaD subunits. Electron microscopy followed by single particle and helical image analysis was used to reconstruct three‐dimensional images of TCs at ∼20 Å resolution. Docking of an IpaD crystal structure, constrained by the crosslinks observed, reveals that TC organisation is different from that of all previously proposed models. Our findings suggest new mechanisms for TC assembly and function. The TC is the only site within these secretion systems targeted by disease‐protecting antibodies. By suggesting how these act, our work will allow improvement of prophylactic and therapeutic strategies.
U NIT R OOTS AND CYCLES IN THE MAIN MACROECONOMIC VARIABLES FOR A RGENTINA

In this paper we study the integration properties of some of the main macroeconomic series of Argentina. We present a robust methodology for the analysis of persistence of shocks affecting macroeconomic series and its consequences on the modeling of the cyclical and permanent components. Our strategy consists on testing the stationarity of the series by using a sequence of indicators in such a way that we can analyze the problem from three converging points of view: Persistence of the series, Unit Root (UR) and UR with a Structural Breaks. In such a way we reach robust results regarding the integration properties of the main 14 Argentinean macroeconomic time series. Thus, we are able to classify them in four homogenous groups according to its order of integration. This allows us to determine the best strategy for modeling the cyclical component of each variable. For example, we found that the GDP can be robustly considered integrated of order one, I(1). Shocks seem to have permanent effects on the GDP and consequently a stochastic process is the best alternative for modeling its behavior. Finally, with respect to the date of the structural break relevant for the Argentinean economy, the years 1988-89 concentrate the greatest number of breaks detected endogenously for the series of these work. Thus, we can conclude that the convertibility does not appear to be a point of structural change in the data generating process of the main macroeconomic series of Argentina.
Factor modeling for high-dimensional time series: inference for the number of factors

This paper deals with the factor modeling for high-dimensional time series based on a dimension-reduction viewpoint. Under stationary settings, the inference is simple in the sense that both the number of factors and the factor loadings are estimated in terms of an eigenanalysis for a nonnegative definite matrix, and is therefore applicable when the dimension of time series is on the order of a few thousands. Asymptotic properties of the proposed method are investigated under two settings: (i) the sample size goes to infinity while the dimension of time series is fixed; and (ii) both the sample size and the dimension of time series go to infinity together. In particular, our estimators for zero-eigenvalues enjoy faster convergence (or slower divergence) rates, hence making the estimation for the number of factors easier. In particular, when the sample size and the dimension of time series go to infinity together, the estimators for the eigenvalues are no longer consistent. However, our estimator for the number of the factors, which is based on the ratios of the estimated eigenvalues, still works fine. Furthermore, this estimation shows the so-called “blessing of dimensionality” property in the sense that the performance of the estimation may improve when the dimension of time series increases. A two-step procedure is investigated when the factors are of different degrees of strength. Numerical illustration with both simulated and real data is also reported.
Enhanced nutrient supply to the California Current Ecosystem with global warming and increased stratification in an earth system model

A leading hypothesis relating productivity with climate variability in the California Current Ecosystem (CCE) describes an alternation between warmer, well‐stratified periods of low productivity and cooler periods of high productivity. This empirical relationship suggests that productivity will decline with global warming. Here, we explore the response of productivity to future climate change in the CCE using an earth system model. This model projects increases in nitrate supply and productivity in the CCE during the 21st century despite increases in stratification and limited change in wind‐driven upwelling. We attribute the increased nitrate supply to enrichment of deep source waters entering the CCE resulting from decreased ventilation of the North Pacific. Decreases in dissolved‐oxygen concentration and increasing acidification accompany projected increases in nitrate. This analysis illustrates that anthropogenic climate change may be unlike past variability; empirical relationships based on historical observations may be inappropriate for projecting ecosystem responses to future climate change.
How to Round Subspaces: A New Spectral Clustering Algorithm

A basic problem in spectral clustering is the following. If a solution obtained from the spectral relaxation is close to an integral solution, is it possible to find this integral solution even though they might be in completely different basis? In this paper, we propose a new spectral clustering algorithm. It can recover a $k$-partition such that the subspace corresponding to the span of its indicator vectors is $O(\sqrt{opt})$ close to the original subspace in spectral norm with $opt$ being the minimum possible ($opt \le 1$ always). Moreover our algorithm does not impose any restriction on the cluster sizes. Previously, no algorithm was known which could find a $k$-partition closer than $o(k \cdot opt)$. We present two applications for our algorithm. First one finds a disjoint union of bounded degree expanders which approximate a given graph in spectral norm. The second one is for approximating the sparsest $k$-partition in a graph where each cluster have expansion at most $\phi_k$ provided $\phi_k \le O(\lambda_{k+1})$ where $\lambda_{k+1}$ is the $(k+1)^{st}$ eigenvalue of Laplacian matrix. This significantly improves upon the previous algorithms, which required $\phi_k \le O(\lambda_{k+1}/k)$.
Justification of radiographic examinations: What are the key issues?

Justification of radiographic examinations is the practice of evaluating requested radiological examinations to assess for clinical merit and appropriateness based on clinical notes and patient information. This implies that justification in radiography requires the evaluation of requested examinations, the justification of exposures being applied and determining whether patients fit the recommended criteria for the procedure. Medico‐legal requirements by the professional registration body, the Medical Radiation Practice Board of Australia (MRPBA), identify justification as an advocated and obligatory practice for radiographers. Yet, justification remains an inconsistent practice implemented amongst Australian radiographers. This review aims to identify associated barriers inhibiting the consistent practice of justification and the hesitance by radiographers in practicing justification responsibilities. It also recommends a change in workplace culture which encourages radiographers to accept a more autonomous role that cultivates critical thinking, reflection and research‐informed decision making as justification will ultimately benefit patients.
High Dynamic Range Image Watermarking

High Dynamic Range (HDR) images represent the future format for digital images since they allow more sensitive rendering. However, nowadays special types of preprocessing collectively known as tone mapping operators are needed to adapt HDR images to currently existing displays. Tone mapped images, although of reduced dynamic range, have nonetheless high quality and hence retain some commercial value. In this paper we propose a solution to the problem of HDR watermarking, e.g. for copyright embedding, that should survive tone mapping. Therefore, the requirements imposed on the watermark encompass imperceptibility, a certain degree of security and robustness to tone mapping operators. The proposed watermarking system belongs to the blind, detectable category, it is based on the QIM paradigm and employs a higher order statistic as feature. Preliminary experimental analysis shows positive results; more work is needed and currently underway.
Musculotendon simulation for hand animation

We describe an automatic technique for generating the motion of tendons and muscles under the skin of a traditionally animated character. This is achieved by integrating the traditional animation pipeline with a novel biomechanical simulator capable of dynamic simulation with complex routing constraints on muscles and tendons. We also describe an algorithm for computing the activation levels of muscles required to track the input animation. We demonstrate the results with several animations of the human hand.
Vaccination for hepatitis C virus: closing in on an evasive target

Hepatitis C virus (HCV) infects more than 170 million people globally and is a leading cause of liver cirrhosis, transplantation and hepatocellular carcinoma. Current gold-standard therapy often fails, has significant side effects in many cases and is expensive. No vaccine is currently available. The fact that a significant proportion of infected people spontaneously control HCV infection in the setting of an appropriate immune response suggests that a vaccine for HCV is a realistic goal. A comparative analysis of infected people with distinct clinical outcomes has enabled the characterization of many important innate and adaptive immune processes associated with viral control. It is clear that a successful HCV vaccine will need to exploit and enhance these natural immune defense mechanisms. New HCV vaccine approaches, including peptide, recombinant protein, DNA and vector-based vaccines, have recently reached Phase I/II human clinical trials. Some of these technologies have generated robust antiviral immunity in healthy volunteers and infected patients. The challenge now is to move forward into larger at-risk or infected populations to truly test efficacy.
Development and Evaluation of an Affordable Real-Time Qualitative Assay for Determining HIV-1 Virological Failure in Plasma and Dried Blood Spots

ABSTRACT Virological failure (VF) has been identified as the earliest, most predictive determinant of HIV-1 antiretroviral treatment (ART) failure. Due to the high cost and complexity of virological monitoring, VF assays are rarely performed in resource-limited settings (RLS). Rather, ART failure is determined by clinical monitoring and to a large extent immunological monitoring. This paper describes the development and evaluation of a low-cost, dried blood spot (DBS)-compatible qualitative assay to determine VF, in accordance with current WHO guideline recommendations for therapy switching in RLS. The assay described here is an internally controlled qualitative real-time PCR targeting the conserved long terminal repeat domain of HIV-1. This assay was applied to HIV-1 subtypes A to H and further evaluated on HIV-1 clinical plasma samples from South Africa (n = 191) and Tanzania (n = 42). Field evaluation was performed in Uganda using local clinical plasma samples (n = 176). Furthermore, assay performance was evaluated for DBS. This assay is able to identify VF for all major HIV-1 group M subtypes with equal specificity and has a lower detection limit of 1.00E+03 copies/ml for plasma samples and 5.00E+03 copies/ml for DBS. Comparative testing yielded accurate VF determination for therapy switching in 89% to 96% of samples compared to gold standards. The assay is robust and flexible, allowing for “open platform” applications and producing results comparable to those of commercial assays. Assay design enables application in laboratories that can accommodate real-time PCR equipment, allowing decentralization of testing to some extent. Compatibility with DBS extends access of sampling and thus access to this test to remote settings.
Phytochemical Studies and Genetic Diversity in Sesame ( Sesamum indicum L . )

Completely Randomized Design (CRD). Extracts from the seeds were screened for phenolics, saponin, alkaloid, flavonoid, tannin, phytate and oxalate. Data obtained were subjected to Analysis of Variance (ANOVA) and means separated using the Duncan Multiple Range Test (DMRT). The results revealed high genetic diversity among the 23 sesame genotypes and showed that the phenolic contents had negative correlation with tannin while flavonoid had positive correlation with saponin and alkaloid. The information provided by this research will help breeders in future breeding programmes to develop improved varieties of sesame.
Achieving eye contact in a one-to-many 3D video teleconferencing system

We present a set of algorithms and an associated display system capable of producing correctly rendered eye contact between a three-dimensionally transmitted remote participant and a group of observers in a 3D teleconferencing system. The participant's face is scanned in 3D at 30Hz and transmitted in real time to an autostereoscopic horizontal-parallax 3D display, displaying him or her over more than a 180° field of view observable to multiple observers. To render the geometry with correct perspective, we create a fast vertex shader based on a 6D lookup table for projecting 3D scene vertices to a range of subject angles, heights, and distances. We generalize the projection mathematics to arbitrarily shaped display surfaces, which allows us to employ a curved concave display surface to focus the high speed imagery to individual observers. To achieve two-way eye contact, we capture 2D video from a cross-polarized camera reflected to the position of the virtual participant's eyes, and display this 2D video feed on a large screen in front of the real participant, replicating the viewpoint of their virtual self. To achieve correct vertical perspective, we further leverage this image to track the position of each audience member's eyes, allowing the 3D display to render correct vertical perspective for each of the viewers around the device. The result is a one-to-many 3D teleconferencing system able to reproduce the effects of gaze, attention, and eye contact generally missing in traditional teleconferencing systems.
Radiosynthesis of 6’-Deoxy-6’[18F]Fluorosucrose via Automated Synthesis and Its Utility to Study In Vivo Sucrose Transport in Maize (Zea mays) Leaves

Sugars produced from photosynthesis in leaves are transported through the phloem tissues within veins and delivered to non-photosynthetic organs, such as roots, stems, flowers, and seeds, to support their growth and/or storage of carbohydrates. However, because the phloem is located internally within the veins, it is difficult to access and to study the dynamics of sugar transport. Radioactive tracers have been extensively used to study vascular transport in plants and have provided great insights into transport dynamics. To better study sucrose partitioning in vivo, a novel radioactive analog of sucrose was synthesized through a completely chemical synthesis route by substituting fluorine-18 (half-life 110 min) at the 6’ position to generate 6’-deoxy-6’[18F]fluorosucrose (18FS). This radiotracer was then used to compare sucrose transport between wild-type maize plants and mutant plants lacking the Sucrose transporter1 (Sut1) gene, which has been shown to function in sucrose phloem loading. Our results demonstrate that 18FS is transported in vivo, with the wild-type plants showing a greater rate of transport down the leaf blade than the sut1 mutant plants. A similar transport pattern was also observed for universally labeled [U-14C]sucrose ([U-14C]suc). Our findings support the proposed sucrose phloem loading function of the Sut1 gene in maize, and additionally demonstrate that the 18FS analog is a valuable, new tool that offers imaging advantages over [U-14C]suc for studying phloem transport in plants.
Consensus in a Box: Inexpensive Coordination in Hardware

Consensus mechanisms for ensuring consistency are some of the most expensive operations in managing large amounts of data. Often, there is a trade off that involves reducing the coordination overhead at the price of accepting possible data loss or inconsistencies. As the demand for more efficient data centers increases, it is important to provide better ways of ensuring consistency without affecting performance. In this paper we show that consensus (atomic broadcast) can be removed from the critical path of performance by moving it to hardware. As a proof of concept, we implement Zookeeper's atomic broadcast at the network level using an FPGA. Our design uses both TCP and an application specific network protocol. The design can be used to push more value into the network, e.g., by extending the functionality of middleboxes or adding inexpensive consensus to in-network processing nodes. To illustrate how this hardware consensus can be used in practical systems, we have combined it with a mainmemory key value store running on specialized microservers (built as well on FPGAs). This results in a distributed service similar to Zookeeper that exhibits high and stable performance. This work can be used as a blueprint for further specialized designs.