Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Mediator Enhances Activator-Facilitated Recruitment of RNA Polymerase II and Promoter Recognition by TATA-Binding Protein (TBP) Independently of TBP-Associated Factors

ABSTRACT Mediator is a general cofactor implicated in the functions of many transcriptional activators. Although Mediator with different protein compositions has been isolated, it remains unclear how Mediator facilitates activator-dependent transcription, independent of its general stimulation of basal transcription. To define the mechanisms of Mediator function, we isolated two forms of human Mediator complexes (Mediator-P.5 and Mediator-P.85) and demonstrated that Mediator-P.5 clearly functions by enhancing activator-mediated recruitment of RNA polymerase II (pol II), whereas Mediator-P.85 works mainly by stimulating overall basal transcription. The coactivator function of Mediator-P.5 was not impaired when TATA-binding protein (TBP) was used in place of TFIID, but it was abolished when another general cofactor, PC4, was omitted from the reaction or when Mediator-P.5 was added after pol II entry into the preinitiation complex. Moreover, Mediator- P.5 is able to enhance TBP binding to the TATA box in an activator-dependent manner. Our data provides biochemical evidence that Mediator functions by facilitating activator-mediated recruitment of pol II and also promoter recognition by TBP, both of which can occur in the absence of TBP-associated factors in TFIID.
Reliability of reporting of self-monitoring of blood glucose in pregnant women.

OBJECTIVE To determine the accuracy of reporting of self-monitored blood glucose in pregnant women with diabetes. DESIGN A descriptive study. Patient-recorded logs of self-monitored blood glucose values were compared to meter memory values. SETTING AND PARTICIPANTS A convenience sample of 85 pregnant women with pregestational and gestational diabetes enrolled in a perinatal diabetes program in an urban teaching hospital. RESULTS Accuracy significantly differed by diabetes type (p = .015). Women with type 1 diabetes did not accurately record on average 36.7% of blood glucose values as compared to 8.5% of type 2, 21.2% of GDMA(1) (gestational diabetes mellitus, diet controlled), and 23.4% of GDMA(2) (gestational diabetes mellitus, insulin controlled). Age positively affected accuracy, but accuracy was not affected by marital status, educational background, or duration of diabetes. Statistical significance was shown between values from women with private health insurance and women with Medicaid. Eighty percent of the sample overreported by adding phantom values in the logbook, which did not differ by diabetes type. Approximately 70% underreported by not logging values in the meter memory that was statistically significant by diabetes type. CONCLUSION Assessment of the reliability of self-monitored blood glucose results from pregnant women with diabetes is recommended owing to a significant degree of falsification.
Evaluation of a direct motion estimation/correction method in respiratory‐gated PET/MRI with motion‐adjusted attenuation

Purpose Respiratory motion compensation in PET/CT and PET/MRI is essential as motion is a source of image degradation (motion blur, attenuation artifacts). In previous work, we developed a direct method for joint image reconstruction/motion estimation (JRM) for attenuation‐corrected (AC) respiratory‐gated PET, which uses a single attenuation‐map (μ‐map). This approach was successfully implemented for respiratory‐gated PET/CT, but since it relied on an accurate μ‐map for motion estimation, the question of its applicability in PET/MRI is open. The purpose of this work is to investigate the feasibility of JRM in PET/MRI and to assess the robustness of the motion estimation when a degraded μ‐map is used. Methods We performed a series of JRM reconstructions from simulated PET data using a range of simulated Dixon MRI sequence derived μ‐maps with wrong attenuation values in the lungs, from −100% (no attenuation) to +100% (double attenuation), as well as truncated arms. We compared the estimated motions with the one obtained from JRM in ideal conditions (no noise, true μ‐map as an input). We also applied JRM on 4 patient datasets of the chest, 3 of them containing hot lesions. Patient list‐mode data were gated using a principal component analysis method. We compared SUVmax values of the JRM reconstructed activity images and non motion‐corrected images. We also assessed the estimated motion fields by comparing the deformed JRM‐reconstructed activity with individually non‐AC reconstructed gates. Results Experiments on simulated data showed that JRM‐motion estimation is robust to μ‐map degradation in the sense that it produces motion fields similar to the ones obtained when using the true μ‐map, regardless of the attenuation errors in the lungs (< 0.5% mean absolute difference with the reference motion field). When using a μ‐map with truncated arms, JRM estimates a motion field that stretches the μ‐map in order to match the projection data. Results on patient datasets showed that using JRM improves the SUVmax values of hot lesions significantly and suppresses motion blur. When the estimated motion fields are applied to the reconstructed activity, the deformed images are geometrically similar to the non‐AC individually reconstructed gates. Conclusion Motion estimation by JRM is robust to variation of the attenuation values in the lungs. JRM successfully compensates for motion when applied to PET/MRI clinical datasets. It provides a potential alternative to existing methods where the motion fields are pre‐estimated from separate MRI measurements.
Investigation of Frame Alignments for GMM-based Digit-prompted Speaker Verification

Frame alignments can be computed by different methods in GMM-based speaker verification. By incorporating a phonetic Gaussian mixture model (PGMM), we are able to compare the performance using alignments extracted from the deep neural networks (DNN) and the conventional hidden Markov model (HMM) in digit-prompted speaker verification. Based on the different characteristics of these two alignments, we present a novel content verification method to improve the system security without much computational overhead. Our experiments on the RSR2015 Part-3 digit-prompted task show that, the DNN-based alignment performs on par with the HMM alignment. The results also demonstrate the effectiveness of the proposed Kullback-Leibler (KL) divergence based scoring to reject speech with incorrect pass-phrases.
Online multiclass learning with "bandit" feedback under a Passive-Aggressive approach

This paper presents a new approach to online multi-class learning with bandit feedback. This algorithm, named PAB (Passive Ag- gressive in Bandit) is a variant of Online Passive-Aggressive Algorithm proposed by (2), the latter being an e↵ective framework for performing max-margin online learning. We analyze some of its operating principles, and show it to provide a good and scalable solution to the bandit classi- fication problem, particularly in the case of a real-world dataset where it outperforms the best existing algorithms.
A Practical Guide to Entity-Relationship Modeling

The Entity-Relationship (ER) model and its accompanying ER diagrams are widely used for database design and Systems Analysis. Many books and articles just provide a definition of each modeling component and give examples of pre-built ER diagrams. Beginners in data modeling have a great deal of difficulty learning how to approach a given problem, what questions to ask in order to build a model, what rules to use while constructing an ER diagram, and why one diagram is better than another. In this paper, therefore, we present step-by-step guidelines, a set of decision rules proven to be useful in building ER diagrams, and a case study problem with a preferred answer as well as a set of incorrect diagrams for the problem. The guidelines and decision rules have been successfully used in our beginning Database Management Systems course for the last eight years. The case study will provide readers with a detailed approach to the modeling process and a deeper understanding of data modeling.
A Test Battery to Measure the Recovery of Voluntary Movement Control following Stroke

Tests of upper limb function and an activities of daily living (ADL) index were selected to measure recovery following stroke. Thirty stroke patients were assessed at intervals for up to 6 months to 1 year post-stroke using the battery. The results showed that the ADL index is insensitive to upper limb recovery. All the tests measured recovery in some of the patients after 24 weeks post-stroke. Since the presentation and recovery of patients was variable, it is argued that it is necessary to offer a selection of assessment tests to measure recovery and to aid treatment planning.
Cold storage to overcome dormancy affects the carbohydrate status and photosynthetic capacity of Rhododendron simsii.

Global warming leads to increasing irregular and unexpected warm spells during autumn, and therefore natural chilling requirements to break dormancy are at risk. Controlled cold treatment can provide an answer to this problem. Nevertheless, artificial cold treatment will have consequences for carbon reserves and photosynthesis. In this paper, the effect of dark cold storage at 7 °C to break flower bud dormancy in the evergreen Rhododendron simsii was quantified. Carbohydrate and starch content in leaves and flower buds of an early ('Nordlicht'), semi-early ('M. Marie') and late ('Mw. G. Kint') flowering cultivar showed that carbon loss due to respiration was lowest in 'M. Marie', while 'Mw. G. Kint' was completely depleted of starch reserves at the end of cold treatment. Gene isolation resulted in a candidate gene for sucrose synthase (SUS) RsSus, which appears to be homologous to AtSus3 and had a clear increase in expression in leaves during cold treatment. Photosynthesis measurements on 'Nordlicht' and the late-flowering cultivar 'Thesla' showed that during cold treatment, dark respiration decreased 58% and 63%, respectively. Immediately after cold treatment, dark respiration increased and stabilised after 3 days. The light compensation point followed the same trend as dark respiration. Quantum efficiency showed no significant changes during the first days after cold treatment, but was significantly higher than in plants with dormant flower buds at the start of cold treatment. In conclusion, photosynthesis stabilised 3 days after cold treatment and was improved compared to the level before cold treatment.
Use of brief psychiatric screening measures in a primary care sample

Patients seen in primary medical clinics report higher rates of major depression [Pérez‐Stable et al., 1990: Arch Intern Med 15:1083–1088], and panic disorder [Sherbourne et al., 1996b: Von Korff et al., 1987: Arch Gen Psychiatry 44:152–156] than the general population. Primary care staff therefore need efficient methods of identifying patients with psychiatric disorders. The current study evaluates the use of several brief psychiatric screening measures for identifying patients with major depression and/or anxiety disorders. Participants were 213 primary care patients who received the Center for Epidemiological Studies Depression Scale (CES‐D), the Beck Anxiety Inventory (BAI), and two new instruments, the Autonomic Nervous System Questionnaire (ANS) for assessing panic disorder and the Social Phobia Questionnaire (SPQ) for assessing social phobia. Participants received both the screening instruments and a structured diagnostic interview. Results suggest that the CES‐D is a useful measure for detecting psychopathology, but it is not particularly specific to depression, the ANS was a highly sensitive and reasonably specific measure for panic disorder, and the SPQ was reasonably sensitive and specific for social phobia. The BAI was a relatively poor screening measure that added no significant information beyond the other measures. Depression and Anxiety 12:21–29, 2000. © 2000 Wiley‐Liss, Inc.
Phosphopeptide detection using automated online IMAC‐capillary LC‐ESI‐MS/MS

IMAC has become a commonly used technique in phosphoprotein analysis because of its affinity for phosphopeptides. However, the commonly used strategy combining offline IMAC enrichment with desalting procedures prior to MS/MS makes this method laborious. Here we report the development of a robust and automatic IMAC‐capillary RP HPLC‐ESI MS/MS technology platform, by which all procedures needed in phosphopeptide analysis including IMAC enrichment, RP HPLC separation and nanospray MS/MS can be done automatically controlled by the MassLynx program. The platform was optimized by analyzing standard phosphopeptide, and was then applied to the identification of phosphorylation sites of recombinant human telomeric repeat binding factor 1 treated with kinase in vitro, and two phosphorylation sites are defined.
MEG Fields of Subjects with Dyslexia During Word and Shape Recognition Tasks

Dyslexia, a poorly understood group of learning disorders, is the inability to read, despite having adequate intelligence and the ability to see and recognize letters [1]. Significant differences have been reported between auditory evoked responses of dyslexic individuals, obtained using the conventional Electroencephalography (EEG) and those of control subjects (normal readers matched in intelligence and age) [2].
Finite control set model predictive control for dc voltage balancing in Vienna rectifier

This paper is concerned with the investigation of Finite Control Set Model Predictive Control (FCS-MPC) for dc link voltage balancing in a Vienna rectifier. Large EV charging stations with common dc bus utilize a high-power rectifier as a front end conversion stage. In this regards, Vienna rectifier, as a central ac-dc stage, with bipolar dc bus structure is an attractive choice. Bipolar dc bus is potentially prone to voltage imbalance which is undesirable. dc link voltage imbalance also lead to distorted input current and more power quality issues. This paper proposes a capacitor voltage balancing technique based on the FCS-MPC method. In order to apply the FCS-MPC method, the discrete time model of the Vienna rectifier in unbalanced conditions is derived. By applying this model, the proper cost function is proposed to balance dc bus voltage. Simulation and experimental results are presented to validate the proposed control strategy in terms of the effectiveness of output voltage balancing and low distortion input current.
An Improved Low-Complexity LMMSE Channel Estimation Algorithm

This paper proposes an improved linear minimum mean square error (LMMSE) algorithm of adaptive order determination by taking advantage of the structure characteristics of time domain least square (LS) channel estimation based on hardware platform, which provides the approximate estimation approach of max-time delay and noise power. In addition, this algorithm achieves a practical channel estimation formula which greatly reduces the complexity of the algorithm by decomposing the autocorrelation matrix into some sub-matrixes on the foundation of correlation bandwidth. Finally, comparisons are made between the simulation performances of improved LMMSE algorithm with those of other estimation methods for further analysis.
Innovativeness in New Product Development (NPD): validating a new measure for inter-/intra-functional technological learning

This paper focuses on developing a measurement model for inter/intra-functional technological learning. A brief overview of innovation and its general importance in the success of any entity (i.e. nation, firm, project or product) is initially provided. Central to this frame is the need to intensify New Product Development (NPD) efforts especially for a developing country such as Malaysia. However, since NPD success remains broadly defined, their measures portray the outcome of NPD efforts, rather than the means. This provided a cause to pursue measurement validation of learning processes in NPD collaboration, through data from 105 project teams across nine multi-national companies located in Malaysia. Four constructs bearing the concept of technological learning (i.e. knowledge acquisition, information distribution, information interpretation and organisational memory) were tested following a series of tests that are more stringent than their predecessors. Significant theoretical aspects are highlighted throughout the paper.
Metabolic Syndrome in Korean Cancer Survivors and Family Members: A Study in a Health Promotion Center

This cross-sectional study evaluated the risk of metabolic syndrome (MetS) in cancer survivors and family members. Subjects were 48,934 adults (24,786 men, 24,148 women) aged ≥40yr who receive a routine health examination at 1 hospital from January 2010 to December 2012. There were 2468 cancer survivors, 18,211 with cancer patients in the family, and 28,255 noncancer subjects, who never experienced cancer and whose family members either. Associations between MetS and cancer experience were assessed using multiple logistic regression analysis. The odds ratio (OR) of MetS in female cancer survivors was significantly higher than noncancer subjects after adjusting for age, smoking, physical activity, and alcohol intake (OR = 1.22, 95% confidence intervals: 1.02–1.47]. However, the OR of MetS for male survivors did not differ from that of noncancer subjects. Gastric cancer survivors had a lower OR of MetS than noncancer subjects (0.37, 0.27–0.50). ORs of breast cancer (1.49, 1.00–2.23) and prostate cancer survivors (1.46, 1.07–1.99) were higher than the OR of MetS for noncancer subjects. There was no difference in the OR of MetS between the family members of cancer patients and non-cancer subjects. These findings suggest that the odds of MetS for cancer survivors may differ by cancer type and by sex.
FlexX‐Scan: Fast, structure‐based virtual screening

We present a new software module, FlexX‐Scan, for high‐throughput, structure‐based virtual screening. FlexX‐Scan was developed with the aim to further speed up the virtual screening process. Based on the incremental construction docking tool FlexX (Rarey et al., J Mol Biol 1996;261:470–489), a compact descriptor for representing favorable protein interaction spots within the protein binding site has been developed. The descriptor is calculated using special‐purpose clustering techniques applied to the usual interaction points created by FlexX. The algorithm automatically detects a small set of interaction spots in the binding site for positioning ligand functional groups. The parametrizations of the base placement and incremental construction algorithms have been adapted to the new interaction model. We tested the software tool on a diverse set of 200 protein–ligand complexes from the protein database (PDB) (Kramer et al., Proteins 1999;37:228–241). On average, the algorithm proposes about 90 interaction spots per binding site compared to about 1000 interaction dots in FlexX. We observe that the docking solutions of FlexX‐Scan have a root‐mean‐square deviation from the crystal structure similar to the deviation of docking solutions of standard FlexX. For further validation we also performed virtual screening experiments for cyclin‐dependent kinase 2, thrombin, angiotensin‐converting enzyme, and dihydrofolat reductase. In these experiments, we screened a set of 34,000 random compounds and a number of known actives for each target. With FlexX‐Scan, we achieved comparable enrichments to standard FlexX, with an averaged computing time of 5–10 s per compound, depending on parametrization. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Evaluation of email alerts in practice: Part 1. Review of the literature on clinical emailing channels.

RATIONALE Methods to systematically assess electronic knowledge resources by health professionals may enhance evaluation of these resources, knowledge exchange between information users and providers, and continuing professional development. We developed the Information Assessment Method (IAM) to document health professional perspectives on the relevance, cognitive impact, potential use and expected health outcomes of information delivered by (push) or retrieved from (pull) electronic knowledge resources. However, little is known about push communication in health sciences, and what we propose to call clinical emailing channels (CECs). CECs can be understood as a communication infrastructure that channels clinically relevant research knowledge, email alerts, from information providers to the inboxes of individual practitioners. AIMS In two companion papers, our objectives are to (part 1) explore CEC evaluation in routine practice, and (part 2) examine the content validity of the cognitive component of IAM. METHODS The present paper (part 1) critically reviews the literature in health sciences and four disciplines: communication, information studies, education and knowledge translation. Our review addresses the following questions. What are CECs? How are they assessed? RESULTS The review contributes to better define CECs, and proposes a 'push-pull-acquisition-cognition-application' evaluation framework, which is operationalized by IAM. CONCLUSION Compared with existing evaluation tools, our review suggests IAM is comprehensive, generic and systematic.
Exercise-induced pulmonary haemorrhage workshop.

Exercise-induced pulmonary haemorrhage (EIPH) occurs frequently during strenuous exercise in the horse (see, for example, Pascoe et al. 198 1; Raphel and Soma 1982; Mason et al. 1983; Roberts et al. 1993). The presence of haemosiderincontaining macrophages in tracheal washes, indicating previous haemorrhage, suggests that EIPH is an ubiquitous condition of horses subjected to strenuous exercise. Despite the importance with which the condition is viewed by clinicians and trainers (Foord 1994), little progress has been made in its control and treatment. At the 4th International Conference on Equine Exercise Physiology, Professor Howard Erickson chaired a successful workshop on EIPH (Erickson 1995). The current workshop followed on from the previous one and sought to address and debate the following topics: (1) the causes and mechanisms of EIPH, (2) the effects of EIPH on performance and (3) the treatment of EIPH.
Plasmids of the pRM/pRF Family Occur in Diverse Rickettsia Species

ABSTRACT The recent discoveries of the pRF and pRM plasmids of Rickettsia felis and R. monacensis have contravened the long-held dogma that plasmids are not present in the bacterial genus Rickettsia (Rickettsiales; Rickettsiaceae). We report the existence of plasmids in R. helvetica, R. peacockii, R. amblyommii, and R. massiliae isolates from ixodid ticks and in an R. hoogstraalii isolate from an argasid tick. R. peacockii and four isolates of R. amblyommii from widely separated geographic locations contained plasmids that comigrated with pRM during pulsed-field gel electrophoresis and larger plasmids with mobilities similar to that of pRF. The R. peacockii plasmids were lost during long-term serial passage in cultured cells. R. montanensis did not contain a plasmid. Southern blots showed that sequences similar to those of a DnaA-like replication initiator protein, a small heat shock protein 2, and the Sca12 cell surface antigen genes on pRM and pRF were present on all of the plasmids except for that of R. massiliae, which lacked the heat shock gene and was the smallest of the plasmids. The R. hoogstraalii plasmid was most similar to pRM and contained apparent homologs of proline/betaine transporter and SpoT stringent response genes on pRM and pRF that were absent from the other plasmids. The R. hoogstraalii, R. helvetica, and R. amblyommii plasmids contained homologs of a pRM-carried gene similar to a Nitrobacter sp. helicase RecD/TraA gene, but none of the plasmids hybridized with a probe derived from a pRM-encoded gene similar to a Burkholderia sp. transposon resolvase gene.