Miracle-dz/UniFAR-FTUs huggingface dataset:
Latency-Associated Nuclear Antigen of Kaposi's Sarcoma-Associated Herpesvirus Recruits Uracil DNA Glycosylase 2 at the Terminal Repeats and Is Important for Latent Persistence of the Virus

ABSTRACT Latency-associated nuclear antigen (LANA) of KSHV is expressed in all forms of Kaposi's sarcoma-associated herpesvirus (KSHV)-mediated tumors and is important for TR-mediated replication and persistence of the virus. LANA does not exhibit any enzymatic activity by itself but is critical for replication and maintenance of the viral genome. To identify LANA binding proteins, we used a LANA binding sequence 1 DNA affinity column and determined the identities of a number of proteins associated with LANA. One of the identified proteins was uracil DNA glycosylase 2 (UNG2). UNG2 is important for removing uracil residues yielded after either misincorporation of dUTP during replication or deamination of cytosine. The specificity of the ′LANA-UNG2 interaction was confirmed by using a scrambled DNA sequence affinity column. Interaction of LANA and UNG2 was further confirmed by in vitro binding and coimmunoprecipitation assays. Colocalization of these proteins was also detected in primary effusion lymphoma (PEL) cells, as well as in a cotransfected KSHV-negative cell line. UNG2 binds to the carboxyl terminus of LANA and retains its enzymatic activity in the complex. However, no major effect on TR-mediated DNA replication was observed when a UNG2-deficient (UNG−/−) cell line was used. Infection of UNG−/− and wild-type mouse embryonic fibroblasts with KSHV did not reveal any difference; however, UNG−/− cells produced a significantly reduced number of virion particles after induction. Interestingly, depletion of UNG2 in PEL cells with short hairpin RNA reduced the number of viral genome copies and produced infection-deficient virus.
Should researchers protect the good name and reputation of institutions in which research is done

The article explores the issue of protecting the good name and reputation of institutions and organisations in which research is being done. It explores current ethical codes in this regard, as well as legal provision for such protection. The issue of balancing the right of the researchers to share information about institutions in which research is done, with the need for organisations to protect their good names is discussed, and recommendations will be made with regard to the inclusion of this aspect of research ethics into the brief of ethics committees and the way in which organisations can be protected without jeopardising the aims of research.
CcpC, a novel regulator of the LysR family required for glucose repression of the citB gene in Bacillus subtilis.

Synergistic carbon catabolite repression of the Bacillus subtilis aconitase (citB) gene by glucose and a source of 2-ketoglutarate is dependent on DNA sequences located upstream of the gene. Mutations in a dyad symmetry element centered at position -66 and in a repeat of the downstream arm of the dyad symmetry at position -27 cause derepressed citB expression. In this work, a protein able to bind to a DNA fragment containing these elements was purified and identified. This protein, named CcpC (Catabolite control protein C), shares sequence similarity with members of the LysR family of transcriptional regulators. In addition to binding to the citB promoter, CcpC bound to the promoter of the citZ gene, which encodes the cell's major citrate synthase and is subject to carbon catabolite repression. In a ccpC null mutant, expression of both citB and citZ was derepressed in glucose-glutamine minimal medium, indicating that CcpC is a negative regulator of citB and citZ gene expression. DNase I footprinting experiments showed that CcpC binds to two sites within the citB promoter region, corresponding to the dyad symmetry and -27 elements. In the presence of citrate, a putative inducer, only the dyad symmetry element was fully protected by CcpC. When the dyad symmetry element was mutated, CcpC was no longer able to bind to either the dyad symmetry or -27 elements. Repression of citB and citZ gene expression during anaerobiosis also proved to be mediated by CcpC.
REPLACE INTERROGATION AND TORTURE ?

Many techniques have been used to extract reliable information from individuals who are unwilling to divulge it, including interrogation, torture, and “lie detectors,” all of which have shortcomings in their ability to get and / or evaluate information. Brain imaging technologies present the possibilities of determining if an individual is lying, concealing information, or has predispositions to particular behaviors. Functional magnetic resonance imaging (fMRI) is the best known brain imaging technique, and can already be used to determine hidden conscious states of an individual, and to determine true and false statements with accuracy greater than chance. Thus, the main empirical question is no longer if brain imaging can be used productively in security situations, but rather how practical it might be and how confident users may be in the information obtained. Ethical questions about appropriate uses of brain imaging technology in security situations are immediate and urgent, but ethical concerns about privacy and similar issues raised by brain imaging appear minor compared to the ethical issues raised by torture. Brain imaging may be able to render some arguments about the use of torture moot by providing a more reliable method of getting and evaluating information from individuals. Global Virtue Ethics Review Volume Six, Number 2, pp. 55-78
Aberrant CXCR4 and β-catenin expression in osteosarcoma correlates with patient survival

To determine the clinical significance of C-X-C chemokine receptor type 4 (CXCR4) and β-catenin in osteosarcoma, their protein expression levels were assessed in 96 osteosarcoma and 20 osteochondroma cases using immunohistochemistry. Additionally, CXCR4 and β-catenin mRNA expression levels were measured in 16 fresh osteosarcoma and 16 adjacent healthy tissue samples using fluorescent reverse transcription-quantitative polymerase chain reaction (RT-qPCR). In the osteosarcoma samples, the positive CXCR4 protein expression rate was significantly higher than the rate in the osteochondroma samples (68.75 vs. 20.00%; P<0.01). Furthermore, β-catenin protein expression was detected in 61.46% of osteosarcoma cases and 25.00% of osteochondroma cases. Similarly, the RT-qPCR data identified increased CXCR4 and β-catenin mRNA expression levels in the osteosarcoma compared with adjacent control tissues. It was determined that CXCR4 (P<0.01) and β-catenin (P<0.05) expression were significantly associated with the clinical Enneking stage, metastasis and survival of osteosarcoma. Furthermore, multivariate analysis identified CXCR4 and β-catenin protein expression levels, as well as clinical stage and metastasis, as significant risk factors for survival in patients with osteosarcoma (P<0.05). In conclusion, the present study determined that CXCR4 and β-catenin are abnormally expressed in osteosarcoma tissues, and, therefore, may be important during osteosarcoma progression.
Mining Sequential Patterns for Appliance Usage Prediction

Reducing the energy consumption in buildings and homes can be achieved by predicting how energy-consuming appliances are used, and by discovering their patterns. To mine these patterns, a smart-metering architecture needs to be in place complemented by appropriate data analysis mechanisms. Once the usage patterns are obtained, they can be employed to optimize the way energy from renewable installations, home batteries, and even micro grids is managed. We present an approach and related experiments for mining sequential patterns in appliance usage. In particular, we mine patterns that allow us to perform device usage prediction, energy usage prediction, and device usage prediction with failed sensors. The focus of this work is on the sequential relationships between the state of distinct devices. We use data sets from three existing buildings, of which two are households and one is an office building. The data is used to train our modified Support-Pruned Markov Models which use a relative support threshold. Our experiments show the viability of the approach, as we achieve an overall accuracy of 87% in device usage predictions, and up to 99% accuracy for devices that have the strongest sequential relationships. For these devices, the energy usage predictions have an accuracy of around 90%. Predicting device usage with failed sensors is feasible, assuming there is a strong sequential relationship for the devices.
Improving phase congruency for EEG data reduction

Real signals are often corrupted by noise. In applications where the noise power spectrum is variable with time, dynamic noise estimation and compensation can potentially improve the performance of signal processing algorithms. One such application is scalp EEG monitoring in epilepsy, where the electrical activity generated by cranio-facial muscle contraction and expansion, often obscures the measured brainwave signals. This work presents a data reduction algorithm which is based on differentiating interictal from normal background activity, in epileptic scalp EEG signals, using a modified phase congruency technique. The modification is based on dynamically estimating muscle activity from the signal and incorporating this estimation in phase congruency computations. The proposed algorithm identifies 90%of interictal spikes whilst transmitting only 45% of EEG data. This is in the order of 15% improvement in data reduction when compared to the performance obtained with the state-of-the-art denoised phase congruency—which calculates a constant noise threshold—applied to the same dataset.
The variability of earnings and non-earnings information and earnings prediction

This paper examines the performance of a 'composite' model of earnings prediction that integrates current earnings and current price as predictors of next year's earnings. The results show that current earnings (current price) play a key role in predicting future earnings when the ratio of earnings variance to price variance is low (high). The composite model is superior to univariate time-series models in out-of-sample predictive accuracy for the overall sample, and is substantially so for the group of firms with a high ratio of earnings variance to price variance. Copyright Blackwell Publishers Ltd 1999.
The role of group configuration in the social transmission of memory: Evidence from identical and reconfigured groups

Collaborating with others during recall shapes both group and individual memories. Individuals contribute less when recalling in groups than when recalling alone, a phenomenon called collaborative inhibition. In contrast, collaboration improves post-collaborative individual memory by providing re-exposure to information that would have been otherwise forgotten. Collaboration also influences collective memory—the overlap in post-collaborative memory among group members. We examined the role of group configuration on such transmission of memory by varying group configuration across repeated recalls. Participants (N = 162) studied words and completed three recall sessions in one of three conditions (N = 54/condition): Individual–Individual–Individual (Control), Collaborative–Collaborative (Identical group)–Individual and Collaborative–Collaborative (Reconfigured group)–Individual. Collaborative inhibition occurred in both the Identical and Reconfigured groups during the first recall but disappeared in the Reconfigured groups during the second recall. Post-collaborative individual memory was greater following Reconfigured than Identical group collaboration. This pattern reversed for collective memories; repeated collaboration increased overlap in the remembered and forgotten items in Identical groups compared to Reconfigured groups. Finally, Reconfigured groups provided a quantifiable index of the influence of distal partners (i.e., no direct collaboration involved) on post-collaborative individual memory. We conclude that group configuration has powerful consequences on the amount, the similarity and the variety of memory representations.
Evidence of silicic acid leakage to the tropical Atlantic via Antarctic Intermediate Water during Marine Isotope Stage 4

Antarctic Intermediate Water (AAIW) and Subantarctic Mode Water (SAMW) are the main conduits for the supply of dissolved silicon (silicic acid) from the deep Southern Ocean to the low latitude surface ocean, and therefore have an important control on low latitude diatom productivity. Enhanced supply of silicic acid by AAIW (and SAMW) during glacial periods may have enabled tropical diatoms to outcompete carbonate-producing phytoplankton, decreasing the relative export of inorganic to organic carbon to the deep ocean and lowering atmospheric pCO2. This mechanism is known as the ‘Silicic Acid Leakage Hypothesis’ (SALH). Here we present records of neodymium and silicon isotopes from the western tropical Atlantic that provide the first direct evidence of increased silicic acid leakage from the Southern Ocean to the tropical Atlantic within AAIW during glacial Marine Isotope Stage (MIS) 4 (~60–70 ka). This leakage was approximately coeval with enhanced diatom export in the NW Atlantic and across the eastern equatorial Atlantic and provides support for the SALH as a contributor to CO2 drawdown during full glacial development.
RE-EXPORT OF FINANCIAL SERVICES

The present article deals with the research of the concept of ‘re-export of financial services’ in banking, the examples of its practical expression and influence on economic processes. For theoretical formulation of the ‘re-export of financial services’ concept the author uses the method of inductive evidence to compare the concepts of export and re-export of goods and services, as well as analyzes historical information on the given subject. Special attention is paid to the comparison of ‘re-export of financial services’ with ‘re-export of capital’. The above mentioned research resulted in the author’s derivation of re-export theory. As practical examples of re-export of financial services the author quotes current schemes used by Latvian banks in their work with fast money transfers and with financial instruments trading on global markets. The article is completed by a disclosure and survey of positive and negative aspects of the influence of re-export, including financial services, on both subjects of economics and economy as a whole.
Locomotor Trajectories of Stroke Patients during Oriented Gait and Turning

Background The Timed Up and Go (TUG) test is widely used to assess locomotion in patients with stroke and is considered to predict the risk of falls. The analysis of locomotor trajectories during the TUG appears pertinent in stroke patients. The aims of this study were i) to analyze locomotor trajectories in patients with stroke during the walking and turning sub-tasks of the TUG, and to compare them with healthy subjects, ii) to determine whether trajectory parameters provide additional information to that provided by the conventional measure (performance time), iii) to compare the trajectory parameters of fallers and non-fallers with stroke and of patients with right and left hemisphere stroke, and iv) to evaluate correlations between trajectory parameters and Berg Balance Scale scores. Methods 29 patients with stroke (mean age 54.2±12.2 years, 18 men, 8 fallers) and 25 healthy subjects (mean age 51.6±8.7 years, 11 men) underwent three-dimensional analysis of the TUG. The trajectory of the center of mass was analyzed by calculation of the global trajectory length, Hausdorff distance and Dynamic Time Warping. The parameters were compared with a reference trajectory during the total task and each sub-task (Go, Turn, Return) of the TUG. Results Values of trajectory parameters were significantly higher for the stroke group during the total TUG and the Go and Turn sub-tasks (p<0.05). Moreover, logistic regression indicated that these parameters better discriminated stroke patients and healthy subjects than the conventional timed performance during the Go sub-task. In addition, fallers were distinguished by higher Dynamic Time Warping during the Go (p<0.05). There were no differences between patients with right and left hemisphere stroke. Discussion and Conclusion The trajectories of the stroke patients were longer and more deviated during the turn and the preceding phase. Trajectory parameters provided additional information to timed performance of this locomotor task. Focusing rehabilitation programs on lead-up to turn and turning could be relevant for stroke patients since the Turn was related to the balance and the phase preceding the turn seemed to distinguish fallers.
GI symptoms in diabetes mellitus are associated with both poor glycemic control and diabetic complications

OBJECTIVE:Diabetes mellitus is associated with an increased prevalence of GI symptoms, but the mechanisms underlying symptoms are poorly defined and controversial. We aimed to determine whether there is a relationship between GI symptoms and both diabetic complications and glycemic control.METHODS:We performed a cross-sectional questionnaire study of 1101 subjects with diabetes mellitus recruited from outpatient clinics (n = 209) and the community (n = 892). Data on eight GI symptom groups, complications of diabetes (retinopathy, neuropathy, nephropathy), and self-reported glycemic control were obtained from a validated questionnaire. Glycated hemoglobin was measured in 463 of the subjects. The association between diabetic complications, glycemic control, and GI symptoms was assessed using logistic regression analysis, adjusted for demographic and clinical factors.RESULTS:Of the 1101 subjects, 57% reported at least one complication. Diabetic complications were independently associated with both symptom complexity (number of symptom groups reported) (adjusted odds ratio = 1.92 per symptom group [95% CI = 1.51–2.45]) and seven of the eight GI symptom groups. For all symptom groups, the association was explained by self-reported symptoms of peripheral neuropathy. Poor glycemic control measured by both self-report and Hb A1c was an independent risk factor for upper GI symptoms, whereas other potential risk indicators, including duration and type of diabetes, were not significant.CONCLUSIONS:GI symptoms in diabetes mellitus may be linked to diabetic complications, particularly peripheral neuropathy, and to poor glycemic control.
Dependence Guided Unsupervised Feature Selection

In the past decade, various sparse learning based unsupervised feature selection methods have been developed. However, most existing studies adopt a two-step strategy, i.e., selecting the top-m features according to a calculated descending order and then performing K-means clustering, resulting in a group of sub-optimal features. To address this problem, we propose a Dependence Guided Unsupervised Feature Selection (DGUFS) method to select features and partition data in a joint manner. Our proposed method enhances the inter-dependence among original data, cluster labels, and selected features. In particular, a projection-free feature selection model is proposed based on l20-norm equality constraints. We utilize the learned cluster labels to fill in the information gap between original data and selected features. Two dependence guided terms are consequently proposed for our model. More specifically, one term increases the dependence of desired cluster labels on original data, while the other term maximizes the dependence of selected features on cluster labels to guide the process of feature selection. Last but not least, an iterative algorithm based on Alternating Direction Method of Multipliers (ADMM) is designed to solve the constrained minimization problem efficiently. Extensive experiments on different datasets consistently demonstrate that our proposed method significantly outperforms state-of-the-art baselines.
Vitamin D Receptor Polymorphisms Are Associated with Reduced Esophageal Vitamin D Receptor Expression and Reduced Esophageal Adenocarcinoma Risk

Epidemiological studies indicate that vitamin D exerts a protective effect on the development of various solid cancers. However, concerns have been raised regarding the potential deleterious role of high vitamin D levels in the development of esophageal adenocarcinoma (EAC). This study investigated genetic variation in the vitamin D receptor (VDR) in relation to its expression and risk of Barrett esophagus (BE) and EAC. VDR gene regulation was investigated by immunohistochemistry, reverse transcriptase-polymerase chain reaction (RT-PCR) and gel shift assays. Fifteen haplotype tagging single-nucleotide polymorphisms (SNPs) of the VDR gene were analyzed in 858 patients with reflux esophagitis (RE), BE or EAC and 202 healthy controls. VDR mRNA expression was higher in BE compared with squamous epithelium. VDR protein was located in the nucleus in BE. An rs1989969T/rs2238135G haplotype was identified in the 5′ regulatory region of the VDR gene. It was associated with an approximately two-fold reduced risk of RE, BE and EAC. Analysis of a replication cohort was done for BE that confirmed this. The rs1989969T allele causes a GATA-1 transcription factor binding site to appear. The signaling of GATA-1, which is regarded as a negative transcriptional regulator, could explain the findings for rs1989969. The rs2238135G allele was associated with a significantly reduced VDR expression in BE; for the rs1989969T allele, a trend in reduced VDR expression was observed. We identified a VDR haplotype associated with reduced esophageal VDR expression and a reduced incidence of RE, BE and EAC. This VDR haplotype could be useful in identifying individuals who benefit most from vitamin D chemoprevention.
Landscape scenarios visualized by Baka and Aka Pygmies in the Congo Basin

We describe our attempts to use visualization techniques to engage the Baka and Aka in the North-West Congo Basin in a debate about their preferred future options. Baka and Aka Pygmies in the Sangha Tri-National landscape live in extreme poverty and score poorly on most development indicators. Their traditional livelihoods have suffered as their forests are taken over by outsiders for farming and logging. Conservation programmes deny them access to their traditional hunting and gathering forest territories. Over ten years we spent time with the Baka and Aka in their camps and joined them on trips into the forests. We used visualization techniques to enable them to portray their present perception of their landscapes and their preferred future scenarios. We compared their representations with those of non-Pygmy communities in the same area. Baka and Aka showed a richer and more nuanced appreciation of the forest landscape in their representations of the present but converged with the non-Pygmies in representations of their preferred future. Agriculture, health, education and employment opportunities emerged as significant elements portrayed in drawings of desired future scenarios. Visualization cannot provide a definitive diagnosis of the very diverse desires of Pygmy communities. Our study suggests that visualization techniques strengthened the ability of Pygmies to communicate their views to other actors in their landscape and to external decision makers. Decisions about programmes to help the Pygmies have often been made by well-intentioned outsiders and the Pygmies themselves had little input. We conclude that visualization empowered Pygmies in discussions and expanded their options for influencing decisions that would impact on their future.