Miracle-dz/UniFAR-FTUs huggingface dataset:
Mapping 5' termini of JC virus early RNAs

Within its enhancer promoter region, the MAD-1 strain of JC virus (JCV) has two 98-base-pair tandem repeats, each containing a TATA box-like sequence. In the present study, polyadenylated early JCV mRNAs were isolated 5 or 29 days after infection of primary human fetal glial (PHFG) cells. By using S1 nuclease, the 5' termini of the early mRNAs were mapped to nucleotide position(s) (np) 122 through 125, which lies within an AT rich region (at np 113 through 127). In contrast, when JCV DNA was transcribed in vitro, we observed a single major cluster of 5' start sites at np 94 through 97, which is approximately 25 base pairs downstream from one of the TATA boxes. By day 5, the earliest time at which JCV RNA was detected, viral DNA replication had begun; it continued for at least an additional 20 days. Since more late than early RNA was present at 5 days postinfection, the early RNAs whose synthesis began at np 122 through 125 may be analogous to SV40 late early mRNA (Ghosh and Lebowitz, J. Virol. 40:224-240, 1981). However, we have not detected RNAs with 5' termini 25 to 30 bp downstream from the TATA box at earlier times. While JCV contains two identical TATA boxes, one in each of the 98-bp repeats, only the upstream TATA box functions as an early promoter element.
Information Diffusion Temporal Dynamic Prediction in Microblog System Based On User Influence Learning

Information diffusion in online social network especially in microblog system, can largely affect the public opinion and even the development of events, so the prediction of the future dynamics of diffusion could be very valuable at many aspects. In this research, a novel graphbased cascades construct algorithm is proposed, with which we build a prediction model for future information diffusion dynamics. By learning user influence features that related with the network topology and users’ interactions from a large scale real Weibo dataset, we successfully predicted the short term topic related tweets population dynamics.
Adherence to Dietary Guidelines and Successful Aging Over 10 Years.

BACKGROUND We aimed to prospectively examine the relationship between overall diet quality (reflecting adherence to dietary guidelines) and successful aging in a population-based cohort of older adults. METHODS In this population-based cohort study, we analyzed 10-year follow-up data from 1,609 adults aged 49 years and older, who were free of cancer, coronary artery disease, and stroke at the baseline and who had complete dietary data. Dietary data were collected using a semiquantitative food frequency questionnaire. Total diet scores (TDS) were allocated for intake of selected food groups and nutrients for each participant as described in the national dietary guidelines. Higher scores indicated closer adherence to dietary guidelines. Successful aging was defined as the absence of disability, depressive symptoms, cognitive impairment, respiratory symptoms, and chronic diseases (cancer, coronary artery disease, and stroke). RESULTS At 10-year follow-up, 610 (37.9%) participants had died and 249 (15.5%) participants aged successfully. After multivariable adjustment, each 1-unit increase in TDS at baseline was associated with a 8% increased odds of successful aging 10 years later, odds ratio 1.08 (95% confidence interval 1.00-1.15). Participants in the highest (high adherence to dietary guidelines) versus lowest quartile (poor adherence to guidelines) of TDS at baseline had 58% higher odds of successful aging after 10 years, odds ratio 1.58 (95% confidence interval 1.02-2.46). CONCLUSIONS Greater compliance with recommended national dietary guidelines (higher diet quality) was associated with an increased likelihood of successful aging, as determined through a multidomain approach.
Bilateral TMJ Disk Displacement Induces Mandibular Retrognathia

Unilateral non-reducing TMJ disk displacement has been shown to retard mandibular growth on the ipsilateral side, with facial asymmetry a sequela. We hypothesized that bilateral affliction would impair mandibular growth bilaterally, generating mandibular retrognathia. Non-reducing TMJ disk displacement was surgically created in 10 growing New Zealand White rabbits. Ten additional rabbits served as a sham-operated control group. Facial growth was followed in serial cephalograms, with tantalum implants, during a period corresponding to childhood and adolescence in man. The results verified that bilateral non-reducing TMJ disk displacement retarded mandibular growth bilaterally, the extent corresponding to mandibular retrognathia in man. Maxillary growth was also retarded, but to a lesser degree. Growth impairment fluctuated over time, the most striking retardation occurring during periods of general growth acceleration. This should be taken into consideration when orthodontic treatment, aimed at stimulating mandibular growth, is initiated in adolescent individuals with non-reducing TMJ disk displacement.
Accuracy in Self-Reported Health Insurance Coverage among Medicaid Enrollees

The largest portion of the Medicaid undercount is caused by survey reporting error—that is, Medicaid recipients misreport their enrollment in health insurance coverage surveys. In this study, we sampled known Medicaid enrollees to learn how they respond to health insurance questions and to document correlates of accurate and inaccurate reports. We found that Medicaid enrollees are fairly accurate reporters of insurance status and type of coverage, but some do report being uninsured. Multivariate analyses point to the prominent role of program-related factors in the accuracy of reports. Our findings suggest that the Medicaid undercount should not undermine confidence in survey-based estimates of uninsurance.
EditorialCultural competence is everyone's responsibility!

Over the past several years, the importance of culture in medical care and medical education has gradually been acknowledged. Increases in literature (e.g. Hall et al., 2004; McLean, 2004; Rosen et al., 2004), healthcare and educational policy recommendations (e.g. Institute of Medicine, 2002; General Medical Council, 2003; World Federation for Medical Education, 2003), and collections of resources (e.g. American Medical Association, 1999) attest to that. Now medical education must develop programs that span the full spectrum of medical education and ensure appropriate teachers. The latter have the dual role of teaching how to provide culturally competent patient care, as well as working with trainees in a culturally effective fashion. This editorial examines how to integrate culture-related training across the continuum of medical education and explores what competences are required of teachers. The concept of culture reflects the breadth and individuality of experience. People have as many cultures as groups they belong to. Figure 1 lists areas where cultural differences frequently occur in patient–clinician and learner–teacher encounters. There are some parallels between communication skills and cultural competence education although the former is probably several years ahead of the latter in terms of development. For a long time communication skills training was relegated to electives, isolated training events and the dedication of a few. Now that this competence is more generally accepted as essential for effective medical care, such training has become more prominent. Programs are not just in basic education but have also been implemented in postgraduate and continuing professional development (CPD). We know that communication skills are not necessarily maintained over time (Pfeiffer et al., 1998). It is likely that cultural competence also represents a lifelong learning need. As physicians (and teachers) cannot be fully competent if they do not communicate effectively, they cannot be fully competent if they are unable to manage cross-cultural encounters effectively.
SensorWebIDS: a web mining intrusion detection system

Purpose – The purpose of this paper is to propose a web intrusion detection system (IDS), SensorWebIDS, which applies data mining, anomaly and misuse intrusion detection on web environment.Design/methodology/approach – SensorWebIDS has three main components: the network sensor for extracting parameters from real‐time network traffic, the log digger for extracting parameters from web log files and the audit engine for analyzing all web request parameters for intrusion detection. To combat web intrusions like buffer‐over‐flow attack, SensorWebIDS utilizes an algorithm based on standard deviation (δ) theory's empirical rule of 99.7 percent of data lying within 3δ of the mean, to calculate the possible maximum value length of input parameters. Association rule mining technique is employed for mining frequent parameter list and their sequential order to identify intrusions.Findings – Experiments show that proposed system has higher detection rate for web intrusions than SNORT and mod security for such classes .
Lung Injury and Lung Cancer

Chronic obstructive pulmonary disease (COPD) and lung cancer are frequently caused by tobacco smoking. However, these diseases present opposite phenotypes involving redox signaling at the cellular level. While COPD is characterized by excessive airway epithelial cell death and lung injury, lung cancer is caused by uncontrolled epithelial cell proliferation. Notably, epidemiological studies have demonstrated that lung cancer incidence is significantly higher in patients who have preexisting emphysema/lung injury. However, the molecular link and common cell signaling events underlying lung injury diseases and lung cancer are poorly understood. This review focuses on studies of molecular mechanism(s) underlying smoking-related lung injury (COPD) and lung cancer. Specifically, the role of the ceramide-generating machinery during cigarette smoke-induced oxidative stress leading to both apoptosis and proliferation of lung epithelial cells is emphasized. Over recent years, it has been established that ceramide is a sphingolipid playing a major role in lung epithelia structure/function leading to lung injury in chronic pulmonary diseases. However, new and unexpected findings draw attention to its potential role in lung development, cell proliferation, and tumorigenesis. To address this dichotomy in detail, evidence is presented regarding several protein targets, including Src, p38 mitogen-activated protein kinase, and neutral sphingomyelinase 2, the major sphingomyelinase that controls ceramide generation during oxidative stress. Furthermore, their roles are presented not only in apoptosis and lung injury but also in enhancing cell proliferation, lung cancer development, and resistance to epidermal growth factor receptor-targeted therapy for treating lung cancer. Antioxid. Redox Signal. 21, 2149–2174.
Donor Site Sensitivity After Breast Reconstruction With Deep Inferior Epigastric Artery Perforator Flap

The aim of this study was to examine pressure sensitivity at the donor site after breast reconstruction with deep inferior epigastric artery perforator (DIEAP). In a cross-sectional survey, 2 groups of patients were analyzed. The DIEAP group consisted of 30 women who had previously had secondary breast reconstruction with DIEAP flap after mastectomy for breast cancer. The control group consisted of 7 women with no previous abdominal incisions planned for secondary breast reconstruction with DIEAP. Pressure thresholds were tested within the margins of the abdominal wall using Semmes-Weinstein monofilaments. In the DIEAP group a pattern of higher pressure thresholds was observed in the proximity of the scar. Comparing the 2 groups, significant higher pressure thresholds were found in the DIEAP group in the scar on both sides and in the midline from the scar to the umbilical level. Our data show that the abdominoplasty performed during breast reconstruction with DIEAP reduces cutaneous sensitivity in the donor site area.
Wavelet Orthonormal Decompositions for Extracting Features in Pattern Recognition

In this paper, a novel approach based on the wavelet orthonormal decomposition is presented to extract features in pattern recognition. The proposed approach first reduces the dimensionality of a two-dimensional pattern, and thereafter performs wavelet transform on the derived one-dimensional pattern to generate a set of wavelet transform subpatterns, namely, several uncorrelated functions. Based on these functions, new features are readily computed to represent the original two-dimensional pattern. As an application, experiments were conducted using a set of printed characters with varying orientations and fonts. The results obtained from these experiments have consistently shown that the proposed feature vectors can yield an excellent classification rate in pattern recognition.
Context switching eye typing using dynamic expanding targets

Text entry by gazing on a virtual keyboard (also known as eye typing) is an important component of any gaze communication system. One of the main challenges for efficient communication is how to avoid unintended key selections due to the Midas' touch problem. The most common selection technique by gaze is dwelling. Though easy to learn, long dwell-times slows down the communication, and short dwells are prone to error. Context switching (CS) is a faster and more comfortable alternative, but the duplication of contexts takes a lot of screen space. In this paper we introduce two new CS designs using dynamic expanding targets that are more appropriate when a reduced interaction window is required. We compare the performance of the two new designs with the original CS design using QWERTY layouts as contexts. Our results with 6 participants typing with the 3 keyboards show that the use of smaller size layouts with dynamic expanding targets are as accurate and comfortable as the larger QWERTY layout, though providing lower typing speeds.
HYBRID COMPRESSION OF VIDEO WITH GRAPHICS IN DTV C 0 M M U N I CAT 1 0 N SYSTEMS

Advanced broadcast manipulation of TV sequences and enhanced user interfaces for TV systems have resul ted i n an increased amount of preand post-editing of video sequences, where graphical information is inserted. However, i n the current broadcast ing chain, there are no provisions for enabling an efficient transmission/storage of these mixed video and graphics signals and, at this emerging stage of DTV systems, introducing new standards is not desired. Nevertheless, in the professional video communicat ion chain be tween content provider and broadcaster and locally, i n the DTV receiver, proprietary video-graphics compression schemes can be used to enable more efficient transmission/storage of mixed video and graphics signals. For example, in the DTV receiver case, this will lead to a significant memory-cost reduction. To preserve a high overall image quality, the video and graphics data require independent coding systems, matched wi th their specific visual and statistical properties. In th is paper, we introduce various efficient a lgori thms that suppor t both the lossless (contour, run length and ar i thmetic coding) and the lossy (block predictive coding) compression of graphics data . If the graphics d a t a are apriori mixed w i t h video and the graphics position is unknown at compression t ime, an accura te detect ion mechanism is applied to distinguish the two signals, such that independent coding algori thms can be employed for each datatype. In the DTV memory-reduct ion scenario, an overall bi t ra te cont rol completes the system, ensuring a fixed compression factor of 2-3 per f rame without sacrificing the quality of the graphics. KeywordsTV c o m m u n i c a t i o n systems, lossless i m a g e c o m p r e s s i o n , graphics , c o n t o u r cod ing , ar i thmet ic cod ing , r u n l e n g t h cod ing , e m b e d d e d c o m p r e s s i o n architecture.
3D gaze estimation in the scene volume with a head-mounted eye tracker

Most applications involving gaze-based interaction are supported by estimation techniques that find a mapping between gaze data and corresponding targets on a 2D surface. However, in Virtual and Augmented Reality (AR) environments, interaction occurs mostly in a volumetric space, which poses a challenge to such techniques. Accurate point-of-regard (PoR) estimation, in particular, is of great importance to AR applications, since most known setups are prone to parallax error and target ambiguity. In this work, we expose the limitations of widely used techniques for PoR estimation in 3D and propose a new calibration procedure using an uncalibrated head-mounted binocular eye tracker coupled with an RGB-D camera to track 3D gaze within the scene volume. We conducted a study to evaluate our setup with real-world data using a geometric and an appearance-based method. Our results show that accurate estimation in this setting still is a challenge, though some gaze-based interaction techniques in 3D should be possible.
Advances in Agriculture and Natural Sciences for Sustainable Agriculture ( October 12 & 13 , 2018 ) In Vitro callus induction and plant regeneration in basmati rice ( Oryza Sativa L . ) varieties

Rice is the most important staple food for a large part of the world’s population. Its production needs increase to meet the predicted demands of increasing population. Biotechnology provides a novel approach for rice improvement through transformation technique. Studies related to the In-vitro culture of plant require a basic protocol for callus induction and subsequent plant regeneration. Efficient callus induction and plant regeneration are pre-requisite for transformation. In the present study, an efficient callus induction and regeneration system was established for basmati rice varieties viz. Basmati-370, Pusa Sugandha-4, Vallabh Basmati-22 and Taroari. A number of factors such as media composition, different concentrations and combinations of hormones were studied. MS media supplemented with 2.0 mg/l of 2, 4-D produced the most desired calli. The callus induction frequency was found to be highest for Pusa Sugandha-4 while Basmati-370 showed the highest regeneration frequency on MS medium supplemented with 2.0 mg/l BAP and 1mg/l of NAA.
Cloning and characterization of DNA polymerase η from Trypanosoma cruzi: Roles for translesion bypass of oxidative damage

We report the cloning and characterization of the DNA polymerase η gene from Trypanosoma cruzi (TcPolη), the causative agent of Chagas disease. This protein, which can bypass cyclobutane pyrimidine dimers, contains motifs that are conserved between Y family polymerases. In vitro assays showed that the recombinant protein is capable of synthesizing DNA in undamaged primer‐templates. Intriguingly, T. cruzi overexpressing TcPolη does not increase its resistance to UV‐light (with or without caffeine) or cisplatin, despite the ability of the protein to enhance UV resistance in a RAD30 mutant of Saccharomyces cerevisiae. Parasites overexpressing TcPolη are also unable to restore growth after treatment with zeocin or gamma irradiation. T. cruzi overexpressing TcPolη are more resistant to treatment with hydrogen peroxide (H2O2) compared to nontransfected cells. The observed H2O2 resistance could be associated with its ability to bypass 8‐oxoguanine lesions in vitro. The results presented here suggest that TcPolη is able to bypass UV and oxidative lesions. However the overexpression of the gene only interferes in response to oxidative lesions, possibly due to the presence of these lesions during the S phase. Environ. Mol. Mutagen. 2009. © 2009 Wiley‐Liss, Inc.
Study of Bulk and Elementary Screw Dislocation Assisted Reverse Breakdown in Low-Voltage ( 250 V ) 4 H – SiC p n Junction Diodes — Part I : DC Properties

Given the high-density ( 10 cm ) of elementary screw dislocations (Burgers vector= 1c with no hollow core) in commercial SiC wafers and epilayers, all large current ( >1 A) SiC power devices will likely contain elementary screw dislocations for the foreseeable future. It is therefore important to ascertain the electrical impact of these defects, particularly in high-field vertical power device topologies where SiC is expected to enable large performance improvements in solid-state high-power systems. This paper compares the dc-measured reverse-breakdown characteristics of low-voltage ( <250 V) small-area (<5 10 4 cm) 4H–SiC pn diodes with and without elementary screw dislocations. Diodes containing elementary screw dislocations exhibited higher pre-breakdown reverse leakage currents, softer reverse breakdown current–voltage ( I V ) knees, and highly localized microplasmic breakdown current filaments compared to screw dislocation-free devices. The observed localized 4H–SiC breakdown parallels microplasmic breakdown observed in silicon and other semiconductors, in which space-charge effects limit current conduction through the local microplasma as reverse bias is increased.
Testing a Model-Directed, Mixed Mode Protocol in the RECS Pilot Study

The Residential Energy Consumption Survey (RECS) is a periodic survey of households that collects energy characteristics, energy usage patterns, and household demographics. The survey has been conducted since 1978 with the most recent iteration in 2009. Currently, the RECS is an in-person survey using computer-assisted personal interviewing (CAPI) for data collection. The sampling design includes labor-intensive area probability sampling with listing and rostering of housing units along with the use of address-based sampling (ABS) in more recent years in areas that have high coverage of an ABS frame. The Energy Information Administration (EIA) conducted a series of pilot tests to determine the feasibility, cost-effectiveness, time efficiency, and response validity of selfadministered modes in the RECS Cities Pilot. The second of these tests, and the subject of this paper, was the RECS Cities Pilot conducted in five localities: Chicago, IL; Jacksonville, FL; San Diego, CA; Seattle, WA; and Worcester, MA. The Cities Pilot study implemented two modes of response – computer assisted web interviewing (CAWI) and paper and pencil interviewing (PAPI). This paper focuses on an experiment to test the so-called “model-directed mode protocol. ” This approach attempts to identify households who do not have internet access and would find it very difficult to respond using the web. These households would (initially) be asked to complete a PAPI questionnaire while other households would be requested to respond by web. The experiment described in this paper was designed to determine whether this approach results in a higher response rate than the CAWI-first protocol without reducing the proportion of respondents that complete the questionnaire by web.
First record of bridal creeper rust, Puccinia myrsiphylli, a classical biocontrol agent of the environmental weed bridal creeper, Asparagus asparagoides, in New Zealand

Puccinia myrsiphylli is reported for the first time on weed infestations of Asparagus asparagoides in New Zealand, where it is concluded to have been introduced either accidentally or autonomously by way of wind-dispersed spores. A detailed description, illustration and genetic sequence of the specimen are provided.