Miracle-dz/UniFAR-FTUs huggingface dataset:
Rab33B Controls Hepatitis B Virus Assembly by Regulating Core Membrane Association and Nucleocapsid Processing

Many viruses take advantage of cellular trafficking machineries to assemble and release new infectious particles. Using RNA interference (RNAi), we demonstrate that the Golgi/autophagosome-associated Rab33B is required for hepatitis B virus (HBV) propagation in hepatoma cell lines. While Rab33B is dispensable for the secretion of HBV subviral envelope particles, its knockdown reduced the virus yield to 20% and inhibited nucleocapsid (NC) formation and/or NC trafficking. The overexpression of a GDP-restricted Rab33B mutant phenocopied the effect of deficit Rab33B, indicating that Rab33B-specific effector proteins may be involved. Moreover, we found that HBV replication enhanced Rab33B expression. By analyzing HBV infection cycle steps, we identified a hitherto unknown membrane targeting module in the highly basic C-terminal domain of the NC-forming core protein. Rab33B inactivation reduced core membrane association, suggesting that membrane platforms participate in HBV assembly reactions. Biochemical and immunofluorescence analyses provided further hints that the viral core, rather than the envelope, is the main target for Rab33B intervention. Rab33B-deficiency reduced core protein levels without affecting viral transcription and hampered core/NC sorting to envelope-positive, intracellular compartments. Together, these results indicate that Rab33B is an important player in intracellular HBV trafficking events, guiding core transport to NC assembly sites and/or NC transport to budding sites.
Cytoplasmic mutated nucleophosmin is stable in primary leukemic cells and in a xenotransplant model of NPMc+ acute myeloid leukemia in SCID mice

Findings of this study indicate that NPM1 mutations are stable in patients with acute myeloid leukemia, providing a rationale for monitoring of minimal residual disease. We investigated the NPM1 mutation status or subcellular expression of NPM protein (nuclear vs. aberrant cytoplasmic) at diagnosis and relapse in 125 patients with acute myeloid leukemia from Italy and Germany. All 52 patients with acute myeloidleukemia carrying at diagnosis mutated or cytoplasmic NPM (NPMc+ acute myeloid leukemia) retained this feature at relapse. Notably, cytoplasmic mutated NPM has now been retained for eight years in a xenotransplant model of NPMc+ acute myeloid leukemia in immunodeficient mice. None of 73 acute myeloid leukemia patients carrying at diagnosis wild-type NPM1 gene or showing at immunohistochemistry nucleus-restricted expression of nucleophosmin (NPMc− acute myeloid leukemia), which is predictive of NPM1 gene in germline configuration, acquired cytoplasmic mutated NPM at relapse. This finding further confirms that NPMc+ acute myeloid leukemia represents a primary event rather than a transformation stage of NPMc− acute myeloid leukemia. The stability of cytoplasmic mutated NPM in patients with acute myeloid leukemia, even at relapse in extramedullary sites, and in a xenotransplant model, suggest this event is crucial for leukemogenesis and represents the rationale for monitoring minimal residual disease and molecular targeted therapy in NPMc+ acute myeloid leukemia.
The Effect of Multichannel Compression on Vowel and Stop‐Consonant Discrimination in Normal‐Hearing and Hearing‐Impaired Subjects

Objective Multichannel compression (MCC) processing can alter the speech spectrum, perhaps reducing spectral contrasts that are important for the discrimination of certain speech sounds. The effect of MCC processing on the discrimination of vowels and voiced stop consonants was studied. Design Vowels and voiced stop consonants were MCC-processed in two ways: 1) FLAT MCC having the same compression ratio in each channel, and 2) SHAPED MCC having compression ratios in each channel adjusted to the auditory area of the particular subject. The stimuli were processed both ways using 2, 4, 8, 16, and 31 independent compression channels. Unprocessed and linearly amplified stimuli were used as control conditions. Normal-hearing and hearing-impaired subjects were tested for changes in discrimination performance as a function of the MCC processing parameters. Results When the MCC processing was adjusted specifically for an individual hearing-impaired subject, no negative effect of increasing numbers of channels (2 to 31) was found. In the case of FLAT MCC processing, increasingly degraded discrimination performance was found for both subject groups as the compression ratio increased and as the number of channels increased. There was also a strong interaction between the effects of the number of channels and the compression ratio, with the negative effects of increasing numbers of channels being much greater at the highest compression ratio. Conclusions Negative effects of MCC were found only for very extreme MCC conditions. MCC processing with compression ratios adjusted in each channel for the individual subject, and having as many as 31 channels, revealed no negative effects on vowel or voiced stop-consonant discrimination. These results do not support the prevalent view that MCC with more than two or three channels will be detrimental and should encourage further research on MCC processing with larger numbers of channels.
Creation of Reliable Relevance Judgments in Information Retrieval Systems Evaluation Experimentation through Crowdsourcing: A Review

Test collection is used to evaluate the information retrieval systems in laboratory-based evaluation experimentation. In a classic setting, generating relevance judgments involves human assessors and is a costly and time consuming task. Researchers and practitioners are still being challenged in performing reliable and low-cost evaluation of retrieval systems. Crowdsourcing as a novel method of data acquisition is broadly used in many research fields. It has been proven that crowdsourcing is an inexpensive and quick solution as well as a reliable alternative for creating relevance judgments. One of the crowdsourcing applications in IR is to judge relevancy of query document pair. In order to have a successful crowdsourcing experiment, the relevance judgment tasks should be designed precisely to emphasize quality control. This paper is intended to explore different factors that have an influence on the accuracy of relevance judgments accomplished by workers and how to intensify the reliability of judgments in crowdsourcing experiment.
Detection of BCR-ABL Positive Cells in an Asymptomatic Patient: A Case Report and Literature Review

We report a case of an asymptomatic 39-year-old male who was incidentally found to have a white blood cell count of 15 000/mm3 associated with a positive BCR-ABL/t(9;22)(q34;q11) chromosomal translocation detected in 51/300 of cells by FISH and RT-PCR from peripheral blood. Within the next 3 months, leukocytosis spontaneously subsided; however, BCR-ABL by RT-PCR and FISH was persistent both in peripheral blood and bone marrow. The patient was not started on any therapy and is being followed regularly with laboratory checkup and physical examination for monitoring signs and symptoms of chronic myeloid leukemia (CML) and biological behavior of his BCR-ABL transcripts. At 1 year of surveillance, he is disease free; however he has persistent detection of BCR-ABL fusion gene. Our case is challenging because actual risk of developing CML in BCR-ABL positive healthy, asymptomatic patients is not known.
CPHD Filtering With Unknown Clutter Rate and Detection Profile

In Bayesian multi-target filtering, we have to contend with two notable sources of uncertainty, clutter and detection. Knowledge of parameters such as clutter rate and detection profile are of critical importance in multi-target filters such as the probability hypothesis density (PHD) and cardinalized PHD (CPHD) filters. Significant mismatches in clutter and detection model parameters result in biased estimates. In practice, these model parameters are often manually tuned or estimated offline from training data. In this paper we propose PHD/CPHD filters that can accommodate model mismatch in clutter rate and detection profile. In particular we devise versions of the PHD/CPHD filters that can adaptively learn the clutter rate and detection profile while filtering. Moreover, closed-form solutions to these filtering recursions are derived using Beta and Gaussian mixtures. Simulations are presented to verify the proposed solutions.
Measuring assessor accuracy: a comparison of nist assessors and user study participants

In many situations, humans judging document relevance are forced to trade-off accuracy for speed. The development of better interactive retrieval systems and relevance assessing platforms requires the measurement of assessor accuracy, but to date the subjective nature of relevance has prevented such measurement. To quantify assessor performance, we define relevance to be a group's majority opinion, and demonstrate the value of this approach by comparing the performance of NIST assessors to a group of assessors representative of participants in many information retrieval user studies. Using data collected as part of a user study with 48 participants, we found that NIST assessors discriminate between relevant and non-relevant documents better than the average participant in our study, but that NIST assessors' true positive rate is no better than that of the study participants. In addition, we found NIST assessors to be conservative in their judgment of relevance compared to the average participant.
Taking , Learning , and Technology Adoption : Results from an Economic Experiment with Farmers 1

This paper examines the complementarities between advice taking and individual learning in technology adoption. We run an economic experiment with US farmers measuring their individual learning ability and their propensity to take advice. We then compare the decisions they make in the experiments with their real-world adoption of genetically modified (GM) corn and soy seeds. The first adopters are those who are both quite able cognitively and disinclined to take advice. We find evidence that individual ability and advice taking from external sources of information are substitutes rather than complements in the agricultural technology decision-making process.
Extracting Information on Pneumonia in Infants Using Natural Language Processing of Radiology Reports

Natural language processing (NLP) is critical for improvement of the healthcare process because it can encode clinical data in patient documents. Many clinical applications such as decision support require coded data to function appropriately. However, in order to be applicable for healthcare, performance must be adequate. A valuable automated application is the detection of infectious diseases, such as surveillance of pneumonia in newborns (e.g., neonates) because the disease produces significant rates of morbidity and mortality, and manual surveillance is challenging. Studies have demonstrated that automated surveillance using NLP is a useful adjunct to manual surveillance and an effective tool for infection control practitioners. This paper presents a study evaluating the feasibility of an NLP-based monitoring system to screen for healthcare-associated pneumonia in neonates. We estimated sensitivity, specificity, and positive predictive value by comparing results with clinicians' judgments. Sensitivity was 71% and specificity was 99%. Our results demonstrated that the automated method was feasible.
Transformation Properties of External Radiation Fields, Energy-Loss Rates and Scattered Spectra, and a Model for Blazar Variability

We treat transformation properties of external radiation fields in the proper frame of a plasma moving with constant speed. The specific spectral energy densities of external isotropic and accretion disk radiation fields are derived in the comoving frame of relativistic outflows, such as those thought to be found near black hole jet and gamma-ray burst sources. Nonthermal electrons and positrons Compton-scatter this radiation field, and high-energy protons and ions interact with this field through photomeson and photopair production. We revisit the problem of the Compton-scattered spectrum associated with an external accretion disk radiation field and clarify a past treatment by the authors. Simple expressions for energy-loss rates and Thomson-scattered spectra are given for ambient soft photon fields consisting of either a surrounding external isotropic monochromatic radiation field or an azimuthally symmetric, geometrically thin accretion disk radiation field. A model for blazar emission is presented that displays a characteristic spectral and variability behavior due to the presence of a direct accretion disk component. The disk component and distinct flaring behavior can be bright enough to be detected from flat-spectrum radio quasars with GLAST. Spectral states of blazars are characterized by the relative importance of the accretion disk and scattered radiation fields and, in the extended jet, by the accretion disk, inner jet, and cosmic microwave background radiation fields.
Clinical characteristics and treatment outcome in a Taiwanese population of patients with Epstein-Barr virus-positive diffuse large B-cell lymphoma.

OBJECTIVE Epstein-Barr virus-positive diffuse large B-cell lymphoma is a provisional entity in the 2008 World Health Organization classification of tumors of hematopoietic and lymphoid tissues. Reports on the characteristics and clinical outcome of this disease in different geographic regions showed great disparities. METHODS To define the clinical characteristics as well as the prognostic impact of Epstein-Barr virus infection on diffuse large B-cell lymphoma in Taiwan, we retrospectively investigated the Epstein-Barr virus status of 89 patients with newly diagnosed diffuse large B-cell lymphoma in our institute. RESULTS Using a cutoff point of positive nuclear staining of Epstein-Barr virus-encoded RNA-1-in situ hybridization in ≥20% of the examined cells, we identified 15 cases (16.9%) of the entire study cohort as Epstein-Barr virus-positive diffuse large B-cell lymphoma. The clinical and laboratory features were not different between Epstein-Barr virus-positive and -negative diffuse large B-cell lymphoma patients. Univariate analysis showed patients with diffuse large B-cell lymphoma that were either Epstein-Barr virus-positive or had activated B-cell-like features had an inferior overall survival. Older age, advanced stage and lymphoma with activated B-cell-like features or Epstein-Barr virus-encoded RNA positivity were independent prognostic factors affecting overall survival on multivariate analysis. Patients with two or three of these adverse-risk factors were considered high risk and fared far worse than patients with no or only one adverse factor. CONCLUSIONS Taken together, we demonstrated that a higher frequency of Epstein-Barr virus association was detected in a Taiwanese cohort of diffuse large B-cell lymphoma patients, and Epstein-Barr virus-encoded RNA positivity was shown to add important prognostic value in these patients.
Co Alloy- ${\hbox{SiO}}_{2}$ Granular-Type Longitudinal Media for Sputtered Tape Applications

We investigated bias-sputtered Co alloy-films (CoCrPt- and CoPt-) for high density magnetic tape media. We used bias sputtering to achieve desirable properties (good in-plane orientation and low noise) in these media. The CoCrPt-sputtered tape media showed a flat frequency response with a of 160 kfci and a corresponding signal-to-noise ratio of 21 dB. The overwrite performance was better than 40 dB for an overwriting frequency of 12 MHz (90 kfci) and overwritten frequency ranging from 1 to 10 MHz (8-75 kfci). An overcoat (carbon nitride) with a thickness of 6 nm resulted in a 4-5 dB spacing loss in the roll-off curve at high recording densities, and a 3-4 dB lower overwrite ratio. In addition, the CoPt-media with no Cr present produced a maximum output 4-5 dB higher, but also higher noise power compared to the CoCrPt-media.
Toward brain correlates of natural behavior: fMRI during violent video games

Modern video games represent highly advanced virtual reality simulations and often contain virtual violence. In a significant amount of young males, playing video games is a quotidian activity, making it an almost natural behavior. Recordings of brain activation with functional magnetic resonance imaging (fMRI) during gameplay may reflect neuronal correlates of real‐life behavior. We recorded 13 experienced gamers (18–26 years; average 14 hrs/week playing) while playing a violent first‐person shooter game (a violent computer game played in self‐perspective) by means of distortion and dephasing reduced fMRI (3 T; single‐shot triple‐echo echo‐planar imaging [EPI]). Content analysis of the video and sound with 100 ms time resolution achieved relevant behavioral variables. These variables explained significant signal variance across large distributed networks. Occurrence of violent scenes revealed significant neuronal correlates in an event‐related design. Activation of dorsal and deactivation of rostral anterior cingulate and amygdala characterized the mid‐frontal pattern related to virtual violence. Statistics and effect sizes can be considered large at these areas. Optimized imaging strategies allowed for single‐subject and for single‐trial analysis with good image quality at basal brain structures. We propose that virtual environments can be used to study neuronal processes involved in semi‐naturalistic behavior as determined by content analysis. Importantly, the activation pattern reflects brain‐environment interactions rather than stimulus responses as observed in classical experimental designs. We relate our findings to the general discussion on social effects of playing first‐person shooter games. Hum Brain Mapp, 2006. © 2006 Wiley‐Liss, Inc.
DESIGN AND VALIDATION OF AN INTERORGANIZATIONAL INFORMATION SYSTEM

This paper presents an interorganizational information system that aims to structure collaboration of engineering activities as well as data sharing across company borders. The paper also describes the approach underlying the system, validates it by designing a system prototype, and tests the system using questionnaire and in-depth interviews in order to further knowledge about the subject. The main results from the test show: collaboration engineering is potentially important for senior managers; end-users were specifically attracted more by the concept rather by its implementation; engineering change management is a complex process; and the support of strategic level is a critical success factor. In addition, the paper describes other factors that emerged during the ongoing project and inhibit success of the system.
Influence of Hypoxia, High Glucose, and Low Serum on the Growth Kinetics of Mesenchymal Stem Cells from Deciduous and Permanent Teeth

The therapeutic potential of mesenchymal stromal cells depends on their ability to survive and proliferate under adverse in vivo scenarios in a particular disease. In most of the sites of injury, especially in diabetic wounds, there can be hypoxia, hyperglycemia, and ischemia, leading to a lack of nutrients. Hence, the aim of our present study was to investigate the influence of hypoxia, high glucose, and low serum concentrations on the growth kinetics and proliferative potential of human dental pulp stem cells from exfoliated deciduous teeth (SHED) and permanent teeth (DPSC). In this study we isolated two types of specialized stem cells from human dental pulp tissues, which were supposedly of neural crest origin, and cultured them in KO-DMEM medium supplemented with 10% fetal bovine serum (FBS). Both SHED and DPSC were characterized for standard CD surface markers, and their ability to differentiate into adipogenic and osteogenic lineages was tested. SHED and DPSC were exposed to either hypoxia or high glucose or low serum conditions, and their growth kinetics and differentiation potentials were compared with those of normal culture conditions. We found that SHED retained their phenotypic expression and differentiation potential under hypoxia, high-glucose, and low-serum conditions and exhibited a higher proliferation in terms of cell yield and a reduced doubling time compared to DPSC. Our findings clearly demonstrate for the first time that SHED are superior to DPSC as evidenced by their enhanced proliferation under adverse culture conditions.
A CMOS Instrumentation Amplifier With 90-dB CMRR at 2-MHz Using Capacitive Neutralization: Analysis, Design Considerations, and Implementation

The benefits of using “current feedback” in instrumentation amplifier (IA) design are well known. In this paper, we analyze the mismatch mechanisms, both random and systematic types, which influence the common-mode rejection ratio (CMRR) performance of the local current feedback IA topology. We derive analytical expressions for the common-mode gain frequency response due to random mismatches (transconductance, drain-source conductance and parasitic capacitance) and verify the integrity of the analysis through simulation. To address the systematic mismatch in the drain capacitance of the input pair transistors, we employ capacitive neutralization and verify its effectiveness in practice from the fabricated IA chip samples in a 0.35- CMOS process technology. The measured average common-mode gain improvement for the 20 fabricated samples employing our neutralization technique is about 20 dB at 2 MHz ( 3 dB bandwidth). When taking into account the differential gain response (33.7 dB), the average CMRR of the neutralized IA at 2 MHz exceeds 90 dB. The IA occupies an area of 0.068 and dissipates 0.85 mW from a 3-V power supply. The circuit is intended for a wideband bioimpedance spectroscopy application.
Gender Differences in Sleep Deprivation Effects on Risk and Inequality Aversion: Evidence from an Economic Experiment

Excessive working hours—even at night—are becoming increasingly common in our modern 24/7 society. The prefrontal cortex (PFC) is particularly vulnerable to the effects of sleep loss and, consequently, the specific behaviors subserved by the functional integrity of the PFC, such as risk-taking and pro-social behavior, may be affected significantly. This paper seeks to assess the effects of one night of sleep deprivation on subjects’ risk and social preferences, which are probably the most explored behavioral domains in the tradition of Experimental Economics. This novel cross-over study employs thirty-two university students (gender-balanced) participating to 2 counterbalanced laboratory sessions in which they perform standard risk and social preference elicitation protocols. One session was after one night of undisturbed sleep at home, and the other was after one night of sleep deprivation in the laboratory. Sleep deprivation causes increased sleepiness and decreased alertness in all subjects. After sleep loss males make riskier decisions compared to the rested condition, while females do the opposite. Females likewise show decreased inequity aversion after sleep deprivation. As for the relationship between cognitive ability and economic decisions, sleep deprived individuals with higher cognitive reflection show lower risk aversion and more altruistic behavior. These results show that one night of sleep deprivation alters economic behavior in a gender-sensitive way. Females’ reaction to sleep deprivation, characterized by reduced risky choices and increased egoism compared to males, may be related to intrinsic psychological gender differences, such as in the way men and women weigh up probabilities in their decision-making, and/or to the different neurofunctional substrate of their decision-making.
A novel inhibitor of p75-neurotrophin receptor improves functional outcomes in two models of traumatic brain injury

The p75 neurotrophin receptor (p75NTR) is a member of the TNF-receptor superfamily. Delbary-Gossart, Lee et al. describe the neuroprotective effects of a novel piperizine derivative that blocks p75NTR. In two rodent models of traumatic brain injury, EVT901 protects neurons and glia, reduces inflammation and seizure susceptibility, and improves neurological outcomes.