Miracle-dz/UniFAR-FTUs huggingface dataset:
Electrophysiological correlates of visual consciousness and selective attention

It is not clear whether attention is necessary or not for consciousness. We studied the relationship between attention and consciousness by tracking their electrophysiological correlates. The participants attended to visual targets, ignored nontargets in the prespecified visual field and ignored all stimuli in the opposite field. Visual consciousness was varied by masking. Our results showed that the earliest electrophysiological correlate of consciousness emerged independent of the manipulations of spatial and nonspatial attention. Conversely, the electrophysiological correlate of attention, selection negativity, was elicited regardless of the presence or absence of consciousness. Only the correlates of later, higher-level conscious processes strongly depended on attention. Thus, the electrophysiological brain responses reflecting visual consciousness and attention are initially independent of each other.
Appendectomy and the risk of developing ulcerative colitis or Crohn's disease: results of a large case-control study. South Limburg Inflammatory Bowel Disease Study Group.

BACKGROUND & AIMS Appendectomy has been pointed out as a protective factor for ulcerative colitis (UC). The aim of this study was to elucidate the role of appendectomy in inflammatory bowel disease (IBD). METHODS Prevalent as well as incident cases with IBD were studied separately using a pairwise age- and sex-matched case-control study design. RESULTS In 232 prevalent UC cases, the risk of developing UC was significantly lower after previous appendectomy (odds ratio [OR], 0.36; 95% confidence interval [CI], 0.15-0.80); subgroup analysis found a protective effect only in pancolitis (OR, 0.2; 95% CI, 0.02-0.7). In 208 patients with Crohn's disease (CD), the OR was not significantly increased but a positive association with appendectomy was observed in ileocecal disease. A significant larger proportion of appendectomies was performed close to the time of diagnosis. Smoking was not a confounding factor. No statistically significant associations were observed in incident IBD patients. Prevalent and incident patients taken together resulted in ORs of 0.44 (95% CI, 0.24-0.78) in UC and 1.65 (95% CI, 0.96-2.91) in CD. CONCLUSIONS An overall protective role of appendectomy for UC was observed. The observations in CD suggest that appendectomy in some cases was a result of still undiagnosed CD.
Engineered G-protein Coupled Receptors are Powerful Tools to Investigate Biological Processes and Behaviors

Understanding how discreet tissues and neuronal circuits function in relation to the whole organism to regulate physiological processes and behaviors is a fundamental goal of modern biological science. Powerful and important new tools in this discovery process are modified G-protein coupled receptors (GPCRs) known as ‘Receptors Activated Solely by Synthetic Ligands (RASSLs),’ and ‘Designer Receptors Exclusively Activated by a Designer Drug (DREADDs). ’ Collectively, these are GPCRs modified either through rational design or directed molecular evolution, that do not respond to native ligand, but functionally respond only to synthetic ligands. Importantly, the utility of these receptors is not limited to examination of the role of GPCR-coupled effector signal transduction pathways. Due to the near ubiquitous expression of GPCRs throughout an organism, this technology, combined with whole animal transgenics to selectively target expression, has the ability to regulate activity of discreet tissues and neuronal circuits through effector pathway modulation to study function and behavior throughout the organism. Advantages over other systems currently used to modify in vivo function include the ability to rapidly, selectively and reversibly manipulate defined signal transduction pathways both in short term and long term studies, and no need for specialized equipment due to convenient systemic treatment with activating ligand.
An outbreak of tuberculosis with accelerated progression among persons infected with the human immunodeficiency virus. An analysis using restriction-fragment-length polymorphisms.

BACKGROUND Tuberculosis typically develops from a reactivation of latent infection. Clinical tuberculosis may also arise from a primary infection, and this is thought to be more likely in persons infected with the human immunodeficiency virus (HIV). However, the relative importance of these two pathogenetic mechanisms in this population is unclear. METHODS Between December 1990 and April 1991, tuberculosis was diagnosed in 12 residents of a housing facility for HIV-infected persons. In the preceding six months, two patients being treated for tuberculosis had been admitted to the facility. We investigated this outbreak using standard procedures plus analysis of the cultured organisms with restriction-fragment-length polymorphisms (RFLPs). RESULTS Organisms isolated from all 11 of the culture-positive residents had similar RFLP patterns, whereas the isolates from the 2 patients treated for tuberculosis in the previous six months were different strains. This implicated the first of the 12 patients with tuberculosis as the source of this outbreak. Among the 30 residents exposed to possible infection, active tuberculosis developed in 11 (37 percent), and 4 others (13 percent) had newly positive tuberculin skin tests. Of 28 staff members with possible exposure, at least 6 had positive tuberculin-test reactions, but none had tuberculosis. CONCLUSIONS Newly acquired tuberculous infection in HIV-infected patients can spread readily and progress rapidly to active disease. There should be heightened surveillance for tuberculosis in facilities where HIV-infected persons live, and investigation of contacts must be undertaken promptly and be focused more broadly than is usual.
Protein glycosylation and advanced glycosylated endproducts (AGEs) accumulation: an avian solution?

The objectives of this study were to determine the effect of diet restriction (DR) and the crosslinking inhibitor, aminoguanidine (AG), on PMA-induced respiratory burst, concentrations of uric acid, and the rate of pentosidine accumulation in the skin (Ps) of naturally hyperglycemic broiler breeder hens. Female chicks (n = 450) were randomly assigned to four groups from 8 to 92 weeks after hatch: ad libitum (AL), diet restricted (DR), AL and DR groups supplemented with 400 ppm AG each (AL + AG and DR + AG). No consistent effects of treatments were observed on plasma concentrations of glucose. The accumulation of Ps in AL birds increased linearly with age (p < .001) and was significantly retarded in all treatment groups (p < .001). Ps in the AL + AG group was comparable to that in the DR or DR + AG groups. PMA-induced respiratory bursts in blood leukocytes were significantly retarded in DR or AG-supplemented (p < .0001) groups. Although there was a marginal increase in overall mean concentrations of plasma uric acid for the DR group, no consistent differences were observed on individual time points. It is concluded that the glycosylation process may not be the primary cause of glucose-derived crosslinks and that the accumulation of Ps can be retarded by DR and AG in broiler breeder hens.
Corticosteroids Increase Protein Breakdown and Loss in Newly Diagnosed Pediatric Crohn Disease

Children with Crohn disease have altered growth and body composition. Previous studies have demonstrated decreased protein breakdown after either corticosteroid or anti-TNF-α therapy. The aim of this study was to evaluate whole body protein metabolism during corticosteroid therapy in children with newly diagnosed Crohn disease. Children with suspected Crohn disease and children with abdominal symptoms not consistent with Crohn disease underwent outpatient metabolic assessment. Patients diagnosed with Crohn disease and prescribed corticosteroid therapy returned in 2 wk for repeat metabolic assessment. Using the stable isotopes [d5] phenylalanine, [1-13C] leucine, and [15N2] urea, protein kinetics were determined in the fasting state. Thirty-one children (18 controls and 13 newly diagnosed with Crohn disease) completed the study. There were no significant differences in protein breakdown or loss between patients with Crohn disease at diagnosis and controls. After corticosteroid therapy in patients with Crohn disease, the rates of appearance of phenylalanine (32%) and leucine (26%) increased significantly, reflecting increased protein breakdown, and the rate of appearance of urea also increased significantly (273%), reflecting increased protein loss. Whole body protein breakdown and loss increased significantly after 2 wk of corticosteroid therapy in children with newly diagnosed Crohn disease, which may have profound effects on body composition.
Management of severe head injury: Institutional variations in care and effect on outcome*

ObjectiveThe purpose of this study was three-fold: a) to examine variations in care of patients with severe head injury in academic trauma centers across the United States; b) to determine the proportion of patients who received care according to the Brain Trauma Foundation guidelines; and c) to correlate the outcome from severe traumatic brain injury with the care received. DesignRetrospective data collection for consecutive patients with closed head injury and long bone fracture admitted over an 8-month period. SettingThirty-four academic trauma centers in the United States PatientsAll patients admitted with a presenting Glasgow Coma Scale score ≤8. Measurements and Main ResultsVariations in care were assessed, including prehospital intubation, intracranial pressure monitoring, use of osmotic agents, hyperventilation, and computed tomography scan utilization. Aggressive centers were defined as those placing intracranial pressure monitors in >50% of patients meeting the Brain Trauma Foundation criteria for intracranial pressure monitoring. The primary outcome variables were mortality, functional status at discharge, and length of stay. Kaplan-Meier survival analysis was performed for aggressive vs. nonaggressive centers. A Cox proportional hazard model was used to evaluate the association between type of center and mortality rate. Length of stay was evaluated by using linear regression. ResultsThere was considerable variation in the rates of prehospital intubation, intracranial pressure monitoring, intracranial pressure-directed therapy, and head computed tomography scan utilization across centers. Management at an aggressive center was associated with a significant reduction in the risk of mortality (hazard ratio, 0.43; 95% confidence interval, 0.27–0.66). There was no statistically significant difference in functional status at the time of discharge for survivors. Adjusted length of stay for survivors at aggressive centers was shorter, compared with the length of stay at nonaggressive centers: −6 days (95% confidence interval, −14 to 2 days). ConclusionConsiderable national variation in the care of severely head-injured patients persists. An “aggressive” management strategy is associated with decreased mortality rate for patients with severe head injury, with no significant difference in functional status at discharge among survivors.
American Cancer Society Guidelines for Breast Screening with MRI as an Adjunct to Mammography

New evidence on breast Magnetic Resonance Imaging (MRI) screening has become available since the American Cancer Society (ACS) last issued guidelines for the early detection of breast cancer in 2003. A guideline panel has reviewed this evidence and developed new recommendations for women at different defined levels of risk. Screening MRI is recommended for women with an approximately 20–25% or greater lifetime risk of breast cancer, including women with a strong family history of breast or ovarian cancer and women who were treated for Hodgkin disease. There are several risk subgroups for which the available data are insufficient to recommend for or against screening, including women with a personal history of breast cancer, carcinoma in situ, atypical hyperplasia, and extremely dense breasts on mammography. Diagnostic uses of MRI were not considered to be within the scope of this review.
Reanalysis and Simulation Suggest a Phylogenetic Microarray Does Not Accurately Profile Microbial Communities

The second generation (G2) PhyloChip is designed to detect over 8700 bacteria and archaeal and has been used over 50 publications and conference presentations. Many of those publications reveal that the PhyloChip measures of species richness greatly exceed statistical estimates of richness based on other methods. An examination of probes downloaded from Greengenes suggested that the system may have the potential to distort the observed community structure. This may be due to the sharing of probes by taxa; more than 21% of the taxa in that downloaded data have no unique probes. In-silico simulations using these data showed that a population of 64 taxa representing a typical anaerobic subterranean community returned 96 different taxa, including 15 families incorrectly called present and 19 families incorrectly called absent. A study of nasal and oropharyngeal microbial communities by Lemon et al (2010) found some 1325 taxa using the G2 PhyloChip, however, about 950 of these taxa have, in the downloaded data, no unique probes and cannot be definitively called present. Finally, data from Brodie et al (2007), when re-examined, indicate that the abundance of the majority of detected taxa, are highly correlated with one another, suggesting that many probe sets do not act independently. Based on our analyses of downloaded data, we conclude that outputs from the G2 PhyloChip should be treated with some caution, and that the presence of taxa represented solely by non-unique probes be independently verified.
Identifying Dormant Functionality in Malware Programs

To handle the growing flood of malware, security vendors and analysts rely on tools that automatically identify and analyze malicious code. Current systems for automated malware analysis typically follow a dynamic approach, executing an unknown program in a controlled environment (sandbox) and recording its runtime behavior. Since dynamic analysis platforms directly run malicious code, they are resilient to popular malware defense techniques such as packing and code obfuscation. Unfortunately, in many cases, only a small subset of all possible malicious behaviors is observed within the short time frame that a malware sample is executed. To mitigate this issue, previous work introduced techniques such as multi-path or forced execution to increase the coverage of dynamic malware analysis. Unfortunately, using these techniques is potentially expensive, as the number of paths that require analysis can grow exponentially. In this paper, we propose Reanimator, a novel solution to determine the capabilities (malicious functionality) of malware programs. Our solution is based on the insight that we can leverage behavior observed while dynamically executing a specific malware sample to identify similar functionality in other programs. More precisely, when we observe malicious actions during dynamic analysis, we automatically extract and model the parts of the malware binary that are responsible for this behavior. We then leverage these models to check whether similar code is present in other samples. This allows us to statically identify dormant functionality (functionality that is not observed during dynamic analysis) in malicious programs. We evaluate our approach on thousands of real-world malware samples, and we show that our system is successful in identifying additional, malicious functionality. As a result, our approach can significantly improve the coverage of malware analysis results.
A 0.8/spl mu/m CMOS programmable IIR SC filter

The design of a 0.8/spl mu/m standard CMOS digitally programmable switched-capacitor recursive (IIR) filter is presented. A digital-to-analog conversion technique, instead conventional capacitor banks, is adopted so that power consumption and silicon area savings are achieved. Using transfer functions with only two poles and positioning zeros structurally on the unit circle, the described design technique ensures low sensitivity in both passband and stopband frequencies. Moreover, non-ideal effects, such as charge injection and opamp offset voltages, are greatly reduced by using a fully differential filter structure. Experimental results verifying the feasibility of the proposed approach are included.
REVIEW ARTICLE: Immune Physiology of the Mammalian Ovary – A Review

The immune system, besides orchestrating the immune response, plays an important role in the regulation of tissue homeostasis. We refer to this later activity as ‘immune physiology. ’ In human ovaries, immune system‐related cells and molecules accompany corpus luteum development and regression and cancer progression. They also accompany the origination of new rat and human germ cells by asymmetric division of ovarian surface epithelium cells, symmetric division and migration of germ cells, and follicular growth. Currently prevailing dogma on the preservation of human oocytes from the fetal period until menopause (‘storage’ doctrine) vs. oocyte renewal in invertebrates and lower vertebrates (‘continued formation’ doctrine) raises question as to the disadvantage from an evolutionary point of view of prolonged oocyte storage in humans. We attempted to reconcile these two opposing views by proposing the prime reproductive period (PRP) doctrine as follows: The ‘storage’ doctrine fits two periods of the life in human females, that between the termination of fetal oogenesis and puberty or pre‐menarcheal period (about 10–12 years), and also that period from the end of PRP (at about 38 years of age) until menopause. On the contrary, the ‘continued formation’ doctrine accounts for oocyte and follicular renewal during the PRP, and insures the availability of fresh oocytes for the development of healthy progeny. Further study on ‘immune physiology’ may help us better understand ovarian physiology and pathology in general, including infertility caused by premature ovarian failure, the pathophysiology of degenerative diseases and mechanisms of malignancy and metastasis.
Design Consideration on the Ontology for Competitive Intelligence in Web

In this paper, we discuss some consideration on designing the ontology for competitive intelligence in Web. The main task of the ontology modeling is to present a general view for competitive intelligence in Web, which is critical for the extraction of competitive intelligence from the Web. We define a set of entities to represent the hierarchy of competitive intelligence in Web, and present some future issues on this direction.
A Structured Multiarmed Bandit Problem and the Greedy Policy

We consider a multiarmed bandit problem where the expected reward of each arm is a linear function of an unknown scalar with a prior distribution. The objective is to choose a sequence of arms that maximizes the expected total (or discounted total) reward. We demonstrate the effectiveness of a greedy policy that takes advantage of the known statistical correlation structure among the arms. In the infinite horizon discounted reward setting, we show that the greedy and optimal policies eventually coincide, and both settle on the best arm. This is in contrast with the Incomplete Learning Theorem for the case of independent arms. In the total reward setting, we show that the cumulative Bayes risk after T periods under the greedy policy is at most O(logT), which is smaller than the lower bound of ¿(log2 T) established by Lai for a general, but different, class of bandit problems. We also establish the tightness of our bounds. Theoretical and numerical results show that the performance of our policy scales independently of the number of arms.
Anti‐inflammatory Activities of an Active Fraction Isolated from the root of Astragalus membranaceus in RAW 264.7 Macrophages

The root of Astragalus membranaceus (AR), which has been widely used in Traditional Chinese herbal formulae for treating foot ulcer, was found to exhibit anti‐inflammatory property, but its molecular mechanism still remains unknown. We previously identified the anti‐inflammatory sub‐fraction using bioassay‐guided fractionation. The objective of the present study was to investigate the anti‐inflammatory mechanism of the major active fraction (MAF) (0.039 to 0.156 mg/mL) using lipopolysaccharide (LPS)‐stimulated mouse macrophage RAW 264.7 cells. MAF was shown to inhibit LPS‐induced mRNA and protein expression of inducible nitric oxide synthase by 54.7% and 65.1%, respectively. Additionally, MAF down‐regulated the protein expression of cyclooxygenase‐2 and MAPK regulator by 45.0% to 74.6%, as well as the reduction of DNA binding activity of nuclear factor kappa B (NFκB) by 66.5%. It also attenuated the production of prostaglandin E2, interleukin‐1 beta (IL‐1β), IL‐6 and tumor necrosis factor alpha by 21.2% to 86.2%. Furthermore, the chemical constituents of MAF were identified. A total of 13 known chemical compounds were found in MAF, including five isoflavonoids and eight saponins. In conclusion, a bioactive fraction of AR was identified which possessed anti‐inflammatory property by reducing the release of inflammatory mediators and inactivation of NFκB through MAPK signalling pathway. Copyright © 2013 John Wiley & Sons, Ltd.
Development of hypogammaglobulinemia in patients treated with imatinib for chronic myeloid leukemia or gastrointestinal stromal tumor

These data demonstrate that imatinib treatment induces hypogammaglobulinemia which can be severe in 10% of cases, both in patients with chronic myeloid leukemia and in those with gastrointestinal stromal tumor. Imatinib mesylate is a tyrosine kinase inhibitor used as first line treatment in chronic myeloid leukemia and gastrointestinal stromal tumorpatients. Although several in vitro and animal studies demonstrated that imatinib affects immune response, few immune alterations are described in humans. We retrospectively studied hematologic and immunological parameters in 72 chronic myeloid leukemia and 15 gastrointestinal stromal tumor patients treated with imatinib at standard dosage and in 20 chronic myeloid leukemia patients treated before the introduction of imatinib in clinical practice. Both chronic myeloid leukemia and gastrointestinal stromal tumor patients developed a significant reduction of gammaglobulin and immunoglobulin serum levels. No significant hypogammaglobulinemia was observed in chronic myeloid leukemia patients in the pre-imatinib era. These data demonstrate that imatinib treatment induces hypogammaglobulinemia that can reach a severe entity in 10% of cases, both in chronic myeloid leukemia and in gastrointestinal stromal tumor patients. Prospective studies are needed to evaluate immune humoral alterations and to define the real incidence of infectious events, including viral reactivations.