Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative Profiling of In Vivo-assembled RNA-Protein Complexes Using a Novel Integrated Proteomic Approach*

Identification of proteins in RNA-protein complexes is an important step toward understanding regulation of RNA-based processes. Because of the lack of appropriate methodologies, many studies have relied on the creation of in vitro assembled RNA-protein complexes using synthetic RNA and cell extracts. Such complexes may not represent authentic RNPs as they exist in living cells as synthetic RNA may not fold properly and nonspecific RNA-protein interactions can form during cell lysis and purification processes. To circumvent limitations in current approaches, we have developed a novel integrated strategy namely MS2 in vivo biotin tagged RNA affinity purification (MS2-BioTRAP) to capture bona fide in vivo-assembled RNA-protein complexes. In this method, HB-tagged bacteriophage protein MS2 and stem-loop tagged target or control RNAs are co-expressed in cells. The tight association between MS2 and the RNA stem-loop tags allows efficient HB-tag based affinity purification of authentic RNA-protein complexes. Proteins associated with target RNAs are subsequently identified and quantified using SILAC-based quantitative mass spectrometry. Here the 1.2 kb internal ribosome entry site (IRES) from lymphoid enhancer factor-1 mRNA has been used as a proof-of-principle target RNA. An IRES target was chosen because of its importance in protein translation and our limited knowledge of proteins associated with IRES function. With a conventionally translated target RNA as control, 36 IRES binding proteins have been quantitatively identified including known IRES binding factors, novel interacting proteins, translation initiation factors (eIF4A-1, eIF-2A, and eIF3g), and ribosomal subunits with known noncanonical actions (RPS19, RPS7, and RPL26). Validation studies with the small molecule eIF4A-1 inhibitor Hippuristanol shows that translation of endogenous lymphoid enhancer factor-1 mRNA is especially sensitive to eIF4A-1 activity. Our work demonstrates that MS2 in vivo biotin tagged RNA affinity purification is an effective and versatile approach that is generally applicable for other RNA-protein complexes.
Antagonistic effect of amphotericin B on carboplatin antitumor activity in human osteosarcoma xenografts

Amphotericin B (AmB), a polyene antifungal antibiotic, has been shown to potentiate the cytotoxic effect of different chemotherapeutic drugs in vivo and in vitro. The purpose of this study was to determine whether AmB could enhance the carboplatin antitumor activity in a human osteosarcoma xenograft model. Nude mice, bearing s.c. transplanted osteosarcoma xenografts, received i.p. an injection of AmB (5 mg/kg) 6 h prior to carboplatin (20 mg/kg) or each of the drugs separately. The effect of treatment was assessed by analyzing tumor growth delay and T/C ratio. Carboplatin clearly reduced tumor growth when administered alone. However, an unexpected interaction was seen where AmB significantly decreased the antitumor effect of carboplatin. The present results contradict some earlier in vitro studies and indicate the complexity of this interaction in vivo. Hence, it seems that interactive phenomena in one experimental model, and especially with regard to AmB, cannot be universally applied to all experimental situations.
Studies on the elimination of exogenous lipids from the blood stream. The kinetics of the elimination of a fat emulsion studied by single injection technique in man.

Hallberg, D. Studies on the elimination of exogenous lipids from the blood stream. The kinetics of the elimination of a fat emulsion studied by single injection technique in man. Acta physiol. scand. 1965. 64, 306–313. – The kinetics of the elimination of a fat emulsion (Intralipid®) from the blood stream was studied after single injections to 10 fasting individuals. Plasma triglycerides (TG) were fractionated by means of polyvinylpyrrolidone density gradients into three fractions. The emulsion TG was found in the top fraction of the gradient and endogenous plasma TG separated into two fractions which were found in the lower part of the density gradient. The kinetics of the emulsion TG fraction were composed of a zero order elimination rate at high TG concentrations and a first order elimination rate at low TG concentrations. Intra-individual variations were only observed in the zero order part of the kinetics; the possible causes of these variations are discussed. Changes in concentration of the lipids found in the lower part of the density gradient were observed during the elimination of the emulsion TG from the circulation. The possibility that the kinetic principle for one of these fractions (middle fraction) is the same as that for the fat emulsion is discussed.
Scoring manual for the Thought Disorder Index.

response to the task. Examples from the WAIS(What direction would you go if you were going from Chicago to Panama? ) If you went by airplane, I imagine you would go south. (Similarity between north-west) They're both opposite south and east. (How far is it from New York to Paris? ) Oh, I don't know. Eighthour flight. Examples from the Rorschach • (VIII) . an insect that's grown huge—oversized. (Okay, what made it look like an overgrown insect7) I could see the outline of an insect, but it was too big to be a normal insect so it had to be overgrown. (VII) Some kind of fancy military jet flying up the card. d. Overspecificity. The overspecific response is similar to the excessively qualified response in that an obsessive disposition has become exaggerated in both cases. However, in an overspecific response, the scorer should look for arbitrary, irrelevant specifications that spoil a response and give it an ovendeational quality. The subject is attempting to be precise, but fails because of excessive obsessionality or compulsivity, and thus tends toward absurdity or bizarreness. Examples from the WAIS: (What is the theme of the book of Genesis? ) It's, uh a fairy tale . tryin' to describe to the . proletariat masses how . life began . for human beings. (What is similar about a coat and a dress? ) They both hang . an' they're opening at the bottom, mmm . they could have buttons, both of them, or zippers. An' they're both worn as clothing. Examples from the Rorschach: (III) A four-legged lamb. (Ill) A bone of a bear. e. Syncretistic Response. Erring in the opposite direction of Overspecificity, the subject is here too general and abstract, instead of restricting a conceptual class, s/he includes too much in it. The Syncretistic Response is seen most often on items in the Similarities subtest of the WAIS. Examples from the WAIS: (What is similar about a fly-tree? ) They both live in the air. (What is similar about an orangebanana? ) They both contain atoms. 2. Flippant Response A Flippant Response also reflects a problem with distance in that the subject adopts a stance toward the testing situation that betrays an absence of seriousness or a tendency to dismiss the test-taking with wisecracks. Flippant Responses are often humorous, and may be very engaging in informal conversation; however, when such remarks are disruptive and inappropriate to the testing situation, they are scored. A difficulty that arises in scoring these responses is that their inappropriateness is due to the situation in which they occur, instead of to the malignancy of the response itself. Whereas there might be no indication of slippage when one makes a flippant response in ordinary conversation, it becomes a problem if one fails to inhibit these responses in the testing
QRS complex detection using zero frequency filtering

QRS complexes of electro cardiogram (ECG) signal are impulse-like in nature, which are considered as reference points in ECG analysis. Motivated by the zero frequency filter (ZFF) based epoch extraction from speech signals, in the present work, the application of ZFF for the QRS detection is exploited. ECG is preprocessed by moving average subtraction method to remove the base line drift and Hilbert envelope is computed. The preprocessed ECG is passed through a cascade of two resonators located at zero frequency and the trend of the resultant signal is removed by local average subtraction method. The proposed method is based only on the presence of impulse information at zero Hz and does not require any kind of decision logic or window for the selection of QRS. The proposed method is validated over MIT-BIH database using standard evaluation techniques and the results are compared with that of existing high performance state-of-the-art techniques.
Trends in immediate breast reconstruction and early complication rates among older women: A big data analysis

Although approximately 57% of breast cancer (BC) diagnoses are in older patients (>60 years), only 4.1‐14% receives breast reconstruction (BR). This has been attributed to physician concerns about operative complications. This paper aims to: 1) analyze the 30‐day complication rates in the older patient population undergoing immediate breast reconstruction (IBR); and 2) analyze links between complication type and category of reconstruction.
Testing antiretroviral drug efficacy in conventional mice infected with chimeric HIV-1

Objective:We previously described chimeric HIV-1, EcoHIV, which can infect mouse cells in culture and cause spreading infection in conventional immunocompetant mice. We have now applied this system as a model for preclinical evaluation of anti-retroviral drugs. Design and methods:We used chimeric virus EcoHIV/NDK constructed on the backbone of subtype D NDK. EcoHIV/NDK expression in mice was characterized 5–10 days after infection by testing viral DNA, RNA, and protein burdens in spleen and macrophages by real-time PCR (QPCR), RT–PCR, and p24 ELISA. For antiviral evaluation, groups of 5–7 mice were pretreated with 2′,3′–dideoxycytidine (ddC), abacavir, or vehicle; mice were then infected with EcoHIV/NDK, treatment maintained for additional 48 h, and tested for viral DNA and RNA burdens in spleens and macrophages by QPCR. Results:EcoHIV/NDK infected mice reproducibly showed viral burdens of up to 1.4 × 104 viral DNA copies and 200 pg p24 per 106 spleen cells and expressed spliced Vif RNA and mature p24 in macrophages 5–10 days after infection. Treatment of mice with 60 or 300 mg ddC/kg/day blocked EcoHIV/NDK infection in a dose-dependent manner with significantly lower viral DNA and RNA burdens at both drug doses (P < 0.001) in the spleens of infected mice. Abacavir tested at 100 mg/kg/day caused 96% inhibition of viral DNA synthesis in spleen and it almost completely abolished viral spliced RNA synthesis in spleens and macrophages. Conclusions:The system of chimeric HIV-1 infection of mice permits rapid, statistically powerful, and inexpensive evaluation of antiretroviral drugs in vivo.
The number needed to treat for second-generation biologics when treating established rheumatoid arthritis: a systematic quantitative review of randomized controlled trials

Objective: To evaluate the number needed to treat (NNT) and the number needed to harm (NNH) of the second-generation biologics abatacept, certolizumab, golimumab, rituximab, and tocilizumab in patients with established rheumatoid arthritis (RA) taking concomitant methotrexate (MTX). Methods: A systematic literature search of MEDLINE, EMBASE, Web of Science, and the Cochrane Register of Controlled Trials was conducted up to 1 November 2009. We selected any published randomized, double-blind, MTX-controlled study including RA patients with a mean disease duration of at least 5 years before entering a pivotal trial on second-generation biological therapy. Studies eligible for inclusion involved patients, who had previously shown inadequate response to conventional disease-modifying anti-rheumatic drug (DMARD) therapy. Pre-specified binary outcomes were extracted with a preference for 1-year data (6-month data were used if no data were available for 1 year). Two reviewers independently extracted the data necessary to estimate the absolute measures in a non-responder intention-to-treat (ITT) analysis. Results: Five randomized controlled trials, one for each of the drugs, were selected and data extracted according to published data at endpoint for American College of Rheumatology 50% (ACR50)-responding patients, and withdrawals due to adverse events. NNT ranged from four to six treated patients to achieve one ACR50 response, while withdrawals due to adverse events were few and non-significant compared to the placebo group, except for rituximab administered as 1000 mg. Conclusion: Comparable efficacy was shown by the five biological agents studied, with few adverse events. However, for rituximab, tocilizumab, and golimumab, only 6-month data were available, hampering the external validity with regard to long-term efficacy and tolerability. A low dose (500 mg) of rituximab may be as effective as the recommended dose of 1000 mg.
Intravenous immunoglobulin inhibits staphylococcal toxin-induced human mononuclear phagocyte tumor necrosis factor alpha production

Intravenous gamma immunoglobulin (IVIG) is used as therapy in superantigen-mediated disease, yet its mode of action is not clear. Pooled immunoglobulin G contains high concentrations of staphylococcal exotoxin (SE)-specific antibodies which inhibit the in vitro activation of T cells. However, SE and streptococcal exotoxins are potent stimulators of monocytes as well. Monocytes exposed to SE in vitro release large amounts of tumor necrosis factor alpha (TNF-alpha). The purpose of the present study was to determine if SE-specific antibodies in IVIG can inhibit the activation of monocytes by SE. We examined the in vitro effect of IVIG on the ability of staphylococcal exotoxin A (SEA) and staphylococcal exotoxin B (SEB) to stimulate release of TNF-alpha from human mononuclear phagocytes (MO). Pretreatment of SEA with 0.1 mg of IVIG per ml resulted in a slight decrease of SEA-induced TNF-alpha secretion by MO. In contrast, pretreatment of SEB with 0.1 mg of IVIG per ml resulted in significant (greater than 50%) inhibition of SEB-induced TNF-alpha secretion at 24, 48, 72, and 96 h (P < 0.05 for TNF-alpha levels induced by SEB alone versus SEB pretreated with IVIG at all time points). Enzyme-linked immunosorbent assay and Western immunoblotting assays of the IVIG revealed high concentrations of antibodies against SEB and lower concentrations of antibodies to SEA. These data indicate that IVIG can act in a toxin-specific manner to decrease the MO TNF-alpha response to superantigens. Such inhibition may be one mechanism by which IVIG exerts an immunoregulatory role in superantigen-mediated disease.
Studying the Ultrafast Dynamics of the Insulator-Metal Transition in Single Crystal VO 2

The focus of my research project this summer was towards the investigation of the insulatormetal transition dynamics of vanadium dioxide. A summary of the currently known, as well as debated, properties of the material is given here. Also given are the various experimental details involved in the measurements. We used femtosecond pulses in pump-probe experimentation to achieve time-resolved reflectivity measurements of single crystallite VO2 . Preliminary results are presented and the eventual undertakings of the experiment are discussed.
Cross-layer anomaly correlation and response selection

A cyber attack modifies the behavior of its target application or system such that it is outside of its intended or desired range of behavior. The challenge is that one cannot predict the attack mechanism that will cause the modified behavior or when and how the target's behavior will diverge. Thus, if one restricts one's sensors to a particular aspect of the system or looks for specific malicious behavior, one is likely to miss the attack. This paper describes an approach for simultaneously examining multiple network and host abstraction layers to discover anomalous behavior and then correlating anomalies to determine whether an attack is taking place and, when applicable, select an automatic response. We have used this approach to implement host-based and network-based intrusion detection systems, HIDAR and NIDAR, for enterprise networks, as well as sister systems for tactical networks. We discuss both the potential performance of the approach and our real-world experiences. In this venue, we focus on our NIDAR experiences in government and corporate networks under both experiments and live operation.
Nurses’ Information Management and Use of Electronic Tools During Acute Care Handoffs

Little evidence is available about nurses’ use of electronic tools during handoffs. This qualitative study explored information management and use of electronic tools during nursing handoffs. The sample included 93 handoffs by 26 nurses on 5 medical/surgical units in 2 western hospitals with a robust electronic health record (EHR). Data collection included audiotaping handoffs, semi-structured interviews, observations, and fieldnotes. The dataset was inductively coded into 33 categories and 5 themes: good nurse expectations for handoffs, paper forms are best, information at a glance, only pertinent information please, and information tools that work. Two-thirds of the nurses abandoned use of the leadership-endorsed electronic handoff form, preferring personal paper forms. The findings suggest effective electronic solutions will require extensive contextually-based information, information integrated across EHR modules and portable, electronic support throughout shifts. This is a call to action for leaders and informaticists as they select and design future electronic tools.
Replacement of Tyrosine 181 by Phenylalanine in Gentisate 1,2-Dioxygenase I from Pseudomonas alcaligenes NCIMB 9867 Enhances Catalytic Activities

ABSTRACT xlnE, encoding gentisate 1,2-dioxygenase (EC 1.13.11.4), from Pseudomonas alcaligenes (P25X) was mutagenized by site-directed mutagenesis. The mutant enzyme, Y181F, demonstrated 4-, 3-, 6-, and 16-fold increases in relative activity towards gentisate and 3-fluoro-, 4-methyl-, and 3-methylgentisate, respectively. The specific mutation conferred a 13-fold higher catalytic efficiency (kcat/Km) on Y181F towards 3-methylgentisate than that of the wild-type enzyme.
Adoption of mobile Location-Based Services with Zaltman Metaphor Elicitation Techniques

The Location-Based Services (LBS) through wireless pervasive devices at right place and right time could be beneficial to both businesses and their customers. However, the adoption rates of LBS are far from satisfactory, implying that there might be some factors keeping the potential users away from using LBS. This research integrated a qualitative method, Zaltman Metaphor Elicitation Techniques, with the quantitative questionnaire survey to elicit and validate underlying factors which influence potential users' attitude and intentions toward LBS. Our findings can be referenced by service providers for designing and developing successful business applications to catch the revolutionary opportunity and benefit of LBS.
Inhibition of hepatitis b virus surface antigen gene expression in carcinogen‐induced liver tumors from transgenic mice

We previously showed that hepatitis B surface antigen (HBsAg)‐producing transgenic mice were more sensitive to hepatocarcinogens than their normal littermates were. We have now investigated the regulation of hepatitis B virus (HBV) gene expression in carcinogen‐induced liver tumors of HBV‐carrier transgenic mice and in three cell lines derived from tumor samples. Transcription of the S gene was repressed in 17 tumors even though they had normal levels of liver‐specific mRNAs such as albumin and transferrin. Three hepatoma cell lines, derived from independent tumor samples, were analyzed for their capacity to express the S gene after transfection of cloned DNA. Although they no longer expressed the endogenous S gene, they were still able to express it from transfected viral DNA both transiently and stably. The loss of HBsAg expression in tumors and in the cell lines was accompanied by de novo methylation of the S region, which is a way to permanently repress gene expression. Our data confirm in an animal model previous observations of S‐gene expression in human hepatocarcinoma and suggest a role for its downregulation in tumor progression. © 1994 Wiley‐Liss, Inc.
Cooperative communication relaying in hybrid heterogeneous networks

Coverage and capacity are the two most vital aspects of any cellular technology. Coverage, in particular, is of prime importance in a Long Term Evolution network. However, both come at a significant cost. Deployment of additional eNodeBs (macro layer) to cover small dead zones might often result in a negative return on investment. Instead a scheme that augments the macro layer by making use of low power relay nodes can satisfy coverage and capacity demands in a satisfactory manner. The same being proven across a number of studies. Research in this domain has so far dealt with the deployment of relay nodes with LTE over either licensed or unlicensed spectrum. Wirth et al. test one such model in an indoor office environment and compare performance results for the cooperative and standalone systems. In this paper, we present a non-transparent, type-1, amplify and forward relaying scheme based on the use of Wi-Fi access points as relays. The link between the eNodeB and the relay node (backhaul) is wireless. In both the uplink and the downlink, the Wi-Fi access point serves as the relay. In the downlink, the eNodeB is the source, while, in the uplink, the user equipment is the source. While the use of LTE for relay nodes causes interference with the macro base station, Wi-Fi based nodes present a lesser probability of interference due to the different bands (2.4 GHz and 5 GHz) in which they operate. The primary purpose of the purported scheme is coverage extension. Further, we analyze the performance of the model by comparing symbol-error-rate versus signal-to-noise ratio curves for direct and cooperative scenarios, using them to determine the ideal position of the relay; and the effect of path loss and variation in eNB-UE distance. Thus, we show that coverage extension can be achieved in a reliable manner without any hardware addition, through this scheme.
Duration of serologic response to five viral antigens in dogs.

OBJECTIVE To determine whether vaccinated dogs either remained seropositive or responded serologically to revaccination for 5 key viral antigens after extended periods since their last vaccination. DESIGN Serologic survey. ANIMALS 322 healthy client-owned dogs. PROCEDURE Dogs were > or = 2 years old and vaccinated against canine distemper virus (CDV), canine adenovirus-1 (CAV-1), canine adenovirus-2 (CAV-2), canine parainfluenza virus (CPIV), and canine parvovirus (CPV). On day 0, dogs were revaccinated with a vaccine from the same vaccine line as they had historically received. Antibody titers were measured in sera collected at day 0 (prevaccination titer) and 5 to 7 days later (postvaccination titer). Dogs were considered to have responded serologically if they had a day-0 serum neutralization titer to CDV > or = 1:32; a serum neutralization titer to CAV-1, CAV-2, or CPIV > or = 1:16; a hemagglutination inhibition titer to CPV > or = 1:80; or a > or = 4-fold increase in antibody titer after revaccination. RESULTS The percentage of dogs that had titers at or greater than the threshold values or responded to revaccination with a > or = 4-fold increase in titer was 98.1% for CDV, 98.4% for CAV-1, 99.0% for CAV-2, 100% for CPIV, and 98.1% for CPV. CONCLUSIONS AND CLINICAL RELEVANCE In most dogs, vaccination induced a response that lasted up to and beyond 48 months for all 5 antigens. Although not equivalent to challenge-of-immunity studies as a demonstration of efficacy, results suggest that revaccination with the same vaccine provides adequate protection even when given less frequently than the traditional 1-year interval. The study provides valuable information for clinicians to help determine appropriate revaccination intervals.