Miracle-dz/UniFAR-FTUs huggingface dataset:
Delayed progression of a murine retrovirus-induced acquired immunodeficiency syndrome in X-linked immunodeficient mice

The murine acquired immunodeficiency syndrome (MAIDS) caused by defective LP-BM5 murine leukemia virus (MuLV) is a disease that shows severe immunodeficiency with abnormal lymphoproliferation, and hypergammaglobulinemia in susceptible C57BL/6 (B6) mice. To examine the cellular mechanisms of development of MAIDS, we injected LP-BM5 MuLV intraperitoneally into B6 mice bearing the X chromosome-linked immunodeficiency (xid). xid mice lack functionally mature B cells including Ly-1 B cells (also known as B-1 cells). All B6 mice died by 20 wk after LP-BM5 MuLV inoculation. In marked contrast, xid mice have continued to survive without any sign of MAIDS-related symptoms till at least 20 wk after the inoculation. The delayed progression of MAIDS in xid mice appears to depend on xid mutation, according to our experiments using both sexes of (B6.xid x B6)F1 and (B6 x B6.xid)F1 mice. Furthermore, Ly-1 B cells, enriched by a FACS, were shown to integrate the defective genome and appeared to be a major virus- infected B cell population. Our data corroborate that Ly-1 B cells play an important role in the induction and progression of MAIDS.
Hepatic Neutrophil Infiltration in the Pathogenesis of Alcohol-Induced Liver Injury

ABSTRACT The histopathologic evidence of the presence of neutrophils within the liver parenchyma is a prominent feature of alcoholic hepatitis in both experimental animals and chronic human alcoholics. However, the precise mechanisms by which neutrophils infiltrate the liver and cause liver injury still remain to be fully elucidated. For neutrophils to infiltrate the liver, they have to undergo systemic activation (priming) by proinflammatory cytokines, chemokines, complement factors, and other biologically active molecules (e.g., platelet-activating factor). Neutrophils accumulated in the hepatic microvasculature (sinusoids and postsinusoidal venules) can extravasate (transmigrate) into the hepatic parenchyma if they receive appropriate signals from previously sensitized or distressed cells. Transmigration can be mediated by a chemokine gradient established toward the hepatic parenchyma and generally involves the interaction between adhesion molecules on neutrophils (β2 integrins) and on endothelial cells (intercellular adhesion molecules [ICAM-1]). Following transmigration, neutrophils adhere to sensitized hepatocytes through their β2 integrins and ICAM-1 expressed on hepatocytes and mediate killing of hepatocytes mostly by oxidant stress and proteases. These neutrophilic events during chronic alcohol ingestion, based mostly on experiments with rodent models, will be emphasized in this review.
Sources and Magnitude of Intralaboratory Variability in a Sequence-Based Genotypic Assay for Human Immunodeficiency Virus Type 1 Drug Resistance

ABSTRACT We assessed the intralaboratory reproducibility of a system for sequencing human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) by using replicate subanalyses of 46 plasma samples collected from HIV-1-infected, antiretroviral-experienced patients in order to determine the relative contributions of the different procedural steps to final sequence variability. Complete sequence concordance between duplicates of each sample was 99.4%. Complete and partial mismatches occurred scattered throughout the PR-RT genome segment at >300 positions. Approximately 75% of the discordances involved mixtures, some of which appeared at key resistance sites. Most differences were the result of the first-round RT-PCR procedure. Inter-rater concordance for sequence analysis and assembly was >99.9%. There was no observed correlation between the number or frequency of mismatches and plasma viral loads. A separate longitudinal analysis of a single routine control sample sequenced 103 times over 9 months consistently gave highly reproducible sequences (median percentage of nucleotide discordances, 0.04%; range, 0 to 0.2%). Finally, sequence data from 168 sequential samples collected from 22 patients with long-term, predominantly wild type HIV showed that intrapatient nucleotide concordance with individual index sequences ranged from 96.5 to 100%. Together, these results confirm that sequence-based genotyping can be a precise and reliable tool for monitoring HIV drug resistance, and they suggest that efforts to reduce variability should focus on the first RT-PCR step. Consequently, the data suggest that the composition of external quality assessment panels should be based on clinical HIV isolates rather than DNA clones.
Operating system performance measurements for Remote Patient Monitoring applications

The Remote Patient Monitoring (RPM) is becoming vital part of healthcare improving quality of care. The RPM system uses variety of sensors and wireless technologies to monitor multiple biological and environmental signals simultaneously providing status and trend data for the patient. The RPM system can also provide alarms/alerts for the patient or the caregiver in real-time so that the patient gets assistance in timely manner when an acute event occurs. The RPM system must detect such events in real-time to generate alarms/alerts. Use of mobile devices like smartphones and/or tablets for RPM enables patient mobility and provides real-time monitoring capability. The mobile device Operating System (OS) used for real-time RPM needs to meet the hard real-time requirements for alerts/alarms generation. The General Purpose OS (GPOS) uses fair scheduling algorithm for multitasking while Real Time OS (RTOS) uses preemptive scheduling. This paper evaluates the real-time performance of GPOS and a RTOS (QNX) under variety of load condition for RPM application. The results of the measurements indicate that the mobile device OS used for RPM must provide a prioritizing mechanism to satisfy the hard real-time requirements when the mobile device is multitasking and/or overloaded.
Effects of Discourse Type on Recall

Discourse can be organized in different ways; four of these ways are comparison, problem/solution, causation, and a collection of descriptions. These four discourse types correspond to schemata that vary in their organizational components; these differences were expected to result in differences in processing text. The more organized discourse types of comparison, problem/solution, and causation were predicted to yield superior recall of information than when this same information was cast as a collection of descriptions about a topic. The data from two studies support the hypothesized facilitation of the more organized types of discourse and have implications for understanding memory and writing instructional materials.
Fish Assemblage Recovery Along a Riverine Disturbance Gradient.

Artificial fluctuations in streamflow have been documented to alter the composition and structure of stream communities. This study tests the hypothesis that a spatial recovery gradient in fish assemblage structure exists downstream of a hydroelectric dam, and that recovery can be identified by the presence and abundance of species largely restricted to flowing-water habitats (fluvial specialists). A longitudinal gradient of change in a shoreline fish assemblage was quantified in a 66-km reach of a mid-sized, species-rich river (Tallapoosa River, Alabama) with daily flow fluctuations from hydropower generation. The shoreline fish assemblage in a nearby and similar river (Cahaba River, Alabama) was quantified as a regional reference for the occurrence of fish assemblage gradients. Fish were collected with prepositioned area electrofishers in 240 randomly located sampling sites, and physical habitat was quantified. Using distributional and habitat use information, fish species were categorized as fluvial specialists or macrohabitat generalists (species that occur in a wide variety of aquatic systems). Sampled habitats were similar between rivers and along each study reach. The longitudinal pattern of species occurrence and fish abundance was consistent in the free-flowing river. A longitudinal gradient of increasing abundance and richness of only fluvial specialist species existed downstream of the hydroelectric dam. No similar spatial gradient existed for macrohabitat generalists in either river. Although a fish community recovery gradient was identified, a recovery endpoint was not evident because assemblage change was gradual and possibly incomplete. The preservation and management of riverine fish faunas will partly depend on incorporating spatial recovery into decisions about permitting and siting of anthropogenic changes like hydroelectric dams.
On the inclusion of solvent molecules in the crystal structures of organic compounds

The Cambridge Structural Database has been searched for all crystal structures including organic solvent molecules (solvates) and solvent water molecules (hydrates). Well above 300 different solvent molecules were identified and the frequencies with which they occur in crystal structures, as a function of the year of publication, were established. The crystal structures are classified as 'organic' and 'metalloorganic'; it is shown that the relative prevalences of various cocrystallized solvents are different in the two groups. Several frequently used organic solvents are also common ligands for metal ions. Special interest has been focused on the existence of heterosolvates, i.e. crystal structures which include more than one type of solvent molecule. Up to five different types of solvent molecules were found in a single crystal structure. It is suggested that the use of solvent mixtures during crystallizations may prove to be a more useful and versatile approach for obtaining crystals of high-molecular-weight organic compounds than has hitherto been recognized.
Thermodynamic Optimization of Turboshaft Engine using Multi-Objective Genetic Algorithm

Abstract— In this paper multi-objective genetic algorithms are employed for Pareto approach optimization of ideal Turboshaft engines. In the multi-objective optimization a number of conflicting objective functions are to be optimized simultaneously. The important objective functions that have been considered for optimization are specific thrust (/ ) Fm & 0 , specific fuel consumption ( S P ), output shaft power (/) 0 & & Wm shaft and overall efficiency ()η O . These objectives are usually conflicting with each other. The design variables consist of thermodynamic parameters (compressor pressure ratio, turbine temperature ratio and Mach number). At the first stage single objective optimization has been investigated and the method of NSGA-II has been used for multi-objective optimization. Optimization procedures are performed for two and four objective functions and the results are compared for ideal Turboshaft engine. In order to investigate the optimal thermodynamic behavior of two objectives, different set, each including two objectives of output parameters, are considered individually. For each set Pareto front are depicted. The sets of selected decision variables based on this Pareto front, will cause the best possible combination of corresponding objective functions. There is no superiority for the points on the Pareto front figure, but they are superior to any other point. In the case of four objective optimization the results are given in tables.
Examining New Event Detection

We examine the accuracy of first story detection on traditional news collections and on a re-purposed source of academic material. The impact on accuracy of detecting an early rather than the first story is examined, showing that accuracy increases under a broader time window, however, the increases on some collections are small. Even on collections where the increase is large, many new events are still missed and there remains an underlying challenge to detecting new events. An analysis of temporal and vocabulary profiles of topics within their source collections is conducted. Analysis of the results establish the underlying causes of the patterns seen in the experimental results with respect to the different source types and performance. The usefulness of new criteria for new event detection and success across source types is discussed.
Dimeric structure of the cell shape protein MreC and its functional implications

The bacterial actin homologue MreB forms helical filaments in the cytoplasm of rod‐shaped bacteria where it helps maintain the shape of the cell. MreB is co‐transcribed with mreC that encodes a bitopic membrane protein with a major periplasmic domain. Like MreB, MreC is localized in a helical pattern and might be involved in the spatial organization of the peptidoglycan synthesis machinery. Here, we present the structure of the major, periplasmic part of MreC from Listeria monocytogenes at 2.5 Å resolution. MreC forms a dimer through an intimate contact along an N‐terminal α‐helix that connects the transmembrane region with two C‐terminal β‐domains. The translational relationship between the molecules enables, in principle, filament formation. One of the β‐domains shows structural similarity to the chymotrypsin family of proteins and possesses a highly conserved Thr Ser dipeptide. Unexpectedly, mutagenesis studies show that the dipeptide is dispensable for maintaining cell shape and viability in both Escherichia coli and Bacillus subtilis. Bacterial two‐hybrid experiments reveal that MreC interacts with high‐molecular‐weight penicillin‐binding proteins (PBPs), rather than with low‐molecular‐weight endo‐ and carboxypeptidases, indicating that MreC might act as a scaffold to which the murein synthases are recruited in order to spatially organize the synthesis of new cell wall material. Deletion analyses indicate which domains of B. subtilis MreC are required for interaction with MreD as well as with the PBPs.
Synthesis and β1-, β2-Adrenergic Receptor Binding Studies of 4-Acylaminosubstituted Phenoxypropanolamine and 5-Acylamino-substituted Naphthyloxypropanolamine Derivatives

Summary The object of this study was to investigate the β-adrenergic receptor binding affinity of 4-acylaminophenoxypropanolamine (10−15) and 5-acylaminonaphthyl-oxypropanolamine (21−24) derivatives,which were prepared from 4-aminophenol (5) and 5-amino-1-naphthol (16), respectively. The in vitro β1-and β2-adrenergic receptor binding affinities of the newly synthesized compounds were assessed in turkey erythrocyte membrane (β1) and lung homogenates of rats (β2). The binding affinities were compared with that of propranolol (3) (propranolol hydrochloride, CAS 318-98-9). The compound N-[5-(3-tert-butylamino-2-hydroxy-propoxy)-naphthalen-1-yl]- acetamide (22) has β-adrenergic receptor affinity comparable with that of propranolol and shows selectivity to β1-adrenergic receptors.
Developmental status and service use among children in the child welfare system: a national survey.

OBJECTIVES To estimate the prevalence of developmental delay and service use among children in the child welfare system and to identify factors that influence these outcomes. DESIGN A descriptive study using wave 1 of the National Survey of Child and Adolescent Well-Being. PARTICIPANTS AND SETTING Children aged 0 to 10 years (n = 4324) and their caregivers were interviewed within 60 days of a report being made to the child welfare system. Children's development was measured directly using standardized assessment tools. Three questions from the caregiver interviews estimated receipt of developmental services. MAIN EXPOSURES Subjects were characterized as having developmental delay if any developmental measure fell more than 2 SDs below the mean. Prevalence of developmental delay and service use by age group, type of maltreatment, type of placement, race, sex, and income were reported. Odds that children aged 0 to 2, 3 to 5, and 6 to 10 years with developmental delay would receive developmental services were calculated using weighted logistic regression. main outcome measure: Receipt of developmental services by children with developmental delay. RESULTS Younger children aged 0 to 2 and 3 to 5 years had higher rates, 33% and 36%, respectively, of developmental delay than school-aged children (13%) (P<.01). Despite their high prevalence of developmental delay, children aged 0 to 2 years were less likely to receive developmental services than preschool-aged children (odds ratio, 2.4; 95% confidence interval, 1.6-3.7) or school-aged children (odds ratio, 4.2; 95% confidence interval, 2.9-6.0). CONCLUSIONS Rates of developmental delay are high and developmental services are underused, particularly by young children in the child welfare system. Strategies for overcoming barriers to using early intervention services should be implemented.
Facilitated Nucleocytoplasmic Shuttling of the Ran Binding Protein RanBP1

ABSTRACT The Ran binding protein RanBP1 is localized to the cytosol of interphase cells. A leucine-rich nuclear export signal (NES) near the C terminus of RanBP1 is essential to maintain this distribution. We now show that RanBP1 accumulates in nuclei of cells treated with the export inhibitor, leptomycin B, and collapse of the nucleocytoplasmic Ran:GTP gradient leads to equilibration of RanBP1 across the nuclear envelope. Low temperature prevents nuclear accumulation of RanBP1, suggesting that import does not occur via simple diffusion. Glutathione S-transferase (GST)–RanBP1(1-161), which lacks the NES, accumulates in the nucleus after cytoplasmic microinjection. In permeabilized cells, nuclear accumulation of GST-RanBP1(1-161) requires nuclear Ran:GTP but is not inhibited by a dominant interfering G19V mutant of Ran. Nuclear accumulation is enhanced by addition of exogenous karyopherins/importins or RCC1, both of which also enhance nuclear Ran accumulation. Import correlates with Ran concentration. Remarkably, an E37K mutant of RanBP1 does not import into the nuclei under any conditions tested despite the fact that it can form a ternary complex with Ran and importin β. These data indicate that RanBP1 translocates through the pores by an active, nonclassical mechanism and requires Ran:GTP for nuclear accumulation. Shuttling of RanBP1 may function to clear nuclear pores of Ran:GTP, to prevent premature release of import cargo from transport receptors.
High‐Throughput Cloning and Expression of Integral Membrane Proteins in Escherichia coli

Recently, several structural genomics centers have been established and a remarkable number of three‐dimensional structures of soluble proteins have been solved. For membrane proteins, the number of structures solved has been significantly trailing those for their soluble counterparts, not least because over‐expression and purification of membrane proteins is a much more arduous process. By using high‐throughput technologies, a large number of membrane protein targets can be screened simultaneously and a greater number of expression and purification conditions can be employed, leading to a higher probability of successfully determining the structure of membrane proteins. This unit describes the cloning, expression, and screening of membrane proteins using high‐throughput methodologies developed in the laboratory. Basic Protocol 1 describes cloning of inserts into expression vectors by ligation‐independent cloning. Basic Protocol 2 describes the expression and purification of the target proteins on a miniscale. Lastly, for the targets that do express on the miniscale, Basic Protocols 3 and 4 outline the methods employed for the expression and purification of targets on a midi‐scale, as well as a procedure for detergent screening and identification of detergent(s) in which the target protein is stable. Curr. Protoc. Protein Sci. 74:29.6. 1‐29.6. 34. © 2013 by John Wiley & Sons, Inc.
Children's use of the Yahooligans! Web search engine. III. Cognitive and physical behaviors on fully self-generated search tasks

This article presents the third part of a research project that investigated the information-seeking behavior and success of seventh-grade science children in using the Yahooligans! Web search engine/directory. In parts 1 and 2, children performed fully assigned tasks to pursue in the engine. In the present study, children generated their tasks fully. Children's information seeking was captured from the cognitive, physical, and affective perspectives using both quantitative and qualitative inquiry methods. Their information-seeking behavior and success on the fully self-generated task was compared to the behavior and success they exhibited in the two fully assigned tasks. Children were more successful on the fully self-generated task than the two fully assigned tasks. Children preferred the fully self-generated task to the two fully assigned tasks due to their ability to find the information sought and satisfaction with search results rather than the nature of the task in itself (i.e., self-generated aspect). Children were more successful when they browsed than when they searched by keyword on the three tasks. Yahooligans! design, especially its poor keyword searching, contributed to the breakdowns children experienced, implications for system design improvement and Web training are discussed.
Psychological and environmental empowerment: antecedents and consequences

Purpose – The aims of this paper are to clarify empowerment as a construct, assess whether environmental and psychological empowerment differentially predicts job outcomes, and investigate the effects of transformation and transactional leadership on empowerment.Design/methodology/approach – University students (n=197) rated leadership and empowerment in their workplaces and a number of job outcomes using an on‐line questionnaire.Findings – Results supported the proposition that empowerment should be separated into its behavioral and psychological components. The dimensions of empowerment also differentially predicted job outcomes. In particular, environmental empowerment was better at predicting outcomes than was psychological empowerment. It was also found that transformational and transactional leadership predicted environmental empowerment more strongly than psychological empowerment.Research limitations/implications – Limitations include that the study was cross‐sectional, used a student sample, and .
In the Eye of the Beholder: Perceptions of the Centrality of Merit in Affirmative Action and Its Psychological Implications

Affirmative action (AA) remains at the forefront of both public and scholarly discourse. Yet there is little empirical investigation of individuals’ perceptions of how AA typically operates, particularly with respect to the centrality of merit in the implementation process. I suggest these perceptions are critical to the extent that they influence psychological reactions to AA. Results from two survey studies confirmed that the perceived centrality of merit in typical AA implementations predicted both endorsement of the policy and the view of beneficiaries’ competence, above and beyond demographic factors. Theoretical and applied implications are discussed.