Miracle-dz/UniFAR-FTUs huggingface dataset:
Palmitoylation of the Autographa californica Multicapsid Nucleopolyhedrovirus Envelope Glycoprotein GP64: Mapping, Functional Studies, and Lipid Rafts

ABSTRACT Budded virions (BV) of the baculovirus Autographa californica multicapsid nucleopolyhedrovirus (AcMNPV) contain a major envelope glycoprotein known as GP64, which was previously shown to be palmitoylated. In the present study, we used truncation and amino acid substitution mutations to map the palmitoylation site to cysteine residue 503. Palmitoylation of GP64 was not detected when Cys503 was replaced with alanine or serine. Palmitoylation-minus forms of GP64 were used to replace wild-type GP64 in AcMNPV, and these viruses were used to examine potential functions of GP64 palmitoylation in the context of the infection cycle. Analysis by immunoprecipitation and cell surface studies revealed that palmitoylation of GP64 did not affect GP64 synthesis or its transport to the cell surface in Sf9 cells. GP64 proteins lacking palmitoylation also mediated low-pH-triggered membrane fusion in a manner indistinguishable from that of wild-type GP64. Cells infected with viruses expressing palmitoylation-minus forms of GP64 produced infectious virions at levels similar to those from cells infected with wild-type AcMNPV. In combination, these data suggest that virus entry and exit in Sf9 cells were not significantly affected by GP64 palmitoylation. To determine whether GP64 palmitoylation affected the association of GP64 with membrane microdomains, the potential association of GP64 with lipid raft microdomains was examined. These experiments showed that: (i) AcMNPV-infected Sf9 cell membranes contain lipid raft microdomains, (ii) GP64 association with lipid rafts was not detected in infected Sf9 cells, and (iii) GP64 palmitoylation did not affect the apparent exclusion of GP64 from lipid raft microdomains.
Concurrent Reasoning with Inference Graphs

Since their popularity began to rise in the mid-2000s there has been significant growth in the number of multi-core and multi-processor computers available. Knowledge representation systems using logical inference have been slow to embrace this new technology. We present the concept of inference graphs, a natural deduction inference system which scales well on multi-core and multi-processor machines. Inference graphs enhance propositional graphs by treating propositional nodes as tasks which can be scheduled to operate upon messages sent between nodes via the arcs that already exist as part of the propositional graph representation. The use of scheduling heuristics within a prioritized message passing architecture allows inference graphs to perform very well in forward, backward, bi-directional, and focused reasoning. Tests demonstrate the usefulness of our scheduling heuristics, and show significant speedup in both best case and worst case inference scenarios as the number of processors increases.
Intestinal parasites in HIV-seropositive Zambian children with diarrhoea.

We undertook a study over a period of 9 months to define the frequency of parasitic infections in hospitalized children with diarrhoea between the ages of 15 months and 5 years. Every alternate day, mothers of all children admitted with diarrhoea between 09.00 hours and 12.00 hours to one of the wards of the Department of Pediatrics and Child Health of the University Teaching Hospital (UTH) in Lusaka, Zambia, were interviewed for enrollment of their children into the study. A total of 178 children with diarrhoea were enrolled in the study. Of these 44 (25 per cent) were HIV seropositive and 134 (75 per cent) were seronegative for HIV. Out of 44 HIV-seropositive patients, 20 (45 per cent) had acute diarrhoea and 24 (55 per cent) had chronic diarrhoea. Of the 134 HIV-seronegative patients, 68 had acute diarrhoea (51 per cent) and 66 (49 per cent) had chronic diarrhoea. At least one intestinal parasite was found in 34 out of the 178 children enrolled. The commonest parasites identified were Ascaris and Cryptosporidia. No associations were identified between parasite isolation and the following: age, sex, or socio-economic status. Cryptosporidium spp. was isolated from 6 out of 44 (14 per cent) HIV-seropositive children, while 8 out of 134 (6 per cent) seronegative children had the parasite (P = 0.01). HIV-seropositive children with chronic diarrhoea had significantly higher cryptosporidium identification rates than those HIV-seropositive children with acute diarrhoea [5 out of 24 (21 per cent) patients with chronic diarrhoea compared to 1 out of 20 (5 per cent) patients with acute diarrhoea; (P > or = 0.01)]. (ABSTRACT TRUNCATED AT 250 WORDS)
Collective Findings, Individual Interpretations: An Illustration of a Pluralistic Approach to Qualitative Data Analysis

The establishment of qualitative approaches in the mainstream of psychology research facilitates innovation in their use, both singly and in combination. In this article, we describe a pluralistic qualitative analysis of the transcript of a semi-structured interview on the topic of second-time motherhood using Grounded Theory, Interpretative Phenomenological Analysis, Narrative Analysis, and Foucauldian Discourse Analysis. Each approach encapsulates different epistemological assumptions and is employed by a different analyst. We present key collective findings and the different interpretations of these findings by each analyst. We discuss how a pluralistic qualitative approach to data analysis can aid the quest to “know more” about a phenomenon by providing a more holistic, multilayered understanding of data that works across epistemologies.
The Jitter Spatial Frequency Sweep VEP: a new paradigm to study spatiotemporal development of pattern- and motion-processing mechanisms in human infants

We introduce a new VEP paradigm - the Jitter Spatial Frequency (JSF) Sweep VEP - that permits efficient mapping of the spatiotemporal tuning of the developmental motion asymmetry (DMA). Vertical sinewave gratings undergoing 90o horizontal oscillatory displacements (6 or 10 Hz) were presented while their SF was swept over 2 to 5 octaves during each VEP trial. JSF sweep VEPs were recorded from 28 infants (8-43 weeks), and symmetric (second-harmonic, F2) and asymmetric (F1) components of the VEP were measured. JSF sweeps can provide four useful estimates: (1,2) the high-SF cutoff of F1 and F2 responses estimates the spatial resolution of direction-selective (DS) and non-DS mechanisms, respectively; (3) the low-SF cutoff for F1 estimate the SF-boundary between mature (F1 absent) and immature (F1 present) DS mechanisms; and (4) the F1 high-SF cutoff estimates the lower velocity limit of cortical DS cells. For 6 Hz, the low-SF F1 cutoffs increased two times faster than traditional (contrast-reversal) VEP grating acuity (0.5 vs ~0.25 octaves/month), and twice that of the high-SF F1 and F2 cutoffs. This implies that no single mechanism can account for the DMA at both low and high SFs. At 10 Hz, the DMA exhibited no significant development, consistent with slower maturation of DS mechanisms at higher ST frequencies. The F2 high-SF cutoffs were higher than F1 at both 6 and 10 Hz, suggesting higher spatial resolution for non-DS (pattern) vs DS (motion) mechanisms. Finally, the lower velocity limit of the DS mechanisms decreased from ~2 deg/sec at 8 weeks, to 0.75 deg/sec at 33 weeks, similar to analogous limits for direction-of-motion identification in adults (~0.5 - 1 deg/sec), and close to prior VEP estimates in infants (0.6 deg/sec).
Evaluation of clinical pharmacist recommendations in the geriatric ward of a Belgian university hospital

Objective To evaluate the type, acceptance rate, and clinical relevance of clinical pharmacist recommendations at the geriatric ward of the Ghent university hospital. Methods The clinical pharmacist evaluated drug use during a weekly 2-hour visit for a period of 4 months and, if needed, made recommendations to the prescribing physician. The recommendations were classified according to type, acceptance by the physician, prescribed medication, and underlying drug-related problem. Appropriateness of prescribing was assessed using the Medication Appropriateness Index (MAI) before and after the recommendations were made. Two clinical pharmacologists and two clinical pharmacists independently and retrospectively evaluated the clinical relevance of the recommendations and rated their own acceptance of them. Results The clinical pharmacist recommended 304 drug therapy changes for 100 patients taking a total of 1137 drugs. The most common underlying drug-related problems concerned incorrect dose, drug–drug interaction, and adverse drug reaction, which appeared most frequently for cardiovascular drugs, drugs for the central nervous system, and drugs for the gastrointestinal tract. The most common type of recommendation concerned adapting the dose, and stopping or changing a drug. In total, 59.7% of the recommendations were accepted by the treating physician. The acceptance rate by the evaluators ranged between 92.4% and 97.0%. The mean clinical relevance of the recommendations was assessed as possibly important (53.4%), possibly low relevance (38.1%), and possibly very important (4.2%). A low interrater agreement concerning clinical relevance between the evaluators was found: kappa values ranged between 0.15 and 0.25. Summated MAI scores significantly improved after the pharmacist recommendations, with mean values decreasing from 9.3 to 6.2 (P < 0.001). Conclusion In this study, the clinical pharmacist identified a high number of potential drug-related problems in older patients; however, the acceptance of the pharmacotherapy recommendations by the treating physician was lower than by a panel of evaluators. This panel, however, rated most recommendations as possibly important and as possibly having low relevance, with low interrater reliability. As the appropriateness of prescribing seemed to improve with decreased MAI scores, clinical pharmacy services may contribute to the optimization of drug therapy in older inpatients.
Ambient Fine Particulate Matter Alters Cerebral Hemodynamics in the Elderly

Background and Purpose— Short-term elevations in fine particulate matter air pollution (PM2.5) are associated with increased risk of acute cerebrovascular events. Evidence from the peripheral circulation suggests that vascular dysfunction may be a central mechanism. However, the effects of PM2.5 on cerebrovascular function and hemodynamics are unknown. Methods— We used transcranial Doppler ultrasound to measure beat-to-beat blood flow velocity in the middle cerebral artery at rest and in response to changes in end-tidal CO2 (cerebral vasoreactivity) and arterial blood pressure (cerebral autoregulation) in 482 participants from the Maintenance of Balance, Independent Living, Intellect, and Zest in the Elderly (MOBILIZE) of Boston study. We used linear mixed effects models with random subject intercepts to evaluate the association between cerebrovascular hemodynamic parameters and mean PM2.5 levels 1 to 28 days earlier adjusting for age, race, medical history, meteorologic covariates, day of week, temporal trends, and season. Results— An interquartile range increase (3.0 µg/m3) in mean PM2.5 levels during the previous 28 days was associated with an 8.6% (95% confidence interval, 3.7%–13.8%; P<0.001) higher cerebral vascular resistance and a 7.5% (95% confidence interval, 4.2%–10.6%; P<0.001) lower blood flow velocity at rest. Measures of cerebral vasoreactivity and autoregulation were not associated with PM2.5 levels. Conclusions— In this cohort of community-dwelling seniors, exposure to PM2.5 was associated with higher resting cerebrovascular resistance and lower cerebral blood flow velocity. If replicated, these findings suggest that alterations in cerebrovascular hemodynamics may underlie the increased risk of particle-related acute cerebrovascular events.
Musical Training and Late-Life Cognition

This study investigated the effects of early- to midlife musical training on cognition in older adults. A musical training survey examined self-reported musical experience and objective knowledge in 237 cognitively intact participants. Responses were classified into low-, medium-, and high-knowledge groups. Linear mixed models compared the groups’ longitudinal performance on the Animal Naming Test (ANT; semantic verbal fluency) and Logical Memory Story A Immediate Recall (LMI; episodic memory) controlling for baseline age, time since baseline, education, sex, and full-scale IQ. Results indicate that high-knowledge participants had significantly higher LMI scores at baseline and over time compared to low-knowledge participants. The ANT scores did not differ among the groups. Ability to read music was associated with higher mean scores for both ANT and LMI over time. Early- to midlife musical training may be associated with improved late-life episodic and semantic memory as well as a useful marker of cognitive reserve.
Assessing Key Informant Methodology in Congregational Research

Surveying key informants is a common methodology in congregational research. While practical and cost-effective, there are limitations in the ability of a single informant to speak for an entire organization. This paper explores potential limitations empirically. Using the 1993 American Congregational Giving Study, we compare demographic descriptions provided by pastors to demographic information taken from random samples of members in the same congregations. Significant differences in congregational profiles appear along dimensions of gender, age, race/ethnicity and, most notably, education and income. The amount of discrepancy between pastor and member profiles varies by congregational factors such as denominational affiliation and employment status of pastor. We construct diversity measures using both pastor descriptions and surveys from samples of congregation members to demonstrate the impact of data type on conclusions drawn from empirical research. Difficulties notwithstanding, key informant methodology has a place in congregational research with appropriate precautions. Of course, the most complete view of congregations is one that combines perceptions from the pulpit with information directly from the pews.
Effective Population Size and the Faster-X Effect: An Extended Model

Current models of X-linked and autosomal evolutionary rates often assume that the effective population size of the X chromosome (NeX ) is equal to three-quarters of the autosomal population size (NeA). However, polymorphism studies of Drosophila melanogaster and D. simulans suggest that there are often significant deviations from this value. We have computed fixation rates of beneficial and deleterious mutations at X-linked and autosomal sites when this occurs. We find that NeX/NeA is a crucial parameter for the rates of evolution of X-linked sites compared to autosomal sites. Faster-X evolution due to the fixation of beneficial mutations can occur under a much wider range of levels of dominance when NeX/NeA > ¾. We also examined various parameters that are known to influence the rates of evolution at X-linked and autosomal sites, such as different mutation rates in males and females and mutations that are sexually antagonistic, to determine which cases can lead to faster-X evolution. We show that, when the rate of nonsynonymous evolution is normalized by the rate of neutral evolution, a sex difference in mutation rate has no influence on the conditions for faster-X evolution.
Prosody, Memory Load, and Memory for Speech

Previous experiments indicate that prosody may facilitate memory for spoken utterances. Memory load, however, has not been systematically manipulated and may interact with such facilitating effects. Therefore, subjects were asked to listen to connected prose passages between one to five intonation phrases long and to repeat as much of each narrative as possible. Stimuli were normal productions or else had been deprived of intonational variation, pauses, or both. Performance on both the normal and the prosodically altered passages decreased as passage length grew. Errors were overwhelmingly omissions and occurred mainly in the middle of a passage. The prosodic manipulations affected memory for the longest passages. These results alongside previous findings suggest that prosody facilitates memory for spoken stimuli that are relatively difficult to process. Lengthy material, infrequent words, unrelated items, citation form prosody, or thematic or grammatical anomalies may create such difficulties.
Assessment of clinical outcomes of cervical epidural neuroplasty using a Racz-catheter and predictive factors of efficacy in patients with cervical spinal pain.

BACKGROUND Epidural neuroplasty using the Racz catheter has a therapeutic effect in patients with cervical disc herniation and central stenosis who do not respond to fluoroscopically guided epidural injections. OBJECTIVE To evaluate the clinical outcomes of cervical epidural neuroplasty in patients with posterior neck and upper extremity pain and to demonstrate correlations between predictive factors and unsuccessful results of cervical epidural neuroplasty. STUDY DESIGN Observational study. SETTING An interventional pain management practice in a university hospital. METHODS Outcome measures were obtained using the numeric rating scale (NRS) for total pain, neck pain, arm pain, and sleep disturbance; and the neck pain and disability scale (NPDS); as well as opioid consumption at preprocedure, one month, 3, 6, and 12 months after procedure. Successful epidural neuroplasty was defined as 50% or greater reduction from the preprocedure NRS for total pain, and at least a 40% reduction in the NPDS. We obtained clinical data and radiologic findings to evaluate correlations between predictive factors and efficacy of epidural neuroplasty. RESULTS Of the 169 patients, successful outcomes were observed in 108 patients (63.9%) at one month following the procedure, in 109 patients (64.5%) at 3 months, in 96 patients (56.8%) at 6 months, and in 89 patients (52.7%) at 12 months. Previous surgery, spondylolisthesis, and ossification of the posterior longitudinal ligament were significantly associated with unsuccessful outcomes as measured by NRS and NPDS (P < 0.05). LIMITATIONS Limitations of this evaluation include the lack of a placebo group. CONCLUSIONS Cervical epidural neuroplasty may be an effective treatment for pain reduction and functional improvement in patients with cervical spinal pain who did not respond to conservative treatment, and may decrease surgical demand. Previous surgery, spondylolisthesis, and ossification of the posterior longitudinal ligament are associated with unsuccessful outcomes of epidural neuroplasty.
Transgene Expression of bcl-xL Permits Anti-immunoglobulin (Ig)–induced Proliferation in xid B Cells

Mutations in the tyrosine kinase, Btk, result in a mild immunodeficiency in mice (xid). While B lymphocytes from xid mice do not proliferate to anti-immunoglobulin (Ig), we show here induction of the complete complement of cell cycle regulatory molecules, though the level of induction is about half that detected in normal B cells. Cell cycle analysis reveals that anti-Ig stimulated xid B cells enter S phase, but fail to complete the cell cycle, exhibiting a high rate of apoptosis. This correlated with a decreased ability to induce the anti-apoptosis regulatory protein, Bcl-xL. Ectopic expression of Bcl-xL in xid B cells permitted anti-Ig induced cell cycle progression demonstrating dual requirements for induction of anti-apoptotic proteins plus cell cycle regulatory proteins during antigen receptor mediated proliferation. Furthermore, our results link one of the immunodeficient traits caused by mutant Btk with the failure to properly regulate Bcl-xL.
Adaptive specialization, conditional plasticity and phylogenetic history in the reproductive cue response systems of birds

Appropriately timed integration of breeding into avian annual cycles is critical to both reproductive success and survival. The mechanisms by which birds regulate timing of breeding depend on environmental cue response systems that regulate both when birds do and do not breed. Despite there being multiple possible explanations for birds' abilities to time breeding appropriately in different environments, and for the distribution of different cue response system characteristics among taxa, many studies infer that adaptive specialization of cue response systems has occurred without explicitly considering the alternatives. In this paper, we make explicit three hypotheses concerning the timing of reproduction and distribution of cue response characteristics among taxa: adaptive specialization; conditional plasticity; and phylogenetic history. We emphasize in particular that although conditional plasticity built into avian cue response systems (e.g. differing rates of gonadal development and differing latencies until onset of photorefractoriness) may lead to maladaptive annual cycles in some novel circumstances, this plasticity also can lead to what appear to be adaptively specialized cue response systems if not viewed in a comparative context. We use a comparative approach to account for the distribution of one important feature of avian reproductive cue response systems, photorefractoriness. Analysis of the distribution within songbirds of one criterion for absolute photorefractoriness, the spontaneous regression of the gonads without any decline in photoperiod, reveals that a failure to display this trait probably represents an adaptive specialization to facilitate a flexible reproductive schedule. More finely resolved analysis of both criteria for absolute photorefractoriness (the second being total lack of a reproductive response even to constant light after gonadal regression has occurred) within the cardueline finches not only provides further confirmation of this interpretation, but also indicates that these two criteria for photorefractoriness can be, and have been, uncoupled in some taxa. We suggest that careful comparative studies at different phylogenetic scales will be extremely valuable for distinguishing between adaptive specialization and non-adaptive explanations, such as phylogenetic history as explanations of cue response traits in particular taxa. We also suggest that particular focus on taxa in which individuals may breed on very different photoperiods (latitudes or times of year) in different years should be particularly valuable in identifying the range of environmental conditions across which conditionally plastic cue responses can be adaptive.
The Difficulty of Mapping Modeled Associations to SQL

Entity-Relationship and UML class diagrams allow users to model the structural relationships, i.e., associations, that occur between entities or objects. By extending these diagrams with Object Relationship Notation (ORN), users can model the semantics of a variety of common association types with improved precision. Mapping these semantics to SQL, however, is very difficult. Here, we provide a brief overview of ORN, show with examples the degree of complexity that is still required to implement common association semantics in standard SQL, and propose a solution. Our purpose is to stimulate efforts to improve SQL in order to close the gap between the modeling of associations and their implementation.