Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV-1 Resistance to the Capsid-Targeting Inhibitor PF74 Results in Altered Dependence on Host Factors Required for Virus Nuclear Entry

ABSTRACT During HIV-1 infection of cells, the viral capsid plays critical roles in reverse transcription and nuclear entry of the virus. The capsid-targeting small molecule PF74 inhibits HIV-1 at early stages of infection. HIV-1 resistance to PF74 is complex, requiring multiple amino acid substitutions in the viral CA protein. Here we report the identification and analysis of a novel PF74-resistant mutant encoding amino acid changes in both domains of CA, three of which are near the pocket where PF74 binds. Interestingly, the mutant virus retained partial PF74 binding, and its replication was stimulated by the compound. The mutant capsid structure was not significantly perturbed by binding of PF74; rather, the mutations inhibited capsid interactions with CPSF6 and Nup153 and altered HIV-1 dependence on these host factors and on TNPO3. Moreover, the replication of the mutant virus was markedly impaired in activated primary CD4+ T cells and macrophages. Our results suggest that HIV-1 escapes a capsid-targeting small molecule inhibitor by altering the virus's dependence on host factors normally required for entry into the nucleus. They further imply that clinical resistance to inhibitors targeting the PF74 binding pocket is likely to be strongly limited by functional constraints on HIV-1 evolution. IMPORTANCE The HIV-1 capsid plays critical roles in early steps of infection and is an attractive target for therapy. Here we show that selection for resistance to a capsid-targeting small molecule inhibitor can result in viral dependence on the compound. The mutant virus was debilitated in primary T cells and macrophages—cellular targets of infection in vivo. The mutations also altered the virus's dependence on cellular factors that are normally required for HIV-1 entry into the nucleus. This work provides new information regarding mechanisms of HIV-1 resistance that should be useful in efforts to develop clinically useful drugs targeting the HIV-1 capsid.
Strengthening Causal Estimates for Links Between Spanking and Children’s Externalizing Behavior Problems

Establishing causal links when experiments are not feasible is an important challenge for psychology researchers. The question of whether parents’ spanking causes children’s externalizing behavior problems poses such a challenge because randomized experiments of spanking are unethical, and correlational studies cannot rule out potential selection factors. This study used propensity score matching based on the lifetime prevalence and recent incidence of spanking in a large and nationally representative sample (N = 12,112) as well as lagged dependent variables to get as close to causal estimates outside an experiment as possible. Whether children were spanked at the age of 5 years predicted increases in externalizing behavior problems by ages 6 and 8, even after the groups based on spanking prevalence or incidence were matched on a range of sociodemographic, family, and cultural characteristics and children’s initial behavior problems. These statistically rigorous methods yield the conclusion that spanking predicts a deterioration of children’s externalizing behavior over time.
Adverse effect of the CCR5 promoter −2459A allele on HIV‐1 disease progression

HIV positive individuals heterozygous for a 32 basepair deletion in the CCR5 encoding gene (CCR5 Δ32) have a reduced number of CCR5 receptors on the cell surface and a slower progression towards AIDS and death. Other human polymorphisms, such as the CCR2 64I and the CCR5 promoter −2459 A/G transition that has been discovered recently, have also been shown to influence HIV progression. Since genetic linkages make these polymorphisms interdependent variables, the aim of the present study was to isolate and evaluate the effect on HIV disease progression for each of these mutations independently. Genotypes were determined in 119 individuals enrolled in the Copenhagen AIDS Cohort. When including the concurrent effects of the CCR5 Δ32 and CCR2 64I mutations, homozygous carriers of the CCR5 promoter −2459A allele had a significantly faster progression towards death than heterozygous A/G individuals (P = 0.03), whereas this adverse effect was not significant when comparing A/A and G/G individuals. However, independent analysis revealed a significant adverse effect of the CCR5 promoter −2459A allele. Homozygous carriers of the −2459A allele that lack the protective effects of the CCR5 Δ32 and CCR2 64I mutations were found to have a median survival of 6.0 years, whereas carriers of the −2459G allele had a median survival of 9.4 years (P < 0.01). J. Med. Virol. 65:441–444, 2001. © 2001 Wiley‐Liss, Inc.
Optic nerve head circulation after topical calcium channel blocker.

PURPOSE Our purpose was to investigate the effects of the calcium channel blocker verapamil on intraocular pressure and blood circulation in the human optic nerve head. METHODS The effects of three different concentrations of topical verapamil (0.063%, 0.125%, and 0.25%) on intraocular pressure and optic nerve head capillary blood speed were measured in 12 healthy normal subjects. In a randomized, double-masked design, each subject received one drop of either verapamil or placebo in one eye and the opposite treatment in the fellow eye. Anterior optic nerve circulation was assessed at baseline and 90 min after instillation of the drops using the laser Doppler technique. RESULTS The intraocular pressure was significantly reduced compared with baseline in both verapamil- and placebo-treated eyes at each concentration. The reductions of intraocular pressure were greater in verapamil-treated eyes (12-17%) than in placebo-treated eyes (9-12%). No systemic effect on heart rate or blood pressure was detected after administration of topical verapamil. The capillary blood speed in the optic nerve head was increased in both verapamil- and placebo-treated eyes at each concentration, although the only statistically significant increases were with the 0.25% concentration. The mean +/- SEM increase compared with baseline at the 0.25% concentration was 10.4 +/- 3.6% in verapamil-treated eyes (p = 0.017), and 11.6 +/- 4.4% in placebo-treated eyes (p = 0.026). CONCLUSIONS These results indicate that topical administration of verapamil lowers the intraocular pressure and increases the capillary blood speed in the optic nerve head in normal subjects. Changes measured in verapamil-treated eyes were also observed in placebo-treated eyes, indicating a crossover effect.
Mechano‐signalling pathways in an experimental intensive critical illness myopathy model

Using an experimental rat intensive care unit (ICU) model, not limited by early mortality, we have previously shown that passive mechanical loading attenuates the loss of muscle mass and force‐generation capacity associated with the ICU intervention. Mitochondrial dynamics have recently been shown to play a more important role in muscle atrophy than previously recognized. In this study we demonstrate that mitochondrial dynamics, as well as mitophagy, is affected by mechanosensing at the transcriptional level, and muscle changes induced by unloading are counteracted by passive mechanical loading. The recently discovered ubiquitin ligases Fbxo31 and SMART are induced by mechanical silencing, an induction that similarly is prevented by passive mechanical loading.
The Size of Suspended Particulate Matter in Air

By means of the NASN cascade impactor the particle sizes of ambient aerosols can be measured by fractionating the particles according to their aerodynamic dimensions, and the fractions can be quantified gravimetrically. Data obtained with this instrument show that particulate matter suspended in urban air in the United States and Great Britain is remarkably uniform in distribution and that the particles are predominantly less than 1 �m in diameter. In Ankara, Turkey, the high proportion of particles larger than 1 �m in diameter are associated with the incomplete combustion of lignite; particulate concentrations in Ankara, however, are considerably higher than those measured elsewhere. The growth of particles in air during temperature inversions occurs in Cincinnati; the greater proportion of large particles found there during inversion periods can account for the reduction in visibility. Aerosols in the vicinity of highways are composed of particles larger than those found some distance away because of the reentrainment of debris by the traffic-induced turbulence. On the other hand, highway configuration and traffic volume have little effect on the size distribution of aerosols in samples collected away from the turbulence area of the roadway. Aerosols measured inside buildings are predominantly smaller in size and exhibit a narrower range of sizes than aerosols outside buildings.
POSSIBLE INVOLVEMENT OF ENDOTHELIN–1 AND NITRIC OXIDE IN THE PATHOGENESIS OF PROLIFERATIVE DIABETIC RETINOPATHY

Background Overproduction of endothelin-1 (ET-1) and nitric oxide (NO) in the retina is demonstrated in experimental diabetic animals. To clarify the possible involvement of ET-1 and NO in the pathogenesis of diabetic retinopathy, the authors examined the vitreous levels of these principal endothelium-derived vasoactive substances in patients with proliferative diabetic retinopathy (PDR). Methods Vitreous fluid was taken from patients with PDR (ET-1, n = 12; NO, n = 12) and from patients with macular holes as controls (ET-1, n = 10; NO, n = 10) at vitreous surgery. Endothelin-1 and NO metabolites were measured by radioimmunoassay and high-performance liquid chromatography based on the Griess method, respectively. Results Endothelin-1 levels (mean ± SE) were 21.5 ± 1.7 pg/mL in the vitreous of patients with PDR and 16.7 ± 0.7 pg/mL in the vitreous of patients with macular hole. There was a significant difference between patients with PDR and controls (P = 0.009, Mann–Whitney). Nitrate (NO3) was 49.8 ± 5.0 &mgr;mol/L in patients with PDR and 24.2 ± 2.8 &mgr;mol/L in patients with macula hole; it was also significantly elevated in patients with PDR (P = 0.004, Mann–Whitney), whereas nitrite (NO2) was not detected in this study. Conclusion These results indicate that ET-1 and NO may be related in the pathogenesis of PDR.
“Candidatus Bacilloplasma,” a Novel Lineage of Mollicutes Associated with the Hindgut Wall of the Terrestrial Isopod Porcellio scaber (Crustacea: Isopoda)

ABSTRACT Pointed, rod-shaped bacteria colonizing the cuticular surface of the hindgut of the terrestrial isopod crustacean Porcellio scaber (Crustacea: Isopoda) were investigated by comparative 16S rRNA gene sequence analysis and electron microscopy. The results of phylogenetic analysis, and the absence of a cell wall, affiliated these bacteria with the class Mollicutes, within which they represent a novel and deeply branched lineage, sharing less than 82.6% sequence similarity to known Mollicutes. The lineage has been positioned as a sister group to the clade comprising the Spiroplasma group, the Mycoplasma pneumoniae group, and the Mycoplasma hominis group. The specific signature sequence was identified and used as a probe in in situ hybridization, which confirmed that the retrieved sequences originate from the attached rod-shaped bacteria from the hindgut of P. scaber and made it possible to detect these bacteria in their natural environment. Scanning and transmission electron microscopy revealed a spherically shaped structure at the tapered end of the rod-shaped bacteria, enabling their specific and exclusive attachment to the tip of the cuticular spines on the inner surface of the gut. Specific adaptation to the gut environment, as well as phylogenetic positioning, indicate the long-term association and probable coevolution of the bacteria and the host. Taking into account their pointed, rod-shaped morphology and their phylogenetic position, the name “Candidatus Bacilloplasma” has been proposed for this new lineage of bacteria specifically associated with the gut surface of P. scaber.
Conceptual and Practical Difficulties with the Economic Evaluation of Health Services Developments

Five recent economic evaluations comparing hospital at home schemes with acute hospital care faced remarkably similar problems. This paper outlines these problems and considers what strategies can be derived from these experiences, which will be relevant to economic evaluations of other aspects of the organisation of care, particularly those crossing the interfaces between primary and secondary health care or the interface between health and social services. The difficulties experienced can be divided into conceptual and practical problems. Conceptual problems were primarily associated with issues of context and related to the choice of comparator, capacity constraints and size of schemes, and the choice between a short or a long run perspective. Practical problems were connected with the time at which schemes were evaluated, the type of clinical study alongside which studies were conducted and the types of data available for use in the analysis. Strategies which can be pursued in conducting economic evaluations of organisational change include giving greater attention to conceptual and hence contextual problems as well as reporting these contextual issues in detail, accepting the need for repeated economic evaluations as organisational changes become more widespread and considering carefully the clinical study design where economic evaluations of organisational change are conducted alongside. These strategies are of importance not just to those conducting economic evaluations but also to those funding appraisals of changes in the organisation of care. Use of different strategies such as those suggested here should be evaluated.
West Nile Virus: The Complex Biology of an Emerging Pathogen

West Nile virus (WNV) is a zoonotic virus that circulates in birds and is transmitted by mosquitoes. Incidentally, humans, horses and other mammals can also be infected. Disease symptoms caused by WNV range from fever to neurological complications, such as encephalitis or meningitis. Mortality is observed mostly in older and immunocompromised individuals. In recent years, epidemics caused by WNV in humans and horses have become more frequent in several Southern European countries, such as Italy and Greece. In 1999, WNV was introduced into the USA and spread over North America within a couple of years. The increasing number of WNV outbreaks is associated with the emergence of novel viral strains, which display higher virulence and greater epidemic potential for humans. Upon infection with WNV, the mammalian immune system counteracts the virus at several different levels. On the other side, WNV has developed elaborated escape mechanisms to avoid its elimination. This review summarizes recent findings in WNV research that help to understand the complex biology associated with this emerging pathogen.
Suppressor gene analysis reveals an essential role for sphingolipids in transport of glycosylphosphatidylinositol-anchored proteins in Saccharomyces cerevisiae

Sphingolipids are normally necessary for growth of Saccharomyces cerevisiae cells, but mutant strains that bypass the need for sphingolipids have been identified. Such bypass mutants fail to grow under stressful conditions, including low pH (pH 4.1), when they lack sphingolipids. To begin to understand why sphingolipids seem to be necessary for coping with low-pH stress, we screened a genomic library and selected a suppressor gene, CWP2 (cell wall protein 2), that when present in multiple copies partially compensates for the lack of sphingolipids and enhances survival at low pH. To explain these results, we present evidence that sphingolipids are required for a normal rate of transport of glycosylphosphatidylinositol (GPI)-anchored proteins, including Cwp2 and Gas1/Gpg1, from the endoplasmic reticulum (ER) to the Golgi apparatus. The effect of sphingolipids is specific for transport of GPI-anchored proteins because no effect on the rate of transport of carboxypeptidase Y, a non-GPI-anchored protein, was observed. Since the Gasl protein accumulated in the ER with a GPI anchor in cells lacking sphingolipids, we conclude that sphingolipids are not necessary for anchor attachment. Therefore, sphingolipids must be necessary for a step in formation of COPII vesicles or for their transport to the Golgi apparatus. Our data identify the Cwp2 protein as a vital component in protecting cells from the stress of low pH.
Trimeric Structure of Major Outer Membrane Proteins Homologous to OmpA in Porphyromonas gingivalis

ABSTRACT The major outer membrane proteins Pgm6 (41 kDa) and Pgm7 (40 kDa) of Porphyromonas gingivalis ATCC 33277 are encoded by open reading frames pg0695 and pg0694, respectively, which form a single operon. Pgm6 and Pgm7 (Pgm6/7) have a high degree of similarity to Escherichia coli OmpA in the C-terminal region and are predicted to form eight-stranded β-barrels in the N-terminal region. By sodium dodecyl sulfate-polyacrylamide gel electrophoresis, Pgm6/7 appear as bands with apparent molecular masses of 40 and 120 kDa, with and without a reducing agent, suggesting a monomer and trimer, respectively. To verify the predicted trimeric structure and function of Pgm6/7, we constructed three mutants with pg0695, pg0694, or both deleted. The double mutant produced no Pgm6/7. The single-deletion mutants appeared to contain less Pgm7 and Pgm6 and to form homotrimers that migrated slightly faster (115 kDa) and slower (130 kDa), respectively, than wild-type Pgm6/7 under nonreducing conditions. N-terminal amino acid sequencing and mass spectrometry analysis of partially digested Pgm6/7 detected only fragments from Pgm6 and Pgm7. Two-dimensional, diagonal electrophoresis and chemical cross-linking experiments with or without a reducing agent clearly showed that Pgm6/7 mainly form stable heterotrimers via intermolecular disulfide bonds. Furthermore, growth retardation and arrest of the three mutants and increased permeability of their outer membranes indicated that Pgm6/7 play an important role in outer membrane integrity. Based on results of liposome swelling experiments, these proteins are likely to function as a stabilizer of the cell wall rather than as a major porin in this organism.
Immune Tolerance Induction with Multiepitope Peptide Derived from Citrullinated Autoantigens Attenuates Arthritis Manifestations in Adjuvant Arthritis Rats

Citrullinated peptides are major targets of disease-specific autoantibodies in rheumatoid arthritis. Currently, citrullinated peptides are used as biomarkers for diagnosing rheumatoid arthritis by measuring anti-citrullinated protein Ab (ACPA) titers in patients’ sera. The accumulation of citrullinated proteins at synovial inflammation sites suggests that they are possible targets for tolerance induction. The objective of the present study was to determine whether citrullinated peptides could induce tolerance in an experimental arthritis model in rats. In view of the multiplicity of target citrullinated autoantigens described for ACPA, we generated a multiepitope citrullinated peptide (Cit-ME), derived from major prevalent citrullinated autoantigens (citrullinated filaggrin, fibrinogen, vimentin, and collagen type II), and studied its effects on arthritic rats. Adjuvant-induced arthritis was induced in Lewis rats. Beginning at day 7 after disease induction, the rats received eight s.c. injections of Cit-ME on alternate days. Differences in clinical status and modulation of T cell populations were analyzed. In adjuvant-induced arthritis rats treated with Cit-ME, disease severity was significantly reduced compared with that of untreated rats. Moreover, amelioration of disease manifestations was related to an increased regulatory T cell subset and an elevated apoptosis rate of T cells associated with reduced Th17 cells. Thus, the use of citrullinated peptides–based immunotherapy may be a promising approach for tolerance induction in experimental arthritis and perhaps even in susceptible individuals that are ACPA-seropositive in human arthritis.
Data processing and airborne experiment results analysis of a fully polarized scatterometer

Scatterometers are key instruments for remotely sensing of ocean surface winds. The Ku-band airborne full polarized scatterometer (AFPSCAT) of the Airborne Remote Sensing System (ARSS) was developed mainly for this application by the Key Laboratory of Microwave Remote Sensing in National Space Science Center of Chinese Academy of Sciences. Its rotating fan-beam antenna is unique among existed fully polarized scatterometers for remote sensing, which is a special type of scatterometer capable of collecting the co-polarized and cross-polarized backscattering as well as providing complex correlation of the scattering matrix. An initial test of this instrument and its potential for measuring wind field was done by flying with a plane over the Yellow Sea area in China. In this paper, the instrument was depicted, and then the experiment was described as well as data processing progress. Finally results were analyzed and conclusions were drawn that the instrument worked well for wind retrieving and further work needed to be done before its forward applications.
Eukaryotic elongation factor 1 complex subunits are critical HIV-1 reverse transcription cofactors

Cellular proteins have been implicated as important for HIV-1 reverse transcription, but whether any are reverse transcription complex (RTC) cofactors or affect reverse transcription indirectly is unclear. Here we used protein fractionation combined with an endogenous reverse transcription assay to identify cellular proteins that stimulated late steps of reverse transcription in vitro. We identified 25 cellular proteins in an active protein fraction, and here we show that the eEF1A and eEF1G subunits of eukaryotic elongation factor 1 (eEF1) are important components of the HIV-1 RTC. eEF1A and eEF1G were identified in fractionated human T-cell lysates as reverse transcription cofactors, as their removal ablated the ability of active protein fractions to stimulate late reverse transcription in vitro. We observed that the p51 subunit of reverse transcriptase and integrase, two subunits of the RTC, coimmunoprecipitated with eEF1A and eEF1G. Moreover eEF1A and eEF1G associated with purified RTCs and colocalized with reverse transcriptase following infection of cells. Reverse transcription in cells was sharply down-regulated when eEF1A or eEF1G levels were reduced by siRNA treatment as a result of reduced levels of RTCs in treated cells. The combined evidence indicates that these eEF1 subunits are critical RTC stability cofactors required for efficient completion of reverse transcription. The identification of eEF1 subunits as unique RTC components provides a basis for further investigations of reverse transcription and trafficking of the RTC to the nucleus.