Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Basis for Cell Tropism of CXCR4-Dependent Human Immunodeficiency Virus Type 1 Isolates

ABSTRACT Laboratory isolates of human immunodeficiency virus type 1 (HIV-1) that utilize CXCR4 as a coreceptor infect primary human macrophages inefficiently even though these express a low but detectable level of cell surface CXCR4. In contrast, infection of primary macrophages by primary CXCR4-tropic HIV-1 isolates is readily detectable. Here, we provide evidence suggesting that this difference in cell tropism results from a higher requirement for cell surface CXCR4 for infection by laboratory HIV-1 isolates. Transfected COS7 cells that express a high level of CD4 but a low level of CXCR4 were infected significantly more efficiently by two primary CXCR4-tropic HIV-1 isolates compared to the prototypic laboratory HIV-1 isolate IIIB. More importantly, overexpression of either wild-type or signaling-defective CXCR4 on primary macrophages dramatically enhanced the efficiency of infection by the laboratory HIV-1 isolate yet only modestly enhanced infection by either primary CXCR4-tropic virus. Overexpression of CD4 had, in contrast, only a limited effect on macrophage infection by the laboratory HIV-1, although infection by the primary isolates was markedly enhanced. We therefore conclude that the laboratory CXCR4-tropic HIV-1 isolate exhibits a significantly higher CXCR4 requirement for efficient infection than do the primary CXCR4-tropic isolates and that this difference can explain the poor ability of the laboratory HIV-1 isolate to replicate in primary macrophages. More generally, we propose that the cell tropisms displayed by different strains of HIV-1 in culture can largely be explained on the basis of differential requirements for cell surface CD4 and/or coreceptor expression levels.
Vaccination timeliness in preterm infants: An integrative review of the literature

AIMS AND OBJECTIVES To take a systematic approach to reviewing the scientific literature examining the timeliness of vaccination in preterm infants and to identify any factors associated with timeliness. BACKGROUND Preterm infants are vulnerable to infection and guidance advocates they are vaccinated in accordance with their full-term peers. Vaccination is well tolerated and protective immune responses are observed, yet some early enquiries suggest that preterm infants experience unwarranted delays. The recent surge in pertussis cases and the increase in vaccinations administered make this a topic requiring further exploration. DESIGN An integrative review of the empirical literature. METHODS Studies were identified following a search of Medline, Academic Search Premier, Cochrane Database of Systematic Reviews and the Cumulative Index to Nursing and Allied Health Literature. The review methods used were influenced by a narrative synthesis approach. The retrieval of papers adhered to recognised reporting standards. RESULTS Fourteen studies were identified, which indicated that infants with the lowest gestational ages and birthweights experience the greatest delays. Vaccination timeliness is influenced by hospitalisation and increased postdischarge follow-up. There was a lack of consensus to indicate that parental socio-economic status and level of education were indicators for a delay. The studies propose that many delays are unjustified and not according to genuine contraindications. CONCLUSION This review indicates that preterm infants are not vaccinated in a timely manner. Those involved in vaccinating preterm infants must be informed of the genuine contraindications to avoid unnecessary delays putting preterm infants at an increased risk of infection. RELEVANCE TO CLINICAL PRACTICE Care providers should acknowledge the risk of a delay in preterm infants and actively promote vaccination in this population. Regular training should help to negate the occurrence of inappropriate delays, and careful discharge planning is needed to ensure that preterm infants are vaccinated on time.
Modeling of the Hysteretic $I{-}V$ Characteristics of ${\rm TiO}_{2}$-Based Resistive Switches Using the Generalized Diode Equation

An equivalent circuit representation for the conduction characteristics of TiO2-based resistive switches based on the generalized diode equation is reported. The proposed model consists of two antiparallel diodes with series and parallel resistances representing the filamentary current pathway spanning the oxide layer and the possible parasitic conduction effects. The model accounts for the pulse-induced hysteretic behavior exhibited by the I-V characteristic after electroforming. Three different approaches, each one of them with increased complexity, are assessed: 1) constant; 2) nanowire-like; and 3) sigmoidal diode amplitude. In all cases, the logarithmic conductance of the diodes is modeled using a logistic-type threshold function.
Interview schedule for children and adolescents (ISCA).

OBJECTIVE To describe the development, use, and psychometric properties of the semistructured, symptom-oriented Interview Schedule for Children and Adolescents (ISCA) and its versions suitable for reevaluation. METHOD Data are summarized on the reliability, construct validity, and predictive validity of symptom ratings and resultant diagnoses, and information regarding the feasibility of a version of the ISCA for young adult subjects is presented. RESULTS The evidence suggests that these instruments yield reliable symptom ratings and diagnoses relevant to a wide range of syndromes and diagnoses over time and that the ISCA is useful with psychiatric and pediatric medical populations. CONCLUSIONS The ISCA and its follow-up versions are useful clinical tools in research focusing on developmental psychopathology.
Identification of a New Iron-Regulated Virulence Gene,ireA, in an Extraintestinal Pathogenic Isolate ofEscherichia coli

ABSTRACT Our laboratory is studying an extraintestinal pathogenic isolate ofEscherichia coli (CP9) as a model pathogen. We have been using human urine, ascites, and blood ex vivo to identify genes with increased expression in these media relative to expression in Luria-Bertani (LB) broth. Such genes may represent new or unrecognized virulence traits. In this study, we report the identification of a new gene, ireA (iron-responsive element). This gene has an open reading frame of 2,049 nucleotides, and its peptide has a molecular mass of 75.3 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Its expression is increased a mean of 3.6-fold in human urine, 16.2-fold in human ascites, and 6.6-fold in human blood relative to expression in LB medium, and it is Fe repressible. IreA also exhibits peptide similarities (48 to 56%) to previously identified proteins that function as siderophore receptors, suggesting that IreA is involved in iron acquisition. PCR-based analysis ofireA's phylogenetic distribution detectedireA in none (0%) of 14 fecal isolates that represented probable commensal strains, but in 13 (26%) of 50 random urine and blood clinical isolates (P = 0.05) and in 5 (100%) of 5 representatives of the J96-like, clonal group of which CP9 is a member (P < 0.001). In a mouse urinary tract infection model, the presence of ireA contributed significantly to CP9's ability to colonize the bladder (P < 0.02), evidence that IreA is a urovirulence factor. Taken together, these findings demonstrate thatireA encodes a new virulence factor, which is likely involved in Fe acquisition.
T-cell proliferation involving the CD28 pathway is associated with cyclosporine-resistant interleukin 2 gene expression

CD28 is a homodimeric glycoprotein expressed on the surface of a major subset of human T cells that has recently been identified as a member of the immunoglobulin supergene family. The binding of monoclonal antibodies to the CD28 antigen on purified T cells does not result in proliferation; however, previous studies have shown that the combination of CD28 stimulation and protein kinase C activation by phorbol myristate acetate (PMA) results in T-cell proliferation that is independent of both accessory cells and activation of the T-cell receptor-CD3 complex. In the present study, effects of stimulation by anti-CD28 on cell cycle progression and on the interleukin 2 (IL-2) and IL-2 receptor system have been investigated on primary cultures of purified peripheral-blood CD28+ T cells. There was no measurable effect on cell size or on DNA synthesis after stimulation of resting (G0) cells by CD28 alone. After 3 h of activation of T cells by PMA alone, a slight (8%) increase in cell volume occurred that did not progress to DNA synthesis. In contrast, T-cell stimulation by CD28 in combination with PMA resulted in a progressive increase in cell volume in approximately 100% of cells at 12 to 14 h after stimulation. Northern blot (RNA blot) analysis revealed that CD28 stimulation alone failed to cause expression of the alpha chain of the IL-2 receptor or of IL-2 mRNA, and in accord with previous studies, stimulation by PMA alone resulted in the accumulation of IL-2 receptor transcripts but no detectable IL-2 mRNA. In contrast, T-cell stimulation by the combination of CD28 and PMA resulted in the appearance of IL-2 transcripts and enhanced expression of IL-2 receptor mRNA. Functional studies revealed that the proliferation induced by CD28 and PMA stimulation was entirely resistant to cyclosporine, in contrast to T-cell activation induced by the CD3-T-cell receptor complex. Cyclosporine was found not to affect the accumulation of IL-2 mRNA after CD28 plus PMA stimulation, although there was no detectable IL-2 mRNA after stimulation by CD3 in the presence of the drug. Furthermore, stimulation by CD28 in combination with immobilized CD3 antibodies caused a striking enhancement of IL-2 mRNA expression that was, in part, resistant to the effects of cyclosporine. These studies indicate that the CD28 molecule synergizes with protein kinase C activation to induce IL-2 gene expression and demonstrate that stimulation by the CD28 pathway can cause vigorous T-cell proliferation even in the presence of cyclosporine and that cyclosporine does not prevent transcription of 16-2 mRNA, as has been suggested previously. Moreover, these findings suggest that a potential role for the CD28 molecule in vivo may be to augment IL-2 production after stimulation of the CD3-T-cell receptor molecular complex and thereby to amplify an antigen-specific immune response. Finally, these results provide further evidence that the CD28 molecule triggers T-cell proliferation in a manner that differs biochemically from CD3-T-cell receptor-induced proliferation.
A Simplified Model to Predict Oxygen Attenuation on Earth-Space Links

A simplified yet accurate model to predict oxygen attenuation for Earth-space applications (10–350 GHz range) is presented in this contribution. The model is developed by taking advantage of an extensive set of high-resolution radiosonde observations (RAOBS) collected in several sites worldwide. It predicts the statistics of oxygen attenuation along the path by retaining the accurate formulation for the specific oxygen attenuation included in the Liebe MPM93 model, but it relies on simplified meteorological input values (namely the mean yearly ground temperature and the statistics of the ground water vapor content), rather than on full atmospheric vertical profile. Tested against attenuation estimates obtained from Liebe MPM93 model coupled with the mentioned RAOBS data, the model provides a very good prediction accuracy in the full 10–350 GHz range, which turns out to be almost independent of the considered site.
Telecommunications IT and navigation for future Mars exploration missions

There are three primary drivers behind current investments in telecommunications information technology and navigation for Mars exploration. One is finding ways to maximize the volume of science data return since instrument data generation often exceeds communication bandwidth. Another is to provide the necessary technology to enable networked spacecraft. The third is to enable more precise landing so in-situ vehicles can be placed in more scientifically interesting regions. This paper describes current NASA investments in these areas funded through the Mars Technology Program (competed via NASA Research Announcements). Current investments are in stereo image compression, next generation Mars relay protocols, and a capability for autonomous approach navigation using in-situ Mars orbiter assets
Cross-Modal Deep Variational Hashing Venice

In this paper, we propose a cross-modal deep variational hashing (CMDVH) method for cross-modality multimedia retrieval. Unlike existing cross-modal hashing methods which learn a single pair of projections to map each example as a binary vector, we design a couple of deep neural network to learn non-linear transformations from imagetext input pairs, so that unified binary codes can be obtained. We then design the modality-specific neural networks in a probabilistic manner where we model a latent variable as close as possible from the inferred binary codes, which is approximated by a posterior distribution regularized by a known prior. Experimental results on three benchmark datasets show the efficacy of the proposed approach.
Differential behaviour of Escherichia coli and Campylobacter spp. in a stream draining dairy pasture.

The faecal indicator bacterium Escherichia coli and thermotolerant Campylobacter spp. , which are potentially pathogenic, were investigated in the Toenepi Stream draining a pastoral catchment dominated by dairying. Bacteria concentrations were monitored routinely at fortnightly intervals over 12 months and intensively during storm events to compare the transport dynamics of bacterial indicator and pathogen under varying hydro-meteorological conditions. Routine monitoring indicated median concentrations of 345 E. coli MPN 100 ml(-1) and relatively low concentrations of 2.3 Campylobacter MPN 100 ml(-1). The bacterial flux was three orders of magnitude greater under elevated stream flow compared with base-flow. E. coli peak concentrations occurred very close to the turbidity peak and consistently ahead of the Campylobacter spp. peak (which was close to the hydrograph peak). We postulate that, under flood conditions, the E. coli peak reflects the entrainment and mobilisation of in-stream stores on the flood wave front. In contrast, Campylobacter spp. are derived from wash-in from land stores upstream and have travelled at the mean water velocity which is slower than the speed of the flood wave. Our findings of different dynamics for E. coli and Campylobacter spp. suggest that mitigation to reduce faecal microbial impacts from farms will need to take account of these differences.
Population‐based case‐control teratogenic study of hydroxyprogesterone treatment during pregnancy

ABSTRACT Hydroxyprogesterone, a synthetic progestin, was used for the treatment of pregnant women with threatened abortion and preterm delivery. Previous studies showed some association between hydroxyprogesterone use during early pregnancy and some specific congenital abnormalities. The population‐based large Hungarian data set seemed to be appropriate to check this possible association. The Hungarian Case‐Control Surveillance of Congenital Abnormalities between 1980 and 1996 includes 22 843 cases with congenital abnormalities and 38 151 controls without any defect. 318 (1.4%) cases, while 433 (1.1%) controls had mothers with hydroxyprogesterone treatment during pregnancy (adjusted POR with 95% CI: 1.3, 1.1–1.5). However, there was no association between risk for any congenital abnormality group and a higher use of maternal hydroxyprogesterone treatment during the second and third month of gestation. On the other hand hydroxyprogesterone is not effective in the prevention of preterm delivery. In conclusion, there was no detectable risk for congenital abnormalities in the offspring of mothers with hydroxyprogesterone treatment during early pregnancy, however, there is no reasonable indication of this treatment during pregnancy.
Selection and simulation of a proper microfluidic for hepatocyte culture

The advent of microfluidics as suitable environments for culturing cells is associated with some challenges as shear stresses applied on the cells. Moreover, among all factors needed for cell viability, feeding hepatocytes with adequate oxygen is of great importance due to their high demand for oxygen compared the other cell types. In this paper three kinds of geometries has been studied in order that shear stresses would be in allowed range and provision of hepatocytes with sufficient oxygen concentrations has been ensured as well. In addition to supplying hepatocytes with oxygen, the range of its concentration has been adjusted in physiologic value so that it would be practical for further medical experiments. The yielded results, as a consequence of comparison, established the fact that the geometry containing hydrogel provides a more satisfactory environment for cell living.
Sexual dysfunction in male schizophrenic patients.

BACKGROUND Neuroleptic treatment in schizophrenic patients is associated with sexual dysfunction. However, it is not clear to what extent the psychiatric disorder and/or the pharmacologic treatment are responsible for the sexual impairment. The aim of the present study was to evaluate the sexual function of untreated and treated male schizophrenic patients in comparison with healthy subjects. METHOD Participants included 122 male subjects: 20 drug-free schizophrenic patients, 51 neuroleptic-treated (depot form) schizophrenic patients, and 51 normal controls. A detailed structured interview was used to quantitatively and qualitatively assess sexual function. RESULTS A high frequency of sexual dysfunction was reported by both schizophrenic groups of patients. Impairments in arousal items (erection) and orgasm during sex were reported mainly by the treated patients. Desire parameters were reduced in both schizophrenic groups, but reduction in the frequency of sexual thoughts was confined to the untreated one. The schizophrenic patients were more involved in masturbatory activity in comparison with the control subjects. Treated patients disclosed dissatisfaction with their sexual function. CONCLUSION Untreated schizophrenic patients exhibit decreased sexual desire. Neuroleptic treatment is associated with restoration of sexual desire yet it entails erectile, orgasmic, and sexual satisfaction problems. Clinicians' awareness and open discussion of sexual problems with patients may improve comprehension and compliance.
Blastogenesis of Large Granular Lymphocytes in Nonlymphoid Organs

High numbers of large granular lymphocytes (LGL) accumulate in the livers and peritoneal cavities of mice during the course of viral infection. Accumulation of natural killer (NK) cells at day 3 postinfection (p.i.) was shown to be radiation‐sensitive, implying that proliferation was required for this response. Accumulation occurred in splenectomized mice, indicating that the spleen, known to be an organ for mature NK cell proliferation, was not the major source for liver and peritoneal NK/LGL.
Internally located and oppositely oriented polymerase II promoters direct convergent transcription of a LINE-like retroelement, the Dictyostelium repetitive element, from Dictyostelium discoideum

The Dictyostelium discoideum NC4 genome harbors approximately 150 individual copies of a retrotransposable element called the Dictyostelium repetitive element (DRE). This element contains nonidentical terminal repeats (TRs) consisting of conserved building blocks A and B in the left TR and B and C in the right TR. Seven different-sized classes of RNA transcripts from these elements were resolved by Northern (RNA) blot analysis, but their combined abundance was very low. When D. discoideum cells were grown in the presence of the respiratory chain blocker antimycin A, steady-state concentrations of these RNA species increased 10- to 20-fold. The D. discoideum genome contains two DRE subtypes, the full-length 5.7-kb DREa and the internally deleted 2.4-kb DREb. Both subtypes are transcribed, as confirmed by analysis of cloned cDNA. Primary transcripts from the sense strand originate at nucleotide +1 and terminate at two dominant sites, located 21 or 28 nucleotides upstream from the 3' end of the elements. The activity of a reasonably strong polymerase II promoter in the 5'-terminal A module is slightly upregulated by the tRNA gene located 50 +/- 4 nucleotides upstream and drastically reduced by the adjacent B module of the DRE. Transcripts from the opposite DNA strand (complementary-sense transcripts) were also detected, directed by an internally located polymerase II promoter residing within the C module. This latter transcription was initiated at multiple sites within the oligo(dA12) stretch which terminates DREs.
Joint subchannel and power allocation in two-tier OFDMA HetNets with clustered femtocells

Efficient power and subchannel allocation methods are required for orthogonal frequency division multiple access (OFDMA)-based femtocells to mitigate both co-tier and cross-tier interferences. In this paper, we study the problem of joint power and subchannel allocation in a densely deployed femtocell network with constraints on co-tier and cross-tier interference and minimum datarate requirements. A convex optimization problem is formulated and the solution of the problem is obtained numerically. For this joint resource allocation problem, the effect of clustering (or cooperation) is studied as well, where femtocells are placed in disjoint groups. The performances of distributed resource allocation (i.e., without clustering) and centralized resource allocation (i.e., with only one cluster) are compared against clustering-based (i.e., semi-distributed) resource allocation. Numerical results show that, in a dense environment, with femtocells closely located to each other, the effect of co-tier interference becomes significantly dominant and clustering is a very effective technique in such a densely deployed environment to improve the sumrate capacity of the femtocells.
Metabolomic prediction of yield in hybrid rice.

Rice (Oryza sativa) provides a staple food source for more than 50% of the world's population. An increase in yield can significantly contribute to global food security. Hybrid breeding can potentially help to meet this goal because hybrid rice often shows a considerable increase in yield when compared with pure-bred cultivars. We recently developed a marker-guided prediction method for hybrid yield and showed a substantial increase in yield through genomic hybrid breeding. We now have transcriptomic and metabolomic data as potential resources for prediction. Using six prediction methods, including least absolute shrinkage and selection operator (LASSO), best linear unbiased prediction (BLUP), stochastic search variable selection, partial least squares, and support vector machines using the radial basis function and polynomial kernel function, we found that the predictability of hybrid yield can be further increased using these omic data. LASSO and BLUP are the most efficient methods for yield prediction. For high heritability traits, genomic data remain the most efficient predictors. When metabolomic data are used, the predictability of hybrid yield is almost doubled compared with genomic prediction. Of the 21 945 potential hybrids derived from 210 recombinant inbred lines, selection of the top 10 hybrids predicted from metabolites would lead to a ~30% increase in yield. We hypothesize that each metabolite represents a biologically built-in genetic network for yield; thus, using metabolites for prediction is equivalent to using information integrated from these hidden genetic networks for yield prediction.