Miracle-dz/UniFAR-FTUs huggingface dataset:
Moderate Influence of Human APOBEC3F on HIV-1 Replication in Primary Lymphocytes

ABSTRACT Multiple APOBEC3 proteins are expressed in HIV-1 target cells, but their individual contributions to viral suppression when expressed at endogenous levels remain largely unknown. We used an HIV NL4-3 mutant that selectively counteracts APOBEC3G (A3G) but not APOBEC3F (A3F) to dissect the relative contribution of A3F to the inhibition of HIV-1 replication in primary human lymphocytes (peripheral blood mononuclear cells [PBMCs]). This HIV Vif mutant replicated similarly to wild-type virus in PBMCs, suggesting that the effect of A3F on HIV restriction in these cells is limited. The different A3F variants found in PMBC donors displayed either comparable activity or less activity than wild-type A3F. Lastly, the endogenous A3F mRNA and protein expression levels in PBMCs were considerably lower than those of A3G. Our results suggest that A3F neutralization is dispensable for HIV-1 replication in primary human T-lymphocytes.
A radioimmunoassay for human thyroglobulin: methodology and clinical applications

Abstract. A specific double‐antibody radioimmunoassay with a sensitivity of 2.5 ng/ml has been developed for measuring thyroglobulin (Tg) in human serum. As endogenous anti‐Tg antibodies in serum interfere in the assay, only sera with a negative tanned red cell (TRC) test are suitable for analysis. Tg was detectable in 84.7% of the euthyroid subjects, with a mean value of 6.1 (values ranging from nondetectable to 43.0 ng/ml). Values were significantly higher in women than in men. Tg release by the thyroid appears to be under pituitary control, as suggested by TSH stimulation and T3 suppression tests. Elevated Tg levels were found in hyperthyroidism, simple goitre, and differentiated thyroid carcinoma. The significance of circulating Tg and the possible application of the Tg RIA are discussed.
Circadian organization and the role of the pineal in birds

All organisms exhibit significant daily rhythms in a myriad of functions from molecular levels to the level of the whole organism. Significantly, most of these rhythms will persist under constant conditions, showing that they are driven by an internal circadian clock. In birds the circadian system is composed of several interacting sites, each of which may contain a circadian clock. These sites include the pineal organ, the suprachiasmatic nucleus (SCN) of the hypothalamus, and, in some species, the eyes. Light is the most powerful entraining stimulus for circadian rhythms and, in birds, light can affect the system via three different pathways: the eyes, the pineal, and extraretinal photoreceptors located in the deep brain. Circadian pacemakers in the pineal and in the eyes of some avian species communicate with the hypothalamic pacemakers via the rhythmic synthesis and release of the hormone melatonin. Often the hypothalamic pacemakers are unable to sustain persistent rhythmicity in constant conditions in the absence of periodic melatonin input from the pineal (or eyes). It has also been proposed that pineal pacemakers may be unable to sustain rhythmicity in constant conditions without periodic neural input from the SCN. Significant variation can occur among birds in the relative roles that the pineal, the SCN, and the eyes play within the circadian system; for example, in the house sparrow pacemakers in the pineal play the predominant role, in the pigeon circadian pacemakers in both the pineal and eyes play a significant role, and in Japanese quail ocular pacemakers play the predominant role. Microsc. Res. Tech. 53:48–62, 2001. © 2001 Wiley‐Liss, Inc.
Noise promotes independent control of gamma oscillations and grid firing within recurrent attractor networks

Neural computations underlying cognitive functions require calibration of the strength of excitatory and inhibitory synaptic connections and are associated with modulation of gamma frequency oscillations in network activity. However, principles relating gamma oscillations, synaptic strength and circuit computations are unclear. We address this in attractor network models that account for grid firing and theta-nested gamma oscillations in the medial entorhinal cortex. We show that moderate intrinsic noise massively increases the range of synaptic strengths supporting gamma oscillations and grid computation. With moderate noise, variation in excitatory or inhibitory synaptic strength tunes the amplitude and frequency of gamma activity without disrupting grid firing. This beneficial role for noise results from disruption of epileptic-like network states. Thus, moderate noise promotes independent control of multiplexed firing rate- and gamma-based computational mechanisms. Our results have implications for tuning of normal circuit function and for disorders associated with changes in gamma oscillations and synaptic strength. DOI: http://dx.doi. org/10.7554/eLife.06444. 001
An exploratory study of marketing international education online

As competition increases in the education industry, public and private schools increasingly view students as consumers and market their institutions. This paper investigates the Internet’s role in communicating educational opportunities from two perspectives: students’ Internet use to facilitate information search and decision making; and educational institutions’ e‐business adoption and implementation. Two surveys of international students and face‐to‐face interviews with marketing executives from nine Australian institutions explored the Internet’s role in marketing international education. Academically, this paper reviews how Rogers’ diffusion of innovations explains individual and organizational adoption of the Internet, and proposes future research areas. Based on this exploratory research, educational institutions gain insights of online customer service and e‐business strategies for successfully recruiting students. The results show that prospective overseas students do indeed use the Internet. Institutions should immediately establish procedures for answering e‐mail and review changing their Web sites to appeal to overseas students.
Capacity and Stable Scheduling in Heterogeneous Wireless Networks

Heterogeneous wireless networks (HetNets) provide a means to increase network capacity by introducing small cells and adopting a layered architecture. HetNets allocate resources flexibly through time sharing and cell range expansion/contraction allowing a wide range of possible schedulers. In this paper, we define the capacity of a HetNet down link in terms of the maximum number of downloads per second, which can be achieved for a given offered traffic density. Given this definition we show that the capacity is determined via the solution to a continuous linear program (LP). If the solution is smaller than 1 then there is a scheduler such that the number of mobiles in the network has ergodic properties with finite mean waiting time. If the solution is greater than 1 then no such scheduler exists. These results have clear implications for network planning. The above results continue to hold if a more general class of schedulers is considered.
MITOCHONDRIAL INTROGRESSION AND INCOMPLETE LINEAGE SORTING THROUGH SPACE AND TIME: PHYLOGENETICS OF CROTAPHYTID LIZARDS

Abstract We investigate the roles of mitochondrial introgression and incomplete lineage sorting during the phylogenetic history of crotaphytid lizards. Our Bayesian phylogenetic estimate for Crotaphytidae is based on analysis of mitochondrial DNA sequence data for 408 individuals representing the 12 extant species of Crotaphytus and Gambelia. The mitochondrial phylogeny disagrees in several respects with a previously published morphological tree, as well as with conventional species designations, and we conclude that some of this disagreement stems from hybridization-mediated mitochondrial introgression, as well as from incomplete lineage sorting. Unidirectional introgression of Crotaphytus collaris (western collared lizard) mitochondria into C. reticulatus (reticulate collared lizard) populations in the Rio Grande Valley of Texas has resulted in the replacement of ancestral C. reticulatus mitochondria over approximately two-thirds of the total range of the species, a linear distance of ∼270 km. Introgression of C. collaris mitochondria into C. bicinctores (Great Basin collared lizard) populations in southwestern Arizona requires a more complex scenario because at least three temporally separated and superimposed introgression events appear to have occurred in this region. We propose an “introgression conveyor” model to explain this unique pattern of mitochondrial variation in this region. We show with ecological niche modeling that the predicted geographical ranges of C. collaris, C. bicinctores, and C. reticulatus during glacial maxima could have provided enhanced opportunities for past hybridization. Our analyses suggest that incomplete lineage sorting and/or introgression has further confounded the phylogenetic placements of additional species including C. nebrius, C. vestigium, C. insularis, C. grismeri, and perhaps G. copei. Despite many independent instances of interspecific hybridization among crotaphytid lizards, the species continue to maintain morphological and geographic cohesiveness throughout their ranges.
On the performance of cognitive access with periodic spectrum sensing

The problem of cognitive access of parallel channels occupied by primary users is considered. The transmissions of primary users are modeled as independent continuous-time Markov processes. A secondary cognitive user employs a slotted transmission format and a periodic sensing strategy such that it decides if and where to transmit according to its sensing outcomes. The objective of the cognitive user is to maximize its throughput while satisfying collision constrains imposed by the primary users. Three access policies are analyzed. The optimal access policy is obtained based on a formulation of constrained Markov decision processes. A simple suboptimal memoryless policy is obtained by the use of instantaneous sensing outcome. As an upper bound of the optimal policy, a memoryless policy assuming the access of full channel states is also considered. For a symmetric system, we show that the simple memoryless policy is asymptotically optimal when the collision constraint is tight by proving that the performances of all three policies converge to the same value.
Bund source separation based on Multi-Stage ICA combining frequency-domain ICA and time-domain ICA

We propose a new algorithm for blind source separation (BSS), in which frequency-domain independent component analysis (FDICA) and time-domain ICA (TDICA) are combined to achieve a superior source-separation performance under reverberant conditions. Generally speaking, the conventional TDICA fails to separate source signals under heavily reverberant conditions because of the low convergence in the iterative learning of the inverse of the mixing system. On the other hand, the separation performance of the conventional FDICA under reverberant conditions also degrades significantly because the independence assumption of narrowband signals collapses when the number of subbands increases. In the proposed method, the separated signals of FDICA are regarded as the input signals for TDICA, and we can remove the residual cross-talk components of FDICA by using TDICA. The experimental results under the reverberant condition reveal that the signal-separation performance of the proposed method is superior to that of the conventional ICA-based BSS methods.
Dealing with uncertainty in image forensics: A fuzzy approach

Image forensics research has mainly focused on the detection of artifacts introduced by a single processing tool. In tamper detection applications, however, the kind of artifacts the forensic analyst should look for is not known beforehand, hence making it necessary that several tools developed for different scenarios are applied. The problem, then, is twofold: i) devise a sound strategy to elaborate the information provided by the different tools into a single output, and ii) deal with the uncertainty introduced by error-prone tools. In this paper, we introduce a framework based on Fuzzy Theory to overcome these problems. We describe a practical implementation of the proposed framework putting the theoretical principles in practice. To validate the proposed approach, we carried out some experiments addressing a simple realistic scenario in which three forensic tools exploit artifacts introduced by JPEG compression to detect cut&paste tampering within a specified region of an image. The results are encouraging, especially when compared with those obtained by simply XOR-ing the output of the the single detection tools.
Reliability issues regarding the beginning, middle and end of continuous emotion ratings to music

Continuous self-reported emotion expressed by four pieces of music were collected on a two-dimensional (valence and arousal) emotion space in a repeated measures (test-retest conditions) design. Initial orientation time (IOT), test-retest reliability and afterglow were examined. Median IOT was 8 seconds. Valence ratings took up to 25 (median 4), and for arousal up to 35 (median 12) seconds. Slower tempi seemed to require longer IOT. Test-retest reliability examined correlation coefficients, and compared periods of sample-by-sample good agreement in response between Test and Retest condition. About 80% of responses were reliable in both the Test and Retest conditions regardless of response dimension. Pearson correlations demonstrated better test-retest reliability for arousal responses than for valence. Retest condition ratings were within 8% of Test condition rating within participant. Average standard deviations for ratings collapsed across dimension, stimulus and conditions was 12.2% of the ratings scale range. Afterglow effects – large outliers in spread of scores just after the end of a piece – were identified. The reliability of continuous emotional response is therefore considered to be quite good, but caution must be taken as to how to deal with the opening and ending of continuous emotional response data.
The role of epidemiology in the era of molecular epidemiology and genomics: Summary of the 2013 AJE-sponsored Society of Epidemiologic Research Symposium.

On June 20, 2013, the American Journal of Epidemiology sponsored a symposium at the Society for Epidemiologic Research's 46th Annual Meeting in Boston, Massachusetts, entitled, "What Is the Role of Epidemiology in the Era of Molecular Biology and Genomics? " The future of epidemiology depends on innovation in generating interesting and important testable hypotheses that are relevant to population health. These new strategies will depend on new technology, both in measurement of agents and environment and in the fields of pathophysiology and outcomes, such as cellular epidemiology and molecular pathology. The populations to be studied, sample sizes, and study designs should be selected based on the hypotheses to be tested and include case-control, cohort, and clinical trials. Developing large mega cohorts without attention to specific hypotheses is inefficient, will fail to address many associations with high-quality data, and may well produce spurious results.
Human CtIP Mediates Cell Cycle Control of DNA End Resection and Double Strand Break Repair*S⃞

In G0 and G1, DNA double strand breaks are repaired by nonhomologous end joining, whereas in S and G2, they are also repaired by homologous recombination. The human CtIP protein controls double strand break (DSB) resection, an event that occurs effectively only in S/G2 and that promotes homologous recombination but not non-homologous end joining. Here, we mutate a highly conserved cyclin-dependent kinase (CDK) target motif in CtIP and reveal that mutating Thr-847 to Ala impairs resection, whereas mutating it to Glu to mimic constitutive phosphorylation does not. Moreover, we show that unlike cells expressing wild-type CtIP, cells expressing the Thr-to-Glu mutant resect DSBs even after CDK inhibition. Finally, we establish that Thr-847 mutations to either Ala or Glu affect DSB repair efficiency, cause hypersensitivity toward DSB-generating agents, and affect the frequency and nature of radiation-induced chromosomal rearrangements. These results suggest that CDK-mediated control of resection in human cells operates by mechanisms similar to those recently established in yeast.
Who needs interaction anyway: exploring mobile playlist creation from manual to automatic

Currently available user interfaces for playlist generation allow creating playlists in various ways, within a spectrum from fully automatic to fully manual. However, it is not entirely clear how users interact with such systems in the field and whether different situations actually demand different interfaces. In this paper we describe Rush 2, a music interface for mobile touch-screen devices that incorporates three interaction modes with varying degrees of automation: Adding songs manually, in quick succession using the rush interaction technique or filling the playlist automatically. For all techniques various filters can be set. In a two- week diary study (with in-depth interaction logging) we gained insight into how people interact with music in their everyday lives and how much automation and interactivity are really necessary.
Bringing the U-Haul: Embracing and Resisting Sexual Stereotypes in a Lesbian Community

I examine the rules of sex and dating in a midwestern white middle-class lesbian community. I interview participants and describe how they comply with these rules, which largely (though not entirely) correspond with stereotypes of white middle-class female sexuality. The participants also describe how through the community rules they resist heterosexual norms of sexuality, which primarily means resistance of stereotypical male sexuality. The women seem unaware of the ways in which they participate in the process of creating and reifying these rules within their community, perceiving themselves instead to be completely ignorant of them. I examine these patterns within the context of the lesbian ‘sex wars’, concluding that the legacy of lesbian feminism has remained surprisingly strong in this community.
Still Divided by a Common Language: Discontentment and the Semantics of Power

In a recent response to an article of mine on the ‘faces of power’ controversy published in this journal (Politics Vol. 18. No. 1), James Doyle provides an important, sophisticated and provocative attempt to rehabilitate Lukes' three-dimensional conception of power from the criticisms of myself and others. He argues, in particular, that Lukes' understanding of power is not compromised by its reliance upon a distinction between subjective and objective interests since such a distinction is, in fact, ‘an integral part of the logical grammar of the concept’. Nor, he suggests, is Lukes wrong to raise the spectre of the concept of false consciousness' since the notion of ‘duping others’ is also ‘internal to the logic of the concept’ of power. Finally, Doyle argues that my chosen reformulation of the concept of power as context- and conduct-shaping unwittingly exposes me to precisely the same criticism(s) which I direct at Lukes. In this brief response I seek to clarify and defend my earlier position in the face of certain obvious misunderstandings in Doyle's reading, whilst re-stating my principal point of departure from Lukes' formulation.
Addressing decisional conflict about fertility preservation: helping young female cancer survivors’ family planning decisions

Background Health professionals are challenged by a growing number of young long-term cancer survivors with their specific needs with regard to family planning. This study aimed at assessing decisional conflict (DC) in young female cancer patients regarding fertility preservation, identifying demographic, fertility and fertility preservation related factors, which may affect DC, and assessing the helpfulness of various decision-supports. Methods A retrospective, cross-sectional, web-based survey via an online questionnaire available in three languages with specific items concerning cancer, fertility, fertility preservation and the validated Decisional Conflict Scale targeted at current or former female cancer patients aged 18–45 years, with cancer types or treatment potentially affecting reproductive function. Results The 155 participating women showed considerable DC, especially with regard to missing information and support. DC was significantly lower in patients when the risk of infertility was discussed with a health professional, when they had undergone any procedure to preserve fertility, and when they had a university education. A longer time interval since cancer diagnosis was associated with higher DC. The most helpful decision-support tools were specialised websites and leaflets. Conclusions Young female cancer patients’ DC with regard to fertility preservation is very high. Information and support seem to be deficient. More information through standardised information tools might be an effective strategy to lower their DC at the time when treatment decisions need to be taken, and to improve their reproductive health after they have overcome cancer in the future.
3D printing of microscopic bacterial communities

Significance Bacteria within the human body commonly thrive within structured three-dimensional (3D) communities composed of multiple bacterial species. Organization of individuals and populations within bacterial aggregates is believed to play key roles in mediating community attributes, affecting, for example, the virulence of infections within the cystic fibrosis lung and oral cavity. To gain detailed insights into how geometry may influence pathogenicity, we describe a strategy for 3D printing bacterial communities in which physically distinct but chemically interactive populations of defined size, shape, and density can be organized into essentially any arrangement. Using this approach, we show that resistance of one pathogenic species to an antibiotic can enhance the resistance of a second species by virtue of their 3D relationship. Bacteria communicate via short-range physical and chemical signals, interactions known to mediate quorum sensing, sporulation, and other adaptive phenotypes. Although most in vitro studies examine bacterial properties averaged over large populations, the levels of key molecular determinants of bacterial fitness and pathogenicity (e.g., oxygen, quorum-sensing signals) may vary over micrometer scales within small, dense cellular aggregates believed to play key roles in disease transmission. A detailed understanding of how cell–cell interactions contribute to pathogenicity in natural, complex environments will require a new level of control in constructing more relevant cellular models for assessing bacterial phenotypes. Here, we describe a microscopic three-dimensional (3D) printing strategy that enables multiple populations of bacteria to be organized within essentially any 3D geometry, including adjacent, nested, and free-floating colonies. In this laser-based lithographic technique, microscopic containers are formed around selected bacteria suspended in gelatin via focal cross-linking of polypeptide molecules. After excess reagent is removed, trapped bacteria are localized within sealed cavities formed by the cross-linked gelatin, a highly porous material that supports rapid growth of fully enclosed cellular populations and readily transmits numerous biologically active species, including polypeptides, antibiotics, and quorum-sensing signals. Using this approach, we show that a picoliter-volume aggregate of Staphylococcus aureus can display substantial resistance to β-lactam antibiotics by enclosure within a shell composed of Pseudomonas aeruginosa.