Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome‐wide differentiation in closely related populations: the roles of selection and geographic isolation

Population divergence in geographic isolation is due to a combination of factors. Natural and sexual selection may be important in shaping patterns of population differentiation, a pattern referred to as ‘isolation by adaptation’ (IBA). IBA can be complementary to the well‐known pattern of ‘isolation by distance’ (IBD), in which the divergence of closely related populations (via any evolutionary process) is associated with geographic isolation. The barn swallow Hirundo rustica complex comprises six closely related subspecies, where divergent sexual selection is associated with phenotypic differentiation among allopatric populations. To investigate the relative contributions of selection and geographic distance to genome‐wide differentiation, we compared genotypic and phenotypic variation from 350 barn swallows sampled across eight populations (28 pairwise comparisons) from four different subspecies. We report a draft whole‐genome sequence for H. rustica, to which we aligned a set of 9493 single nucleotide polymorphisms (SNPs). Using statistical approaches to control for spatial autocorrelation of phenotypic variables and geographic distance, we find that divergence in traits related to migratory behaviour and sexual signalling, as well as geographic distance, together explain over 70% of genome‐wide divergence among populations. Controlling for IBD, we find 42% of genomewide divergence is attributable to IBA through pairwise differences in traits related to migratory behaviour and sexual signalling alone. By (i) combining these results with prior studies of how selection shapes morphological differentiation and (ii) accounting for spatial autocorrelation, we infer that morphological adaptation plays a large role in shaping population‐level differentiation in this group of closely related populations.
Break point of serum creatine kinase release after endurance exercise.

We investigated whether there is a break point of creatine kinase (CK) release after daily endurance exercise and whether CK response depends on individual physical characteristics. Fifteen healthy young men performed 90 min of bicycle exercise for 3 consecutive days. Body composition, properties of the quadriceps femoris muscle (QFM), and aerobic and anaerobic capacities were estimated before the test. Blood samples were obtained 22 times during the experimental period. Endurance exercise significantly elevated serum CK from 3 h after the first exercise session (P < 0.05) and gradually increased thereafter. Subjects were classified into two groups according to their peak CK values: high responders (HR; >500 IU/l of CK) and low responders (LR; <300 IU/l of CK). Peak CK values during the experimental period correlated (P < 0.01) with workload/cross-sectional area of the QFM (r = 0.658), workload/volume of the QFM (r = 0.648), and knee extensor strength/body mass (r = -0.634); however, the HR and LR groups were separated in each variable. Thus the break point of CK release after endurance exercise under these conditions is 300-500 IU/l, two or three times higher than in the resting condition, and is associated with properties of the QFM.
How Bureaucratic Writing Style Affects Source Credibility

This study examines whether bureaucratic writing style affects readers' perception of source credibility. The experiment required 172 college students to read bureaucratic and simple writing and to rate their impressions of the author and the writing quality. Results indicate that the subjects rated the author of the bureaucratic style higher in expertise, but not significantly different from the author of the simple style in trustworthiness and open-mindedness. Source occupational status was not a necessary condition for the perceived differences in credibility. The differences in expertise ratings were significantly greater for readers with more years of schooling. However, the subjects consistently preferred the simple to the bureaucratic writing.
Chicken and Duck Myotubes Are Highly Susceptible and Permissive to Influenza Virus Infection

ABSTRACT Skeletal muscle, at 30 to 40% of body mass, is the most abundant soft tissue in the body. Besides its primary function in movement and posture, skeletal muscle is a significant innate immune organ with the capacity to produce cytokines and chemokines and respond to proinflammatory cytokines. Little is known about the role of skeletal muscle during systemic influenza A virus infection in any host and particularly avian species. Here we used primary chicken and duck multinucleated myotubes to examine their susceptibility and innate immune response to influenza virus infections. Both chicken and duck myotubes expressed avian and human sialic acid receptors and were readily susceptible to low-pathogenicity (H2N3 A/mallard duck/England/7277/06) and high-pathogenicity (H5N1 A/turkey/England/50-92/91 and H5N1 A/turkey/Turkey/1/05) avian and human H1N1 (A/USSR/77) influenza viruses. Both avian host species produced comparable levels of progeny H5N1 A/turkey/Turkey/1/05 virus. Notably, the rapid accumulation of viral nucleoprotein and matrix (M) gene RNA in chicken and duck myotubes was accompanied by extensive cytopathic damage with marked myotube apoptosis (widespread microscopic blebs, caspase 3/7 activation, and annexin V binding at the plasma membrane). Infected chicken myotubes produced significantly higher levels of proinflammatory cytokines than did the corresponding duck cells. Additionally, in chicken myotubes infected with H5N1 viruses, the induction of interferon beta (IFN-β) and IFN-inducible genes, including the melanoma differentiation-associated protein 5 (MDA-5) gene, was relatively weak compared to infection with the corresponding H2N3 virus. Our findings highlight that avian skeletal muscle fibers are capable of productive influenza virus replication and are a potential tissue source of infection. IMPORTANCE Infection with high-pathogenicity H5N1 viruses in ducks is often asymptomatic, and skeletal muscle from such birds could be a source of infection of humans and animals. Little is known about the ability of influenza A viruses to replicate in avian skeletal muscle fibers. We show here that cultured chicken and duck myotubes were highly susceptible to infection with both low- and high-pathogenicity avian influenza viruses. Infected myotubes of both avian species displayed rapid virus accumulation, apoptosis, and extensive cellular damage. Our results indicate that avian skeletal muscle fibers of chicken and duck could be significant contributors to progeny production of highly pathogenic H5N1 viruses.
A NEW LOOK AT AN OLD ISSUE

In 1997, the Office of Child Support Enforcement initiated the State Child Access and Visitation (AV) Grant Program, which involves annual awards of $10 million to states to promote the development of programs to alleviate access problems. Telephone interviews with 970 parents who used mediation, parent education, and supervised visitation programs funded by AV grants in nine states revealed that the programs are reaching diverse groups of parents including many low-income, non-White, and unmarried parents who receive no other type of access assistance. The programs also appear to be achieving the major objectives posited for them by the federal government. One-third to one-half of noncustodial parents in every program type reported that parent–child contact increased following program participation, with supervised visitation users who typically had the lowest levels of parent–child contact reporting a significant increase in the number of days of contact. A review of child support records for 173 program users in three states revealed that child support payments increased among participants following program participation, especially for never-married parents who paid a significantly higher proportion of what they owed. These findings are similar to results reported in a five-state study of mediation programs funded by AV grants that was conducted by the Office of the Inspector General. However, both studies have some serious limitations, including low response rates and the absence of a nontreatment comparison group.
The Association Between Irregular Menstruations and Acne With Asthma and Atopy Phenotypes

Earlier menarche and irregular periods, among other markers of sex-hormone levels, have been associated with a higher risk of asthma and allergic diseases. This has suggested an etiologic role of sex hormones in the development of these conditions. The authors investigated the association of age at menarche, irregular periods, duration of menstruation, and acne with reported medical history of asthma and/or atopy (hay fever and/or eczema/urticaria) in a historical cohort of students born before the rise in asthma prevalence in the United Kingdom and attending university in 1948–1968. Finding consistent associations in a cohort that has experienced different life-course exposures and has different confounding structure can help to identify causal associations. In the Glasgow Alumni Cohort, irregular periods were associated with atopic asthma (multinomial odds ratio (MOR) = 2.79, 95% confidence interval (CI): 1.33, 5.83) and atopy alone (MOR = 1.40, 95% CI: 1.06, 1.84) but not with nonatopic asthma (MOR = 1.02, 95% CI: 0.45, 2.30), compared with students reporting no asthma and no atopy. The authors found no association with acne, a marker of high testosterone levels, that they hypothesized could point to polycystic ovary syndrome underpinning these associations. In summary, the authors found evidence for a potentially etiologic role of irregular menstruations with some specific asthma phenotypes, namely, atopic asthma and atopy, but not with nonatopic asthma.
A sea urchin homologue of the chordate Brachyury (T) gene is expressed in the secondary mesenchyme founder cells.

Chordates are thought to have emerged from some common ancestor of deuterostomes by organizing shared anatomical and embryological features including a notochord, a dorsal nerve cord and pharyngeal gill slits. Because the notochord is the most prominent feature of chordates and because the Brachyury (T) gene is essential for notochord formation, the T gene is a key molecular probe with which to explore the origin and evolution of chordates. We investigated whether the sea urchin (echinoderm) conserves the T gene and, if so, where the sea urchin T gene is expressed. A cDNA clone for the sea urchin T (HpTa) gene contained a long open reading frame that encodes a polypeptide of 434 amino acids. Although the overall degree of amino acid identity was not very high (52%, sea urchin/mouse), in the T domain of the N terminus the amino acid identity was 73% (sea urchin/mouse). The HpTa gene is present as a single copy per haploid genome. As with the chordate T gene, the expression of HpTa is transient, being first detected in the swimming blastula, maximally transcribed in the gastrula, decreasing at the prism larval stage and barely detectable at the pluteus larval stage. HpTa transcripts were found in the secondary mesenchyme founder cells, vegetal plate of the mesenchyme blastula, extending tip of the invaginating archenteron and, finally, the secondary mesenchyme cells at the late-gastrula stage. (ABSTRACT TRUNCATED AT 250 WORDS)
CLIQUE: Role-Free Clustering with Q-Learning for Wireless Sensor Networks

Clustering and aggregation inherently increase wireless sensor network (WSN) lifetime by collecting information within a cluster at a cluster head, reducing the amount of data through computation, then forwarding it. Traditional approaches, however, both spend extensive communication energy to identify the cluster heads and are inflexible to network dynamics such as those arising from sink mobility, node failure, or dwindling battery reserves. This paper presents Clique, an approach for data clustering that saves cluster head selection energy by using machine learning to enable nodes to independently decide whether or not to act as a cluster head on a per-packet basis. We refer to this lack of actual cluster head assignment as being role-free, and demonstrate through simulations that, when combined with learning dynamic network properties such as battery reserves, up to 25% less energy is consumed in comparison to a traditional, random cluster head selection approach.
Unwinding the "hairball" graph: a pruning algorithm for weighted complex networks

Empirical networks of weighted dyadic relations often contain "noisy" edges that alter the global characteristics of the network and obfuscate the most important structures therein. Graph pruning is the process of identifying the most significant edges according to a generative null model and extracting the subgraph consisting of those edges. Here, we focus on integer-weighted graphs commonly arising when weights count the occurrences of an "event" relating the nodes. We introduce a simple and intuitive null model related to the configuration model of network generation and derive two significance filters from it: the marginal likelihood filter (MLF) and the global likelihood filter (GLF). The former is a fast algorithm assigning a significance score to each edge based on the marginal distribution of edge weights, whereas the latter is an ensemble approach which takes into account the correlations among edges. We apply these filters to the network of air traffic volume between US airports and recover a geographically faithful representation of the graph. Furthermore, compared with thresholding based on edge weight, we show that our filters extract a larger and significantly sparser giant component.
Arabinogalactan Proteins From Baobab and Acacia Seeds Influence Innate Immunity of Human Keratinocytes In Vitro

Plant derived arabinogalactan proteins (AGP) were repeatedly confirmed as immunologically as well as dermatologically active compounds. However, little is currently known regarding their potential activity toward skin innate immunity. Here, we extracted and purified AGP from acacia (Acacia senegal) and baobab (Adansonia digitata) seeds to investigate their biological effects on the HaCaT keratinocyte cell line in an in vitro system. While AGP from both sources did not exhibit any cytotoxic effect, AGP from acacia seeds enhanced cell viability. Moreover, real‐time quantitative reverse transcription‐polymerase chain reaction (qRT‐PCR) analysis showed that AGP extracted from both species induced a substantial overexpression of hBD‐2, TLR‐5, and IL1‐α genes. These data suggest that plant AGP, already known to control plant defensive processes, could also modulate skin innate immune responses. J. Cell. Physiol. 232: 2558–2568, 2017. © 2016 Wiley Periodicals, Inc.
SCMDOT: Spatial Clustering with Multiple Density-Ordered Trees

With the rapid explosion of information based on location, spatial clustering plays an increasingly significant role in this day and age as an important technique in geographical data analysis. Most existing spatial clustering algorithms are limited by complicated spatial patterns, which have difficulty in discovering clusters with arbitrary shapes and uneven density. In order to overcome such limitations, we propose a novel clustering method called Spatial Clustering with Multiple Density-Ordered Trees (SCMDOT). Motivated by the idea of the Density-Ordered Tree (DOT), we firstly represent the original dataset by the means of constructing Multiple Density-Ordered Trees (MDOT). In the constructing process, we impose additional constraints to control the growth of each Density-Ordered Tree, ensuring that they all have high spatial similarity. Furthermore, a series of MDOT can be successively generated from regions of sparse areas to the dense areas, where each Density-Ordered Tree, also treated as a sub-tree, represents a cluster. In the merging process, the final clusters are obtained by repeatedly merging a suitable pair of clusters until they satisfy the expected clustering result. In addition, a heuristic strategy is applied during the process of our algorithm for suitability for special applications. The experiments on synthetic and real-world spatial databases are utilised to demonstrate the performance of our proposed method.
Connecting Terror Management and Dissonance Theory: Evidence that Mortality Salience Increases the Preference for Supporting Information after Decisions

From the perspective of terror management theory, reminders of mortality should intensify the desire to pursue cognitive consistency. The authors investigated this notion with regard to dissonance theory starting from the finding of research on “selective exposure to information” that after having made a decision, people prefer consonant over dissonant information. The authors found that following mortality salience, people indeed showed an increased preference for information that supported their decision compared to information conflicting with it. However, this only occurred with regard to a worldview-relevant decision case. For a fictitious decision scenario, mortality salience did not affect information seeking. Practical and theoretical implications are discussed.
INTEGRATED INFORMATION RETRIEVAL : THE ENTREZ SYSTEM

As discussed earlier in this book, GenBank was created in response to the explosion in sequence information resulting from a panoply of scientific efforts such as the Human Genome Project. To review, GenBank is an annotated collection of all publicly available DNA and protein sequences and is maintained by the National Center for Biotechnology Information (NCBI). As of this writing, GenBank contains 7 million sequence records covering almost 9 billion nucleotide bases. Sequences find their way into GenBank in several ways, most often by direct submission by individual investigators through tools such as Sequin or through ‘‘direct deposit’’ by large genome sequencing centers. GenBank, or any other biological database for that matter, serves little purpose unless the database can be easily searched and entries retrieved in a usable, meaningful format. Otherwise, sequencing efforts have no useful end, since the biological community as a whole cannot make use of the information hidden within these millions of bases and amino acids. Much effort has gone into making such data accessible to the average user, and the programs and interfaces resulting from these efforts are the focus of this chapter. The discussion centers on querying the NCBI databases because these more ‘‘general’’ repositories are far and away the ones most often accessed by biologists, but attention is also given to a number of smaller, specialized databases that provide information not necessarily found in GenBank.
Simple Latex Agglutination Assay for Rapid Serodiagnosis of Human Leptospirosis

ABSTRACT A newly developed latex agglutination assay for the detection of genus-specific Leptospira antibodies in human sera was evaluated. The assay is performed by mixing, on an agglutination card, serum with equal volumes of stabilized antigen-coated, dyed test and control latex beads and is read within 2 min. The latex agglutination test was evaluated with groups of serum samples from patients with leptospirosis and control patients from Hawaii, the Seychelles, Thailand, and The Netherlands. The mean overall sensitivity was 82.3%, and the mean overall specificity was 94.6%. The assay is easy to perform and does not require special skills or equipment. The reagents have a long shelf life, even at tropical temperatures. Together, these factors make the assay suitable for use even at the peripheral level of a health care system as a rapid screening test for leptospirosis.
Revolving Doors?

This article analyzes the movement of personnel among elite positions in business and government, contrasting the staffing patterns at higher rungs of the executive branch during the Clinton and G. W. Bush administrations. We find that the Bush administration recruited far more heavily from among corporate officers and directors than did the Clinton administration, particularly when staffing ambassadorships. We also find that both administrations served as springboards for subsequent corporate board appointments. There were relatively few patterns with respect to industry or geography, with the exception of the military: All but one of the Joint Chiefs of Staff at the turn of the millennium ended up serving on the board of a military contractor after completing their government service.
Optic perineuritis: clinical and radiographic features.

BACKGROUND Optic perineuritis is an uncommon variety of orbital inflammatory disease that is distinct from demyelinating optic neuritis. OBJECTIVE To describe the clinical and radiographic features of idiopathic optic perineuritis, with particular emphasis on those features that help to distinguish this condition from optic neuritis. METHODS We reviewed the medical records of 14 patients with optic perineuritis who were seen in 2 neuro-ophthalmology clinics. RESULTS Patients ranged in age from 24 to 60 years; 5 were older than 50 years. All patients had visual loss, eye pain, or both. The visual acuity was 20/20 or better in 8 of the 15 eyes. The results of visual field testing were normal in 2 eyes, and a paracentral scotoma or an arcuate defect was seen in 7. Magnetic resonance imaging scans demonstrated circumferential enhancement around the optic nerve, sometimes with intraorbital extension. Response to corticosteroids was dramatic; however, 4 patients had a relapse with lowering of the dose. CONCLUSIONS In contrast to those with optic neuritis, patients with optic perineuritis are often older at onset and are more likely to show sparing of central vision. Magnetic resonance imaging scans demonstrate enhancement around, rather than within, the optic nerve. Response to corticosteroids is more dramatic than in patients with optic neuritis, and patients are more likely to experience recurrence after stopping treatment.
Epidermal growth factor responsiveness of a new human neuroblastoma cell line

A human neuroblastoma cell line, CA‐2E, has been established from a bone‐marrow aspirate of a 16‐month‐old boy with progressive disease. The karyotype and antigen pheno‐type of the cells correspond to those of a neuroblastoma. This cell line grows well in liquid cultures supplemented with 5% fetal calf serum; conversely, colony formation in semi‐solid medium by cells from early passages is dependent upon exogenous EGF. With time in continuous culture, the cloning efficiency in the absence of EGF increases, but the line remains sensitive to EGF, as evidenced by an enhancement of the number and size of colonies. A relative dependence upon EGF in liquid cultures has also been clearly demonstrated by limiting the concentration of serum. Long‐term (over 2 weeks) treatment with EGF results in a decreased rate of proliferation, a decreased proportion of clonogenic cells, and the appearance of flat, epithelial‐type cells. In some experiments, EGF also has a remarkable effect in inducing neurite outgrowth and process branching. Our results suggest that EGF may have both proliferation‐ and differentiation‐inducing effects on this neuroblastoma cell line. We have also shown that EGF induces increased proliferation in 7 out of 8 other human neuroblastoma cell lines. Functional response of neuroblastoma cells to EGF appears to be a general phenomenon which may be related to a block in the normal maturation pathway of the neural crest cells from which this tumor originates.