Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and high genetic diversity in dwarf mountain toads (Capensibufo) from South Africa

Traditional models of amphibian dispersal and gene flow point to low dispersal and high philopatry. In recent years, this traditional view has been challenged and it appears that no general model holds across taxa. Conservation of amphibians cannot be addressed on an over-arching scale, but must come on a case-by-case basis, especially for range-restricted species where information on gene flow and migration must be incorporated into conservation efforts. The only two members of the genus Capensibufo Grandison, 1980 (Anura: Bufonidae) are range restricted small bufonids, with distributions limited to montane areas in South Africa. Using a Bayesian analysis of two mitochondrial markers (16S and ND2), we examined the genetic patterns in Capensibufo rosei and Capensibufo tradouwi in order to understand both taxonomic and geographic boundaries. These species were not monophyletic, and demonstrate no clear taxonomic boundaries. Instead, the genus is extremely diverse genetically, with distinct lineages confined to isolated mountains that represent geographic boundaries. In addition, bioclimatic modelling using MAXENT and scenarios of climatic conditions at both the present and last glacial maximum suggest multiple bioclimatic and physical barriers to gene flow at present and in the past. We conclude that members of the genus have very low vagility, that current taxonomic boundaries are inadequate, and that strong geographic structuring has undoubtedly contributed to genetic diversity at the species level, rather than the population level. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 822–834.
Non-Informative Effects of Stimuli Functioning as Cues

The category of a first stimulus (S1) serving as a cue may allow a subject to predict the category of a second stimulus (S2). However, a cue may have effects on RT to S2 that are independent of those derived from its intended role as a predictor. These non-informative effects of a cue may add to or subtract from the benefits associated with its predictive function. Two experiments demonstrate that when S1 is in the same category as S2 (as is frequently the case for valid cues in cueing experiments) but provides no information about S2, RT is slower than when S1 is in a different category from S2. It is suggested that this category relation effect arises because inhibition of a response to S1 is still present when S2 arrives and that, in some cueing experiments, it may subtract from the RT benefits derived from the cue as a predictor of S2. Also, RT to a visual but not to an auditory S2 was faster after an auditory S1 than after a visual S1. It is argued that this modality combination effect is consistent with the view that auditory signals are more alerting than visual ones and that this is another factor to be taken into account in the design of cueing and other experiments.
Who does not get screened? A simple model of the complex relationships in mammogram non-attendance

With increasing mammogram rates, identifying attributes of non-attending women entails going beyond differences in demographic groups to reveal complex interactions among personality attributes. In this study, we analyzed survey data from 474 women aged 41 years and older using decision trees. By incorporating personality, religiousness, and age, we were able to correctly classify 42.9 percent of non-attenders compared to 4.4 percent with logistic regression analysis. Our findings suggest that incorporating personality and religiousness attributes may increase non-attender identification. Furthermore, the simple profile generated by decision trees provides a clear map useful for intervention planning.
Moving experiences: Understanding television's influences and effects

The possible effect of television on its viewers has been a source of controversy for decades. Over the years, the flickering box has been blamed for every kind of social problem and antisocial act, and in many cases has been found guilty by an audacious but often surprisingly shaky range of studies. The hypothesis that television makes people mad, bad, or otherwise dangerous to know, has been tested in multifarious ways, whilst researchers have also investigated whether television might actually do viewers good.
Vitamin D Deficiency Promotes Skeletal Muscle Hypersensitivity and Sensory Hyperinnervation

Musculoskeletal pain affects nearly half of all adults, most of whom are vitamin D deficient. Previous findings demonstrated that putative nociceptors (“pain-sensing” nerves) express vitamin D receptors (VDRs), suggesting responsiveness to 1,25-dihydroxyvitamin D. In the present study, rats receiving vitamin D-deficient diets for 2–4 weeks showed mechanical deep muscle hypersensitivity, but not cutaneous hypersensitivity. Muscle hypersensitivity was accompanied by balance deficits and occurred before onset of overt muscle or bone pathology. Hypersensitivity was not due to hypocalcemia and was actually accelerated by increased dietary calcium. Morphometry of skeletal muscle innervation showed increased numbers of presumptive nociceptor axons (peripherin-positive axons containing calcitonin gene-related peptide), without changes in sympathetic or skeletal muscle motor innervation. Similarly, there was no change in epidermal innervation. In culture, sensory neurons displayed enriched VDR expression in growth cones, and sprouting was regulated by VDR-mediated rapid response signaling pathways, while sympathetic outgrowth was not affected by different concentrations of 1,25-dihydroxyvitamin D. These findings indicate that vitamin D deficiency can lead to selective alterations in target innervation, resulting in presumptive nociceptor hyperinnervation of skeletal muscle, which in turn is likely to contribute to muscular hypersensitivity and pain.
Men are from Mars, Women are from Venus: An Analysis of a Potential Meme

The purpose of this study was to discover whether the phrase "men are from Mars, women are from Venus, " from John Gray's book, had become a meme and to explore what its usage implied. Analysis of 510 references was guided by grounded theory. Coding over a decade of newspaper usage of the phrase into seven emergent themes allowed examination of usage against the theories of gender research, communication research, media research and meme theory research. This analysis revealed that this phrase meets the requirements to be considered a meme, and as a meme it has successfully assisted the survival, evolution and permeance of Gray's premise that communication differences are inherent and immutable. While this premise is not based on established clinical and academic principles, it is an example of how incorrect and baseless ideas can displace good reasoned thinking based on research. iv DEDICATION To Patrick, for his boundless support on this " 2-year " journey. To Paul and Will, for doing their own laundry. To Nelson and Mary, for never saying, " You can't do that. " v ACKNOWLEDGMENTS
Phylogenetic relationships inferred from ribosomal its sequences and biogeographic patterns in representatives of the genus Calopteryx (Insecta: Odonata) of the West Mediterranean and adjacent West European zone.

Western Europe is a reinvasion zone for the riverine dragonfly genus Calopteryx (Insecta: Odonata). Reinvasion may have been from central West Asia or from the West Mediterranean refugium. Phylogenetic relationships of West Mediterranean and West European taxa of the genus Calopteryx from different localities were inferred from sequences of the internal transcribed spacers (ITS1 and ITS2) of the nuclear ribosomal RNA genes. Twenty-six taxa belonging to the species groups C. splendens, C. meridionalis, C. haemorrhoidalis, C. virgo, C. xanthostoma, and C. exul were analyzed, with two North American species, C. amata and C. aequabilis, as outgroup. Sequence data and phylogenetic analyses were used to infer biogeographical patterns. The ribosomal spacers (ITS1 and ITS2) and the intervening 5.8S rDNA gene were amplified by PCR and sequenced. The ITS2 sequences of the West Mediterranean and West European calopterygids show no length variation but the ITS1 region was slightly variable in length. The sequence variation for ITS1 and ITS2 regions between different West Mediterranean and West European calopterygids was 14.5 and 6.1%, respectively. Phylogenetic relationships inferred from ITS sequences only partly confirm morphological data. A monophyletic origin of all West Mediterranean and West European species emerged. They are separated into two main clades; the splendens-like forms and the virgo/meridionalis/haemorrhoidalis group. Intraspecific variability, indicating different stages of speciation, was detected only in West Mediterranean representatives (e.g., C. xanthostoma) but not in invasive representatives in West Europe. The North African endemic C. exul is more closely related to the Italian C. s. caprai than to C. splendens sensu strictu. Based on the present information, Cretan populations are the only splendens-like taxa in addition to C. s. caprai that deserve subspecies status.
Intra- and interbrain synchronization and network properties when playing guitar in duets

To further test and explore the hypothesis that synchronous oscillatory brain activity supports interpersonally coordinated behavior during dyadic music performance, we simultaneously recorded the electroencephalogram (EEG) from the brains of each of 12 guitar duets repeatedly playing a modified Rondo in two voices by C.G. Scheidler. Indicators of phase locking and of within-brain and between-brain phase coherence were obtained from complex time-frequency signals based on the Gabor transform. Analyses were restricted to the delta (1–4 Hz) and theta (4–8 Hz) frequency bands. We found that phase locking as well as within-brain and between-brain phase-coherence connection strengths were enhanced at frontal and central electrodes during periods that put particularly high demands on musical coordination. Phase locking was modulated in relation to the experimentally assigned musical roles of leader and follower, corroborating the functional significance of synchronous oscillations in dyadic music performance. Graph theory analyses revealed within-brain and hyperbrain networks with small-worldness properties that were enhanced during musical coordination periods, and community structures encompassing electrodes from both brains (hyperbrain modules). We conclude that brain mechanisms indexed by phase locking, phase coherence, and structural properties of within-brain and hyperbrain networks support interpersonal action coordination (IAC).
75 Kiloparsec Trails of Ionized Gas behind Two Irregular Galaxies in A1367

In a 6 hr Hα exposure of the northwest region of the cluster of galaxies A1367, we discovered a 75 kpc cometary emission of ionized gas trailing behind two Irr galaxies. The Hα trails correspond in position and length with tails of syncrotron radiation. At the galaxy side opposite to the tails, the two galaxies show bright H II regions aligned along arcs, where the star formation takes place at the prodigious rate of ∼1 M⊙ yr-1. From the morphology of the galaxies and of the trailing material, we infer that the two galaxies are suffering from ram pressure due to their high-velocity motion through the cluster intergalactic medium. We estimate that ∼109 M⊙ of gas, probably ionized in the giant H II regions, is swept out, forming the tails. The tails cross each other at some 100 kpc from the present galaxy location, indicating that a major tidal event occurred some ∼5 × 107 yr ago. We exclude that mutual harassment produced the observed morphology, and we show with numerical simulations that it could have marginally aided ram pressure stripping by loosening the potential well of the galaxies.
Salt-stress-induced ABA accumulation is more sensitively triggered in roots than in shoots.

Salt-stress-induced ABA accumulation in maize root tissues was compared with that in leaf tissues. While salt stress with NaCl resulted in a significant ABA accumulation in root tissues (up to 10-fold), the same stress only led to a small ABA accumulation in leaf tissues (about 1-fold). Pretreatment with ethylene glycol (EG), a permeable and inert monomer of PEG, could prevent the shrinkage of cell volume and completely block the ABA accumulation in leaf tissues under salt stress, but substantial salt-induced ABA accumulation was still observed in root tissues following such pretreatment. Hypotonic salt solutions, i.e. below 100 mM NaCl, still induced a significant ABA accumulation (more than 3-fold) in roots, but showed no effect on that in leaf tissues. Results suggest that the salt-stress-induced ABA accumulation in roots may also be triggered by an osmosensing mechanism, which is in addition to the perception of the changes in reduced cellular volume or plasmalemma tension that leads to ABA accumulation in leaves. When leaf and root tissues were immersed into salt solutions, salt entered into the cells as a function of time and salt concentrations. Such entrance apparently led to a loss of sensitivity of leaf tissues to accumulate ABA under the salt stress, and also prevented the leaf tissues from responding to further air-drying in terms of ABA accumulation. Roots showed no such responses. Results suggest that the entrance of salt into leaf cells brought about some toxic effect that might have reduced the capability of leaf cells to produce ABA under dehydration.
ASAGA: Asynchronous Parallel SAGA

We describe ASAGA, an asynchronous parallel version of the incremental gradient algorithm SAGA that enjoys fast linear convergence rates. Through a novel perspective, we revisit and clarify a subtle but important technical issue present in a large fraction of the recent convergence rate proofs for asynchronous parallel optimization algorithms, and propose a simplification of the recently introduced "perturbed iterate" framework that resolves it. We thereby prove that ASAGA can obtain a theoretical linear speedup on multi-core systems even without sparsity assumptions. We present results of an implementation on a 40-core architecture illustrating the practical speedup as well as the hardware overhead.
Body mass index in relation to oesophageal and oesophagogastric junction adenocarcinomas: a pooled analysis from the International BEACON Consortium

Background Previous studies suggest an association between obesity and oesophageal (OA) and oesophagogastric junction adenocarcinomas (OGJA). However, these studies have been limited in their ability to assess whether the effects of obesity vary by gender or by the presence of gastro-oesophageal reflux (GERD) symptoms. Methods Individual participant data from 12 epidemiological studies (8 North American, 3 European and 1 Australian) comprising 1997 OA cases, 1900 OGJA cases and 11 159 control subjects were pooled. Logistic regression was used to estimate study-specific odds ratios (ORs) and 95% confidence intervals (CIs) for the association between body mass index (BMI, kg/m2) and the risk of OA and OGJA. Random-effects meta-analysis was used to combine these ORs. We also investigated effect modification and synergistic interaction of BMI with GERD symptoms and gender. Results The association of OA and OGJA increased directly with increasing BMI (P for trend <0.001). Compared with individuals with a BMI <25, BMI ≥40 was associated with both OA (OR 4.76, 95% CI 2.96–7.66) and OGJA (OR 3.07, 95% CI 1.89–4.99). These associations were similar when stratified by gender and GERD symptoms. There was evidence for synergistic interaction between BMI and GERD symptoms in relation to OA/OGJA risk. Conclusions These data indicate that BMI is directly associated with OA and OGJA risk in both men and women and in those with and without GERD symptoms. Disentangling the relationship between BMI and GERD will be important for understanding preventive efforts for OA and OGJA.
Global scale climate–crop yield relationships and the impacts of recent warming

Changes in the global production of major crops are important drivers of food prices, food security and land use decisions. Average global yields for these commodities are determined by the performance of crops in millions of fields distributed across a range of management, soil and climate regimes. Despite the complexity of global food supply, here we show that simple measures of growing season temperatures and precipitation—spatial averages based on the locations of each crop—explain ∼30% or more of year-to-year variations in global average yields for the world’s six most widely grown crops. For wheat, maize and barley, there is a clearly negative response of global yields to increased temperatures. Based on these sensitivities and observed climate trends, we estimate that warming since 1981 has resulted in annual combined losses of these three crops representing roughly 40 Mt or $5 billion per year, as of 2002. While these impacts are small relative to the technological yield gains over the same period, the results demonstrate already occurring negative impacts of climate trends on crop yields at the global scale.
Unique geometry of sister kinetochores in human oocytes during meiosis I may explain maternal age-associated increases in chromosomal abnormalities

ABSTRACT The first meiotic division in human oocytes is highly error-prone and contributes to the uniquely high incidence of aneuploidy observed in human pregnancies. A successful meiosis I (MI) division entails separation of homologous chromosome pairs and co-segregation of sister chromatids. For this to happen, sister kinetochores must form attachments to spindle kinetochore-fibres emanating from the same pole. In mouse and budding yeast, sister kinetochores remain closely associated with each other during MI, enabling them to act as a single unified structure. However, whether this arrangement also applies in human meiosis I oocytes was unclear. In this study, we perform high-resolution imaging of over 1900 kinetochores in human oocytes, to examine the geometry and architecture of the human meiotic kinetochore. We reveal that sister kinetochores in MI are not physically fused, and instead individual kinetochores within a pair are capable of forming independent attachments to spindle k-fibres. Notably, with increasing female age, the separation between kinetochores increases, suggesting a degradation of centromeric cohesion and/or changes in kinetochore architecture. Our data suggest that the differential arrangement of sister kinetochores and dual k-fibre attachments may explain the high proportion of unstable attachments that form in MI and thus indicate why human oocytes are prone to aneuploidy, particularly with increasing maternal age. Summary: Sister kinetochores in meiosis I human oocytes are not physically fused, with the degree of separation increasing with maternal age. This may have implications for the high incidence of aneuploidy in human oocytes.
Detailed Kinetics of the Direct Allo-Response in Human Liver Transplant Recipients: New Insights from an Optimized Assay

Conventional assays for quantification of allo-reactive T-cell precursor frequencies (PF) are relatively insensitive. We present a robust assay for quantification of PF of T-cells with direct donor-specificity, and establish the kinetics of circulating donor-specific T cells after liver transplantation (LTx). B cells from donor splenocytes were differentiated into professional antigen-presenting cells by CD40-engagement (CD40-B cells). CFSE-labelled PBMC from LTx-recipients obtained before and at several time points after LTx, were stimulated with donor-derived or 3rd party CD40-B cells. PF of donor-specific T cells were calculated from CFSE-dilution patterns, and intracellular IFN-γ was determined after re-stimulation with CD40-B cells. Compared to splenocytes, stimulations with CD40-B cells resulted in 3 to 5-fold higher responding T-cell PF. Memory and naïve T-cell subsets responded equally to allogeneic CD40-B cell stimulation. Donor-specific CD4+ and CD8+ T-cell PF ranged from 0.5 to 19% (median: 5.2%). One week after LTx, PF of circulating donor-specific CD4+ and CD8+ T cells increased significantly, while only a minor increase in numbers of T cells reacting to 3rd party allo-antigens was observed. One year after LTx numbers of CD4+ and CD8+ T cells reacting to donor antigens, as well as those reacting to 3rd party allo-antigens, were slightly lower compared to pre-transplant values. Moreover, CD4+ and CD8+ T cells responding to donor-derived, as well as those reacting to 3rd party CD40-B cells, produced less IFN-γ. In conclusion, our alternative approach enables detection of allo-reactive human T cells at high frequencies, and after application we conclude that donor-specific T-cell PF increase immediately after LTx. However, no evidence for a specific loss of circulating T-cells recognizing donor allo-antigens via the direct pathway up to 1 year after LTx was obtained, underscoring the relative insensitiveness of previous assays.
Scleral Cross-Linking Using Riboflavin UVA Irradiation for the Prevention of Myopia Progression in a Guinea Pig Model: Blocked Axial Extension and Altered Scleral Microstructure

Purpose To develop methods of collagen cross-linking (CXL) in the sclera for the treatment of progressive myopia and to investigate the biomechanical and histological changes that occur in as a result. Methods Twenty 14-day-old guinea pigs were divided into 3 groups: the cross-linking group (CL, n = 8), non cross-linking group (NCL, n = 8), and control group (n = 4). The scleras of the right eyes of the guinea pigs in the CL group were surgically exposed and riboflavin was dropped onto the irradiation zone for 20 seconds prior to ultraviolet-A (UVA) irradiation. The same procedure was conducted on the NCL group but without UVA irradiation. No procedure was conducted on the control group. The right eyes of the guinea pigs in the CL and NCL groups were then fitted with -10.00DS optics for six weeks. Retinoscopy and the axial lengths (AXL) were measured at baseline, and at the second, fourth and sixth weeks post-treatment in all three groups. All animal subjects were euthanized after the sixth week and then biomechanical and histopathological examinations of the scleras were conducted. Results The mean AXL of the NCL group was longer than both the control and CL groups at six weeks (P = 0.001). The mean refractive error in the NCL group was statistically significantly more negative than both the control and the CL groups at six weeks (P = 0.001). The scleral collagen fiber arrangements of the CL and control groups were denser and more regularly distributed than the NCL group. Ultimate stress of the sclera was lowest in the NCL group, followed by the CL then the control group (P<0.05). Ultimate strain (%) of the sclera was lowest in the CL group followed by the NCL and then the control group (P<0.05). Conclusion Our study demonstrates that scleral CXL using riboflavin UVA irradiation effectively prevents the progression of myopia by increasing scleral biomechanical strength in a guinea pig model.