Miracle-dz/UniFAR-FTUs huggingface dataset:
A Conserved Carbon Starvation Response Underlies Bud Dormancy in Woody and Herbaceous Species

Plant shoot systems give rise to characteristic above-ground plant architectures. Shoots are formed from axillary meristems and buds, whose growth and development is modulated by systemic and local signals. These cues convey information about nutrient and water availability, light quality, sink/source organ activity and other variables that determine the timeliness and competence to maintain development of new shoots. This information is translated into a local response, in meristems and buds, of growth or quiescence. Although some key genes involved in the onset of bud latency have been identified, the gene regulatory networks (GRNs) controlled by these genes are not well defined. Moreover, it has not been determined whether bud dormancy induced by environmental cues, such as a low red-to-far-red light ratio, shares genetic mechanisms with bud latency induced by other causes, such as apical dominance or a short-day photoperiod. Furthermore, the evolution and conservation of these GRNs throughout angiosperms is not well established. We have reanalyzed public transcriptomic datasets that compare quiescent and active axillary buds of Arabidopsis, with datasets of axillary buds of the woody species Vitis vinifera (grapevine) and apical buds of Populus tremula x Populus alba (poplar) during the bud growth-to-dormancy transition. Our aim was to identify potentially common GRNs induced during the process that leads to bud para-, eco- and endodormancy. In Arabidopsis buds that are entering eco- or paradormancy, we have identified four induced interrelated GRNs that correspond to a carbon (C) starvation syndrome, typical of tissues undergoing low C supply. This response is also detectable in poplar and grapevine buds before and during the transition to dormancy. In all eukaryotes, C-limiting conditions are coupled to growth arrest and latency like that observed in dormant axillary buds. Bud dormancy might thus be partly a consequence of the underlying C starvation syndrome triggered by environmental and endogenous cues that anticipate or signal conditions unfavorable for sustained shoot growth.
Effects of social gaze on visual-spatial imagination

Previous research suggests that closing one’s eyes or averting one’s gaze from another person can benefit visual-spatial imagination by interrupting cognitive demands associated with face-to-face interaction (Markson and Paterson, 2009). The present study further investigated this influence of social gaze on adults’ visual-spatial imagination, using the matrix task (Kerr, 1987, 1993). Participants mentally kept track of a pathway through an imaginary 2-dimensional (2D) or 3-dimensional (3D) matrix. Concurrent with this task, participants either kept their eyes closed or maintained eye contact with another person, mutual gaze with a person whose eyes were obscured (by wearing dark glasses), or unreciprocated gaze toward the face of a person whose own gaze was averted or whose face was occluded (by placing a paper bag over her head). Performance on the 2D task was poorest in the eye contact condition, and did not differ between the other gaze conditions, which produced ceiling performance. However, the more difficult 3D task revealed clear effects of social gaze. Performance on the 3D task was poorest for eye contact, better for mutual gaze, and equally better still for the unreciprocated gaze and eye-closure conditions. The findings reveal the especially disruptive influence of eye contact on concurrent visual-spatial imagination and a benefit for cognitively demanding tasks of disengaging eye contact during face-to-face interaction.
Plasma selenium concentration and prostate cancer risk: results from the European Prospective Investigation into Cancer and Nutrition (EPIC).

BACKGROUND Some evidence indicates that a low selenium intake may be associated with an increased risk of prostate cancer. OBJECTIVE The aim of this study was to investigate the association of plasma selenium concentration with subsequent prostate cancer risk and to examine this association by stage and grade of disease and other factors. DESIGN A nested case-control study was performed among men in the European Prospective Investigation into Cancer and Nutrition (EPIC). The association between plasma selenium concentration and prostate cancer risk was assessed in 959 men with incident prostate cancer and 1059 matched controls. RESULTS Overall, plasma selenium concentration was not associated with prostate cancer risk; the multivariate relative risk for men in the highest fifth of selenium concentration compared with the lowest fifth was 0.96 (95% CI: 0.70, 1.31; P for trend = 0.25). There were no significant differences in the association of plasma selenium with risk when analyzed by stage or grade of disease. Similarly, the association of selenium with risk did not differ by smoking status or by plasma alpha- or gamma-tocopherol concentration. CONCLUSION Plasma selenium concentration was not associated with prostate cancer risk in this large cohort of European men.
Putative TetR Family Transcriptional Regulator SCO1712 Encodes an Antibiotic Downregulator in Streptomyces coelicolor

ABSTRACT A tetR family transcriptional regulatory gene (SCO1712) was identified as a global antibiotic regulatory gene from a Streptomyces interspecies DNA microarray analysis. SCO1712 disruption in Streptomyces coelicolor not only upregulated antibiotic biosynthesis through pathway-specific regulators when a previously identified pleiotropic downregulatory wblA was expressed but also further stimulated antibiotic production in a wblA deletion mutant, implying that SCO1712 might encode a novel antibiotic downregulator.
Chronic eosinophilic pneumonia after radiation therapy for breast cancer

The priming of bronchiolitis obliterans organising pneumonia by radiation therapy (RT) to the breast is now a well recognised syndrome. This study describes the occurrence of chronic eosinophilic pneumonia following RT after surgery for breast cancer in five female patients, with a mean age of 68 yrs (range 49–77). All patients had a history of asthma and/or allergy. At the onset of eosinophilic pneumonia, all patients were symptomatic. Chest radiograph showed pulmonary infiltrates, unilateral and limited to the irradiated lung in three patients, and bilateral in two. Pulmonary opacities were migratory in one patient. All patients had blood eosinophilia >1.0 109·L−1 and/or eosinophilia >40% at bronchoalveolar lavage differential cell count. The median time interval between the end of radiation therapy and the onset of eosinophilic pneumonia was 3.5 months (range 1–10). All patients rapidly improved with oral corticosteroids without sequelae. Relapse occurred in two patients after treatment withdrawal. Priming of alveolitis by radiation therapy to the breast might promote either bronchiolitis obliterans organising pneumonia or chronic eosinophilic pneumonia, with the latter depending on genetic or acquired characteristics of patients and/or further stimulation that may trigger a T‐helper cell type 2 form of lymphocyte response, especially in patients with asthma or other atopic manifestations.
To what extent will women accept HPV self-sampling for cervical cancer screening? A qualitative study conducted in Switzerland

Objectives Human papillomavirus self-sampling (self-HPV) is regarded as an alternative to Pap smear testing for women who do not participate in cervical cancer screening. This qualitative study aimed to determine women’s views on cervical cancer screening and the various obstacles to participation in screening, and to evaluate the perceived benefits and disadvantages of self-HPV. Method Twenty-four focus groups were conducted in 2012, with a total of 125 participants aged between 24 and 67 years. They were recruited through different channels, including flyers and posters, personal contacts, and an ongoing clinical trial focused on the unscreened population. Interview transcripts have been coded with the ATLAS.ti CAQDAS. Results Fifty-seven participants regularly attended screening and 68 had not been screened in the past 3 years. While some participants considered self-HPV as an acceptable screening method, others expressed concerns. Benefits included access, reduced costs, and time-saving. Disadvantages included the fear of not performing the test correctly, hurting oneself, and the accuracy of the test. Participants expressed concern that self-HPV would replace gynecological visits. Conclusion Self-HPV is not likely to rapidly or substantially modify women’s behaviors in regard to screening. While it may offer benefits in some specific situations, most women emphasized the advantages of regular gynecologist visits.
Endoscopic orbital decompression for dysthyroid eye disease

Abstract Orbital decompression for dysthyroid eye disease is traditionally performed either through an external approach or transantrally. The introduction of endoscopic sinus surgery over the last decade has led to a better understanding of the intranasal surgical landmarks of orbital walls and the development of endoscopic orbital decompression. We have adopted the endoscopic technique as the treatment of choice for orbital decompression in dysthyroid eye disease for the last two years. The surgical technique is described and illustrated, and the results of our first series of 15 patients (30 orbits) are presented.
Rapid Correction of Aimed Movements by Summation of Force-Field Primitives

Spinal circuits form building blocks for movement construction. In the frog, such building blocks have been described as isometric force fields. Microstimulation studies showed that individual force fields can be combined by vector summation. Summation and scaling of a few force-field types can, in theory, produce a large range of dynamic force-field structures associated with limb behaviors. We tested for the first time whether force-field summation underlies the construction of real limb behavior in the frog. We examined the organization of correction responses that circumvent path obstacles during hindlimb wiping trajectories. Correction responses were triggered on-line during wiping by cutaneous feedback signaling obstacle collision. The correction response activated a force field that summed with an ongoing sequence of force fields activated during wiping. Both impact force and time of impact within the wiping motor pattern scaled the evoked correction response amplitude. However, the duration of the correction response was constant and similar to the duration of other muscles activated in different phases of wiping. Thus, our results confirm that both force-field summation and scaling occur during real limb behavior, that force fields represent fixed-timing motor elements, and that these motor elements are combined in chains and in combination contingent on the interaction of feedback and central motor programs.
Low power 4-bit full adder cells in subthreshold regime

In this work, low power 4-bit adder cells based on subthreshold logic in nanometer CMOS technology is presented. Twelve different subthreshold 1-bit full adders are used for designing 4-bit adders in two different topologies. These topologies are Carry-Ripple and Carry Look-Ahead adders. To compare these adders, HSpice simulations in 65nm and 90nm standard CMOS technologies are used. Different performance parameters of the adder including power, delay, power-delay product and energy-delay product as a function of supply voltage, transistor sizing, frequency, technology, and temperature are investigated. The best adder with the smallest power and power-delay product and the highest achievable frequency is determined.
Risk of Stroke in Chronic Heart Failure Patients Without Atrial Fibrillation: Analysis of the Controlled Rosuvastatin in Multinational Trial Heart Failure (CORONA) and the Gruppo Italiano per lo Studio della Sopravvivenza nell’Insufficienza Cardiaca-Heart Failure (GISSI-HF) Trials

Background— Our aim was to describe the incidence and predictors of stroke in patients who have heart failure without atrial fibrillation (AF). Methods and Results— We pooled 2 contemporary heart failure trials, the Controlled Rosuvastatin in Multinational Trial Heart Failure (CORONA) and the Gruppo Italiano per lo Studio della Sopravvivenza nell’Insufficienza cardiaca-Heart Failure trial (GISSI-HF). Of the 9585 total patients, 6054 did not have AF. Stroke occurred in 165 patients (4.7%) with AF and in 206 patients (3.4%) without AF (rates 16.8/1000 patient-years and 11.1/1000 patient-years, respectively). Using Cox proportional-hazards models, we identified the following independent predictors of stroke in patients without AF (ranked by &khgr;2 value): age (hazard ratio, 1.34; 95% confidence interval, 1.18–1.63 per 10 years), New York Heart Association class (1.60, 1.21–2.12 class III/IV versus II), diabetes mellitus treated with insulin (1.87, 1.22–2.88), body mass index (0.74, 0.60–0.91 per 5 kg/m2 up to 30), and previous stroke (1.81, 1.19–2.74). N-terminal pro B-type natriuretic peptide (available in 2632 patients) was also an independent predictor of stroke (hazard ratio, 1.31; 1.11–1.57 per log unit) when added to this model. With the use of a risk score formulated from these predictors, we found that patients in the upper third of risk had a rate of stroke that approximated the risk in patients with AF. Conclusions— A small number of demographic and clinical variables identified a subset of patients who have heart failure without AF at a high risk of stroke.
The Bartonella henselae VirB/Bep system interferes with vascular endothelial growth factor (VEGF) signalling in human vascular endothelial cells

The vasculotropic pathogen Bartonella henselae (Bh) intimately interacts with human endothelial cells (ECs) and subverts multiple cellular functions. Here we report that Bh specifically interferes with vascular endothelial growth factor (VEGF) signalling in ECs. Bh infection abrogated VEGF‐induced proliferation and wound closure of EC monolayers as well as the capillary‐like sprouting of EC spheroids. On the molecular level, Bh infection did not alter VEGF receptor 2 (VEGFR2) expression or cell surface localization, but impeded VEGF‐stimulated phosphorylation of VEGFR2 at tyrosine1175. Consistently, we observed that Bh infection diminished downstream events of the tyrosine1175‐dependent VEGFR2‐signalling pathway leading to EC proliferation, i.e. phospholipase‐Cγ activation, cytosolic calcium fluxes and mitogen‐activated protein kinase ERK1/2 phosphorylation. Pervanadate treatment neutralized the inhibitory activity of Bh on VEGF signalling, suggesting that Bh infection may activate a phosphatase that alleviates VEGFR2 phosphorylation. Inhibition of VEGFR2 signalling by Bh infection was strictly dependent on a functional VirB type IV secretion system and thereby translocated Bep effector proteins. The data presented in this study underscore the role of the VirB/Bep system as important factor controlling EC proliferation in response to Bh infection; not only as previously reported by counter‐acting an intrinsic bacterial mitogenic stimulus, but also by restricting the exogenous angiogenic stimulation by Bh‐induced VEGF.
Effect of Therapeutic Inhibition of TNF on Circulating Endothelial Progenitor Cells in Patients with Rheumatoid Arthritis

Endothelial dysfunction has been detected in RA patients and seems to be reversed by control of inflammation. Low circulating endothelial progenitor cells (EPCs) have been described in many conditions associated with increased cardiovascular risk, including RA. The aim of this study was to investigate the effect of inhibition of TNF on EPCs in RA patients. Seventeen patients with moderate-severe RA and 12 sex and age-matched controls were evaluated. Endothelial biomarkers were tested at baseline and after 3 months. EPCs were identified from peripheral blood mononuclear cells by cytofluorimetry using anti-CD34 and anti-vascular endothelial growth factor-receptor 2. Asymmetric dimethylarginine (ADMA) was tested by ELISA and flow-mediated dilatation (FMD) by ultrasonography. Circulating EPCs were significantly lower in RA patients than in controls (P = 0.001). After 3 months EPCs increased significantly (P = 0.0006) while ADMA levels significantly decreased (P = 0.001). An inverse correlation between mean increase in EPCs number and mean decrease of DAS28 after treatment was observed (r = −0.56, P = 0.04). EPCs inversely correlated with ADMA (r = −0.41, P = 0.022). No improvement of FMD was detected. Short-term treatment with anti-TNF was able to increase circulating EPCs concurrently with a proportional decrease of disease activity suggesting that therapeutic intervention aimed at suppressing the inflammatory process might positively affect the endothelial function.
Unconstrained evolution in short introns? – An analysis of genome‐wide polymorphism and divergence data from Drosophila

An unconstrained reference sequence facilitates the detection of selection. In Drosophila, sequence variation in short introns seems to be least influenced by selection and dominated by mutation and drift. Here, we test this with genome‐wide sequences using an African population (Malawi) of D. melanogaster and data from the related outgroup species D. simulans, D. sechellia, D. erecta and D. yakuba. The distribution of mutations deviates from equilibrium, and the content of A and T (AT) nucleotides shows an excess of variance among introns. We explain this by a complex mutational pattern: a shift in mutational bias towards AT, leading to a slight nonequilibrium in base composition and context‐dependent mutation rates, with G or C (GC) sites mutating most frequently in AT‐rich introns. By comparing the corresponding allele frequency spectra of AT‐rich vs. GC‐rich introns, we can rule out the influence of directional selection or biased gene conversion on the mutational pattern. Compared with neutral equilibrium expectations, polymorphism spectra show an excess of low frequency and a paucity of intermediate frequency variants, irrespective of the direction of mutation. Combining the information from different outgroups with the polymorphism data and using a generalized linear model, we find evidence for shared ancestral polymorphism between D. melanogaster and D. simulans, D. sechellia, arguing against a bottleneck in D. melanogaster. Generally, we find that short introns can be used as a neutral reference on a genome‐wide level, if the spatially and temporally varying mutational pattern is accounted for.
CYP 3 A 4 and CYP 3 A 5 Genotypes , Haplotypes , and Risk of Prostate Cancer 1

Previous case-only studies have shown that men with the CYP3A4*1B promoter variant are at an increased risk of developing more aggressive forms of prostate cancer. However, no changes in CYP3A4 activity have been found in CYP3A4*1B carriers, suggesting that its association with disease may simply reflect linkage disequilibrium with another functional variant. CYP3A5 is located within 200 kb of CYP3A4, and a variant in CYP3A5 (*1/*3) correlates with function of the CYP3A5 enzyme. In this study, the potential effect of CYP3A4*1B and CYP3A5*1 on prostate cancer risk and aggressiveness were evaluated in a family-based case-control population. The CYP3A4*1B variant was positively associated with prostate cancer among Caucasians with more aggressive disease [odds ratio (OR), 1.91; 95% confidence interval (CI), 1.02–3.57; P 0.04], and inversely associated with risk among Caucasians with less aggressive disease (OR, 0.08; 95% CI, 0.01–0.49; P 0.006) and men with an age of diagnosis <63 (OR, 0.51; 95% CI, 0.26–1.00; P 0.05). The CYP3A5*1 variant was inversely associated with prostate cancer, especially among Caucasians with less aggressive disease (OR, 0.42; 95% CI, 0.22–0.78; P 0.006). As expected based on these genotype-level results, the CYP3A4*1B/CYP3A5*3 haplotype was positively associated with disease (OR, 2.91; 95% CI, 1.36–6.23; P 0.006), and the CYP3A4*1B/CYP3A5*1 haplotype was inversely associated with risk among Caucasians with less aggressive disease (OR, 0.07; 95% CI, 0.01–0.51; P 0.009). These findings suggest that the CYP3A4 and CYP3A5 variants, or other alleles on the haplotypes they help distinguish, are associated with prostate cancer risk and aggressiveness.
Co-occurrence of Point Mutations in the Voltage-Gated Sodium Channel of Pyrethroid-Resistant Aedes aegypti Populations in Myanmar

Background Single amino acid substitutions in the voltage-gated sodium channel associated with pyrethroid resistance constitute one of the main causative factors of knockdown resistance in insects. The kdr gene has been observed in several mosquito species; however, point mutations in the para gene of Aedes aegypti populations in Myanmar have not been fully characterized. The aim of the present study was to determine the types and frequencies of mutations in the para gene of Aedes aegypti collected from used tires in Yangon City, Myanmar. Methodology/Principal Findings We determined high pyrethroid resistance in Aedes aegypti larvae at all collection sites in Yangon City, by using a simplified knockdown bioassay. We showed that V1016G and S989P mutations were widely distributed, with high frequencies (84.4% and 78.8%, respectively). By contrast, we were unable to detect I1011M (or I1011V) or L1014F mutations. F1534C mutations were also widely distributed, but with a lower frequency than the V1016G mutation (21.2%). High percentage of co-occurrence of the homozygous V1016G/S989P mutations was detected (65.7%). Additionally, co-occurrence of homozygous V1016G/F1534C mutations (2.9%) and homozygous V1016G/F1534C/S989P mutations (0.98%) were detected in the present study. Conclusions/Significance Pyrethroid insecticides were first used for malaria control in 1992, and have since been constantly used in Myanmar. This intensive use may explain the strong selection pressure toward Aedes aegypti, because this mosquito is generally a domestic and endophagic species with a preference for indoor breeding. Extensive use of DDT for malaria control before the use of this chemical was banned may also explain the development of pyrethroid resistance in Aedes aegypti.