Miracle-dz/UniFAR-FTUs huggingface dataset:
Measuring and simulating crown respiration of Scots pine with increased temperature and carbon dioxide enrichment.

Acclimation to elevated atmospheric carbon dioxide concentration and temperature of respiration by the foliage in the crown of Scots pine (Pinus sylvestris) trees is measured and modelled. Starting in 1996, individual 20-year-old trees were enclosed in chambers and exposed to either normal ambient conditions (CON), elevated CO2 concentration (EC), elevated temperature (ET) or a combination of EC and ET (ECT). Respiration of individual leaves within the crown was measured in 2000. To extrapolate the response of respiration of individual leaves to the whole crown, a multi-layer model was developed and used to predict daily and annual crown respiration, in which the crown structure and corresponding microclimate data were used as input. Respiration measurements showed that EC led to higher Q10 values (4.6%) relative to CON, but lower basal respiration rates at 20 degrees C [R1.d(20)] (-7.1%) during the main growth season (days 120-240), whereas ET and ECT both reduced Q10 (-12.0 and -9.8%, respectively) throughout the year but increased R1.d(20) (27.2 and 21.6%, respectively) during the period of no-growth, and slightly reduced R1.d(20) (-1.7 and -2.8%, respectively) during the main growth season. Model computations showed that annual crown respiration increased: (1) by 16% in EC, with 92% of this increase attributable to the increase in foliage area; (2) by 35% in ET, with 66% related to the increase in foliage area and 17% to the rise in ambient temperature; and (3) by 27% in the case of ECT, with 43% attributable to the increase in foliage area and 29% to the rise in ambient temperature. Changed respiration parameters for individual leaves, induced by treatments, made only a small contribution to the annual crown respiration compared with the increased foliage area. The effects of changes in crown architecture and nitrogen distribution, caused by treatments, on the daily and annual course of crown respiration are discussed.
Arterial stiffness, cardiovagal baroreflex sensitivity and postural blood pressure changes in older adults: The Rotterdam Study

Objective Arterial stiffness may be involved in the impairment of the arterial baroreflex. In the present study the associations between arterial stiffness and cardiovagal baroreflex sensitivity (BRS) and between BRS and postural blood pressure (BP) changes were investigated within the framework of the Rotterdam Study. Methods Arterial stiffness was determined by aortic pulse wave velocity and the carotid distensibility coefficient. Continuous recording of the R–R interval and finger BP was performed with the subject resting supine, and BRS was estimated from the spontaneous changes in systolic BP and corresponding interbeat intervals. Measures of aortic stiffness or carotid distensibility and BRS were available in 2490 and 2083 subjects, respectively. The association between arterial stiffness and ln BRS was investigated by multivariate linear regression analysis and then by analysis of covariance, comparing BRS by quartiles of arterial stiffness. Results The mean age of the subjects was 71.7 ± 6.6 (41.7% men). Aortic stiffness was negatively associated [β = −0.029; 95% confidence interval (CI): −0.040, −0.019] and the carotid distensibility coefficient positively associated with BRS (β = 0.017; 95% CI: 0.010, 0.024). An orthostatic decrease in systolic BP was absent in 1609 subjects, between 1 and 10 mmHg in 502 and >10 mmHg in 269 subjects, with corresponding mean values (95% CI) of ln BRS of 1.47 (1.44–1.51), 1.43 (1.37–1.49) and 1.36 (1.28–1.44) ms/mmHg (test for trend P < 0.019). An orthostatic decrease in diastolic BP was absent in 1123 subjects, 1–10 mmHg in 1057 and >10 mmHg in 209 subjects, with corresponding mean values of ln BRS of 1.49 (1.45–1.53), 1.41 (1.37–1.45) and 1.45 (1.36–1.54) ms/mmHg (P < 0.04). Conclusion In a large population of older subjects, arterial stiffness appears to be an independent determinant of impaired BRS. Within the same population, impaired BRS was associated with orthostatic BP changes.
An Integrated Gene Regulatory Network Controls Stem Cell Proliferation in Teeth

Epithelial stem cells reside in specific niches that regulate their self-renewal and differentiation, and are responsible for the continuous regeneration of tissues such as hair, skin, and gut. Although the regenerative potential of mammalian teeth is limited, mouse incisors grow continuously throughout life and contain stem cells at their proximal ends in the cervical loops. In the labial cervical loop, the epithelial stem cells proliferate and migrate along the labial surface, differentiating into enamel-forming ameloblasts. In contrast, the lingual cervical loop contains fewer proliferating stem cells, and the lingual incisor surface lacks ameloblasts and enamel. Here we have used a combination of mouse mutant analyses, organ culture experiments, and expression studies to identify the key signaling molecules that regulate stem cell proliferation in the rodent incisor stem cell niche, and to elucidate their role in the generation of the intrinsic asymmetry of the incisors. We show that epithelial stem cell proliferation in the cervical loops is controlled by an integrated gene regulatory network consisting of Activin, bone morphogenetic protein (BMP), fibroblast growth factor (FGF), and Follistatin within the incisor stem cell niche. Mesenchymal FGF3 stimulates epithelial stem cell proliferation, and BMP4 represses Fgf3 expression. In turn, Activin, which is strongly expressed in labial mesenchyme, inhibits the repressive effect of BMP4 and restricts Fgf3 expression to labial dental mesenchyme, resulting in increased stem cell proliferation and a large, labial stem cell niche. Follistatin limits the number of lingual stem cells, further contributing to the characteristic asymmetry of mouse incisors, and on the basis of our findings, we suggest a model in which Follistatin antagonizes the activity of Activin. These results show how the spatially restricted and balanced effects of specific components of a signaling network can regulate stem cell proliferation in the niche and account for asymmetric organogenesis. Subtle variations in this or related regulatory networks may explain the different regenerative capacities of various organs and animal species.
Towards Comprehensive Modelling by Inter-model Links Using an Integrating Repository

Model-based development techniques enable a high efficiency and the mastering of complexity. For many domains more than one model has to be used to express the relevant information. Many methods use different models without a tight coupling, with a high risk of inconsistencies. Other approaches are based on metamodel extension or unified metamodels, with a limited tool support as consequence. We present an approach for the interconnection between several models in a joint repository by means of dependency relationships. The interconnection is shown between UML models, BPMN models and feature models by examples for variable workflows in mobile systems. The presented approach is implemented by the EMF-based repository EMF Trace, with XML for model representation. Dependencies are determined either automatically by a rule set or manually by explicit references.
Tensile and elastic behavior of tencel continuous filaments

Tencel is a regenerated cellulose fiber produced using an environmentally-responsible dry-jet wet-spinning process, which contributes to its excellent mechanical properties. In this study, the tensile properties of Tencel continuous filaments are characterized and the effect of twist on mechanical properties, including breaking load and extension, are considered. Peak strength was obtained in Tencel filaments of 140 t m−1. The elastic behavior of Tencel monofilament was observed by assessing the recovery from strain-induced energy and the elastic recovery was found to be low. Along with time dependency, Tencel has the ability to stabilize its deformed state by forming new crosslinks, and this influences the elastic behavior. In simple extension cycles, the same low elasticity was observed. Cumulative extension cycles were also performed to characterize the behavior of filaments subjected to repeated strain and to determine the resultant hysteresis effects. Permanent elongation was observed at 2% imposed strain, which suggests that the filament has low extensibility. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 99: 1496–1503, 2006
Aesthetic Design of Skin-Sparing Mastectomy Incisions for Immediate Autologous Tissue Breast Reconstruction in Asian Women

Background The advent of skin-sparing mastectomy has allowed for the reconstruction of the breast and nipple with improved cosmesis. However, the nipple-areolar complex (NAC) in Asian patients is more pigmented and scars easily. Therefore, commonly described incisions tend to result in poor aesthetic outcomes in Asian patients with breast cancer. Methods We describe an algorithmic approach to skin-sparing mastectomy incisions in Asian patients on the basis of the location of the biopsy scar and the tumor site and size. Four incision types are described: peri-areolar, a peri-areolar incision with a second distant skin paddle, "racquet handle," and peri-areolar with adjacent skin excision. Results 281 immediate breast reconstructions were performed between May 2001 and February 2012 after skin-sparing mastectomy. The mastectomy incisions used included the peri-areolar design (n=124, 44%), peri-areolar design with a second distant skin paddle (n=39, 14%), "racquet handle" (n=21, 7.5%), and peri-areolar design with adjacent skin excision (n=42, 14%). The traditional elliptical incision and other variants where the NAC outline was not preserved were performed in the remaining 55 patients. The average follow-up was 44.7 months during which there was 1 case of total flap loss and 7 cases of partial flap necrosis; all remaining flaps survived. 24% of the patients (68/281) underwent subsequent nipple reconstruction. Conclusions Our algorithm avoids breast incisions that are randomly placed or excessively long and prevents the unnecessary sacrifice of normal breast skin. This allows skin-sparing mastectomy and immediate breast reconstruction to be performed with a consistently achievable aesthetic result in Asian women without neglecting oncological safety.
Developmental processes associated with longitudinal declines in parental responsibility and adherence to type 1 diabetes management across adolescence.

OBJECTIVE To identify whether changes in pubertal status and self-efficacy for diabetes management are associated with longitudinal declines in parental responsibility for diabetes, and to determine whether these factors moderate associations between declining parental responsibility and deteriorating adherence across adolescence. METHODS Adolescents (N = 252; 53.6% females) with type 1 diabetes, mothers, and 188 fathers participated in a 2.5-year longitudinal study. Self-reports of pubertal status, adolescent efficacy, parental responsibility, and adherence were completed every 6 months (6 time points). RESULTS Latent growth curve modeling revealed that longitudinal increases in efficacy and pubertal maturation were uniquely associated with longitudinal declines in parental responsibility. Declines in parental responsibility were related to deterioration in adherence especially when adolescents did not report concomitant growth in self-efficacy. CONCLUSIONS Transfer of responsibility for diabetes management across adolescence may be more optimal when adolescents' increased independence is titrated to their changing self-efficacy beliefs.
Microblog Emotion Classification by Computing Similarity in Text, Time, and Space

Most work in NLP analysing microblogs focuses on textual content thus neglecting temporal and spatial information. We present a new interdisciplinary method for emotion classification that combines linguistic, temporal, and spatial information into a single metric. We create a graph of labeled and unlabeled tweets that encodes the relations between neighboring tweets with respect to their emotion labels. Graph-based semi-supervised learning labels all tweets with an emotion.
Consumption of Sutherlandia frutescens by HIV-Seropositive South African Adults: An Adaptive Double-Blind Randomized Placebo Controlled Trial

Background Sutherlandia frutescens (L.) R. Br. is widely used as an over the counter complementary medicine and in traditional medications by HIV seropositive adults living in South Africa; however the plant’s safety has not been objectively studied. An adaptive two-stage randomized double-blind placebo controlled study was used to evaluate the safety of consuming dried S. frutescens by HIV seropositive adults with CD4 T-lymphocyte count of >350 cells/μL. Methods In Stage 1 56 participants were randomized to S. frutescens 400, 800 or 1,200 mg twice daily or matching placebo for 24 weeks. In Stage 2 77 additional participants were randomized to either 1,200 mg S. frutescens or placebo. In the final analysis data from Stage 1 and Stage 2 were combined such that 107 participants were analysed (54 in the S. frutescens 1,200 mg arm and 53 in the placebo arm). Results S. frutescens did not change HIV viral load, and CD4 T-lymphocyte count was similar in the two arms at 24 weeks; however, mean and total burden of infection (BOI; defined as days of infection-related events in each participant) was greater in the S. frutescens arm: mean (SD) 5.0 (5.5) vs. 9.0 (12.7) days (p = 0.045), attributed to two tuberculosis cases in subjects taking isoniazid preventive therapy (IPT). Conclusion A possible interaction between S. frutescens and IPT needs further evaluation, and may presage antagonistic interactions with other herbs having similar biochemical (antioxidant) properties. No other safety issues relating to consumption of S. frutescens in this cohort were identified. Trial Registration ClinicalTrials.gov NCT00549523
The influence of intrauterine exposure to immunosuppressive treatment on changes in the immune system in juvenile Wistar rats

Background In our study, we assessed the impact of immunosuppressive drug combinations on changes in the immune system of juvenile Wistar rats exposed to these drugs during pregnancy. We primarily concentrated on changes in two organs of the immune system – the thymus and the spleen. Methods The study was conducted on 40 (32+8) female Wistar rats administered full and half dose of drugs, respectively, subjected to regimens commonly used in therapy of human kidney transplant recipients ([1] cyclosporine A, mycophenolate mofetil, and prednisone; [2] tacrolimus, mycophenolate mofetil, and prednisone; [3] cyclosporine A, everolimus, and prednisone). The animals received drugs by oral gavage 2 weeks before pregnancy and during 3 weeks of pregnancy. Results There were no statistically significant differences in the weight of the thymus and spleen, but changes were found in the results of blood hematology, cytometry from the spleen, and a histologic examination of the examined immune organs of juvenile Wistar rats. In the cytokine assay, changes in the level of interleukine 17 (IL-17) after increasing amounts of concanavaline A were dose-dependent; the increase of IL-17 was blocked after administration of higher doses of immunosuppressive drugs. However, after a reduction of doses, its increase resumed. Conclusion Qualitative, quantitative, and morphological changes in the immune system of infant rats born to pharmacologically immunosuppressed females were observed. Thymus structure, spleen composition, and splenocyte IL-17 production were mostly affected in a drug regimen–dependent manner.
A prefoldin-associated WD-repeat protein (WDR92) is required for the correct architectural assembly of motile cilia

WDR92 is a highly conserved component of a prefoldin-like cochaperone complex that has a phylogenetic signature compatible with a role in motile cilia assembly or function. Lack of this component in planaria causes pleiomorphic defects in ciliary architecture, resulting in immotile or poorly motile structures.
PACER: proportional detection of data races

Data races indicate serious concurrency bugs such as order, atomicity, and sequential consistency violations. Races are difficult to find and fix, often manifesting only after deployment. The frequency and unpredictability of these bugs will only increase as software adds parallelism to exploit multicore hardware. Unfortunately, sound and precise race detectors slow programs by factors of eight or more and do not scale to large numbers of threads. This paper presents a precise, low-overhead sampling-based data race detector called Pacer. PACER makes a proportionality guarantee: it detects any race at a rate equal to the sampling rate, by finding races whose first access occurs during a global sampling period. During sampling, PACER tracks all accesses using the dynamically sound and precise FastTrack algorithm. In nonsampling periods, Pacer discards sampled access information that cannot be part of a reported race, and Pacer simplifies tracking of the happens-before relationship, yielding near-constant, instead of linear, overheads. Experimental results confirm our theoretical guarantees. PACER reports races in proportion to the sampling rate. Its time and space overheads scale with the sampling rate, and sampling rates of 1-3% yield overheads low enough to consider in production software. The resulting system provides a "get what you pay for" approach that is suitable for identifying real, hard-to-reproduce races in deployed systems.
Maternal smoking in pregnancy and asthma in preschool children: a pooled analysis of eight birth cohorts.

RATIONALE Although epidemiological studies suggest that exposure to maternal smoking during fetal and early life increases the risk of childhood wheezing and asthma, previous studies were not able to differentiate the effects of prenatal from postnatal exposure. OBJECTIVES To assess the effect of exposure to maternal smoking only during pregnancy on wheeze and asthma among preschool-age children. METHODS A pooled analysis was performed based on individual participant data from eight European birth cohorts. Cohort-specific effects of maternal smoking during pregnancy, but not during the first year, on wheeze and asthma at 4 to 6 years of age were estimated using logistic regression and then combined using a random effects model. Adjustments were made for sex, parental education, parental asthma, birth weight, and siblings. MEASUREMENTS AND MAIN RESULTS Among the 21,600 children included in the analysis, 735 children (3.4%) were exposed to maternal smoking exclusively during pregnancy but not in the first year after birth. In the pooled analysis, maternal smoking only during pregnancy was associated with wheeze and asthma at 4 to 6 years of age, with adjusted odds ratios of 1.39 (95% confidence interval, 1.08-1.77) and 1.65 (95% confidence interval, 1.18-2.31), respectively. The likelihood to develop wheeze and asthma increased statistically significantly in a linear dose-dependent manner in relation to maternal daily cigarette consumption during the first trimester of pregnancy. CONCLUSIONS Maternal smoking during pregnancy appears to increase the risk of wheeze and asthma among children who are not exposed to maternal smoking after birth.
Interleukin 3 Prevents Delayed Neuronal Death in the Hippocampal CA1 Field

In the central nervous system, interleukin (IL)-3 has been shown to exert a trophic action only on septal cholinergic neurons in vitro and in vivo, but a widespread distribution of IL-3 receptor (IL-3R) in the brain does not conform to such a selective central action of the ligand. Moreover, the mechanism(s) underlying the neurotrophic action of IL-3 has not been elucidated, although an erythroleukemic cell line is known to enter apoptosis after IL-3 starvation possibly due to a rapid decrease in Bcl-2 expression. This in vivo study focused on whether IL-3 rescued noncholinergic hippocampal neurons from lethal ischemic damage by modulating the expression of Bcl-xL, a Bcl-2 family protein produced in the mature brain. 7-d IL-3 infusion into the lateral ventricle of gerbils with transient forebrain ischemia prevented significantly hippocampal CA1 neuron death and ischemia-induced learning disability. TUNEL (terminal deoxynucleotidyltransferase–mediated 2′-deoxyuridine 5′-triphosphate-biotin nick end labeling) staining revealed that IL-3 infusion caused a significant reduction in the number of CA1 neurons exhibiting DNA fragmentation 7 d after ischemia. The neuroprotective action of IL-3 appeared to be mediated by a postischemic transient upregulation of the IL-3R α subunit in the hippocampal CA1 field where IL-3Rα was barely detectable under normal conditions. In situ hybridization histochemistry and immunoblot analysis demonstrated that Bcl-xL mRNA expression, even though upregulated transiently in CA1 pyramidal neurons after ischemia, did not lead to the production of Bcl-xL protein in ischemic gerbils infused with vehicle. However, IL-3 infusion prevented the decrease in Bcl-xL protein expression in the CA1 field of ischemic gerbils. Subsequent in vitro experiments showed that IL-3 induced the expression of Bcl-xL mRNA and protein in cultured neurons with IL-3Rα and attenuated neuronal damage caused by a free radical–producing agent FeSO4. These findings suggest that IL-3 prevents delayed neuronal death in the hippocampal CA1 field through a receptor-mediated expression of Bcl-xL protein, which is known to facilitate neuron survival. Since IL-3Rα in the hippocampal CA1 region, even though upregulated in response to ischemic insult, is much less intensely expressed than that in the CA3 region tolerant to ischemia, the paucity of IL-3R interacting with the ligand may account for the vulnerability of CA1 neurons to ischemia.
Making designer mutants in model organisms

Recent advances in the targeted modification of complex eukaryotic genomes have unlocked a new era of genome engineering. From the pioneering work using zinc-finger nucleases (ZFNs), to the advent of the versatile and specific TALEN systems, and most recently the highly accessible CRISPR/Cas9 systems, we now possess an unprecedented ability to analyze developmental processes using sophisticated designer genetic tools. In this Review, we summarize the common approaches and applications of these still-evolving tools as they are being used in the most popular model developmental systems. Excitingly, these robust and simple genomic engineering tools also promise to revolutionize developmental studies using less well established experimental organisms.