Miracle-dz/UniFAR-FTUs huggingface dataset:
Fine roots of pedunculate oak (Quercus robur L.) in the Netherlands seven years after liming

A liming experiment was initiated in 1988 in which an equivalent dose of 1.6 t/ha CaO was applied to a young and an old stand of Q. robur (planted in 1980 and 19953, respectively), growing on acidic sandy soils in southeast Netherlands. Seven years after the liming treatments, the effects on soil and roots were intensively studied. Prior to liming, the young stand suffered from a deficiency in N, P, Mg, Zn and Fe, whereas the older stand had a deficiency in Mg and Zn. The results indicated that, 7 years after the application of lime, cation availability and soil pH were increased. Liming increased specific root length and number of apices with mycorrhizas per cm of fine root length in most of the profile in the young stand, but stimulated fine root biomass and length only in the top soil of the old stand. The leaf nutrient status was improved the most in the youngest stand, where lime had greatest impact on the area of soil exploited by the root and mycorrhizas system.
Glyceraldehyde-3-phosphate Dehydrogenase Aggregates Accelerate Amyloid-β Amyloidogenesis in Alzheimer Disease*

Background: There is currently no strong evidence for a linkage between glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and Alzheimer disease (AD). Results: GAPDH aggregates enhanced amyloid-β peptide (Aβ) amyloidogenesis and augmented Aβ40-induced neurotoxicity, both in vitro and in vivo, concomitant with mitochondrial dysfunction. Conclusion: GAPDH aggregates accelerate Aβ amyloidogenesis. Significance: Aβ amyloidogenesis associated with GAPDH aggregation might underlie AD pathogenesis. Alzheimer disease (AD) is a progressive neurodegenerative disorder characterized by loss of neurons and formation of pathological extracellular deposits induced by amyloid-β peptide (Aβ). Numerous studies have established Aβ amyloidogenesis as a hallmark of AD pathogenesis, particularly with respect to mitochondrial dysfunction. We have previously shown that glycolytic glyceraldehyde-3-phosphate dehydrogenase (GAPDH) forms amyloid-like aggregates upon exposure to oxidative stress and that these aggregates contribute to neuronal cell death. Here, we report that GAPDH aggregates accelerate Aβ amyloidogenesis and subsequent neuronal cell death both in vitro and in vivo. Co-incubation of Aβ40 with small amounts of GAPDH aggregates significantly enhanced Aβ40 amyloidogenesis, as assessed by in vitro thioflavin-T assays. Similarly, structural analyses using Congo red staining, circular dichroism, and atomic force microscopy revealed that GAPDH aggregates induced Aβ40 amyloidogenesis. In PC12 cells, GAPDH aggregates augmented Aβ40-induced cell death, concomitant with disruption of mitochondrial membrane potential. Furthermore, mice injected intracerebroventricularly with Aβ40 co-incubated with GAPDH aggregates exhibited Aβ40-induced pyramidal cell death and gliosis in the hippocampal CA3 region. These observations were accompanied by nuclear translocation of apoptosis-inducing factor and cytosolic release of cytochrome c from mitochondria. Finally, in the 3×Tg-AD mouse model of AD, GAPDH/Aβ co-aggregation and mitochondrial dysfunction were consistently detected in an age-dependent manner, and Aβ aggregate formation was attenuated by GAPDH siRNA treatment. Thus, this study suggests that GAPDH aggregates accelerate Aβ amyloidogenesis, subsequently leading to mitochondrial dysfunction and neuronal cell death in the pathogenesis of AD.
High degree of genetic differentiation in marine three‐spined sticklebacks (Gasterosteus aculeatus)

Populations of widespread marine organisms are typically characterized by a low degree of genetic differentiation in neutral genetic markers, but much less is known about differentiation in genes whose functional roles are associated with specific selection regimes. To uncover possible adaptive population divergence and heterogeneous genomic differentiation in marine three‐spined sticklebacks (Gasterosteus aculeatus), we used a candidate gene‐based genome‐scan approach to analyse variability in 138 microsatellite loci located within/close to (<6 kb) functionally important genes in samples collected from ten geographic locations. The degree of genetic differentiation in markers classified as neutral or under balancing selection—as determined with several outlier detection methods—was low (FST = 0.033 or 0.011, respectively), whereas average FST for directionally selected markers was significantly higher (FST = 0.097). Clustering analyses provided support for genomic and geographic heterogeneity in selection: six genetic clusters were identified based on allele frequency differences in the directionally selected loci, whereas four were identified with the neutral loci. Allelic variation in several loci exhibited significant associations with environmental variables, supporting the conjecture that temperature and salinity, but not optic conditions, are important drivers of adaptive divergence among populations. In general, these results suggest that in spite of the high degree of physical connectivity and gene flow as inferred from neutral marker genes, marine stickleback populations are strongly genetically structured in loci associated with functionally relevant genes.
The Penicillium digitatum protein O-mannosyltransferase Pmt2 is required for cell wall integrity, conidiogenesis, virulence and sensitivity to the antifungal peptide PAF26.

The activity of protein O-mannosyltransferases (Pmts) affects the morphogenesis and virulence of fungal pathogens. Recently, PMT genes have been shown to determine the sensitivity of Saccharomyces cerevisiae to the antifungal peptide PAF26. This study reports the identification and characterization of the three Pdpmt genes in the citrus post-harvest pathogen Penicillium digitatum. The Pdpmt genes are expressed during fungal growth and fruit infection, with the highest induction for Pdpmt2. Pdpmt2 complemented the growth defect of the S. cerevisiae Δpmt2 strain. The Pdpmt2 gene mutation in P. digitatum caused pleiotropic effects, including a reduction in fungal growth and virulence, whereas its constitutive expression had no phenotypic effect. The Pdpmt2 null mutants also showed a distinctive colourless phenotype with a strong reduction in the number of conidia, which was associated with severe alterations in the development of conidiophores. Additional effects of the Pdpmt2 mutation were hyphal morphological alterations, increased sensitivity to cell wall-interfering compounds and a blockage of invasive growth. In contrast, the Pdpmt2 mutation increased tolerance to oxidative stress and to the antifungal activity of PAF26. These data confirm the role of protein O-glycosylation in the PAF26-mediated antifungal mechanism present in distantly related fungal species. Important to future crop protection strategies, this study demonstrates that a mutation rendering fungi more resistant to an antifungal peptide results in severe deleterious effects on fungal growth and virulence.
Mutational activation of the STE5 gene product bypasses the requirement for G protein beta and gamma subunits in the yeast pheromone response pathway

The STE5 gene encodes an essential element of the pheromone response pathway which is known to act either after the G subunit encoded by the STE4 gene or at the same step. Mutations in STE5, designated STE5Hyp, that partially activate the pathway in the absence of pheromone were isolated. One allele (STE5Hyp-2) was shown to cause a single amino acid substitution near the N terminus of the predicted STE5 protein. Immunoblotting with anti-Ste5 antibodies indicated that the phenotype was not due to an increased level of the mutant STE5 protein. A multicopy episomal plasmid containing a STE5Hyp allele partially suppressed both the block in pheromone-inducible transcription and the sterility phenotype caused by null alleles of the STE2, STE4, or STE18 gene, indicating that the STE5 product acts after the receptor (STE2 product) and after the G protein beta and gamma subunits (STE4 and STE18 products, respectively). However, the phenotypes of the STE5Hyp mutations were less pronounced in ste4 and ste18 mutants, suggesting that the STE5Hyp-generated signal partially depends on the proposed G beta gamma complex. The STE5Hyp alleles did not suppress ste7, ste11, ste12, or fus3 kss1 null mutants, consistent with previous findings that the STE5 product acts before the protein kinases encoded by STE7, STE11, FUS3, and KSS1 and the transcription factor encoded by STE12. The mating defects of the ste2 deletion mutant and the temperature-sensitive ste4-3 mutant were also suppressed by overexpression of wild-type STE5. The slow-growth phenotype manifested by cells carrying STE5Hyp alleles was enhanced by the sst2-1 mutation; this effect was eliminated in ste4 mutants. These results provide the first evidence that the STE5 gene product performs its function after the G protein subunits.
VEGF‐A Promotes Intussusceptive Angiogenesis in the Developing Chicken Chorioallantoic Membrane

Please cite this paper as: Baum, Suter, Gerber, Tschanz, Buergy, Blank, Hlushchuk and Djonov (2010). VEGF‐A Promotes Intussusceptive Angiogenesis in the Developing Chicken Chorioallantoic Membrane. Microcirculation17(6), 447–457.
Improvement of I/sub c/ by loading and unloading bending strain for high strength Nb/sub 3/Sn wires

We investigated the influence of the repeated bending strain on the critical current properties. The bending strain was applied to the Ti-added high strength CuNb/Nb/sub 3/Sn wires at room temperature and released. We define this loading and unloading bending strain at room temperature as a "pre-bending" treatment. We found that the critical current I/sub c/ is much enhanced by applying the pre-bending treatment. The maximum enhancement of I/sub c/ due to the pre-bending treatment is about twice at 17 T, for instance. The stress dependence of I/sub c/ shows that I/sub c/ is improved in low stress states by pre-bending treatment. This phenomenon can be described well by the uniaxial strain analysis on the basis of the strain distribution. In addition, the increase of the maximum critical current of the strain dependent I/sub c/ is also observed. This may be related to the reduction of the radial/tangential prestrain.
Prestige and dominance-based hierarchies exist in naturally occurring human groups, but are unrelated to task-specific knowledge

Prestige and dominance are thought to be two evolutionarily distinct routes to gaining status and influence in human social hierarchies. Prestige is attained by having specialist knowledge or skills that others wish to learn, whereas dominant individuals use threat or fear to gain influence over others. Previous studies with groups of unacquainted students have found prestige and dominance to be two independent avenues of gaining influence within groups. We tested whether this result extends to naturally occurring social groups. We ran an experiment with 30 groups of people from Cornwall, UK (n = 150). Participants answered general knowledge questions individually and as a group, and subsequently nominated a representative to answer bonus questions on behalf of the team. Participants then anonymously rated all other team-mates on scales of prestige, dominance, likeability and influence on the task. Using a model comparison approach with Bayesian multi-level models, we found that prestige and dominance ratings were predicted by influence ratings on the task, replicating previous studies. However, prestige and dominance ratings did not predict who was nominated as team representative. Instead, participants nominated team members with the highest individual quiz scores, despite this information being unavailable to them. Interestingly, team members who were initially rated as being high status in the group, such as a team captain or group administrator, had higher ratings of both dominance and prestige than other group members. In contrast, those who were initially rated as someone from whom others would like to learn had higher prestige, but not higher dominance, supporting the claim that prestige reflects social learning opportunities. Our results suggest that prestige and dominance hierarchies do exist in naturally occurring social groups, but that these hierarchies may be more domain-specific and less flexible than we anticipated.
Identification of Distal cis-Regulatory Elements at Mouse Mitoferrin Loci Using Zebrafish Transgenesis

ABSTRACT Mitoferrin 1 (Mfrn1; Slc25a37) and mitoferrin 2 (Mfrn2; Slc25a28) function as essential mitochondrial iron importers for heme and Fe/S cluster biogenesis. A genetic deficiency of Mfrn1 results in a profound hypochromic anemia in vertebrate species. To map the cis-regulatory modules (CRMs) that control expression of the Mfrn genes, we utilized genome-wide chromatin immunoprecipitation (ChIP) datasets for the major erythroid transcription factor GATA-1. We identified the CRMs that faithfully drive the expression of Mfrn1 during blood and heart development and Mfrn2 ubiquitously. Through in vivo analyses of the Mfrn-CRMs in zebrafish and mouse, we demonstrate their functional and evolutionary conservation. Using knockdowns with morpholinos and cell sorting analysis in transgenic zebrafish embryos, we show that GATA-1 directly regulates the expression of Mfrn1. Mutagenesis of individual GATA-1 binding cis elements (GBE) demonstrated that at least two of the three GBE within this CRM are functionally required for GATA-mediated transcription of Mfrn1. Furthermore, ChIP assays demonstrate switching from GATA-2 to GATA-1 at these elements during erythroid maturation. Our results provide new insights into the genetic regulation of mitochondrial function and iron homeostasis and, more generally, illustrate the utility of genome-wide ChIP analysis combined with zebrafish transgenesis for identifying long-range transcriptional enhancers that regulate tissue development.
Deaths Attributable to Injuries in Infants, United States, 1983–1991

Objective To describe risk factors for injury death among infants in the United States by the specific external cause of death. Methods. Data were analyzed from the US-linked birth/infant death files for the years 1983–1991. Potential risk factors for injury death were identified from birth certificate data and included both maternal and infant factors. Injury rates were calculated by external cause of death. Characteristics of infants who died from an injury were compared with those of the entire birth cohort. The independent effect of potential risk factors was assessed in multivariate analyses using a case–control study design. Results. A total of 10 370 injury deaths were identified over the 9-year study period (29.72/100 000 live births). The leading causes of death were homicide, suffocation, motor vehicle crashes, and choking (inhalation of food or objects). There was no significant temporal trend in the overall rate of injury death; however, this was because significant increases in the rates of death from homicide (6.4%/year) and mechanical suffocation (3.7%/year) were offset by decreases in rates of death from fires (−4.7%/year) and choking (−4.6%/year). In adjusted analyses, infants born to mothers with no prenatal care, <12 years of education, two or more previous live births, Native American race, or <20 years of age were at twice the risk of injury death compared with the lowest risk groups (initiation of prenatal care in the first trimester, ≥16 years of education, no previous live births, white, or ≥25 years of age). When analyzed by the specific cause of death, the factors that were associated most strongly with death varied. For example, Native Americans were at greatest risk of a motor vehicle related death (compared with whites: OR: 3.6; 95% CI: 1.8–7.1), and infants with birth weights of <1500 g were at greatest risk of death attributable to inhalation of food (compared with ≥2500 g: OR: 9.6; 95% CI: 3.3–28.0) or objects (OR: 11.8; 95% CI: 4.5–30.5). Conclusion. A number of sociodemographic characteristics are associated with an increased risk of injury-related death in infants. The strength of associations between specific risk factors and death varies with the external cause of death, thus identifying high-risk subgroups for targeting of cause-specific interventions and simultaneously increasing our understanding of the individual and societal mechanisms underlying these tragedies. infant, injury, suffocation, motor vehicle, homicide, drowning, inhalation, fire.
An Alternative Model of Expected Returns and its Implications for Return Predictability

Empirical studies have found that during bad times return predictability is higher. Thus, variation in discount rate news should be relatively higher as economic conditions worsen. We propose a parsimonious model for expected returns that captures the countercyclical dynamics of stock return predictability. The implications of the model are studied within a flexible Bayesian predictive system. In our empirical tests, the estimates from the proposed model of expected return present lower prediction errors than the historical mean, and than the predictive regression using the dividend yield. Furthermore, the persistence parameter of expected returns presents long-term dynamics similar to the autocorrelation of realized returns.
Biased Multi-LED Beamforming for Multicarrier Visible Light Communications

Visible light communication (VLC) equipped with multiple light-emitting diodes (LEDs) can provide near ubiquitous indoor coverage for both communication and illumination. This paper introduces the concept of biased beamforming to explore the full potential of multicarrier multi-LED VLC systems. Biased beamforming includes two components to be jointly designed: a direct current (DC) bias on each LED and a beamforming vector on each subcarrier. We first analyze the impact on clipping in multi-LED VLC systems. Next, we consider the joint optimization of beamforming and biasing to maximize data rate. We find the optimal beamformer and analytically characterize its structure. We further optimize the bias on each LED and provide the globally optimal solution in closed form for flat channels, which leads to several critical insights that are helpful for practical systems. We also derive a simplified near-optimal solution for dispersive channels and develop an efficient method for biased beamforming. The performance of the proposed biased beamforming design outperforms existing solutions.
Spontaneous ovarian tumors in twelve baboons: a review of ovarian neoplasms in non‐human primates

Abstract: Twelve spontaneous ovarian tumors were found in the Southwest Foundation for Biomedical Research baboon colony. These included four granulosa cell tumors, three teratomas, two endometrioid carcinomas, one seromucinous cystadenofibroma, a cystic papillary adenocarcinoma, and an ovarian carcinoma. Age was a pre‐disposing factor. With one exception, the tumors of surface epithelial‐ and sex cord‐stromal origin occurred in baboons over 17 years of age. The exceptional animal was 7 years of age when a malignant granulosa cell tumor with Sertoli cell differentiation was identified. The two endometrioid tumors, which were found in 17‐ and 30‐year‐old animals, were both associated with endometriosis. In contrast, the teratomas, which are tumors of germ cell origin, were found in younger animals, i.e. 17 years of age or younger. One case of an ovarian carcinoma with metastases was observed in a 6‐month‐old infant. Cases of spontaneous ovarian tumors from the literature are reviewed.
Anterior cruciate ligament: functional anatomy of its bundles in rotatory instabilities

The functional anatomy of the anterior cruciate ligament was studied in 18 freshly amputated specimens. The cruciates were observed in the extremes of flexion and extension, and in midposition in simulated weight-bearing and nonweight-bearing conditions. Five femoral shafts were split longitudinally so that the femoral and tibial attachments of the ligament could be inspected. The findings indicated that (1) the anterior cruciate ligament is a secondary static stabilizer against rotatory in stabilities of the knee; (2) the anteromedial bundle contributes to anterolateral stability; (3) the intermediate bundle adds to straight and anteromedial stability; and (4) the posterolateral bundle assists in posterolateral stability. Specific bundles and functions of bundles must be considered in reconstruction, substitution, or replacement of the anterior cruciate ligament.
Parathyroidectomy improves bone geometry and microarchitecture in female patients with primary hyperparathyroidism: A one‐year prospective controlled study using high‐resolution peripheral quantitative computed tomography

Following parathyroidectomy (PTX), bone mineral density (BMD) increases in patients with primary hyperparathyroidism (PHPT), yet information is scarce concerning changes in bone structure and strength following normalization of parathyroid hormone levels postsurgery. In this 1‐year prospective controlled study, high‐resolution peripheral quantitative computed tomography (HR‐pQCT) was used to evaluate changes in bone geometry, volumetric BMD (vBMD), microarchitecture, and estimated strength in female patients with PHPT before and 1 year after PTX, compared to healthy controls. Twenty‐seven women successfully treated with PTX (median age 62 years; range, 44–75 years) and 31 controls (median age 63 years; range, 40–76 years) recruited by random sampling from the general population were studied using HR‐pQCT of the distal radius and tibia as well as with dual‐energy X‐ray absorptiometry (DXA) of the forearm, spine, and hip. The two groups were comparable with respect to age, height, weight, and menopausal status. In both radius and tibia, cortical (Ct.) vBMD and Ct. thickness increased or were maintained in patients and decreased in controls (p < 0.01). Radius cancellous bone architecture was improved in patients through increased trabecular number and decreased trabecular spacing compared with changes in controls (p < 0.05). No significant cancellous bone changes were observed in tibia. Estimated bone failure load by finite element modeling increased in patients in radius but declined in controls (p < 0.001). Similar, albeit borderline significant changes in estimated failure load were found in tibia (p = 0.06). This study showed that females with PHPT had improvements in cortical bone geometry and increases in cortical and trabecular vBMD in both radius and tibia along with improvements in cancellous bone architecture and estimated strength in radius 1 year after PTX, reversing or attenuating age‐related changes observed in controls. © 2012 American Society for Bone and Mineral Research.