Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional trait differences and the outcome of community assembly: an experimental test with vernal pool annual plants

Functional trait-based approaches have seen rapid development in community ecology and biogeography in recent years, as they promise to offer a better mechanistic and predictive understanding of community structure. However, several key challenges remain. First, while many studies have explored connections between functional traits and abiotic gradients, far fewer have directly tested the common assumption that functional trait differences influence interspecific interactions. Second, empirical studies often ignore intraspecific trait variation within communities, even though intraspecific variation has been known to have substantial impacts on community dynamics. Here we present an experiment designed to assess the role of functional trait differences in predicting the outcome of interspecific species interactions among a suite of California vernal pool annual plants. Eight species were grown in pairwise combinations in two levels of inundation in a greenhouse and functional traits were measured on all individuals. Nested models predicting focal plant performance were fit to the data. For seven of the eight species in the experiment, the best model included a functional trait difference term that was consistent with a competitive hierarchy, indicating that focal species tended to do better when they had larger leaf size, lower specific leaf area, and greater investment in lateral canopy spread than their neighbors. Models that included individually measured trait values generally performed better than models using species trait averages. We tested if the same trait measurements predicted tolerance of inundation (a feature of vernal pool habitats), and species depth distributions from extensive field surveys, though we did not find strong relationships. Our results suggest that functional traits can be used to make inferences about the outcome of interspecific interactions, and that greater predictive power can come from considering intraspecific variation in functional traits, particularly in low diversity communities.
Interplay between Selenium Levels, Selenoprotein Expression, and Replicative Senescence in WI-38 Human Fibroblasts*

Background: Selenoproteins are important enzymes for antioxidant defense, redox homeostasis, and redox signaling. Results: We report that, in WI-38 human fibroblasts, replicative senescence is controlled by selenium levels and selectively modulates selenoprotein expression. Conclusion: Our data indicate that the selenoproteome is regulated at the translational and mRNA levels in WI-38 cells. Significance: We have characterized a strong interplay between selenium levels, selenoprotein expression, and replicative senescence. Selenium is an essential trace element, which is incorporated as selenocysteine into at least 25 selenoproteins using a unique translational UGA-recoding mechanism. Selenoproteins are important enzymes involved in antioxidant defense, redox homeostasis, and redox signaling pathways. Selenium levels decline during aging, and its deficiency is associated with a marked increase in mortality for people over 60 years of age. Here, we investigate the relationship between selenium levels in the culture medium, selenoprotein expression, and replicative life span of human embryonic lung fibroblast WI-38 cells. Selenium levels regulate the entry into replicative senescence and modify the cellular markers characteristic for senescent cells. Whereas selenium supplementation extends the number of population doublings, its deficiency impairs the proliferative capacity of WI-38 cells. We observe that the expression of several selenoproteins involved in antioxidant defense is specifically affected in response to cellular senescence. Their expression is selectively controlled by the modulation of mRNA levels and translational recoding efficiencies. Our data provide novel mechanistic insights into how selenium impacts the replicative life span of mammalian cells by identifying several selenoproteins as new targets of senescence.
Minicore myopathy with ophthalmoplegia caused by mutations in the ryanodine receptor type 1 gene

Background: Minicore myopathy (multi-minicore disease [MmD]) is a congenital myopathy characterized by multifocal areas with loss of oxidative activity on muscle biopsy. MmD is clinically heterogeneous and distinct phenotypes have been associated with recessive mutations in either the selenoprotein N (SEPN1) or the skeletal muscle ryanodine receptor (RYR1) gene, also implicated in central core disease and malignant hyperthermia. External ophthalmoplegia is an additional finding in a subset of patients with MmD. Objective: To clinically and genetically examine families with MmD and external ophthalmoplegia. Methods: The authors investigated 11 affected individuals from 5 unrelated families. Clinical, histopathologic, and imaging studies were performed and RYR1 haplotyping and mutational analysis were carried out. Results: All patients had multiple cores involving the entire fiber diameter on longitudinal sections. Weakness and wasting in the shoulder girdle, scoliosis, moderate respiratory impairment, and feeding difficulties were prominent. In contrast to SEPN1-related myopathies, soleus was more severely affected than gastrocnemius on muscle MRI. Haplotyping suggested linkage to the RYR1 locus in informative families and mutational screening revealed four novel RYR1 mutations in three unrelated families; in addition, functional haploinsufficiency was found in one allele of two recessive cases. Conclusion: These findings expand the phenotypic spectrum associated with mutations in the skeletal muscle ryanodine receptor (RYR1) gene. Recessive mutations of domains commonly affected in malignant hyperthermia appear to be particularly prevalent in multi-minicore disease with external ophthalmoplegia and might suggest a different pathomechanism from that involved in central core disease.
Renal morphology, phylogenetic history and desert adaptation of South American hystricognath rodents

Summary 1 To determine whether variation in kidney morphology is associated with environmental aridity in South American hystricognaths, we used conventional and phylogenetic analysis (independent contrasts) to correlate mass-independent renal variables (kidney size; relative medullar thickness, RMT; medulla/cortex ratio, MC; inner medulla/cortex ratio, MIC; relative medullar area, RMA) with environmental variables such as precipitation, temperature and a measure of primary productivity (NDVI). 2 Body mass and most renal indexes showed significant phylogenetic signal (the tendency of closely related species to resemble each other), as well as latitude, one index of minimum daily temperature (Tmin) and NDVI, indicating that correcting for phylogenetic effects is necessary, hence results from independent contrasts are more reliable for these traits. 3 All renal indexes except RMA and MIC were significantly correlated with body mass. After correcting for size effects, inclusion of precipitation or NDVI improved significantly the regression model for kidney size and MIC regardless of the analyses employed, whereas Tmin was also a significant predictor of both indices according to independent contrasts. Precipitation was the best predictor of kidney size, with animals from dryer environments having larger kidneys. RMT was not correlated with any of the environmental indexes employed here. 4 Our results suggest that hystricognaths from environments with lower rainfall have evolved larger kidneys, probably to cope with aridity. Additional renal indices (RMT, MC and RMA) were not correlated with any environmental variable, and their relative importance as predictors of urine concentration ability for this group of rodents remains unclear.
Allatostatin-A neurons inhibit feeding behavior in adult Drosophila

How the brain translates changes in internal metabolic state or perceived food quality into alterations in feeding behavior remains poorly understood. Studies in Drosophila larvae have yielded information about neuropeptides and circuits that promote feeding, but a peptidergic neuron subset whose activation inhibits feeding in adult flies, without promoting metabolic changes that mimic the state of satiety, has not been identified. Using genetically based manipulations of neuronal activity, we show that activation of neurons (or neuroendocrine cells) expressing the neuropeptide allatostatin A (AstA) inhibits or limits several starvation-induced changes in feeding behavior in adult Drosophila, including increased food intake and enhanced behavioral responsiveness to sugar. Importantly, these effects on feeding behavior are observed in the absence of any measurable effects on metabolism or energy reserves, suggesting that AstA neuron activation is likely a consequence, not a cause, of metabolic changes that induce the state of satiety. These data suggest that activation of AstA-expressing neurons promotes food aversion and/or exerts an inhibitory influence on the motivation to feed and implicate these neurons and their associated circuitry in the mechanisms that translate the state of satiety into alterations in feeding behavior.
Antibiotic resistance of faecal Escherichia coli from healthy volunteers from eight developing countries.

OBJECTIVES To determine the prevalence of antibiotic-resistant faecal Escherichia coli from adult volunteers from urban (U) areas in Kenya, Mexico, Peru and the Philippines, and non-urban (NU) locations in Curacao, Mexico, Venezuela, Ghana, Zimbabwe and the Philippines. METHODS Faecal samples of adult volunteers (n=1290) were analysed in one laboratory for the presence of antimicrobial-resistant E. coli using Eosin Methylene Blue agar plates containing, respectively, ampicillin, oxytetracycline, cefazolin, ciprofloxacin, gentamicin, chloramphenicol and trimethoprim at breakpoint concentrations. RESULTS The mean age of the volunteers was approximately 35 years; most of them were female. Ciprofloxacin resistance was in the range 1%-63%: the highest percentages were found in the urban populations of Asia and South America. In Peru and the Philippines (U and NU), the prevalence of gentamicin resistance was >20%. Cefazolin resistance was the highest in the urban Philippines (25%). Higher prevalences for ampicillin, oxytetracycline and trimethoprim were found for urban areas compared with non-urban ones of Asia, Africa and South America, respectively (P<0.05). CONCLUSIONS In the populations studied, antibiotic resistance in faecal E. coli from adult volunteers was emerging for cefazolin, gentamicin and ciprofloxacin and was high for the older drugs ampicillin, oxytetracycline, trimethoprim and chloramphenicol.
Differential expression of microRNAs and other small RNAs in barley between water and drought conditions

Drought is a major constraint to crop production, and microRNAs (miRNAs) play an important role in plant drought tolerance. Analysis of miRNAs and other classes of small RNAs (sRNAs) in barley grown under water and drought conditions reveals that drought selectively regulates expression of miRNAs and other classes of sRNAs. Low-expressed miRNAs and all repeat-associated siRNAs (rasiRNAs) tended towards down-regulation, while tRNA-derived sRNAs (tsRNAs) had the tendency to be up-regulated, under drought. Antisense sRNAs (putative siRNAs) did not have such a tendency under drought. In drought-tolerant transgenic barley overexpressing DREB transcription factor, most of the low-expressed miRNAs were also down-regulated. In contrast, tsRNAs, rasiRNAs and other classes of sRNAs were not consistently expressed between the drought-treated and transgenic plants. The differential expression of miRNAs and siRNAs was further confirmed by Northern hybridization and quantitative real-time PCR (qRT-PCR). Targets of the drought-regulated miRNAs and siRNAs were predicted, identified by degradome libraries and confirmed by qRT-PCR. Their functions are diverse, but most are involved in transcriptional regulation. Our data provide insight into the expression profiles of miRNAs and other sRNAs, and their relationship under drought, thereby helping understand how miRNAs and sRNAs respond to drought stress in cereal crops.
On the Difference Between Closest, Furthest, and Orthogonal Pairs: Nearly-Linear vs Barely-Subquadratic Complexity

Point location problems for n points in d-dimensional Euclidean space (and ep spaces more generally) have typically had two kinds of running-time solutions: (Nearly-Linear) less than dpoly(d) · n logO(d) n time, or (Barely-Subquadratic) f(d) · n2−1/Θ(d) time, for various f. For small d and large n, "nearly-linear" running times are generally feasible, while the "barely-subquadratic" times are generally infeasible, requiring essentially quadratic time. For example, in the Euclidean metric, finding a Closest Pair among n points in Rd is nearly-linear, solvable in 2o(d) · n logO(1) n time, while the known algorithms for finding a Furthest Pair (the diameter of the point set) are only barely-subquadratic, requiring Ω(n2--1/Θ(d)) time. Why do these proximity problems have such different time complexities? Is there a barrier to obtaining nearly-linear algorithms for problems which are currently only barely-subquadratic? We give a novel exact and deterministic self-reduction for the Orthogonal Vectors problem on n vectors in {0, 1}d to n vectors in Zω(log d) that runs in 2o(d) time. As a consequence, barely-subquadratic problems such as Euclidean diameter, Euclidean bichromatic closest pair, and incidence detection do not have O(n2−ϵ) time algorithms (in Turing models of computation) for dimensionality d = ω(log log n)2, unless the popular Orthogonal Vectors Conjecture and the Strong Exponential Time Hypothesis are false. That is, while the poly-log-log-dimensional case of Closest Pair is solvable in n1+o(1) time, the poly-log-log-dimensional case of Furthest Pair can encode difficult large-dimensional problems conjectured to require n2−o(1) time. We also show that the All-Nearest Neighbors problem in ω(log n) dimensions requires n2−o(1) time to solve, assuming either of the above conjectures.
Incidence of neoplasia in Hashimoto's thyroiditis: A fine‐needle aspiration study

There is a recognized association between Hashimoto's thyroiditis (HT) and thyroid neoplasms. We reviewed fine‐needle aspirations (FNAs) from 90 patients with HT to assess the contribution of this procedure. For seven patients, FNA showed HT and follicular neoplasm (n = 6) or HT and papillary carcinoma (n = 1). Eighteen patients underwent thyroid resection. Three patients had follicular adenomas which were not detected by FNA, one patient had papillary carcinoma confirmed, and six patients with follicular neoplasm by FNA were negative for tumor. Thus, 4% of our patients had confirmed neoplasms, an incidence lower than usually reported. One reason for the lower rate of neoplasia in our series was misinterpretation of follicular neoplasia in the background of HT. The cytologic changes in the hyperplastic follicular and metaplastic oncocytic epithelium are similar to those seen in follicular neoplasm. Our study suggests that these processes may be indistinguishable, and thus, in the presence of HT, the diagnosis of follicular neoplasm probably should not be rendered. Diagn Cytopathol 1996;14:38–42. © 1996 Wiley‐Liss, Inc.
The Ras Target AF-6 is a Substrate of the Fam Deubiquitinating Enzyme

The Ras target AF-6 has been shown to serve as one of the peripheral components of cell–cell adhesions, and is thought to participate in cell–cell adhesion regulation downstream of Ras. We here purified an AF-6-interacting protein with a molecular mass of ∼220 kD (p220) to investigate the function of AF-6 at cell–cell adhesions. The peptide sequences of p220 were identical to the amino acid sequences of mouse Fam. Fam is homologous to a deubiquitinating enzyme in Drosophila, the product of the fat facets gene. Recent genetic analyses indicate that the deubiquitinating activity of the fat facets product plays a critical role in controlling the cell fate. We found that Fam accumulated at the cell–cell contact sites of MDCKII cells, but not at free ends of plasma membranes. Fam was partially colocalized with AF-6 and interacted with AF-6 in vivo and in vitro. We also showed that AF-6 was ubiquitinated in intact cells, and that Fam prevented the ubiquitination of AF-6.
Gene delivery with low molecular weight linear polyethylenimines

Linear polyethylenimine (LPEI) with a molecular weight (MW) of 22 kDa has been described as having a superior ability to induce gene transfer compared to its branched form. However, the transfection efficiency of the polymer cannot be enhanced beyond a certain limit due to cytotoxicity. We explored the potential of utilizing LPEIs with MWs ranging from 1.0 to 9.5 kDa to overcome this limitation.
Branchial placenta in the viviparous teleost Ilyodon whitei (Goodeidae)

Intraluminal gestation, as it occurs in viviparous goodeids, allows a wide diversity of embryo‐maternal metabolic exchanges. The branchial placenta occurs in embryos developing in intraluminal gestation when ovarian folds enter through the operculum, into the branchial chamber. The maternal ovarian folds may extend to the embryonic pharyngeal cavity. A branchial placenta has been observed in few viviparous teleosts, and there are not previous histological analyses. This study analysis the histological structure in the goodeid Ilyodon whitei. The moterno ovarian folds extend through the embryonic operculum and reach near the gills, occupying part of the branchial chamber. These folds extend also into the pharyngeal cavity. In some regions, the epithelia of the ovarian folds and embryo were in apposition, developing a placental structure in which, maternal and embryonic capillaries lie in close proximity. The maternal epithelium has desquamated cells which may enter through the branchial chamber to the pharyngeal cavity and the alimentary tract. The complex processes that occur in the ovaries of viviparous teleosts, and its diverse adaptations for viviparity, as the presence of branchial placenta, are relevant in the study of the evolution of vertebrate viviparity. J. Morphol. 275:1406–1417, 2014. © 2014 Wiley Periodicals, Inc.
Model‐Based Assessment of the CO2 Sequestration Potential of Coastal Ocean Alkalinization

The potential of coastal ocean alkalinization (COA), a carbon dioxide removal (CDR) climate engineering strategy that chemically increases ocean carbon uptake and storage, is investigated with an Earth system model of intermediate complexity. The CDR potential and possible environmental side effects are estimated for various COA deployment scenarios, assuming olivine as the alkalinity source in ice‐free coastal waters (about 8.6% of the global ocean's surface area), with dissolution rates being a function of grain size, ambient seawater temperature, and pH. Our results indicate that for a large‐enough olivine deployment of small‐enough grain sizes (10 µm), atmospheric CO2 could be reduced by more than 800 GtC by the year 2100. However, COA with coarse olivine grains (1000 µm) has little CO2 sequestration potential on this time scale. Ambitious CDR with fine olivine grains would increase coastal aragonite saturation Ω to levels well beyond those that are currently observed. When imposing upper limits for aragonite saturation levels (Ωlim) in the grid boxes subject to COA (Ωlim = 3.4 and 9 chosen as examples), COA still has the potential to reduce atmospheric CO2 by 265 GtC (Ωlim = 3.4) to 790 GtC (Ωlim = 9) and increase ocean carbon storage by 290 Gt (Ωlim = 3.4) to 913 Gt (Ωlim = 9) by year 2100.
Mutational analysis of class III receptor tyrosine kinases (C‐KIT, C‐FMS, FLT3) in idiopathic myelofibrosis

Summary. Genomic DNA from patients with idiopathic myelofibrosis (IMF) was screened by polymerase chain reaction (PCR) and conformation sensitive gel electrophoresis (CSGE) for mutations in the C‐KIT gene (60 patients), as well as the C‐FMS and FLT3 genes (40 patients). Intronic primers were used to amplify the entire coding region of both the C‐KIT and C‐FMS genes, and selected regions of the FLT3 gene. CSGE and direct DNA sequencing detected all previously reported as well as several novel polymorphisms in each of the genes. A novel c‐fms exon 9 mutation (Gly413Ser) was detected in two patients. Its functional significance remains to be determined. The c‐kit mutation Asp52Asn, previously described in two of six IMF patients in Japan, was not detected in this study. In addition, the reported c‐fms mutations involving codons 301 and 969 were not identified. Therefore, in contrast to acute myeloid leukaemia, mutations in RTKs class III do not appear to play a significant pathogenetic role in idiopathic myelofibrosis.
Cholesterol oxidase production from entrapped cells of Streptomyces sp.

Production of cholesterol oxidase (COD) under batch conditions through Ca‐alginate immobilized cells of Streptomyces sp. was investigated. The process was studied for optimal immobilization conditions, beads operational stability and comparisons were made with the COD production via free cells. Influence of Na‐alginate concentration (1–5 g L−1) and initial biomass loading on enzyme production were studied. Effects of initial pH of the production medium, temperature, shaker speed, as well as reuse of beads on the COD production were also investigated. It was observed that COD production with immobilized cells (5.6 U ml−1) was higher in comparison to free cells (4.5 U ml−1) under optimized conditions. The maximum COD production by free cells was observed with initial pH 7.0, rpm 200 after 96 h of incubation while immobilized cells sustain a broad pH range 6.0–9.0, rpm 300 for maximum production after 72 h. The immobilized and free cells produced maximum COD in the culture incubated at 37 and 30 °C, respectively. Other parameters bead size and Na‐alginate concentration found to be optimum with 1.5 mm and 4% w/v, respectively. Scanning electron microscope study of the immobilized cells indicated that the cells in Ca‐alginate beads remained in normal shape with no alterations in the morphology.
Cost-Efficient SHA Hardware Accelerators

This paper presents a new set of techniques for hardware implementations of secure hash algorithm (SHA) hash functions. These techniques consist mostly in operation rescheduling and hardware reutilization, therefore, significantly decreasing the critical path and required area. Throughputs from 1.3 Gbit/s to 1.8 Gbit/s were obtained for the SHA implementations on a Xilinx VIRTEX II Pro. Compared to commercial cores and previously published research, these figures correspond to an improvement in throughput/slice in the range of 29% to 59% for SHA-1 and 54% to 100% for SHA-2. Experimental results on hybrid hardware/software implementations of the SHA cores, have shown speedups up to 150 times for the proposed cores, compared to pure software implementations.