Miracle-dz/UniFAR-FTUs huggingface dataset:
Natural Genetic Variation and Candidate Genes for Morphological Traits in Drosophila melanogaster

Body size is a complex character associated to several fitness related traits that vary within and between species as a consequence of environmental and genetic factors. Latitudinal and altitudinal clines for different morphological traits have been described in several species of Drosophila and previous work identified genomic regions associated with such variation in D. melanogaster. However, the genetic factors that orchestrate morphological variation have been barely studied. Here, our main objective was to investigate genetic variation for different morphological traits associated to the second chromosome in natural populations of D. melanogaster along latitudinal and altitudinal gradients in Argentina. Our results revealed weak clinal signals and a strong population effect on morphological variation. Moreover, most pairwise comparisons between populations were significant. Our study also showed important within-population genetic variation, which must be associated to the second chromosome, as the lines are otherwise genetically identical. Next, we examined the contribution of different candidate genes to natural variation for these traits. We performed quantitative complementation tests using a battery of lines bearing mutated alleles at candidate genes located in the second chromosome and six second chromosome substitution lines derived from natural populations which exhibited divergent phenotypes. Results of complementation tests revealed that natural variation at all candidate genes studied, invected, Fasciclin 3, toucan, Reticulon-like1, jing and CG14478, affects the studied characters, suggesting that they are Quantitative Trait Genes for morphological traits. Finally, the phenotypic patterns observed suggest that different alleles of each gene might contribute to natural variation for morphological traits. However, non-additive effects cannot be ruled out, as wild-derived strains differ at myriads of second chromosome loci that may interact epistatically with mutant alleles.
On Log-Structured Merge for Solid-State Drives

Log-structure merge (LSM) is an increasingly prevalent approach to indexing, especially for modern writeheavy workloads. LSM organizes data in levels with geometrically increasing sizes. Records enter the top level, whenever a level fills up, it is merged down into the next level. Hence, the index is updated only through merges and records are never updated inplace. While originally conceived to avoid slow random accesses of hard drives, LSM also turns out to be especially suited to solidstate drives, or any block-based storage with expensive writes. We study how to further reduce writes in LSM. Traditionally, LSM always merges an overflowing level fully into the next. We investigate in depth how partial merges save writes and prove bounds on their effectiveness. We propose new algorithms that make provably good decisions on whether to perform a partial merge, and if yes, which part of a level to merge. We also show how to further reduce writes by reusing data blocks during merges. Overall, our approach offers better worst-case guarantees and better practical performance than existing LSM variants.
Crossover control in selection hyper-heuristics : case studies using MKP and HyFlex

Hyper-heuristics are a class of high-level search methodologies which operate over a search space of heuristics rather than a search space of solutions. Hyper-heuristic research has set out to develop methods which are more general than traditional search and optimisation techniques. In recent years, focus has shifted considerably towards cross-domain heuristic search. The intention is to develop methods which are able to deliver an acceptable level of performance over a variety of different problem domains, given a set of low-level heuristics to work with. This thesis presents a body of work investigating the use of selection hyper-heuristics in a number of different problem domains. Specifically the use of crossover operators, prevalent in many evolutionary algorithms, is explored within the context of single-point search hyper-heuristics. A number of traditional selection hyper-heuristics are applied to instances of a well-known NP-hard combinatorial optimisation problem, the multidimensional knapsack problem. This domain is chosen as a benchmark for the variety of existing problem instances and solution methods available. The results suggest that selection hyper-heuristics are a viable method to solve some instances of this problem domain. Following this, a framework is defined to describe the conceptual level at which crossover low-level heuristics are managed in single-point selection hyper-heuristics. HyFlex is an existing software framework which supports the design of heuristic search methods over multiple problem domains, i.e. cross-domain optimisation. A traditional heuristic selection mechanism is modified in order to improve results in the context of cross-domain optimisation. Finally the effect of crossover use in cross-domain optimisation is explored.
Current Trend of Water Hyacinth Expansion and Its Consequence on theFisheries around North Eastern Part of Lake Tana, Ethiopia

The study was conducted from June, 2015 to October, 2016 to assess the effect of water hyacinth on fishing and fishers around the North-Eastern part of Lake Tana. The presence of water hyacinth in Lake Tana has been recognized in 2011. Starting from the last five years, especially after 2014, fishing in the study area becomes tiring due to the expansion of this invasive weed. Water hyacinth entangles the fishing nets and boats’ propeller, making it difficult to fish and resulting in reduced fish catches. Hence, a reduced fish catch would have an adverse effect on the quality of life of the communities around the lake and consequently affect sustainable development in the region. Despite the fact that several efforts have been made by different parties, water hyacinth in Lake Tana continues to expand itself year after year. Therefore, o its expansion is not easy to manage and complete eradication is unimaginable. Therefore, if the expansion of water hyacinth continues in this trend, it can negatively affect the livelihood of fishers in both directions by increasing costs of fishing and reducing the amount of fish caught.
A new isoflavone from the fruits of Madhuca latifolia

A new isoflavone, 3′,4′-dihydroxy-5,2′-dimethoxy-6,7-methylendioxy isoflavone, was isolated from the Madhuca latifolia fruit coatings. The structure was elucidated on the basis of spectral and chemical evidence.
Cross-Language Distributions of High Frequency and Phonetically Similar Cognates

The coinciding form and meaning similarity of cognates, e.g. ‘flamme’ (French), ‘Flamme’ (German), ‘vlam’ (Dutch), meaning ‘flame’ in English, facilitates learning of additional languages. The cross-language frequency and similarity distributions of cognates vary according to evolutionary change and language contact. We compare frequency and orthographic (O), phonetic (P), and semantic similarity of cognates, automatically identified in semi-complete lexicons of six widely spoken languages. Comparisons of P and O similarity reveal inconsistent mappings in language pairs with deep orthographies. The frequency distributions show that cognate frequency is reduced in less closely related language pairs as compared to more closely related languages (e.g., French-English vs. German-English). These frequency and similarity patterns may support a better understanding of cognate processing in natural and experimental settings. The automatically identified cognates are available in the supplementary materials, including the frequency and similarity measurements.
Integrative Genetic Characterization and Phenotype Correlations in Pheochromocytoma and Paraganglioma Tumours

Background About 60% of Pheochromocytoma (PCC) and Paraganglioma (PGL) patients have either germline or somatic mutations in one of the 12 proposed disease causing genes; SDHA, SDHB, SDHC, SDHD, SDHAF2, VHL, EPAS1, RET, NF1, TMEM127, MAX and H-RAS. Selective screening for germline mutations is routinely performed in clinical management of these diseases. Testing for somatic alterations is not performed on a regular basis because of limitations in interpreting the results. Aim The purpose of the study was to investigate genetic events and phenotype correlations in a large cohort of PCC and PGL tumours. Methods A total of 101 tumours from 89 patients with PCC and PGL were re-sequenced for a panel of 10 disease causing genes using automated Sanger sequencing. Selected samples were analysed with Multiplex Ligation-dependent Probe Amplification and/or SNParray. Results Pathogenic genetic variants were found in tumours from 33 individual patients (37%), 14 (16%) were discovered in constitutional DNA and 16 (18%) were confirmed as somatic. Loss of heterozygosity (LOH) was observed in 1/1 SDHB, 11/11 VHL and 3/3 NF1-associated tumours. In patients with somatic mutations there were no recurrences in contrast to carriers of germline mutations (P = 0.022). SDHx/VHL/EPAS1 associated cases had higher norepinephrine output (P = 0.03) and lower epinephrine output (P<0.001) compared to RET/NF1/H-RAS cases. Conclusion Somatic mutations are frequent events in PCC and PGL tumours. Tumour genotype may be further investigated as prognostic factors in these diseases. Growing evidence suggest that analysis of tumour DNA could have an impact on the management of these patients.
Multi-Media Campaigns, Interpersonal Contacts and Contraceptive Behaviour in Southwest Nigeria

Recent evidence suggests that mass media may be an effective tool for motivating people to adopt family planning. Little is known, however, about the process by which this takes place. In this exploratory study, we argue that following an exposure to mass media message(s) about family planning, interpersonal discussion of such message(s) is an important intermediate stage in the process of deciding to use or not to use contraception. If this is the case, interpersonal discussion is expected to enhance or attenuate the effects of exposure to media messages on contraceptive behaviour. Our results show that there is a significant positive relationship between exposure to media messages and contraceptive use in Southwest Nigeria. Furthermore, among women who are exposed to media messages, those who discuss the messages with other people are more likely to use contraception compared with those who did not discuss the messages.
SPEECH RECOGNITION USING THE MELLIN TRANSFORM THESIS

The purpose of this research was to improve performance in speech recognition. Specifically, a new approach was investigating by applying an integral transform known as the Mellin transform (MT) on the output of an auditory model to improve the recognition rate of phonemes through the scale-invariance property of the Mellin transform. Scale-invariance means that as a time-domain signal is subjected to dilations, the distribution of the signal in the MT domain remains unaffected. An auditory model was used to transform speech waveforms into images representing how the brain “sees” a sound. The MT was applied and features were extracted. The features were used in a speech recognizer based on Hidden Markov Models. The results from speech recognition experiments showed an increase in recognition rates for some phonemes compared to traditional methods.
Effect of arbuscular mycorrhizal fungi on young vines in copper-contaminated soil

Abstract High copper (Cu) levels in uprooted old vineyard soils may cause toxicity in transplanted young vines, although such toxicity may be reduced by inoculating plants with arbuscular mycorrhizal fungi (AMF). The objective of this study was to evaluate the effects of AMF on the plant growth, chlorophyll contents, mycorrhizal colonization, and Cu and phosphorus (P) absorption in young vines cultivated in a vineyard soil contaminated by Cu. Commercial vineyard soil with high Cu levels was placed in plastic tubes and transplanted with young vines, which were inoculated with six AMF species (Dentiscutata heterogama, Gigaspora gigantea, Acaulospora morrowiae, A. colombiana, Rhizophagus clarus, R. irregularis) and a control treatment on randomized blocks with 12 replicates. After 130 days, the mycorrhizal colonization, root and shoot dry matter (DM), height increment, P and Cu absorption, and chlorophyll contents were evaluated. The height increment, shoot DM and chlorophyll contents were not promoted by AMF, although the root DM was increased by R. clarus and R. irregularis, which had the greatest mycorrhizal colonization and P uptake. AMF increased Cu absorption but decreased its transport to shoots. Thus, AMF species, particularly R. clarus and R. irregularis, contribute to the establishment of young vines exposed to high Cu levels.
Interleukin-6 promotes androgen-independent growth in LNCaP human prostate cancer cells.

PURPOSE Prostate cancer frequently progresses from an initial androgen dependence to androgen independence, rendering the only effective androgen ablation therapy useless. The mechanism underlying the androgen-independent progression is incompletely understood. Interleukin (IL)-6 has been implicated in this androgen-independent progression. In this study, we tested whether IL-6 induces androgen-independent growth both in vitro and in vivo. EXPERIMENTAL DESIGN IL-6 was expressed in androgen-sensitive LNCaP cells. The effects of IL-6 on androgen receptor activity was determined by Northern blots and gel shift assays. The effects of IL-6 on LNCaP cell growth were determined in vitro by MTT assay and in vivo. RESULTS IL-6 can enhance the growth of androgen-sensitive LNCaP cells in the androgen-deprived condition in vitro, which is accompanied by elevation of androgen-regulated prostate-specific antigen mRNA expression. IL-6 promotes androgen-sensitive LNCaP cell tumor growth in the castrated male mice. IL-6 enhances androgen receptor DNA binding activity and nuclear translocation. The androgen-independent phenotype induced by IL-6 in LNCaP cells is accompanied by significant activation of signal transducers and activators of transcription 3 and mitogen-activated protein kinase signal pathways. CONCLUSIONS These studies clearly provide experimental evidence that IL-6 initiates and/or enhances the transition of prostate cancer cells from an androgen-dependent to an androgen-independent phenotype.
Commentary: but why should women be weighed routinely during pregnancy?

Kleinman and colleagues 1 argue that the pattern of weight gain during pregnancy, as assessed by utilizing both the amount and timing of maternal weight in their area under the weight gain curve (AUC) method, is a more reliable predictor of weight retention after delivery than weight gain alone. Certainly, it seems plausible that weight gained early in pregnancy may be more difficult to shed, as this is likely to reflect maternal fat stores; rather than weight gained later in pregnancy which is more likely to be due to the growing fetus. Although this association may have a value for epidemiological analyses, does measuring maternal weight throughout pregnancy have a role in clinical practice? Routine measurement of maternal weight was introduced into antenatal care during the Second World War in London, as a screening test for poor maternal nutrition. Decades later, the clinical value of this practice was challenged and found wanting. 2 Although there is an association between maternal weight and birthweight, 3 the AUC data 1 provide further evidence that the correlation is too weak to be of clinical value. Nevertheless, maternal weight, weight gain and weight loss are associated with pregnancy outcome. Underweight women and those with weight loss during pregnancy have an increased risk of complications such as pre-term birth and low infant birthweight; whilst overweight women and those with excessive weight gain are at increased risk of a range of adverse
Hidden starbursts and active galactic nuclei at 0< z <4 from the Herschel-VVDS-CFHTLS-D1 field: Inferences on coevolution and feedback

We investigate of the properties of ~2000 Herschel/SPIRE far-infrared-selected galaxies from 0 0.5), the highest LTIR galaxies in a given redshift bin are unobserved by SPIRE at subsequently lower redshifts, a trend linked to downsizing. In conjunction with other results, this evidence is used to argue for prevalent AGN-driven quenching in starburst galaxies across cosmic time.
Two‐Pass Tests of Asset Pricing Models with Useless Factors

In this paper we investigate the properties of the standard two-pass methodology of testing beta pricing models with misspecified factors. In a setting where a factor is useless, defined as being independent of all the asset returns, we provide theoretical results and simulation evidence that the second-pass cross-sectional regression tends to find the beta risk of the useless factor priced more often than it should. More surprisingly, this misspecification bias exacerbates when the number of time series observations increases. Possible ways of detecting useless factors are also examined. WHEN TESTING ASSET PRICING MODELS relating risk premiums on assets to their betas, the primary question of interest is whether the beta risk of a particular factor is priced (i.e., whether the estimated risk premium associated with a given factor is significantly different from zero). Black, Jensen, and Scholes (1972) and Fama and MacBeth (1973) develop a two-pass methodology in which the beta of each asset with respect to a factor is estimated in a first-pass time series regression, and estimated betas are then used in second-pass cross-sectional regressions (CSRs) to estimate the risk premium of the factor. This two-pass methodology is very intuitive and has been widely used in the literature. The properties of the test statistics and goodness-offit measures under the two-pass methodology are usually developed under the assumptions that the asset pricing model is correctly specified and that the factors are correctly identified. Shanken (1992) provides an excellent discussion of this two-pass methodology, especially the large sample proper
KMT2D maintains neoplastic cell proliferation and global histone H3 lysine 4 monomethylation

KMT2D (lysine (K)-specific methyltransferase 2D), formerly named MLL2 (myeloid/lymphoid or mixed-lineage leukemia 2, also known as ALR/MLL4), is a histone methyltransferase that plays an important role in regulating gene transcription. In particular, it targets histone H3 lysine 4 (H3K4), whose methylations serve as a gene activation mark. Recently, KMT2D has emerged as one of the most frequently mutated genes in a variety of cancers and in other human diseases, including lymphoma, medulloblastoma, gastric cancer, and Kabuki syndrome. Mutations in KMT2D identified thus far point to its loss-of-function in pathogenesis and suggest its role as a tumor suppressor in various tissues. To determine the effect of a KMT2D deficiency on neoplastic cells, we used homologous recombination- and nuclease-mediated gene editing approaches to generate a panel of isogenic colorectal and medulloblastoma cancer cell lines that differ with respect to their endogenous KMT2D status. We found that a KMT2D deficiency resulted in attenuated cancer cell proliferation and defective cell migration. Analysis of histone H3 modifications revealed that KMT2D was essential for maintaining the level of global H3K4 monomethylation and that its enzymatic SET domain was directly responsible for this function. Furthermore, we found that a majority of KMT2D binding sites are located in regions of potential enhancer elements. Together, these findings revealed the role of KMT2D in regulating enhancer elements in human cells and shed light on the tumorigenic role of its deficiency. Our study supports that KMT2D has distinct roles in neoplastic cells, as opposed to normal cells, and that inhibiting KMT2D may be a viable strategy for cancer therapeutics.
The Effect of Topic Sampling on Sensitivity Comparisons of Information Retrieval Metrics

The Voorhees/Buckley swap method is useful for comparing the discrimination power of Information Retrieval (IR) and Question Answering (QA) metrics. Given a test collection, a set of runs and an evaluation metric, it derives the swap rate, the chance of observing inconsistencies when two completely different topic sets are used for comparing a pair of runs. Recently, however, Sanderson and Zobel claimed that the method overestimates swap rates as it samples topics without replacement. The main question we address in this paper is whether sampling with and without replacement produce any different results for the purpose of comparing the sensitivity of different metrics. Our IR and QA experiments show that the two methods do generally yield similar results, which suggests that the original Voorhees/Buckley method is valid.
Reliability and the adaptive utility of discrimination among alarm callers

Unlike individually distinctive contact calls, or calls that aid in the recognition of young by their parents, the function or functions of individually distinctive alarm calls is less obvious. We conducted three experiments to study the importance of caller reliability in explaining individual–discriminative abilities in the alarm calls of yellow–bellied marmots (Marmota flaviventris). In our first two experiments, we found that calls from less reliable individuals and calls from individuals calling from a greater simulated distance were more evocative than calls from reliable individuals or nearby callers. These results are consistent with the hypothesis that marmots assess the reliability of callers to help them decide how much time to allocate to independent vigilance. The third experiment demonstrated that the number of callers influenced responsiveness, probably because situations where more than a single caller calls, are those when there is certain to be a predator present. Taken together, the results from all three experiments demonstrate the importance of reliability in explaining individual discrimination abilities in yellow–bellied marmots. Marmots' assessment of reliability acts by influencing the time allocated to individual assessment and thus the time not allocated to other activities.
The Potential of Unique Words in OFDM

In this paper we propose a novel transmit signal structure and an adjusted and optimized receiver for OFDM (orthogonal frequency division multiplexing). Instead of the conventional cyclic prefix (CP) we use a deterministic sequence, which we call unique word (UW), as guard interval. We show how unique words, which are already well investigated for single carrier frequency domain equalization (SC/FDE) systems, can also be introduced in OFDM symbols. Since unique words represent known sequences, they can advantageously be used for synchronization and channel estimation purposes. Furthermore, the proposed approach introduces correlations along the subcarrier symbols. This allows to apply a highly efficient Wiener LMMSE (linear minimum mean square error) smoother for noise reduction at the receiver. We present simulation results in an indoor multipath environment to highlight the advantageous properties of the proposed scheme.