Miracle-dz/UniFAR-FTUs huggingface dataset:
Sex Differences in the Recombination Landscape*

Sex differences in overall recombination rates are well known, but little theoretical or empirical attention has been given to how and why sexes differ in their recombination landscapes: the patterns of recombination along chromosomes. In the first scientific review of this phenomenon, we find that recombination is biased toward telomeres in males and more uniformly distributed in females in most vertebrates and many other eukaryotes. Notable exceptions to this pattern exist, however. Fine-scale recombination patterns also frequently differ between males and females. The molecular mechanisms responsible for sex differences remain unclear, but chromatin landscapes play a role. Why these sex differences evolve also is unclear. Hypotheses suggest that they may result from sexually antagonistic selection acting on coding genes and their regulatory elements, meiotic drive in females, selection during the haploid phase of the life cycle, selection against aneuploidy, or mechanistic constraints. No single hypothesis, however, can adequately explain the evolution of sex differences in all cases. Sex-specific recombination landscapes have important consequences for population differentiation and sex chromosome evolution.
Rare loss-of-function variants in KMT2F are associated with schizophrenia and developmental disorders

Schizophrenia is a common, debilitating psychiatric disorder with a substantial genetic component. By analysing the whole-exome sequences of 4,264 schizophrenia cases, 9,343 controls, and 1,077 parent-proband trios, we identified a genome-wide significant association between rare loss-of-function (LoF) variants in KMT2F and risk for schizophrenia. In this dataset, we observed three de novo LoF mutations, seven LoF variants in cases, and none in controls (P = 3.3x10−9). To search for LoF variants in KMT2F in individuals without a known neuropsychiatric diagnosis, we examined the exomes of 45,376 individuals in the ExAC database and found only two heterozygous LoF variants, showing that KMT2F is significantly depleted of LoF variants in the general population. Seven of the ten individuals with schizophrenia carrying KMT2F LoF variants also had varying degrees of learning difficulties. We further identified four KMT2F LoF carriers among 4,281 children with diverse, severe, undiagnosed developmental disorders, and two additional carriers in an independent sample of 5,720 Finnish exomes, both with notable neuropsychiatric phenotypes. Together, our observations show that LoF variants in KMT2F cause a range of neurodevelopmental disorders, including schizophrenia. Combined with previous common variant evidence, we more generally implicate epigenetic dysregulation, specifically in the histone H3K4 methylation pathway, as an important mechanism in the pathogenesis of schizophrenia.
Serum microRNA Signature Is Capable of Early Diagnosis for Non-Small Cell Lung Cancer

Despite decades of efforts, non-small-cell lung cancer (NSCLC) remains the leading cause of cancer mortality globally primarily due to the challenge in early detection of the cancer. Being an important player in cancer development, the dysregulated miRNAs have been shown promising values as non-invasive diagnostic and prognostic biomarkers for NSCLC. The aim of our study is to access the efficacy and reliability of a potential circulating miRNA panel in early diagnosis of NSCLC. We first selected eight candidate miRNAs, miR-146b, miR-205, miR-29c, miR-31, miR-30b, miR-337, miR-411, and miR-708, which have been shown frequently aberrant in primary NSCLC patients based on our previous studies and other reports. The serum level of each of these miRNAs was evaluated by quantitative real-time PCR (qRT-PCR) in training and testing sets. We found that 5 out of 8 miRNAs (miR-146b, miR-205, miR-29c, miR-30b, and miR-337) were significantly up-regulated in NSCLCs patients compared to healthy or cancer-free controls in both training and testing sets. Based on the logistic regression model, a 4-miRNAs set (miR-146b, miR-205, miR-29c and miR-30b) was picked out of the 5 miRNAs owing to its excellent diagnostic power for NSCLC patients in the training set (AUC=0.99, accuracy=95.00%), the testing set (AUC=0.93, accuracy=89.69%), and the training-testing combined set ( AUC=0.96, accuracy=92.00%). When pathological subtypes of NSCLC are compared, this 4-miRNA panel carried a relatively higher prediction power and higher sensitivity for adenocarcinoma (AC) (AUC=0.98, sensitivity=99.10%) than for squamous cell carcinoma (SCC) (AUC=0.93, sensitivity=90.32%). Additionally, this panel demonstrated a comparable diagnostic capacity for stage I (AUC=0.96) and stage II-III (AUC=0.95) of NSCLC, suggesting its role in reflecting the tumor load. Importantly, the high levels of miR-146b and miR-29c in serum were significantly associated with poor 5-year overall survival (OS) (both p=0.04). Further survival analysis showed that high level of miR-146b in serum is specifically correlated with poor survival rate in SCC patients (p=0.0035) but not in AC patients (p=0.83), consistent with our previous finding that the high tissue expression of miR-146b in lung cancer specimen is indicative of a poor prognosis for SCC patients. Altogether, our study demonstrated that the 4-miRNA panel is a novel, sensitive and non-invasive serum marker for the early diagnosis of NSCLC.
Phylogenetic effective sample size

In this paper I address the question — how large is a phylogenetic sample? I propose a definition of a phylogenetic effective sample size for Brownian motion and Ornstein–Uhlenbeck processes — the regression effective sample size. I discuss how mutual information can be used to define an effective sample size in the non-normal process case and compare these two definitions to an already present concept of effective sample size (the mean effective sample size). Through a simulation study I find that the AICc is robust if one corrects for the number of species or effective number of species. Lastly I discuss how the concept of the phylogenetic effective sample size can be useful for biodiversity quantification, identification of interesting clades and deciding on the importance of phylogenetic correlations.
Differentiating spatial from environmental effects on foliar fungal communities of Populus trichocarpa

Foliar fungi – pathogens, endophytes, epiphytes – form taxonomically diverse communities that affect plant health and productivity. The composition of foliar fungal communities is variable at spatial scales both small (e.g. individual plants) and large (e.g. continents), yet few studies have attempted to tease apart spatial from climatic factors influencing these communities. Moreover, few studies have sampled in more than 1 year to gauge interannual variation in community structure.
Pseudo-lemmatization in Croatian-English SMT

One of the first difficulties in conducting a thorough analysis of statistical machine translation involving Croatian as a morphologically rich and resource poor language is the lack of quality language resources. This paper presents results of two standard fourteen feature Croatian-English phrase-based statistical machine translation systems. Prior to building the second system a partial pseudo-lemmatization of the Croatian parts of training and test sets is made in an attempt to simplify the translation process. Besides automatic evaluation, manual evaluation is conducted in order to gain insight into the nature of the translation differences achieved between two systems.
Effect of storage methods on the germination and early growth performance of African bread fruits ( Treculia africana )

Inadequate drying and storage devices, large volumes of high quality seeds are lost for planting as well as for eating, and so there is a need in getting appropriate storage methods. The study is set to evaluate effect of storage methods on germination and early growth performances of African breadfruits were investigated. A total of 360 seeds in three replications of 60 seeds were subjected to six storage media clay pot, open basket, jute bag, wooden boxes, Jerrican and control (fresh seed) the storage aspect was monitored for 4 weeks. The seedlings produced were thereafter transplanted into the nursery bed with poly bags in a Complete Randomized Design (CRD). The seedlings were assessed for plant height, number of leaves, number of branches and leaf area. Data was analyzed using descriptive statistics. Germination percentage across the storage methods revealed that seeds without storage (control) recorded the highest germination percentage of (96%) closely followed by wooden box (93%) while Jute bags (78%). The least percentage germination (63%) was recorded for Seed stored in open basket. Plant height recorded the highest mean value (98.5cm) from seed without storage; the control closely followed by seed stored in Wooden Box (95.6cm) open basket recorded the least value (33.4cm). There was significant increase in the number of leaves ( P > 0.05). The control recorded the highest number of leaves (40.3) followed by wooden box (35.4) while seeds planted in open basket obtained the least leaves count (10.5). The mean number of branches was higher for T. africana seed without storage (Control) which recorded (30) branches, while the least numbers of branches was obtained from seed stored in clay pot 9 branches. Leave area was significantly higher ( P >0.05) (65.5cm 2 ) from the control, wooden box closely followed (54.6cm 2 ) with the Jerrican device recording the least leave area (25.3cm 2 ). It is therefore recommended that fresh seeds of T. africana be sown fresh. Where long term storage is needed, wooden boxes should be used, but the local farmers may employ the use of jute bag to store T. africana seed meant for planting. Keywords: Storage Methods, Germination, Growth Performance, Wooden box, African breadfruits
Chemical fractions and bioavailability of nickel in a Ni-treated calcareous soil amended with plant residue biochars

ABSTRACT Recently, the use of biochars for stabilization of soil heavy metals has been expanded due to their adsorption characteristics, low cost and carbon storage potential. A factorial experiment was performed to investigate the effects of two plant residue biochars (licorice root pulp and rice husk biochar each applied at 2.5% (w/w)) produced at two temperatures (350 and 550 °C), and three Ni application rates (0, 150 and 300 mg Ni kg−1) on bioavailability and chemical fractions of Ni in a calcareous soil after spinach cultivation. Application of all the biochars significantly reduced Ni bioavailability factor (5–15%) and spinach Ni concentration (54–77%) in Ni-treated soil. The biochars produced at 550 °C were more effective at reducing Ni mobility and Ni uptake by spinach than those produced at 350 °C, attributed to higher CaCO3 and lower acidic functional group content, which resulted in greater enhancement of soil pH. When comparing the biochars produced at the same temperature, the rice husk biochars were the most effective in reducing Ni bioavailability, likely due to their lower acidic functional group content and higher nano-silica content which resulted in higher soil pH values and potentially promoted the formation of Ni-silicates and hydroxides. Abbreviations : Ni: Nickel; RHB: rice husk biochar; LRB: licorice root pulp biochar; WsEx: water soluble and exchangeable; CARB: carbonate form; RES: residual; MnOx; manganese oxides bound; AFeOx; amorphous iron oxides bound; CFeOx: crystalline iron oxides bound; OM: organic bound.
Polarimetric passive remote sensing of ocean wind vectors

Presents the first experimental evidence that the polarimetric brightness temperatures of sea surfaces are sensitive to ocean wind direction in the incidence angle range of 30 to 50 degrees. The experimental data were collected by a K-band (19.35 GHz) polarimetric radiometer (WINDRAD) mounted on the NASA DC-8 aircraft. A set of aircraft radiometer flights was successfully completed in November 1993. The first WINDRAD flight was made on November 4, 1993. There was clear weather with a wind speed of 12 m/s at 330 degrees around the Pt. Arena buoy. The buoy was circled at three incidence angles, and all data when plotted as functions of azimuth angles show clear modulations of several degrees Kelvin. At 40 degrees incidence angle, there is a 5 degrees Kelvin peak-to-peak signal in the second Stokes parameter and and the third Stokes parameter U. The Q data maximum is in the upwind direction and U has a 45 degrees phase shift in azimuth -as predicted by theory. There is also an up/downwind asymmetry of 2 degrees Kelvin in the Q data, and 1 degree Kelvin in the U data. At 50 degrees incidence angle, the collected data show very similar wind direction signatures to the SSM/I model function. Additional flight's were made on other days under cloudy conditions. Data taken at a wind speed of 8 m/s show that at 40 degrees incidence Q and U have a smaller azimuthal modulation of 3 degrees Kelvin, probably due to the lower wind speed. Additionally, the simultaneously recorded video images of sea surfaces suggested that and and U data were less sensitive to clouds, breaking waves and whitecaps, while the T/sub /spl upsi// and T/sub h/ increased by a few degrees Kelvin when the radiometer beam crossed over clouds, or there was a sudden increase of whitecaps in the radiometer footprint. The results of the authors' aircraft flights clearly indicate that passive polarimetric radiometry is a viable option in space remote sensing of ocean surface wind direction as well as wind speed. <<ETX>>
Parsimonious Relevance and Concept Models

We describe our participation in the CLEF 2008 Domain Specific track. The research questions we address are threefold: (i) what are the effects of estimating and applying relevance models to the domain specific collection used at CLEF 2008, (ii) what are the results of parsimonizing these relevance models, and (iii) what are the results of applying concept models for blind relevance feedback? Parsimonization is a technique by which the term probabilities in a language model may be re-estimated based on a comparison with a reference model, making the resulting model more sparse and to the point. Concept models are term distributions over vocabulary terms, based on the language associated with concepts in a thesaurus or ontology and are estimated using the documents which are annotated with concepts. Concept models may be used for blind relevance feedback, by first translating a query to concepts and then back to query terms. We find that applying relevance models helps significantly for the current test collection, in terms of both mean average precision and early precision. Moreover, parsimonizing the relevance models helps mean average precision on title-only queries and early precision on title+narrative queries. Our concept models are able to significantly outperform a baseline query-likelihood run, both in terms of mean average precision and early precision on both title-only and title+narrative queries.
Aggregation of Direct and Indirect Positioning Sensors for Vehicle Guidance

Advanced Vehicle Control Systems (AVCS) require large numbers of sensors for different levels within the control hierarchy. Whereas all sensors contain uncertainty to some degree, different sensors are particularly useful for specific environmental conditions. Therefore, sensor redundancy is essential to achieving high sensor data fidelity for use in real-world, non-ideal, unpredictable environments. In this work, a positioning sensor system, which includes Global Positioning System (GPS) receivers, a radar sensor, and a linear transducer is investigated. Positioning sensors provide information about the absolute or relative position of vehicles, a crucial component of the control system. GPS is potentially powerful for AVCS because of its high accuracy achievable by Differential GPS (DGPS) and other advanced GPS techniques. Field tests using these three sensors have been performed in cooperation with SRI International. Sensor noise models of GPS, radar, and linear Transducer sensors are developed based on the test data. A synchronization method is suggested for the scenario in which sensors output data at different frequencies and time delays. Two types of validation and fusion algorithms, PDAF and FUSVAF, are implemented for the open loop test data and the results are compared. A closed loop simulation has been performed using a simple PDD controller as the follower control law within a platoon. The sensor models developed here are applied in the simulation, and the two fusion algorithms are implemented and the results are compared. Finally, additional simulations incorporate results into VDL. Key words: sensor modeling, sensor validation, sensor fusion, data fusion, data synchronization, supervisory control, VDL, management of uncertainty, reliability
Effects of two management systems on the growth performance of juvenile African giant land snails ( Archachatina marginata )

The study of the effects of two management systems on the Growth Performance of juvenile African Giant Land Snails ( Archachatina marginata ) was carried out in the wildlife domestication unit of the Department of Forest Resources and Wildlife Management, University of Benin, Benin City, Nigeria. One hundred and twenty (120) African giant land snails ( Archachatina marginata ) of average body weight 36.35g ± 0.32g were used for the study. Sixty (60) snails were raised in an intensive system of management while sixty (60) snails were raised in an extensive system of management. Each of the system of management served as the treatment and each treatment was replicated three (3) times with twenty (20) snails per replicate and sixty (60) snails per treatment in a Completely Randomize Design. Results showed that there was a significant difference at ( p <0.05) in the weight gain of the Archachatina marginata of the two management systems. The intensive management system had a higher weight gain of 136.53g with mean value of 5.25 while the extensive management system had a weight gain of 106.53g with mean value of 4.10. There was also a significant difference at ( p <0.05) in the shell length increment and shell width increment of the Archachatina marginata of the two management systems. The snails in the extensive management system had a higher shell length increment of 9.94cm with mean value of 0.38 while the snails in the intensive management system had a shell length increment of 8.02cm with mean value of 0.31. The snails in the extensive management system had a higher shell width increment of 10.46cm with mean value of 0.40 while the snails in the intensive management system had a shell width increment of 9.02cm with mean value of 0.35. The Feed Conversion Ratio (FCR) of the snails in the intensive system of management was 1.99. It was concluded that formulated feed used in feeding the snails in the intensive system of management contributed to the higher weight gain. Keywords: Juvenile, Archachatina marginata , intensive system, extensive system, weight gain
From plasmodesma geometry to effective symplasmic permeability through biophysical modelling

Regulation of molecular transport via intercellular channels called plasmodesmata (PDs) is important for both coordinating developmental and environmental responses among neighbouring cells, and isolating (groups of) cells to execute distinct programs. Cell-to-cell mobility of fluorescent molecules and PD dimensions (measured from electron micrographs) are both used as methods to predict PD transport capacity (i.e., effective symplasmic permeability), but often yield very different values. Here, we build a theoretical bridge between both experimental approaches by calculating the effective symplasmic permeability from a geometrical description of individual PDs and considering the flow towards them. We find that a dilated central region has the strongest impact in thick cell walls and that clustering of PDs into pit fields strongly reduces predicted permeabilities. Moreover, our open source multi-level model allows to predict PD dimensions matching measured permeabilities and add a functional interpretation to structural differences observed between PDs in different cell walls.
Development, growth and metabolic rate of Hermetia illucens larvae

The larvae of Hermetia illucens are known to successfully bio‐convert a vast range of organic substrates into high protein and fat biomass, but little is known about the larval instars. During this research, larval head capsules and biomass growth were measured daily and the specific metabolic rate of larger instars were considered. The head capsule measurements revealed that H. illucens pass through 6 actively feeding larval stadia before entering the last nonfeeding but migrating 7th stadium. Larval growth follows a sigmoid curve with slowly accelerating growth in the earlier stadia and decelerating growth in the latest stadia. In contrast, development was fast until reaching stadium 6 and then slowed down. Accordingly, the specific metabolic rate was high in instars 3, 4 and 5 and reduced in instars 6 and 7.
The Other Woman: Mate Poaching Across the Menstrual Cycle

The goal of the present work was to empirically examine how mate poaching, or romantically pursuing an individual already in a committed relationship (Schmitt & Buss, 2001), varies across the menstrual cycle. The existing literature strongly suggests that partnered women are wary of ovulating women because they are deemed threatening rivals (Krems, Neel, Neuberg, Puts, & Kenrick, 2016). The series of experiments described here tested this assumption by examining both the mate poaching behaviors and perceptions of ovulating women across the menstrual cycle. The first experiment examined if ovulating women would be more willing to mate poach an attractive man. The results were significant, finding that normally ovulating women near peak fertility were more likely to engage in mate poaching behaviors to steal the attractive man away from his relationship than they were for the average-looking man. The second and third experiments examined how women viewed other, ovulating women in the context of potential mate poaching across the menstrual cycles of both the rival and the observer. The second experiment finding, which approached significance, was that normally ovulating women were more likely to view rival near peak fertility as more threatening than women on hormonal contraceptives. The third experiment found perception of poaching is impacted by women’s own conception risk. Implications of these findings, as well as future directions, are discussed. Acknowledgements I would like to express my gratitude to my thesis advisor, Dr. Erin O’Mara, for all the guidance she has provided to bring this thesis to life. I would also like to thank the University of Dayton Psychology Department, Honors Program, and Stander Fellowship for the support provided to complete this research.