Miracle-dz/UniFAR-FTUs huggingface dataset:
A Likelihood Approach for Uncovering Selective Sweep Signatures from Haplotype Data

Selective sweeps are frequent and varied signatures in the genomes of natural populations, and detecting them is consequently important in understanding mechanisms of adaptation by natural selection. Following a selective sweep, haplotypic diversity surrounding the site under selection decreases, and this deviation from the background pattern of variation can be applied to identify sweeps. Multiple methods exist to locate selective sweeps in the genome from haplotype data, but none leverage the power of a model-based approach to make their inference. Here, we propose a likelihood ratio test statistic T to probe whole genome polymorphism datasets for selective sweep signatures. Our framework uses a simple but powerful model of haplotype frequency spectrum distortion to find sweeps and additionally make an inference on the number of presently sweeping haplotypes in a population. We found that the T statistic is suitable for detecting both hard and soft sweeps across a variety of demographic models, selection strengths, and ages of the beneficial allele. Accordingly, we applied the T statistic to variant calls from European and sub-Saharan African human populations, yielding primarily literature-supported candidates, including LCT, RSPH3, and ZNF211 in CEU, SYT1, RGS18, and NNT in YRI, and HLA genes in both populations. We also searched for sweep signatures in Drosophila melanogaster, finding expected candidates at Ace, Uhg1, and Pimet. Finally, we provide open-source software to compute the T statistic and the inferred number of presently sweeping haplotypes from whole-genome data.
Introducing extra bicarbonate transporters bicA and sbtA in the cyanobacterium synechocystis sp. PCC 6803 for enhanced ethanol production

i Declaration . ii List of Publications . iii Acknowledgements . iv List of Figures . viii List of Tables . xii List of Abbreviations . xiv Units of Measurement . xvii Chapter 1: Introduction . 1 1.1 Aim of Study . 2 1.2 Synechocystis sp. PCC 6803 . 3 1.2.1 Cultivation . 5 1.2. 2 Neutral Sites and Selection . 6 1.2. 3 Synechocystis Sub-Strains . 8 1.3 Carbon Concentrating Mechanisms . 9 1.3. 1 The RuBisCO Enzyme . 11 1.3. 2 Carboxysome . 12 1.3. 3 Bicarbonate Transporters . 13 1.3. 4 Carbon Dioxide Transporters . 15 1.3. 5 Selection of Bicarbonate Transporter Genes . 17 1.4 Ethanol Production . 18 1.4. 1 Ethanol Production Pathway . 19 1.4. 2 UL004 . 22 1.4. 3 UL030 . 23 1.4. 4 Zymomonas mobilis PDC/ADH . 25 1.4. 5 Synechocystis sp. PCC 6803 Native ADH . 27 1.5 Increasing Ethanol Yield . 28 1.5. 1 Native Plasmids. 28 1.5. 2 Gene Dosage and Pyruvate Diversion. 29 1.5. 3 Pathway Knockout . 30 1.5. 4 Promoters . 31 1.5. 5 pdc and adh gene Fusion . 32 1.6 Ethanol Tolerance . 33 Chapter 2: Materials and Methods . 35 2.1 Materials and Methods . 36
Web mining techniques for query log analysis and expertise retrieval

With the large increase in the amount of information available online, rich Web data can be obtained on the Internet, such as over one trillion Web pages, millions of scientific literature, and different interactions with society, like question answers, query logs. Currently, Web mining techniques has emerged as an important research area to help Web users find their information need. In general, Web users express their information need as queries, and expect to obtain the needed information from the Web data through Web mining techniques. To better understand what users want in terms of the given query, it is very essential to analyze the query logs. On the other hand, the returned information may be Web pages, images, and other types of data. Beyond the traditional information, it would be quite interesting and important to identify relevant experts with expertise for further consulting about the query topic, which is also called expertise retrieval. The objective of this thesis is to establish automatic content analysis methods and scalable graph-based models for query log analysis and expertise retrieval. One important aspect of this thesis is therefore to develop a framework to combine the content information and the graph information with the following two purposes: 1) analyzing Web contents with graph structures, more specifically, mining query logs; and 2) identifying high-level information needs, such as expertise retrieval, behind the contents. For the first purpose, a novel entropy-biased framework is proposed for modeling bipartite graphs, which is applied to the click graph for better query representation by treating heterogeneous query-URL pairs differently and diminishing the effect of noisy links. Based on the graph information, there is a lack of constraints to make sure the final relevance of the score propagation on the graph. To tackle this problem, a general Co-HITS algorithm is developed to incorporate the bipartite graph with the content information from both sides as well as the constraints of relevance. Extensive evaluations on query log analysis demonstrate the effectiveness of the proposed models. For the second purpose, a weighted language model is proposed to aggregate the expertise of a candidate from the associated documents. The model not only considers the relevance of documents against a given query, but also incorporates important factors of the documents in the form of document priors. Moreover, an important approach is presented to boost the expertise retrieve by incorporating the content with other implicit link information through the graph-based re-ranking model. Furthermore, two community-aware strategies are developed and investigated to enhance the expertise retrieval, which are motivated by the observation that communities could provide valuable insight and distinctive information. Experimental results on the expert finding task demonstrate these methods can improve and enhance traditional the traditional expertise retrieval models with better performance.
Senescence in wild insects: Key questions and challenges

Insects are key laboratory models for research on the fitness effects, genetics and plasticity of senescence. It was long believed that insects almost never survive long enough to senesce in the wild, but it is now clear that senescence occurs and can exact substantial fitness costs in natural insect populations. Yet, given the practical challenges of obtaining longitudinal field data on small, motile animals, we still know remarkably little about the evolution, expression and fitness consequences of senescence in wild insects. We argue that the study of senescence in wild insects is important because many insights and hypotheses based on laboratory experiments must be tested in natural populations. Examples of research areas where conclusions from laboratory studies could be misleading include the roles of candidate senescence genes, the effects of nutrition and dietary restriction on life span and senescence patterns, and the roles of viability selection and sexual selection in shaping senescence through trade‐offs and antagonistic pleiotropy. Several emerging model species (such as antler flies, crickets, damselflies, dragonflies and butterflies) offer opportunities for field research on senescence using a range of observational and experimental techniques, as well as new genomic approaches. Insects provide valuable and increasingly tractable models for research on senescence in natural populations. We believe that such work will shed light on many important questions in ecology and evolutionary biology. A free Plain Language Summary can be found within the Supporting Information of this article.
Determination of the normalized-surface-height autocorrelation function of a two-dimensional randomly rough dielectric surface by the inversion of light-scattering data

Author(s): Simonsen, I; Hetland, OS; Kryvi, JB; Maradudin, AA | Abstract: An expression is obtained on the basis of phase perturbation theory for the contribution to the mean differential reflection coefficient from the in-plane co-polarized component of the light scattered diffusely from a two-dimensional randomly rough dielectric surface when the latter is illuminated by s-polarized light. This result forms the basis for an approach to inverting experimental light scattering data to obtain the normalized surface height autocorrelation function of the surface. Several parametrized forms of this correlation function, and the minimization of a cost function with respect to the parameters defining these representations, are used in the inversion scheme. This approach also yields the rms height of the surface roughness, and the dielectric constant of the dielectric substrate if it is not known in advance. The input data used in validating this inversion consists of computer simulation results for surfaces defined by exponential and Gaussian surface height correlation functions, without and with the addition of multiplicative noise, for a single or multiple angles of incidence. The reconstructions obtained by this approach are quite accurate for weakly rough surfaces, and the proposed inversion scheme is computationally efficient.
Connexin 43 impacts the chick premigratory cranial neural crest cell population without affecting the neural crest cell epithelial-to-mesenchymal transition

Gap junctions are intercellular channels that allow for the diffusion of small ions and solutes between coupled cells. Connexin 43 (Cx43), also known as Gap Junction Protein α1, is the most broadly expressed gap junction protein in vertebrate development. Cx43 is strongly expressed in premigratory cranial neural crest cells and is maintained throughout the neural crest cell epithelial-to-mesenchymal transition (EMT), but its function in these cells is not known. To this end, we have used a combination of in vivo and ex vivo live imaging with confocal microscopy, immunohistochemistry, and functional assays to assess gap junction formation, and Cx43 function, in chick premigratory cranial neural crest cells. Our results demonstrate that gap junctions exist between chick premigratory and migratory cranial neural crest cells, with Cx43 depletion inhibiting the function of gap junctions. While a reduction in Cx43 levels just prior to neural crest cell EMT did not affect EMT and subsequent emigration of neural crest cells from the neural tube, the size of the premigratory neural crest cell domain was decreased in the absence of any changes in cell proliferation or death. Collectively, these data identify a role for Cx43 within the chick premigratory cranial neural crest cell population prior to EMT and migration.
Sample design for small area estimation

Sample surveys have long been used as cost-effective means for data collection. Such data are used to provide suitable statistics not only for the population targeted by the survey but also for a variety of subpopulations, often called domains or areas. Sampling designs and in particular sample sizes are chosen in practice so as to provide reliable estimates for aggregates of the small areas such as large geographical regions or broad demographic groups. Budget and other constraints usually prevent the allocation of sufficiently large samples to each of the sub-domains or small areas to provide reliable estimates using traditional techniques. This thesis will develop approaches for sample design to support small area estimation. Sample designs for small areas can be classified into two major categories: • when it is feasible to select sample units in every small area; • when only a subset of small areas can be surveyed. The first case will be represented by stratified sampling where strata are small areas. The second case will be represented by two-stage sampling where clusters are small areas and are selected either by equal probability (simple two-stage) or unequal probability sampling (general two-stage).
Facial Feature Location and Extraction for Computerized Human Face Recognition

Facial feature extraction is an important step in automated visual interpretation and human face recognition. Deformable template is a method used in extracting the eye boundaries. However, a weakness of the deformable template is the lengthy processing time. In this paper, the head boundary is first located in a head-and-shoulders image. The approximate positions of the eyes are estimated by means of average anthropometric measures. Corners, the salient features of the eyes, are detected and used to set the initial parameters of the eye templates. This scheme can accurately position the templates in relation to the eye images and greatly reduce the processing time for the templates. In order to illustrate this performance, a simplified eye template model is used in the experiment.
Making Useful Programming Objects Available for a Programmer: at the Right Time in the Right Way through the Right Peers

Programming is a complex ill-defined problemsolving task. It requires not only knowledge in the head of a programmer, but also existing information in the world and relevant knowledge of his/her peers in the community. Traditional software reuse techniques do not serve for programmers to a full extent because they are not built from this perspective. Our research addresses the issue from a cognitive perspective, trying to help a programmer reuse existing software objects from software repositories and locate peer programmers who can help him/her solving the current task even when (1) the programmer is not aware of his/her information needs, (2) does not know that potentially useful information exist, and (3) does not know how to ask for help in related programming communities. This paper discusses the design principle called layered informationon-demand that guides the location and presentation of external information and knowledge in response to an individual’s unique information needs determined by his/her current task and background knowledge. The principle is illustrated with the CodeBroker system and the UMCM (user-modeling and community-modeling) engine.
Detection of oil slick signatures in SAR images by fusion of hysteresis thresholding responses

A new method is proposed in this paper to detect oil slick signatures in oceanographic SAR images. This method is based on directional behavioural oil slick in the sea surface. Therefore, directional hysteresis thresholding responses are first computed in order to bring to the fore dark spots, and increase pixels connexity in each Freeman direction. Those responses are then merged with the help of a Context Independent Constant Behaviour (CICB) operator. The proposed method is tested on ERS SAR amplitude images of Mediterranean and Atlantic seas. The obtained results are promising and show a good qualitative detection.
Seven Unrecorded Fungal Species from Field Soils in Korea

Seven unrecorded species in the phylum Ascomycota, Emericellopsis pallida (KNU16-167), Scedosporium aurantiacum (KNU16-190), Duddingtonia flagrans (KNU16-279), Bionectria rossmaniae (KNU16-309), Exophiala xenobiotica (KNU16-79), Pseudocercosporella fraxini (KNU16-102), and Stachybotrys sansevieriae (KNU16-141), were isolated in 2016 from field soils collected from various locations in Korea. All of the species were identified and described based on morphological characteristics and rDNA internal transcribed spacer sequence data. Morphological features of these fungi were examined on potato dextrose agar, oatmeal agar, malt extract agar, Czapek yeast extract agar, and yeast extract sucrose agar. Full descriptions and illustrations of their morphological characteristics are provided.
Branched-chain amino acid interactions in growing pig diets

Abstract The branched-chain amino acids (BCAA) Leu, Ile, and Val share the first steps of their catabolism due to similarities in their structure. The BCAA are reversibly transaminated in skeletal muscle through the activity of branched-chain aminotransferase and then transported to the liver. They undergo an irreversible decarboxylation catalyzed by the branched-chain α-keto acid dehydrogenase complex. Both enzymes are common to Leu, Ile, and Val and increased enzymatic activity stimulated by an excess of one of them will increase the catabolism of all BCAA, which can result in antagonisms. Leucine and its keto acid are the most potent stimulators of BCAA catabolic enzymes. Moreover, BCAA and large neutral amino acids (LNAA) share common brain transporters. Research has shown that high concentrations of BCAA, especially Leu, can decrease the absorption of LNAA, such as Trp, which is a precursor of serotonin and can have a significant impact in feed intake regulation. Finally, high Leu concentrations have the ability to overstimulate the mTOR signaling pathway, resulting in an inhibitory effect on feed intake. Most of the research conducted to evaluate the impact of BCAA on growth performance of pigs seems to agree that high levels of Leu decrease weight gain, mostly due to a reduction in feed intake. However, some studies, mostly with finishing pigs, observed no evidence for an impact on growth performance even with extremely high levels of Leu. It could be hypothesized that these inconsistencies are driven by the entire dietary amino acid profile as opposed to only considering the level of Leu. Grow-finish diets typically contain high levels of Leu, but the other BCAA are also well above the requirement and could potentially mitigate the negative impact of Leu on BCAA catabolism. Indeed, some studies suggest that when diets contain high levels of Leu, more Ile and Val are needed to optimize growth performance. However, the precise relationship between BCAA and their balance in swine diets is not fully understood. More research is needed to understand and quantify the relationship between LNAA and BCAA.
From genomes to forest management – tackling invasive Phytophthora species in the era of genomics

Abstract Species of Phytophthora pose one of the most serious biosecurity threats to forest ecosystems worldwide. Despite management efforts and increased awareness of forest pathogens, there is continued introduction and spread of Phytophthora species. Uncertainty about the center of origin for many of the invasive species hampers disease control efforts. Additionally, the management efforts are often made impossible either by the vast host range or the extreme susceptibility of naïve hosts. In this review, we discuss how genomics has shed light on the extent of spread and destruction caused by invasive Phytophthora species, and how approaches leveraged by genomics can be applied to enhance the management of these invasive forest pathogens. Four case studies, Phytophthora ramorum, Phytophthora lateralis, Phytophthora cinnamomi, and Phytophthora pluvialis are used to illustrate how genomics can be applied to forest management. We urge researchers, governmental research institutes, private companies, and citizens to collaborate in order to stop the spread of invasive Phytophthora species. To accomplish this, we see the following themes as critical parts of resolving this forest health crisis: i) integration of DNA-based pathogen detection into forest inventory programs; ii) development of practical and affordable DNA-based diagnostic methods; iii) sequence hosts as models for resistance gene identification; iv) prediction of pathogen impact based on genomic data; and v) increase collaborative projects and outreach to raise awareness of forest diseases.
An Complex Field Network Coding Scheme in Wireless Communication

Keywords—wireless communication, network coding, diversity gain, relay Abstract—Complex field network coding (CFNC) is a new network coding approach proposed to improve network throughput and achieve full diversity gain in wireless networks. In this paper, a novel complex-field network coding scheme is developed based on cooperative communication. Different from traditional network coding scheme, transmissions are not restricted to binary symbols. The proposed scheme can achieve throughput to approximately XXX symbols per source per channel use. Theoretic analysis demonstrate that, the improved CFNC scheme can obtain the same network throughput and diversity gain as CFNC, while it can decrease the transmission delay of source symbols, and reduce the detection complexity of destination.
Enhancing Czech Valency Lexicon with Semantic Information from FrameNet: The Case of Communication Verbs

In this paper, we report on our attempt at assigning semantic information from FrameNet to lexical units in VALLEX, a valency lexicon of Czech verbs. We focus on the class of communication verbs. We experiment with assigning FrameNet semantic frames to lexical units for communication verbs. The second task consists in linking their valency complementations with FrameNet frame elements. The exact pairwise inter-annotator agreement reaches almost 69% on the semantic frames and 84.6% on the frame elements. We propose enhancing VALLEX with missing semantic information from FrameNet based on exploitation of the semantic relation ‘Inheritance’.
Melanism in the pond slider (Trachemys scripta) in northern Indiana, USA

Melanism in turtles is generally rare among species, but can be extremely common in some species and subspecies. Pond Sliders (Trachemys scripta) show ontogenetic melanism with larger, and presumably older, individuals often showing melanism of the plastron and other body parts (Lovich et al., 1990). Previous studies of melanism in T. scripta have found that the proportion of melanistic individuals can vary among populations. for example, some populations from oklahoma show 100% melanism for both adult males and females, whereas other populations from that state show percentages of melanistic adults ranging from 44% to 75% (mccoy, 1967; hays & mcBee, 2009). in southeastern missouri, 81% of adult males were melanistic (Glorioso et al., 2010), and in southern illinois, approximately 18.7% of adult male T. scripta were melanistic (reehl et al., 2006). Some authors have argued the observed variation in the proportion of melanistic T. scripta does not appear to be related to geographic parameters, such as latitude (see mccoy, 1967), but cahn (1937) suggested that melanism was more frequent in T. scripta from southern illinois than those from northern illinois. however, relatively few populations have been examined to quantify melanism, especially northern populations. here we report on melanism in a population of T. scripta at the northeastern extreme of the range of the species in the Wabash river drainage in indiana (see Seidel & ernst, 2006 for distribution). this population is believed to be natural, although supplementation by pet trade releases over many decades cannot be ruled out.
TWIST1 homo- and heterodimers orchestrate specificity control in embryonic stem cell lineage differentiation and craniofacial development

Combinations of bHLH factors dimers generate great functional diversity required for cell type specification in development. The bHLH factor TWIST1 plays pleiotropic roles in craniofacial development. However, which combination of TWIST1 dimers are involved in craniofacial development, and what impact each dimer impose on gene regulation network remained elusive. Proteome profiling of human-TWIST1 expressing cell lines and transcriptome analysis of mouse cranial mesenchyme revealed TWIST1 homodimer and heterodimers with TCF3, TCF4 and TCF12 E-proteins as preferred combinations. We found that balance of homo- and heterodimers were impaired by human disease mutations in TWIST1 Helix domains, which may underpin the developmental defects in haploinsufficiency. Further, loss or gain of function analysis of TWIST1-E-protein dimers in differentiating embryonic stem cells revealed their previously unappreciated roles in lineage specification. TWIST1-E-protein heterodimers activate mesoderm and neural crest differentiation through epithelial-to-mesenchymal transition, whilst TWIST1 homodimers maintained a progenitor-like state and blocked entry to endoderm lineages.