Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Methylation Changes in Atypical Adenomatous Hyperplasia, Adenocarcinoma In Situ, and Lung Adenocarcinoma

Background Aberrant DNA methylation is common in lung adenocarcinoma, but its timing in the phases of tumor development is largely unknown. Delineating when abnormal DNA methylation arises may provide insight into the natural history of lung adenocarcinoma and the role that DNA methylation alterations play in tumor formation. Methodology/Principal Findings We used MethyLight, a sensitive real-time PCR-based quantitative method, to analyze DNA methylation levels at 15 CpG islands that are frequently methylated in lung adenocarcinoma and that we had flagged as potential markers for non-invasive detection. We also used two repeat probes as indicators of global DNA hypomethylation. We examined DNA methylation in 249 tissue samples from 93 subjects, spanning the putative spectrum of peripheral lung adenocarcinoma development: histologically normal adjacent non-tumor lung, atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS, formerly known as bronchioloalveolar carcinoma), and invasive lung adenocarcinoma. Comparison of DNA methylation levels between the lesion types suggests that DNA hypermethylation of distinct loci occurs at different time points during the development of lung adenocarcinoma. DNA methylation at CDKN2A ex2 and PTPRN2 is already significantly elevated in AAH, while CpG islands at 2C35, EYA4, HOXA1, HOXA11, NEUROD1, NEUROD2 and TMEFF2 are significantly hypermethylated in AIS. In contrast, hypermethylation at CDH13, CDX2, OPCML, RASSF1, SFRP1 and TWIST1 and global DNA hypomethylation appear to be present predominantly in invasive cancer. Conclusions/Significance The gradual increase in DNA methylation seen for numerous loci in progressively more transformed lesions supports the model in which AAH and AIS are sequential stages in the development of lung adenocarcinoma. The demarcation of DNA methylation changes characteristic for AAH, AIS and adenocarcinoma begins to lay out a possible roadmap for aberrant DNA methylation events in tumor development. In addition, it identifies which DNA methylation changes might be used as molecular markers for the detection of preinvasive lesions.
Fishy Aroma of Social Status: Urinary Chemo-Signalling of Territoriality in Male Fathead Minnows (Pimephales promelas)

Chemical structures of several urinary reproductive pheromones in fish have been identified, and their role in the chemical communication of reproductive condition is well characterized. On the contrary, the role of chemical communication in signalling of social/territorial status in fish is poorly understood. Fathead minnows are an example of a fish species whose life history traits appear conducive to evolution of chemical communication systems that confer information about social/territorial status. Male reproduction in this species is dependent upon their ability to acquire and defend a high quality nesting territory, and to attract a female to the nest. We hypothesized that fathead minnow males use visual and urine-derived chemical cues to signal territorial status. To test this hypothesis, effects of territorial acquisition on male-specific secondary sex characteristics (SSCs) and urine volumes were first assessed. Second, frequencies of male urination in varying social contexts were examined. Finally, nuclear magnetic resonance-based metabolomics was used to identify urinary metabolites that were differentially excreted in the urine of territorial versus non-territorial males. The expression of SSCs, sperm, and urine volumes increased with territory acquisition, and either remained unchanged or decreased in non-territorial males. Frequency of male urination increased significantly in the presence of females (but not males), suggesting that females are the main target of the urinary signals. Territorial and non-territorial males had distinct urinary metabolomic profiles. An unforeseen finding was that one could discern future territorial status of males, based on their initial metabolomic profiles. Bile acids and volatile amines were identified as potential chemical signals of social status in the fathead minnow. The finding that trimethylamine (a fishy smelling volatile amine) may be a social cue is particularly interesting, because it is known to bind trace amine-associated receptors, indicating that these receptors may play role in chemical signalling of social status in fish.
Using Social Interaction Between Friends in Knowledge-Based Personalized Recommendation

Over the last decade, ontologies have been increasingly used in recommender systems. Domain ontologies are mainly used to analyze the user behaviour with reference to knowledge structure in order to build user profiles. In addition, ontologies are useful for modelling the trust between users extracted from a social network. We, accordingly, propose to combine two approaches to improve the recommendation process in tourism domain. The first is the trusted friends' preference based on the assumption that users generally have a tendency to use items recommended by friends rather than strangers. The second is the ontology based user interest to represent the semantics of these interests. A Trusted Friends' Application is developed to determine social trusted friends by analyzing user's profile on Facebook. Afterwards, we have represented the user's model as an ontology that takes into consideration all trusted friends' preferences and the degree of trust between friends. Finally, we have used this ontology in a knowledge-based tourism recommender system as a smart e-tourism tool able to recommend items based on the users' preferences and their trusted friends' preferences.
Dissertation Interaction with Sound and Pre-Recorded Music : Novel Interfaces and Use Patterns Tue Haste

Computers are changing the way sound and recorded music are listened to and used. The use of computers to playback music makes it possible to change and adapt music to different usage situations in ways that were not possible with analog sound equipment. In this thesis, interaction with pre-recorded music is investigated using prototypes and user studies. First, different interfaces for browsing music on consumer or mobile devices were compared. It was found that the choice of input controller, mapping and auditory feedback influences how the music was searched and how the interfaces were perceived. Search performance was not affected by the tested interfaces. Based on this study, several ideas for the future design of music browsing interfaces were proposed. Indications that search time depends linearly on distance to target were observed and examined in a related study where a movement time model for searching in a text document using scrolling was developed. Second, work practices of professional disc jockeys (DJs) were studied and a new design for digital DJing was proposed and tested. Strong indications were found that the use of beat information could reduce the DJ’s cognitive workload while maintaining flexibility during the musical performance. A system for automatic beat extraction was designed based on an evaluation of a number of perceptually important parameters extracted from audio signals. Finally, auditory feedback in pen-gesture interfaces was investigated through a series of informal and formal experiments. The experiments point to several general rules of auditory feedback in pen-gesture interfaces: a few simple functions are easy to achieve, gaining further performance and learning advantage is difficult, the gesture set and its computerized recognizer can be designed to minimize visual dependence, and positive emotional or aesthetic response can be achieved using musical auditory feedback.
Few versatile vs. many specialized collections: how to design a collection library for exploratory programming?

While an integral part of all programming languages, the design of collection libraries is rarely studied. This work briefly reviews the collection libraries of 14 languages to identify possible design dimensions. Some languages have surprisingly few but versatile collections, while others have large libraries with many specialized collections. Based on the identified design dimensions, we argue that a small collection library with only a sequence, a map, and a set type are a suitable choice to facilitate exploratory programming. Such a design minimizes the number of decisions programmers have to make when dealing with collections, and it improves discoverability of collection operations. We further discuss techniques that make their implementation practical from a performance perspective. Based on these arguments, we conclude that languages which aim to support exploratory programming should strive for small and versatile collection libraries.
Objective tests for the stickiness of cooked rice.

The suitability of a sieve test and an adhesion test as objective tests for determining the stickiness of cooked rice was examined. 6 rice var. (2 each from dwarf indica, tall indica and japonica classes) stored for 1 and 2 yr at 3 different temp. (3-4 degree C, 23-35 degree C, 37 degree C) were used. The consistency of the cooked rices was also determined by the Haake consistometer. The sieve test gave a very good indication of the stickiness of cooked rice. The adhesion test also gave a fair indication, but the correlation was less sharp and the test needs improvement. Consistency of cooked rice was negatively correlated with stickiness. The water-insoluble amylose content of rice seemed to be related to stickiness and consistency after cooking.
The complete mitochondrial genome of Bactrocera diaphora (Diptera: Tephtitidae)

Abstract We sequenced and annotated the complete mitochondrial genome (mitogenome) of Bactrocera diaphora (Diptera: Tephtitidae), which is an economically important pest in the southwest area of China, India, Sri Lanka, Vietnam and Malaysia. This mitogenome is 15 890 bp in length with an A + T content of 74.103%, and contains 37 typical animal mitochondrial genes that are arranged in the same order as that of the inferred ancestral insects. All protein-coding genes (PCGs) start with a typical ATN codon, except cox1 that begins with TCG. Ten PCGs stop with termination codon TAA or TAG, whereas cox1, nad1 and nad5 have single T–– as the incomplete stop codon. All of the transfer RNA genes present the typical clover leaf secondary structure except trnS1 (AGN) with a looping D-arm. The A + T-rich region is located between rrnS and trnI with a length of 946 bp, and contains a 20 bp poly-T stretch and 22 bp poly-A stretch. Except the control region, the longest intergenic spacer is located between trnR and trnN that is 94 bp long with an excessive high A + T content (95.74%) and a microsatellite-like region (TA)13.
Is There a Classical Nonsense-Mediated Decay Pathway in Trypanosomes?

In many eukaryotes, messenger RNAs with premature termination codons are destroyed by a process called “nonsense-mediated decay”, which requires the RNA helicase Upf1 and also, usually, an interacting factor, Upf2. Recognition of premature termination codons may rely on their distance from either a splice site or the polyadenylation site, and long 3′-untranslated regions can trigger mRNA decay. The protist Trypanosoma brucei relies heavily on mRNA degradation to determine mRNA levels, and 3′-untranslated regions play a major role in control of mRNA decay. We show here that trypanosomes have a homologue of Upf1, TbUPF1, which interacts with TbUPF2 and (in an RNA-dependent fashion) with poly(A) binding protein 1, PABP1. Introduction of a premature termination codon in either an endogenous gene or a reporter gene decreased mRNA abundance, as expected for nonsense-mediated decay, but a dependence of this effect on TbUPF1 could not be demonstrated, and depletion of TbUPF1 by over 95% had no effect on parasite growth or the mRNA transcriptome. Further investigations of the reporter mRNA revealed that increases in open reading frame length tended to increase mRNA abundance. In contrast, inhibition of translation, either using 5′-secondary structures or by lengthening the 5′-untranslated region, usually decreased reporter mRNA abundance. Meanwhile, changing the length of the 3′-untranslated region had no consistent effect on mRNA abundance. We suggest that in trypanosomes, translation per se may inhibit mRNA decay, and interactions with multiple RNA-binding proteins preclude degradation based on 3′-untranslated region length alone.
Optimization of Cholinesterase-Based Catalytic Bioscavengers Against Organophosphorus Agents

Organophosphorus agents (OPs) are irreversible inhibitors of acetylcholinesterase (AChE). OP poisoning causes major cholinergic syndrome. Current medical counter-measures mitigate the acute effects but have limited action against OP-induced brain damage. Bioscavengers are appealing alternative therapeutic approach because they neutralize OPs in bloodstream before they reach physiological targets. First generation bioscavengers are stoichiometric bioscavengers. However, stoichiometric neutralization requires administration of huge doses of enzyme. Second generation bioscavengers are catalytic bioscavengers capable of detoxifying OPs with a turnover. High bimolecular rate constants (kcat/Km > 106 M−1min−1) are required, so that low enzyme doses can be administered. Cholinesterases (ChE) are attractive candidates because OPs are hemi-substrates. Moderate OP hydrolase (OPase) activity has been observed for certain natural ChEs and for G117H-based human BChE mutants made by site-directed mutagenesis. However, before mutated ChEs can become operational catalytic bioscavengers their dephosphylation rate constant must be increased by several orders of magnitude. New strategies for converting ChEs into fast OPase are based either on combinational approaches or on computer redesign of enzyme. The keystone for rational conversion of ChEs into OPases is to understand the reaction mechanisms with OPs. In the present work we propose that efficient OP hydrolysis can be achieved by re-designing the configuration of enzyme active center residues and by creating specific routes for attack of water molecules and proton transfer. Four directions for nucleophilic attack of water on phosphorus atom were defined. Changes must lead to a novel enzyme, wherein OP hydrolysis wins over competing aging reactions. Kinetic, crystallographic, and computational data have been accumulated that describe mechanisms of reactions involving ChEs. From these studies, it appears that introducing new groups that create a stable H-bonded network susceptible to activate and orient water molecule, stabilize transition states (TS), and intermediates may determine whether dephosphylation is favored over aging. Mutations on key residues (L286, F329, F398) were considered. QM/MM calculations suggest that mutation L286H combined to other mutations favors water attack from apical position. However, the aging reaction is competing. Axial direction of water attack is not favorable to aging. QM/MM calculation shows that F329H+F398H-based multiple mutants display favorable energy barrier for fast reactivation without aging.
囊性纤维化跨膜转导调节子（CFTR）对肺癌A549细胞恶性特性的影响研究

背景与目的 肺癌发病率逐年上升，有必要寻找新型的治疗靶点，而最新研究发现囊状纤维化跨膜转导调节子（cystic fibrosis transmembrane conductance regulator, CFTR）与多种肿瘤的发生和恶性转化有关。 本研究探讨CFTR对肺癌A549细胞恶性特性的影响。 方法 应用CCK8细胞增殖实验、细胞划痕实验、Transwell细胞侵袭实验以及克隆形成实验等方法分别检测CFTR的表达对非小细胞肺癌A549细胞的增殖、迁移、侵袭等细胞恶性特性的影响。 同时通过免疫印迹（Western blot）分析CFTR基因表达对肿瘤干细胞相关转录因子表达的影响。 结果 过表达CFTR基因显著抑制A549细胞的增殖、迁移、侵袭和克隆形成等肿瘤恶性特征，而RNA干扰A549细胞CFTR的表达导致细胞上述特征的明显增强。 免疫印迹实验进一步发现CFTR基因过表达抑制A549细胞中干细胞相关转录因子SOX2和OCT3/4，以及细胞表面CD133蛋白的表达；相反，RNA干扰A549细胞中CFTR基因的表达增加SOX2、OCT4和CD133的表达。 然而，免疫印迹和流式细胞术发现CFTR基因表达对A549细胞肺癌干细胞标志乙醛脱氢酶1的表达和阳性细胞数量无显著影响。 结论 CFTR基因在肺癌A549细胞中具有抑制细胞恶性特征的作用，提示其可能是肺腺癌治疗的一个新的靶点，但其对其他肺腺癌细胞的作用与分子机制还有待进一步研究。
Cross-Lingual Neighborhood Effects in Generalized Lexical Decision and Natural Reading

The present study assessed intra- and cross-lingual neighborhood effects, using both a generalized lexical decision task and an analysis of a large-scale bilingual eye-tracking corpus (Cop, Dirix, Drieghe, & Duyck, 2016). Using new neighborhood density and frequency measures, the general lexical decision task yielded an inhibitory cross-lingual neighborhood density effect on reading times of second language words, replicating van Heuven, Dijkstra, and Grainger (1998). Reaction times for native language words were not influenced by neighborhood density or frequency but error rates showed cross-lingual neighborhood effects depending on target word frequency. The large-scale eye movement corpus confirmed effects of cross-lingual neighborhood on natural reading, even though participants were reading a novel in a unilingual context. Especially second language reading and to a lesser extent native language reading were influenced by lexical candidates from the nontarget language, although these effects in natural reading were largely facilitatory. These results offer strong and direct support for bilingual word recognition models that assume language-independent lexical access.
Vibration Influences Haptic Perception of Surface Compliance During Walking

Background The haptic perception of ground compliance is used for stable regulation of dynamic posture and the control of locomotion in diverse natural environments. Although rarely investigated in relation to walking, vibrotactile sensory channels are known to be active in the discrimination of material properties of objects and surfaces through touch. This study investigated how the perception of ground surface compliance is altered by plantar vibration feedback. Methodology/Principal Findings Subjects walked in shoes over a rigid floor plate that provided plantar vibration feedback, and responded indicating how compliant it felt, either in subjective magnitude or via pairwise comparisons. In one experiment, the compliance of the floor plate was also varied. Results showed that perceived compliance of the plate increased monotonically with vibration feedback intensity, and depended to a lesser extent on the temporal or frequency distribution of the feedback. When both plate stiffness (inverse compliance) and vibration amplitude were manipulated, the effect persisted, with both factors contributing to compliance perception. A significant influence of vibration was observed even for amplitudes close to psychophysical detection thresholds. Conclusions/Significance These findings reveal that vibrotactile sensory channels are highly salient to the perception of surface compliance, and suggest that correlations between vibrotactile sensory information and motor activity may be of broader significance for the control of human locomotion than has been previously acknowledged.
The Effects of Herbivory by a Mega- and Mesoherbivore on Tree Recruitment in Sand Forest, South Africa

Herbivory by megaherbivores on woody vegetation in general is well documented; however studies focusing on the individual browsing effects of both mega- and mesoherbivore species on recruitment are scarce. We determined these effects for elephant Loxodonta africana and nyala Tragelaphus angasii in the critically endangered Sand Forest, which is restricted to east southern Africa, and is conserved mainly in small reserves with high herbivore densities. Replicated experimental treatments (400 m2) in a single forest patch were used to exclude elephant, or both elephant and nyala. In each treatment, all woody individuals were identified to species and number of stems, diameter and height were recorded. Results of changes after two years are presented. Individual tree and stem densities had increased in absence of nyala and elephant. Seedling recruitment (based on height and diameter) was inhibited by nyala, and by elephant and nyala in combination, thereby preventing recruitment into the sapling stage. Neither nyala or elephant significantly reduced sapling densities. Excluding both elephant and nyala in combination enhanced recruitment of woody species, as seedling densities increased, indicating that forest regeneration is impacted by both mega- and mesoherbivores. The Sand Forest tree community approached an inverse J-shaped curve, with the highest abundance in the smaller size classes. However, the larger characteristic tree species in particular, such as Newtonia hildebrandtii, were missing cohorts in the middle size classes. When setting management goals to conserve habitats of key importance, conservation management plans need to consider the total herbivore assemblage present and the resulting browsing effects on vegetation. Especially in Africa, where the broadest suite of megaherbivores still persists, and which is currently dealing with the ‘elephant problem’, the individual effects of different herbivore species on recruitment and dynamics of forests and woodlands are important issues which need conclusive answers.
Adaptive probabilistic tracking with discriminative feature selection for mobile robot

Object tracking is one of the important tasks for mobile robot, and developing a robust and real-time visual tracking algorithm which can adaptively capture the varying appearance of target under challenging conditions for mobile robot is still an open problem. The main challenges of visual tracking for mobile robot come from variation of target's appearance and disturbance of environment. To cope with these problems, one of the most important topics is how to select the best tracking features. In this paper, we propose a novel adaptive probabilistic tracking method with discriminative feature selection for mobile robot Different from the existing adaptive tracking algorithms which select the discriminative features in a finite feature set, the proposed method treats feature selection as an estimation problem of the best feature tunable parameters in a continuous space. The estimation of the best tunable parameters and object tracking are implemented via different particle filters with novel observation models. A novel target model updating strategy is also proposed to adapt to the varying appearance of target and resist gradual drift. Experiments show the robustness of the proposed method under challenging conditions.
Hessian Fly-Associated Bacteria: Transmission, Essentiality, and Composition

Plant-feeding insects have been recently found to use microbes to manipulate host plant physiology and morphology. Gall midges are one of the largest groups of insects that manipulate host plants extensively. Hessian fly (HF, Mayetiola destructor) is an important pest of wheat and a model system for studying gall midges. To examine the role of bacteria in parasitism, a systematic analysis of bacteria associated with HF was performed for the first time. Diverse bacteria were found in different developmental HF stages. Fluorescent in situ hybridization detected a bacteriocyte-like structure in developing eggs. Bacterial DNA was also detected in eggs by PCR using primers targeted to different bacterial groups. These results indicated that HF hosted different types of bacteria that were maternally transmitted to the next generation. Eliminating bacteria from the insect with antibiotics resulted in high mortality of HF larvae, indicating that symbiotic bacteria are essential for the insect to survive on wheat seedlings. A preliminary survey identified various types of bacteria associated with different HF stages, including the genera Enterobacter, Pantoea, Stenotrophomonas, Pseudomonas, Bacillus, Ochrobactrum, Acinetobacter, Alcaligenes, Nitrosomonas, Arcanobacterium, Microbacterium, Paenibacillus, and Klebsiella. Similar bacteria were also found specifically in HF-infested susceptible wheat, suggesting that HF larvae had either transmitted bacteria into plant tissue or brought secondary infection of bacteria to the wheat host. The bacteria associated with wheat seedlings may play an essential role in the wheat-HF interaction.