Miracle-dz/UniFAR-FTUs huggingface dataset:
Rice domestication: histories and mysteries

Domesticated rice (Oryza sativa) is one of the world’s most important food crops, culturally, nutritionally and economically ( Khush 1997 ). Thus, it is no surprise that there is intense curiosity about its genetic and geographical origins, its response to selection under domestication, and the genetic structure of its wild relative, Oryza rufipogon. Studies of Oryza attempting to answer these questions have accompanied each stage of the development of molecular markers, starting with allozymes and continuing to genome sequencing. While many of these studies have been restricted to small sample sizes, in terms of either the number of markers used or the number and distribution of the accessions, costs are now low enough that researchers are including large numbers of molecular markers and accessions. How will these studies relate to previous findings and long‐held assumptions about rice domestication and evolution? If the paper in this issue of Molecular Ecology ( Huang et al. 2012 ) is any indication, there will be some considerable surprises in store. In this study, a geographically and genomically thorough sampling of O. rufipogon and O. sativa revealed two genetically distinct groups of wild rice and also indicated that only one of these groups appears to be related to domesticated rice. While this fits well with previous studies indicating that there are genetic subdivisions within O. rufipogon, it stands in contrast to previous findings that the two major varieties of O. sativa (indica and japonica) were domesticated from two (or more) subpopulations of wild rice.
AFLP genome scans suggest divergent selection on colour patterning in allopatric colour morphs of a cichlid fish

Genome scan‐based tests for selection are directly applicable to natural populations to study the genetic and evolutionary mechanisms behind phenotypic differentiation. We conducted AFLP genome scans in three distinct geographic colour morphs of the cichlid fish Tropheus moorii to assess whether the extant, allopatric colour pattern differentiation can be explained by drift and to identify markers mapping to genomic regions possibly involved in colour patterning. The tested morphs occupy adjacent shore sections in southern Lake Tanganyika and are separated from each other by major habitat barriers. The genome scans revealed significant genetic structure between morphs, but a very low proportion of loci fixed for alternative AFLP alleles in different morphs. This high level of polymorphism within morphs suggested that colour pattern differentiation did not result exclusively from neutral processes. Outlier detection methods identified six loci with excess differentiation in the comparison between a bluish and a yellow‐blotch morph and five different outlier loci in comparisons of each of these morphs with a red morph. As population expansions and the genetic structure of Tropheus make the outlier approach prone to false‐positive signals of selection, we examined the correlation between outlier locus alleles and colour phenotypes in a genetic and phenotypic cline between two morphs. Distributions of allele frequencies at one outlier locus were indeed consistent with linkage to a colour locus. Despite the challenges posed by population structure and demography, our results encourage the cautious application of genome scans to studies of divergent selection in subdivided and recently expanded populations.
Clinical Investigation : Lymphoma Involved Node Radiation Therapy : An Effective Alternative in Early-Stage Hodgkin Lymphoma

We present treatment outcomes for a cohort of 97 clinical stage I-II Hodgkin lymphoma (HL) patients using involved node radiation therapy (INRT). The 4year freedom from disease progression was 96.4% (95% confidence interval: 92.4%100.4%). The 4-year overall survival was 94% (95% confidence interval: 88.8%99.1%). Eight patients died, none from HL; 7 malignancies were diagnosed, and 5 patients developed heart disease. INRT represents an effective alternative to more extended radiation therapy in the combined modality treatment for early-stage HL.
Migration distance rather than migration rate explains genetic diversity in human patrilocal groups

In patrilocal groups, females preferentially move to join their mate’s paternal relatives. The gender‐biased gene flow generated by this cultural practice is expected to affect genetic diversity across human populations. Greater female than male migration is predicted to result in a larger decrease in between‐group differentiation for mitochondrial DNA (mtDNA) than for the non‐recombining part of the Y chromosome (NRY). We address the question of how patrilocality affects the distribution of genetic variation in human populations controlling for confounding factors such as ethno‐linguistic heterogeneity and geographic distance which possibly explain the contradictory results observed in previous studies. By combining genetic and bio‐demographic data from Lesotho and Spain, we show that preferential female migration over short distances appears to minimize the impact of a generally higher female migration rate in patrilocal communities, suggesting patrilocality might influence genetic variation only at short ranges.
A likelihood‐based comparison of population histories in a parasitoid guild

Little is known about the stability of trophic relationships in complex natural communities over evolutionary timescales. Here, we use sequence data from 18 nuclear loci to reconstruct and compare the intraspecific histories of major Pleistocene refugial populations in the Middle East, the Balkans and Iberia in a guild of four Chalcid parasitoids (Cecidostiba fungosa, Cecidostiba semifascia, Hobbya stenonota and Mesopolobus amaenus) all attacking Cynipid oak galls. We develop a likelihood method to numerically estimate models of divergence between three populations from multilocus data. We investigate the power of this framework on simulated data, and—using triplet alignments of intronic loci—quantify the support for all possible divergence relationships between refugial populations in the four parasitoids. Although an East to West order of population divergence has highest support in all but one species, we cannot rule out alternative population tree topologies. Comparing the estimated times of population splits between species, we find that one species, M. amaenus, has a significantly older history than the rest of the guild and must have arrived in central Europe at least one glacial cycle prior to other guild members. This suggests that although all four species may share a common origin in the East, they expanded westwards into Europe at different times.
COIN: A Large-Scale Dataset for Comprehensive Instructional Video Analysis

There are substantial instruction videos on the Internet, which enables us to acquire knowledge for completing various tasks. However, most existing datasets for instruction video analysis have the limitations in diversity and scale, which makes them far from many real-world applications where more diverse activities occur. Moreover, it still remains a great challenge to organize and harness such data. To address these problems, we introduce a large-scale dataset called “COIN" for COmprehensive INstruction video analysis. Organized with a hierarchical structure, the COIN dataset contains 11,827 videos of 180 tasks in 12 domains (e.g., vehicles, gadgets, etc.) related to our daily life. With a new developed toolbox, all the videos are annotated effectively with a series of step descriptions and the corresponding temporal boundaries. Furthermore, we propose a simple yet effective method to capture the dependencies among different steps, which can be easily plugged into conventional proposal-based action detection methods for localizing important steps in instruction videos. In order to provide a benchmark for instruction video analysis, we evaluate plenty of approaches on the COIN dataset under different evaluation criteria. We expect the introduction of the COIN dataset will promote the future in-depth research on instruction video analysis for the community.
Genome‐wide patterns of divergence and gene flow across a butterfly radiation

The Heliconius butterflies are a diverse recent radiation comprising multiple levels of divergence with ongoing gene flow between species. The recently sequenced genome of Heliconius melpomene allowed us to investigate the genomic evolution of this group using dense RAD marker sequencing. Phylogenetic analysis of 54 individuals robustly supported reciprocal monophyly of H. melpomene and Heliconius cydno and refuted previous phylogenetic hypotheses that H. melpomene may be paraphylectic with respect to H. cydno. Heliconius timareta also formed a monophyletic clade closely related but distinct from H. cydno with Heliconius heurippa falling within this clade. We find evidence for genetic admixture between sympatric populations of the sister clades H. melpomene and H. cydno/timareta, particularly between H. cydno and H. melpomene from Central America and between H. timareta and H. melpomene from the eastern slopes of the Andes. Between races, divergence is primarily explained by isolation by distance and there is no detectable genetic population structure between parapatric races, suggesting that hybrid zones between races are not zones of secondary contact. Our results also support previous findings that colour pattern loci are shared between populations and species with similar colour pattern elements. Furthermore, this pattern is almost unique to these genomic regions, with only a very small number of other loci showing significant similarity between populations and species with similar colour patterns.
Electrostatic interactions between the CTX phage minor coat protein and the bacterial host receptor TolA drive the pathogenic conversion of Vibrio cholerae

Vibrio cholerae is a natural inhabitant of aquatic environments and converts to a pathogen upon infection by a filamentous phage, CTXΦ, that transmits the cholera toxin-encoding genes. This toxigenic conversion of V. cholerae has evident implication in both genome plasticity and epidemic risk, but the early stages of the infection have not been thoroughly studied. CTXΦ transit across the bacterial periplasm requires binding between the minor coat protein named pIII and a bacterial inner-membrane receptor, TolA, which is part of the conserved Tol-Pal molecular motor. To gain insight into the TolA–pIII complex, we developed a bacterial two-hybrid approach, named Oxi-BTH, suited for studying the interactions between disulfide bond-folded proteins in the bacterial cytoplasm of an Escherichia coli reporter strain. We found that two of the four disulfide bonds of pIII are required for its interaction with TolA. By combining Oxi-BTH assays, NMR, and genetic studies, we also demonstrate that two intermolecular salt bridges between TolA and pIII provide the driving forces of the complex interaction. Moreover, we show that TolA residue Arg-325 involved in one of the two salt bridges is critical for proper functioning of the Tol-Pal system. Our results imply that to prevent host evasion, CTXΦ uses an infection strategy that targets a highly conserved protein of Gram-negative bacteria essential for the fitness of V. cholerae in its natural environment.
Sentence Embedding Alignment for Lifelong Relation Extraction

Conventional approaches to relation extraction usually require a fixed set of pre-defined relations. Such requirement is hard to meet in many real applications, especially when new data and relations are emerging incessantly and it is computationally expensive to store all data and re-train the whole model every time new data and relations come in. We formulate such challenging problem as lifelong relation extraction and investigate memory-efficient incremental learning methods without catastrophically forgetting knowledge learned from previous tasks. We first investigate a modified version of the stochastic gradient methods with a replay memory, which surprisingly outperforms recent state-of-the-art lifelong learning methods. We further propose to improve this approach to alleviate the forgetting problem by anchoring the sentence embedding space. Specifically, we utilize an explicit alignment model to mitigate the sentence embedding distortion of learned model when training on new data and new relations. Experiment results on multiple benchmarks show that our proposed method significantly outperforms the state-of-the-art lifelong learning approaches.
ScholarWorks @ UVM ScholarWorks @ UVM Genetic diversity of Chamaecrista fasciculata (Fabaceae) from Genetic diversity of Chamaecrista fasciculata (Fabaceae) from the USDA germplasm collection the USDA germplasm collection

Objective: Chamaecrista fasciculata is a widespread annual legume across Eastern North America, with potential as a restoration planting, biofuel crop, and genetic model for non-papillinoid legumes. As a non-Papilinoid, C. fasciculata , belongs to the Caesalpiniod group in which nodulation likely arose independently of the nodulation in Papilinoid and Mimosoid legumes. Thus, C. fasciculata is an attractive model system for legume evolution. In this study, we describe population structure and genetic diversity among 32 USDA germplasm accessions of C. fasciculata using 317 AFLP markers developed from 12 primer pairs, to assess where geographically there is the most genetic variation. Results: We found that the C. fasciculata germplasm collection fall into four clusters with admixture among them. After correcting for outliers, our analysis shows two primary groups across Eastern and Central North America. To bet-ter understand the population biology of this species, further sampling of the full range of this widespread species is needed across North America, as well as the development of a larger set of markers providing denser coverage of the genome. Further sampling will help clarify geographical relationships in this widespread temperate species.
A versatile system for the neuronal subtype specific expression of lentiviral vectors

Lentiviral expression vectors are powerful tools for gene therapy and long‐term gene expression/repression in the mammalian brain. However, no specificity of transduction has been reported so far in the central nervous system. Here we have developed a novel system to achieve a neuronal subtype specific expression in either dopaminergic (DA) or GABAergic neurons. We employed a delivery strategy by which the transgene is not expressed until its activation by Cre recombinase. We successfully tested the system in vitro and then used this novel lentivector, containing loxP sites, in 2 different transgenic mouse lines expressing Cre either in DA or in GABAergic neurons. In both lines the reporter gene was detected exclusively in Cre‐positive cells, demonstrating that with this experimental approach we were able to achieve completely specific expression of transgenes delivered by lentiviral vectors. This universal system can be applied to all neural subtypes making use of the growing number of specific Cre driver lines. —Tolu, S. , Avale, M. E. , Nakatani, H. , Pons, S. , Parnaudeau, S. , Tronche, F. , Vogt, A. , Monyer, H. , Vogel, R. , de Chaumont, F. , Olivo‐Marin, J.‐C. , Changeux, J.‐P., Maskos, U. A versatile system for the neuronal subtype specific expression of lentiviral vectors. FASEB J. 24, 723–730 (2010). www.fasebj. org
A2A adenosine receptor overexpression and functionality, as well as TNF‐α levels, correlate with motor symptoms in Parkinson's disease

The antagonistic interaction between adenosine and dopamine receptors could have important pathophysiological and therapeutic implications in Parkinson's disease (PD). The primary aim of this study was to investigate the expression, affinity, and density of A1, A2A, A2B, and A3 adenosine receptors (ARs) and D2 dopamine receptors (D2Rs) in PD. An increase in A2AAR density in putamen was found. The presence and functionality of ARs in human lymphocyte and neutrophil membranes from patients with PD revealed a specific A2AAR alteration compared with healthy subjects. A statistically significant linear correlation among the A2AAR density, functionality, or tumor necrosis factor‐α (TNF‐α) levels and Unified Parkinson's Disease Rating Scale (UPDRS) motor score was reported. Adenosine concentration and TNF‐α levels were increased in plasma of patients with PD. In rat adrenal pheochromocytoma (PC12) cells, a widely useful model, adenosine antagonists decreased dopamine uptake, and an opposite effect was mediated by A2A agonists. This is the first report showing the presence of an A2AAR alteration in putamen in PD that mirrors a similar up‐regulation in human peripheral blood cells. Moreover, the correlation found between A2AAR density or A2A agonist potency and UPDRS motor score highlights the central role of A2AARs in the pharmacological treatment of PD. —Varani, K. , Vincenzi, F. , Tosi, A. , Gessi, S. , Casetta, I. , Granieri, G. , Fazio, P., Leung, E. , MacLennan, S. , Granieri, E. , Borea, P. A. A2A adenosine receptor overexpression and functionality, as well as TNF‐α levels, correlate with motor symptoms in Parkinson's disease. FASEB J. 24, 587–598 (2010). www.fasebj. org
Inverse transcriptional activities during complementary chromatic adaptation are controlled by the response regulator RcaC binding to red and green light‐responsive promoters

Complementary chromatic adaptation (CCA) provides cyanobacteria with the ability to shift between red and blue‐green phenotypes that are optimized for absorption of different wavelengths of light. Controlled by the ratio of green to red light, this process results from differential expression of two groups of operons, many of which encode proteins involved in photosynthetic light harvesting antennae biogenesis. In the freshwater species Fremyella diplosiphon, the inverse regulation of these two classes is complex and occurs through different mechanisms. It also involves a two‐component pathway that includes a phytochrome‐class photoreceptor and the response regulator RcaC. Here we uncover the mechanism through which this system controls CCA by demonstrating that RcaC binds to the L Box within promoters of both classes of light‐regulated operons. We provide functional evidence that complementary regulation of these operons occurs by RcaC's simultaneous activation and repression of transcription in red light. We identify rcaC and L Boxes in the genome of a marine cyanobacterium capable of CCA, suggesting widespread use of this control system. These results provide important insights into the long‐standing enigma of CCA regulation and complete the first description of an entire two‐component system controlled by a phytochrome‐class photoreceptor.
Estrogen receptor (cid:2) – dependent Notch1 activation protects vascular endothelium against tumor necrosis factor (cid:3) (TNF (cid:3) )-induced apoptosis

from Estrogens apoptosis of (ECs), of the hallmarks of to cardiovascular the EC survival. We have previously reported that 17 (cid:2) -estradiol (E2) treatment activates Notch signaling in ECs. Here, we sought to assess whether in TNF (cid:3) -induced inflammation Notch is involved in E2-mediated protection of the endothelium. We treated human umbilical vein endothelial cells (HUVECs) with E2, TNF (cid:3) , or both and found that E2 counteracts TNF (cid:3) -in-duced apoptosis. When Notch1 was inhibited, this E2-mediated protection was not observed, whereas ectopic overexpression of Notch1 diminished TNF (cid:3) -induced apoptosis. Moreover, TNF (cid:3) reduced the levels of active Notch1 protein, which were partially restored by E2 treatment. Moreover, siRNA-mediated knockdown of estrogen receptor (cid:2) (ER (cid:2) ), but not ER (cid:3) , abolished the effect of E2 on apoptosis. Additionally, the E2-mediated regulation of the levels of active Notch1 was abrogated after silencing ER (cid:2) . In summary, our results indicate that E2 requires active Notch1 through a mechanism involving ER (cid:2) to protect the endothelium in TNF (cid:3) -induced inflammation. These findings could be relevant for assessing the efficacy and applicability of menopausalhormonetreatment,becausetheymayindicatethat in women with impaired Notch signaling, hormone therapy might not effectively protect the endothelium.
The small GTPase Rac and the p21‐activated kinase Cla4 in Claviceps purpurea: interaction and impact on polarity, development and pathogenicity

Claviceps purpurea, the ergot fungus, is a highly specialized pathogen of grasses; its colonization of host ovarian tissue requires an extended period of strictly polarized, oriented growth towards the vascular tissue. To understand this process, we study the role of signalling factors affecting polarity and differentiation. We showed that the small GTPase Cdc42 is involved in polarity, sporulation and in planta growth in C. purpurea. Here we present evidence that the GTPase Rac has an even stronger and, in some aspects, inverse impact on growth and development: Δrac mutants form coralline‐like colonies, show hyper‐branching, loss of polarity, sporulation and ability to penetrate. Functional analyses and yeast two‐hybrid studies prove that the p21‐activated kinase Cla4 is a major downstream partner of Rac. Phosphorylation assays of MAP kinases and expression studies of genes encoding reactive oxygen species (ROS)‐scavenging and ‐generating enzymes indicate a function of Rac and Cla4 in fungal ROS homoeostasis which could contribute to their drastic impact on differentiation.
Prolactin—a novel neuroendocrine regulator of human keratin expression in situ

The controls of human keratin expression in situ remain to be fully elucidated. Here, we have investigated the effects of the neurohormone prolactin (PRL) on keratin expression in a physiologically and clinically relevant test system: organ‐cultured normal human hair follicles (HFs). Not only do HFs express a wide range of keratins, but they are also a source and target of PRL. Microarray analysis revealed that PRL differentially regulated a defined subset of keratins and keratin‐associated proteins. Quantitative immunohistomorphometry and quantitative PCR confirmed that PRL up‐regulated expression of keratins K5 and K14 and the epithelial stem cell‐associated keratins K15 and K19 in organ‐cultured HFs and/or isolated HF keratinocytes. PRL also up‐regulated K15 promoter activity and K15 protein expression in situ, whereas it inhibited K6 and K31 expression. These regulatory effects were reversed by a pure competitive PRL receptor antagonist. Antagonist alone also modulated keratin expression, suggesting that “tonic stimulation” by endogenous PRL is required for normal expression levels of selected keratins. Therefore, our study identifies PRL as a major, clinically relevant, novel neuroendocrine regulator of both human keratin expression and human epithelial stem cell biology in situ. —Ramot, Y. , Bíro´, T. , Tiede, S. To´th, B. I. , Langan, E. A. , Sugawara, K. , Foitzik, K. , Ingber, A. , Goffin, V. , Langbein, L. , Paus, R. Prolactin—a novel neuroendocrine regulator of human keratin expression in situ. FASEB J. 24, 1768–1779 (2010). www.fasebj. org