Miracle-dz/UniFAR-FTUs huggingface dataset:
Inaugural Article: Different mechanisms for phytoalexin induction by pathogen and wound signals in Medicago truncatula

Many plant natural products have antimicrobial or antiinsect activity in vitro, and genetically reducing or increasing levels of certain natural products can reduce or enhance resistance or tolerance to microbes or pests (1–3). Antimicrobial plant natural products have been classified as phytoanticipins, which are preformed inhibitory compounds, or phytoalexins, which are derived from often distant precursors via de novo synthesis in response to microbial challenge (4). Consistent with de novo synthesis of phytoalexins, many studies have documented rapid activation of their diverse biosynthetic genes in response to fungal or bacterial infection of plant organs or treatment of plant cell cultures with microbial-derived elicitor molecules (5–7). However, some reports fail to demonstrate a link between phytoalexin accumulation and increased transcription of related biosynthetic genes (e.g., ref. 8). Utilization of additional approaches such as determination of metabolite levels and/or enzymatic activities might help explain the rare cases in which phytoalexin induction is observed in the apparent absence of changes at the transcriptional level. Some natural products, for example, isoflavonoids and triterpenes, show activity against both microbial and insect challengers of the plants that produce them (9–11). Root-derived cell suspension lines of the model legume Medicago truncatula studied previously accumulated the isoflavonoid-derived pterocarpan phytoalexin medicarpin in response to treatment with yeast elicitor (YE), and triterpene saponins after exposure to the wound signal methyl jasmonate (MJ) (12–14). To investigate the different molecular mechanisms underlying metabolic responses to pathogen and wound signals, we have used an integrated transcriptome/metabolome analysis of a different root-derived Medicago cell suspension culture line that accumulates medicarpin in response to both YE and MJ. This culture was of the same genotype (A17) as the previously studied cultures and was propagated under the same conditions (13), the only differences being the independent initial root explant and the passage number at which the experiments were performed. Surprisingly, transcript profiling analysis revealed that none of the genes encoding early enzymes of phenylpropanoid/isoflavonoid biosynthesis was induced before accumulation of medicarpin in response to MJ in this culture line, although the downstream pathway genes specific for medicarpin formation were induced by both treatments. MJ-inducible β-glucosidases were functionally characterized and shown to be active with (iso)flavonoid glycosides and therefore potentially involved in precursor mobilization for medicarpin biosynthesis. Our results suggest that MJ acts as a signal for the rapid deployment of preexisting intermediates into phytoalexin biosynthesis during wound responses.
Setd1a and NURF mediate chromatin dynamics and gene regulation during erythroid lineage commitment and differentiation

The modulation of chromatin structure is a key step in transcription regulation in mammalian cells and eventually determines lineage commitment and differentiation. USF1/2, Setd1a and NURF complexes interact to regulate chromatin architecture in erythropoiesis, but the mechanistic basis for this regulation is hitherto unknown. Here we showed that Setd1a and NURF complexes bind to promoters to control chromatin structural alterations and gene activation in a cell context dependent manner. In human primary erythroid cells USF1/2, H3K4me3 and the NURF complex were significantly co-enriched at transcription start sites of erythroid genes, and their binding was associated with promoter/enhancer accessibility that resulted from nucleosome repositioning. Mice deficient for Setd1a, an H3K4 trimethylase, in the erythroid compartment exhibited reduced Ter119/CD71 positive erythroblasts, peripheral blood RBCs and hemoglobin levels. Loss of Setd1a led to a reduction of promoter-associated H3K4 methylation, inhibition of gene transcription and blockade of erythroid differentiation. This was associated with alterations in NURF complex occupancy at erythroid gene promoters and reduced chromatin accessibility. Setd1a deficiency caused decreased associations between enhancer and promoter looped interactions as well as reduced expression of erythroid genes such as the adult β-globin gene. These data indicate that Setd1a and NURF complexes are specifically targeted to and coordinately regulate erythroid promoter chromatin dynamics during erythroid lineage differentiation.
A comparison of the fat composition and prices of margarines between 2002 and 2006, when new Canadian labelling regulations came into effect

Abstract Objective To examine the effect of the new Canadian labelling regulations on the fat composition and prices of margarines. Study design A survey of all margarines sold in major supermarkets in the Greater Toronto area was conducted in 2006, and results were compared with those of a similar survey conducted in 2002. Average fat composition, proportion of ‘trans fat-free’ margarines and average prices of margarines were compared. A general linear model procedure was used to compare the relationship between price and fat composition in 2002 and 2006. Results Average amounts of trans fatty acids (TFA) and MUFA decreased, while average amounts of PUFA increased significantly from 2002 to 2006. The proportion of margarines with less than 0·2 g TFA/10 g serving rose significantly from 31 % in 2002 to 69 % in 2006. Margarines lower in TFA on average cost significantly more than margarines with greater amounts of these fats, and this relationship appeared stronger in 2006 relative to 2002. Conclusions There is evidence of reductions in TFA in margarines since new labelling regulations came into effect in Canada; however, TFA reductions appeared to be restricted to higher-priced margarines. Results suggest that voluntary approaches (i.e. manufacturer incentives via labelling) to reduce population intakes of TFA will yield little changes in TFA content of low-cost products and thus may have limited benefit for lower-income groups, who are at higher risk of heart disease.
Hellfire and Delinquency: Another Look

Hirschi and Stark (1969) reported very little relationship between religious involvement and adolescent delinquency. They concluded that religion is therefore "irrelevant to delinquency. " The present paper offers an alternative interpretation of their findings and tests one of its implications. It is hypothesized that Hirschi and Stark's findings apply only to offenses against persons and property, and that a clear relationship between religion and delinquency should be found for "victimless" crimes. Data from high-school students in the Pacific Northwest replicate Hirschi and Stark's findings but also reveal a moderately strong relationship between religion and the use of marijuana and alcohol. Suggestions are made for further tests of the alternative interpretation.
Postembryonic development of the dorsal longitudinal flight muscle and its innervation in Manduca sexta

The neuromuscular systems of holometabolous insects must be remodeled during metamorphosis to allow striking behavioral changes, such as the acquisition of flight. The fast contracting dorsal longitudinal flight muscle (DLM) of Manduca arises from an anlage containing both remnants of specific larval dorsal body wall muscles and extrinsic myoblasts. In the mesothorax, the DLM is innervated by five persisting larval motoneurons: one in the mesothoracic and four in the prothoracic ganglion. These motoneurons innervate two slowly contracting body wall muscles in the larva. 2 days before pupation, the DLM template fibers begin to degenerate, whereas other muscles remain intact until pupation. Correspondingly, the motor terminals retract from the template fibers while they remain on other muscle fibers until pupation. Accumulation and proliferation of putative myoblasts also starts 2 days before pupation in close spatial relationship to the retracted motor tufts around the degenerating larval template fibers. Proliferation increases through the early pupal stages, and is detected within the anlage until the ninth day after pupation. 2 days after pupation, the anlage splits into five bundles, each innervated by one motoneuron. Striations occur on the seventh day after pupation when the growing motor axons reach the attachment sites. Subsequently, the muscle grows in volume and higher‐order motor branches are formed. Within the central nervous system, there is dramatic regression of larval dendrites followed by growth of new dendrites as the persistent motoneurons assume their new role in flight behavior. Both central and peripheral remodeling follow similar time courses. J. Comp. Neurol. 422:1–17, 2000. © 2000 Wiley‐Liss, Inc.
Building Usable Menu-Based Natural Language Interfaces To Databases

Natural language interfaces to databases are not in couunon use today for two main reasons: they are difficult to use and they are expensive to build and maintain. This paper presents a functional overview of a new kind of natural language interface that goes far in overcoming both of these problems. The “ease-of-use” problem is solved by wedding a menu-based interaction technique to a traditional semantic graaauar-driven natural language system. Using this approach, all user queries are “understood” by the system. The “creation and maintenance problem” is solved by designing a core grannnar with parameters supplied by the data dictionary and then automatically generating semantic graumars covering some selected subpart of the user’s data. Automatically generated natural language interfaces offer the user an attractive way to group semantically related tables together, to model a user’s access rights, and to model a user's view of supported joins paths in a database.
Should We Move the Whitebark Pine? Assisted Migration, Ethics and Global Environmental Change

Some species face extinction if they are unable to keep pace with climate change. Yet proposals to assist threatened species’ poleward or uphill migration (‘assisted migration’) have caused significant controversy among conservationists, not least because assisted migration seems to threaten some values, even as it protects others. To date, however, analysis of ethical and value questions about assisted migration has largely remained abstract, removed from the ultimately pragmatic decision about whether or not to move a particular species. This paper uses the case study of the whitebark pine, a keystone species of sub-alpine habitats in western North America, to consider how particular cases of assisted migration may be ethically approached. After taking into account the value of species, wildness, place, ecosystems, culture and sentient animals, we conclude that, on balance, there appear to be good reasons to move the whitebark pine.
Comparing the Effects of Methadone Maintenance Treatment, Therapeutic Community, and Residential Rehabilitation on Quality of Life and Mental Health of Drug Addicts

Background This study compared the effects of three drug addiction treatment methods on quality of life and mental health of drug addicts. Methods In this study, 227 Iranian male drug addicts were selected from Mazandaran Province (northern Iran). They were randomized to be treated with methadone maintenance treatment, therapeutic community, or residential rehabilitation. The Short Form Health Survey (SF-36) and the General Health Questionnaire (GHQ) were completed by the subjects at the start and end of the study. The length of intervention and SF-36 and GHQ scores before and after treatment were compared between groups. All statistical analyses were performed in SPSS. Findings Significant differences in quality of life and mental health scores were found between the three groups. We found that if drug addicts stay in the therapeutic community center for more than 6 months, this method will be the most effective intervention to improve quality of life and mental health of drug abusers. Conclusion Evaluation of different methods drug addiction treatment is very difficult. Therefore, further studies are required to better understand the effects of therapeutic community.
Honesty and beliefs about honesty in 15 countries

The honesty of resident nationals of 15 countries was measured in two experiments: reporting a coin flip with a reward for "heads", and an online quiz with the possibility of cheating. There are large differences in honesty across countries. Average honesty correlates with per capita GDP: this relationship is driven mostly by GDP differences arising before 1950, rather than by GDP growth since 1950, suggesting that the growth-honesty relationship was more important in earlier periods than today. The experiment also elicited participants' beliefs about honesty in different countries. Beliefs were not correlated with reality. Instead they appear to be driven by cognitive biases, including self-projection.
Radial Velocities of Stars in the Galactic Center

We present results from K-band slit scan observations of a ~20″ × 20″ region of the Galactic center (GC) in two separate epochs more than 5 years apart. The high-resolution (R = λ/Δ λ ⩾ 14,000) observations allow the most accurate radial velocity and acceleration measurements of the stars in the central parsec of the Galaxy. Detected stars can be divided into three groups based on the CO absorption band heads at ~2.2935 μm and the He II lines at ~2.0581 and ~2.112, 2.113 μm: cool, narrow-line hot, and broad-line hot. The radial velocities of the cool, late-type stars have approximately a symmetrical distribution with its center at ~–7.8 ± 10.3 km s−1 and a standard deviation ~113.7 ± 10.3 km s−1. Although our statistics are dominated by the brightest stars, we estimate a central black hole mass of (3.9 ± 1.1) × 106 M☉, consistent with current estimates from complete orbits of individual stars. Our surface density profile and the velocity dispersion of the late-type stars support the existence of a low-density region at the Galactic center suggested by earlier observations. Many hot, early-type stars show radial velocity changes higher than maximum values allowed by pure circular orbital motions around a central massive object, suggesting that the motions of these stars greatly deviate from circular orbital motions around the Galactic center. The correlation between the radial velocities of the early-type He I stars and their declination offsets from Sagittarius A* suggests that a systematic rotation is present for the early-type population. No figure rotation around the Galactic center for the late-type stars is supported by the new observations.
Social Work Research in the Child Protection Field in Australia

Social work makes an important contribution to child protection practice and policy in Australia, but data are limited about the discipline's contribution to research. The aim of this scoping review was to examine the quantity and nature of Australian social work child protection research for the period 2007–14. A comprehensive search of nine bibliographic databases identified 255 peer-reviewed articles. The papers were authored by 287 researchers, most of whom published only one paper during the period. The research was published in seventeen Australian and thirty-five international journals. Non-empirical papers and those using qualitative methodologies were most prevalent, and there was a lack of research depth and quantum on particular child protection topics. The findings indicate that developing more sustained programmes of research, underpinned by a balanced portfolio of methods and approaches, would maximise the potential for research impact on child protection policy and practice.
A superconducting bandpass delta-sigma modulator for direct analog-to-digital conversion of microwave radio

Direct analog-to-digital conversion of multi-GHz radio frequency (RF) signals is the ultimate goal in software radio receiver design but remains a daunting challenge for any technology. This thesis examines the potential of superconducting technology for realizing RF analogto-digital converters (ADCs) with improved performance. A bandpass delta-sigma (∆Σ) modulator is an attractive architecture for digitizing narrowband signals with high linearity and a large signal-to-noise ratio (SNR). The design of a superconducting bandpass ∆Σ modulator presented here exploits several advantages of superconducting electronics: the high quality factor of resonators, the high sampling rates of comparators realized with Josephson junctions, natural quantization of voltage pulses, and high circuit sensitivity. Demonstration of a superconducting circuit operating at clock rates in the tens of GHz is often hindered by the difficulty of high speed interfacing with room-temperature test equipment. In this work, a test chip with integrated acquisition memory is used to simplify high speed testing in a cryogenic environment. The small size (256 bits) of the on-chip memory severely limits the frequency resolution of spectra based on standard fast Fourier transforms. Higher resolution spectra are obtained by “segmented correlation”, a new method for testing ADCs. Two different techniques have been found for clocking the superconducting modulator at frequencies in the tens of GHz. In the first approach, an optical clocking technique was developed, in which picosecond laser pulses are delivered via optical fiber to an on-chip metal-semiconductor-metal (MSM) photodiode, whose output current pulses trigger the Josephson circuitry. In the second approach, the superconducting modulator is clocked by an on-chip Josephson oscillator. These testing methods have been applied in the successful demonstration of a superconducting bandpass ∆Σ modulator fabricated in a niobium integrated circuit process with 1 kA/cm2 critical current density for the Josephson junctions. At a 42.6 GHz sampling rate, the center frequency of the experimental modulator is 2.23 GHz, the measured SNR is 49 dB over a 20.8 MHz bandwidth, and a full-scale (FS) input is -17.4 dBm. At a 40.2 GHz sampling rate, the measured in-band noise is -57 dBFS over a 19.6 MHz bandwidth. Thesis Supervisor: Hae-Seung Lee Title: Professor of Electrical Engineering and Computer Science Thesis Supervisor: Mark B. Ketchen Title: Manager, Design/Technology Integration, IBM Research In memory of Robert V. Bulzacchelli
Combing Context and Commonsense Knowledge Through Neural Networks for Solving Winograd Schema Problems

This paper proposes a general framework to combine context and commonsense knowledge for solving the Winograd Schema (WS) and Pronoun Disambiguation Problems (PDP). In the proposed framework, commonsense knowledge bases (e.g. cause-effect word pairs) are quantized as knowledge constraints. The constraints guide us to learn knowledge enhanced embeddings (KEE) from large text corpus. Based on the pre-trained KEE models, this paper proposes two meth-ods to solve the WS and PDP problems. The ﬁrst method is an unsupervised method, which represents all the pronouns and candidate mentions in continuous vector spaces based on their contexts and calculates the semantic similarities be-tween all the possible word pairs. The pronoun disambiguation procedure could then be implemented by comparing the semantic similarities between the pronoun (to be resolved) and all the candidate mentions. The second method is a supervised method, which extracts features for all the pronouns and candidate mentions and solves the WS problems by training a typical mention pair classiﬁcation model. Similar to the ﬁrst method, the features used in the second method are also extracted based on the KEE models. Experiments conducted on the available PDP and WS test sets show that, these two methods both achieve consistent improvements over the base-line systems. The best performance reaches 62% in accuracy on the PDP test set of the ﬁrst Winograd Schema Challenge
A New Morphologically Distinct Avian Malaria Parasite That Fails Detection By Established Polymerase Chain Reaction–Based Protocols for Amplification of the Cytochrome B Gene

Abstract: Plasmodium polymorphum n. sp. (Haemosporida, Plasmodiidae) was found in the skylark, Alauda arvensis (Passeriformes: Alaudidae), during autumnal migration in southern Italy. This organism is illustrated and described based on the morphology of its blood stages. The most distinctive feature of this malaria parasite is the clear preference of its blood stages (trophozoites, meronts, and gametocytes) for immature red blood cells, including erythroblasts. Based on preference of erythrocytic meronts for immature red blood cells, P. polymorphum is most similar to species of the subgenus Huffia. This parasite can be readily distinguished from all other bird malaria parasites, including Plasmodium (Huffia) spp. , due to preferential development and maturation of its gametocytes in immature red blood cells, a unique character for avian Plasmodium spp. In addition, the margins of nuclei in blood stages of P. polymorphum are markedly smooth and distinct; this is also a distinct diagnostic feature of this parasite. Plasmodium polymorphum has been recorded only in the skylark; it is probably a rare parasite, whose host range and geographical distribution remain unclear. Microscopic examination detected a light infection of Plasmodium relictum (lineage GRW11, parasitemia of <0.01%) in the same sample with P. polymorphum; the latter parasite clearly predominated (3.5% parasitemia). However, experienced researchers were unable to detect sequences of mitochondrial cytochrome b gene (cyt b) of P. polymorphum from the microscopically positive sample by using published and newly designed primers for DNA amplification of avian Plasmodium spp. The light parasitemia of P. relictum was easily detectable using several polymerase chain reaction (PCR)–based assays, but P. polymorphum was undetectable in all applied assays. Quantitative PCR also showed the presence of light parasitemia (0.06%) of the lineage GRW11 in this sample. This supports the conclusion that the morphologically distinct parasite observed along with P. relictum and predominant in the sample is genetically dissimilar from the lineage GRW11 based on cyt b sequence. In samples with co-infections, general PCR protocols tend to favor the amplification of the parasite with the higher parasitemia or the amplification with the best matching sequence to the primers. Because the parasitemia of P. polymorphum was >50-fold higher than that of P. relictum and several different primers were tested, we suggest that the failure to amplify P. polymorphum is a more complex problem than why co-infections are commonly overlooked in PCR-based studies. We suggest possible explanations of these results and call for additional research on evolution of mitochondrial genome of hemosporidian parasites.
Building peace in hybrid spaces: women's agency in Iraqi NGOs

International peacebuilding efforts in Iraq have been widely criticised by practitioners and academics. Without neglecting these critiques, I elaborate how external intervention has also created spaces for Iraqi women to exercise different forms of agency. Critical approaches in peace and conflict studies often limit so-called ‘local’ agency to resisting liberal agendas, assuming persistent binaries between local and international spaces. I argue here that upholding those binaries implicitly fosters an absolute understanding of space that fails to meet realities on the ground. This article seeks to outline a concept of gendered agency that integrates a relational conceptualisation of space into the hitherto applied understandings of agency. Drawing on empirical evidence from Iraq, it elaborates how a relational theory of space contributes to grasping hybrid realities and notions of agency on the ground. Beyond analysing spaces of agency for women in (post-)conflict Iraq, the article discusses the value of incorporating a relational understanding of space into critical peacebuilding studies.