Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome-Wide Gene Expression Profiling of Fertilization Competent Mycelium in Opposite Mating Types in the Heterothallic Fungus Podospora anserina

Background Mating-type loci in yeasts and ascomycotan filamentous fungi (Pezizomycotina) encode master transcriptional factors that play a critical role in sexual development. Genome-wide analyses of mating-type-specification circuits and mating-type target genes are available in Saccharomyces cerevisiae and Schizosaccharomyces pombe; however, no such analyses have been performed in heterothallic (self-incompatible) Pezizomycotina. The heterothallic fungus Podospora anserina serves as a model for understanding the basic features of mating-type control. Its mat+ and mat− mating types are determined by dissimilar allelic sequences. The mat− sequence contains three genes, designated FMR1, SMR1 and SMR2, while the mat+ sequence contains one gene, FPR1. FMR1 and FPR1 are the major regulators of fertilization, and this study presents a genome-wide view of their target genes and analyzes their target gene regulation. Methodology/Principal Findings The transcriptomic profiles of the mat+ and mat− strains revealed 157 differentially transcribed genes, and transcriptomic analysis of fmr1− and fpr1− mutant strains was used to determine the regulatory actions exerted by FMR1 and FPR1 on these differentially transcribed genes. All possible combinations of transcription repression and/or activation by FMR1 and/or FPR1 were observed. Furthermore, 10 additional mating-type target genes were identified that were up- or down-regulated to the same level in mat+ and mat− strains. Of the 167 genes identified, 32 genes were selected for deletion, which resulted in the identification of two genes essential for the sexual cycle. Interspecies comparisons of mating-type target genes revealed significant numbers of orthologous pairs, although transcriptional profiles were not conserved between species. Conclusions/Significance This study represents the first comprehensive genome-wide analysis of mating-type direct and indirect target genes in a heterothallic filamentous fungus. Mating-type transcription factors have many more target genes than are found in yeasts and exert a much greater diversity of regulatory actions on target genes, most of which are not directly related to mating.
Evaluation of scenario-generation methods for stochastic programming

Stochastic programs can only be solved with discrete distributions of limited cardinality. Input, however, normally comes in the form of continuous distributions or large data sets. Creating a limited discrete distribution from input is called scenario generation. In this paper, we discuss how to evaluate the quality or suitability of scenario generation methods for a given stochastic programming model. We formulate minimal requirements that should be imposed on a scenario generation method before it can be used for solving the stochastic programming model. We also show how the requirements can be tested. The procedures for testing a scenario generation method is illustrated on a case from portfolio management.
Social preferences: Some thoughts from the field

This review steps back from the burgeoning economics literature on measuring social preferences and considers more carefully the empirical evidence from the lab and the field. I place the claims from the ardent supporters of the literature into three bins: one for claims that are supported by the data upon closer scrutiny, one for claims that are not supported by the data upon closer scrutiny, and one for claims that may or may not be true. The third set of claims highlights important theoretical and empirical investigations that need to be done to further our understanding of the nature and import of social preferences.
Mapping Reef Fish and the Seascape: Using Acoustics and Spatial Modeling to Guide Coastal Management

Reef fish distributions are patchy in time and space with some coral reef habitats supporting higher densities (i.e., aggregations) of fish than others. Identifying and quantifying fish aggregations (particularly during spawning events) are often top priorities for coastal managers. However, the rapid mapping of these aggregations using conventional survey methods (e.g., non-technical SCUBA diving and remotely operated cameras) are limited by depth, visibility and time. Acoustic sensors (i.e., splitbeam and multibeam echosounders) are not constrained by these same limitations, and were used to concurrently map and quantify the location, density and size of reef fish along with seafloor structure in two, separate locations in the U.S. Virgin Islands. Reef fish aggregations were documented along the shelf edge, an ecologically important ecotone in the region. Fish were grouped into three classes according to body size, and relationships with the benthic seascape were modeled in one area using Boosted Regression Trees. These models were validated in a second area to test their predictive performance in locations where fish have not been mapped. Models predicting the density of large fish (≥29 cm) performed well (i.e., AUC = 0.77). Water depth and standard deviation of depth were the most influential predictors at two spatial scales (100 and 300 m). Models of small (≤11 cm) and medium (12–28 cm) fish performed poorly (i.e., AUC = 0.49 to 0.68) due to the high prevalence (45–79%) of smaller fish in both locations, and the unequal prevalence of smaller fish in the training and validation areas. Integrating acoustic sensors with spatial modeling offers a new and reliable approach to rapidly identify fish aggregations and to predict the density large fish in un-surveyed locations. This integrative approach will help coastal managers to prioritize sites, and focus their limited resources on areas that may be of higher conservation value.
Chondrogenic and Adipogenic Potential of Microvascular Pericytes

Background—Previous studies have shown that pericytes can differentiate into osteoblasts and form bone. This study investigated whether pericytes can also differentiate into chondrocytes and adipocytes. Methods and Results—Reverse transcription–polymerase chain reaction demonstrated that pericytes express mRNA for the chondrocyte markers Sox9, aggrecan, and type II collagen. Furthermore, when cultured at high density in the presence of a defined chondrogenic medium, pericytes formed well-defined pellets comprising cells embedded in an extracellular matrix rich in sulfated proteoglycans and type II collagen. In contrast, when endothelial cells were cultured under the same conditions, the pellets disintegrated after 48 hours. In the presence of adipogenic medium, pericytes but not endothelial cells expressed mRNA for peroxisome proliferator–activated receptor-γ2 (an adipocyte-specific transcription factor) and incorporated lipid droplets that stained with oil red O. To confirm that pericytes can differentiate along the chondrocytic and adipocytic lineages in vivo, these cells were inoculated into diffusion chambers and implanted into athymic mice for 56 days. Accordingly, mineralized cartilage, fibrocartilage, and a nonmineralized cartilaginous matrix with lacunae containing chondrocytes were observed within these chambers. Small clusters of cells that morphologically resembled adipocytes were also identified. Conclusions—These data demonstrate that pericytes are multipotent cells that may contribute to growth, wound healing, repair, and/or the development and progression of various pathological states.
LANTERN: a randomized study of QVA149 versus salmeterol/fluticasone combination in patients with COPD

Background The current Global initiative for chronic Obstructive Lung Disease (GOLD) treatment strategy recommends the use of one or more bronchodilators according to the patient’s airflow limitation, their history of exacerbations, and symptoms. The LANTERN study evaluated the effect of the long-acting β2-agonist (LABA)/long-acting muscarinic antagonist (LAMA) dual bronchodilator, QVA149 (indacaterol/glycopyrronium), as compared with the LABA/inhaled corticosteroid, salmeterol/fluticasone (SFC), in patients with moderate-to-severe COPD with a history of ≤1 exacerbation in the previous year. Methods In this double-blind, double-dummy, parallel-group study, 744 patients with moderate-to-severe COPD with a history of ≤1 exacerbations in the previous year were randomized (1:1) to QVA149 110/50 μg once daily or SFC 50/500 μg twice daily for 26 weeks. The primary endpoint was noninferiority of QVA149 versus SFC for trough forced expiratory volume in 1 second (FEV1) at week 26. Results Overall, 676 patients completed the study. The primary objective of noninferiority between QVA149 and SFC in trough FEV1 at week 26 was met. QVA149 demonstrated statistically significant superiority to SFC for trough FEV1 (treatment difference [Δ]=75 mL; P<0.001). QVA149 demonstrated a statistically significant improvement in standardized area under the curve (AUC) from 0 hours to 4 hours for FEV1 (FEV1 AUC0–4h) at week 26 versus SFC (Δ=122 mL; P<0.001). QVA149 and SFC had similar improvements in transition dyspnea index focal score, St George Respiratory Questionnaire total score, and rescue medication use. However, QVA149 significantly reduced the rate of moderate or severe exacerbations by 31% (P=0.048) over SFC. Overall, the incidence of adverse events was comparable between QVA149 (40.1%) and SFC (47.4%). The incidence of pneumonia was threefold lower with QVA149 (0.8%) versus SFC (2.7%). Conclusion These findings support the use of the LABA/LAMA, QVA149 as an alternative treatment, over LABA/inhaled corticosteroid, in the management of moderate-to-severe COPD patients (GOLD B and GOLD D) with a history of ≤1 exacerbation in the previous year.
Visualization of the joining of ribosomal subunits reveals the presence of 80S ribosomes in the nucleus

The debate continues concerning translation in the nucleus. In this work from the Brogna lab, the authors use fluorescent complementation between the large and small subunits of the ribosome to show that ribosome joining can occur in the nucleus, and accumulate in the nucleolus in particular, in fly tissues and cultured cells. Puromycin incorporation occurred at these sites indicating the possibility that the association is functional.
Reducing the genetic risk of age-related macular degeneration with dietary antioxidants, zinc, and ω-3 fatty acids: the Rotterdam study.

OBJECTIVE To investigate whether dietary nutrients can reduce the genetic risk of early age-related macular degeneration (AMD) conferred by the genetic variants CFH Y402H and LOC387715 A69S in a nested case-control study. METHODS For 2167 individuals (≥55 years) from the population-based Rotterdam Study at risk of AMD, dietary intake was assessed at baseline using a semiquantitative food frequency questionnaire and genetic variants were determined using TaqMan assay. Incident early AMD was determined on fundus photographs at 3 follow-up visits (median follow-up, 8.6 years). The synergy index was used to evaluate biological interaction between risk factors; hazard ratios were calculated to estimate risk of early AMD in strata of nutrient intake and genotypes. RESULTS Five hundred seventeen participants developed early AMD. Significant synergy indices supported the possibility of biological interaction between CFH Y402H and zinc, β-carotene, lutein/zeaxanthin, and eicosapentaenoic/docosahexaenoic acid (EPA/DHA) and between LOC387715 A69S and zinc and EPA/DHA (all P < .05). Homozygotes of CFH Y402H with dietary intake of zinc in the highest tertile reduced their hazard ratio of early AMD from 2.25 to 1.27. For intakes of β-carotene, lutein/zeaxanthin, and EPA/DHA, these risk reductions were from 2.54 to 1.47, 2.63 to 1.72, and 1.97 to 1.30, respectively. Carriers of LOC387715 A69S with the highest intake of zinc and EPA/DHA reduced their risk from 1.70 to 1.17 and 1.59 to 0.95, respectively (all P trends <.05). CONCLUSIONS High dietary intake of nutrients with antioxidant properties reduces the risk of early AMD in those at high genetic risk. Therefore, clinicians should provide dietary advice to young susceptible individuals to postpone or prevent the vision-disabling consequences of AMD.
Hormone‐dependent processing of the avian progesterone receptor

Avian progesterone receptor exists as two forms, A and B, with molecular weights of 79,000 and 110,000 daltons, respectively. The origin and significance of these two forms is an area of active investigation and debate. Monoclonal antibodies produced against these two forms were used to examine receptor stability in cytosol and changes in the receptor forms induced by hormone binding.
Example-Based Automatic Music-Driven Conventional Dance Motion Synthesis

We introduce a novel method for synthesizing dance motions that follow the emotions and contents of a piece of music. Our method employs a learning-based approach to model the music to motion mapping relationship embodied in example dance motions along with those motions' accompanying background music. A key step in our method is to train a music to motion matching quality rating function through learning the music to motion mapping relationship exhibited in synchronized music and dance motion data, which were captured from professional human dance performance. To generate an optimal sequence of dance motion segments to match with a piece of music, we introduce a constraint-based dynamic programming procedure. This procedure considers both music to motion matching quality and visual smoothness of a resultant dance motion sequence. We also introduce a two-way evaluation strategy, coupled with a GPU-based implementation, through which we can execute the dynamic programming process in parallel, resulting in significant speedup. To evaluate the effectiveness of our method, we quantitatively compare the dance motions synthesized by our method with motion synthesis results by several peer methods using the motions captured from professional human dancers' performance as the gold standard. We also conducted several medium-scale user studies to explore how perceptually our dance motion synthesis method can outperform existing methods in synthesizing dance motions to match with a piece of music. These user studies produced very positive results on our music-driven dance motion synthesis experiments for several Asian dance genres, confirming the advantages of our method.
Factors Affecting Students’ Performance in Chemistry: Case Study in Zanzibar Secondary Schools

The purpose of this study was to investigate the performance of chemistry in Zanzibar Secondary Schools. It was conducted in all regions of Zanzibar in public and private secondary schools and Ministry of Education officials. The objective of the study included finding out causes of poor performance in chemistry. Views, opinions, and suggestions of teachers and students to improve performance of chemistry and a descriptive survey was adopted for the study. 45 teachers and 200 students were randomly sampled from 15 secondary schools in Zanzibar and ten Ministry of Education officials were purposively sampled for the study. Questionnaires and open-ended interview schedules were the main instruments used in obtaining relevant data from respondents. Data collected from the field was analyzed both qualitatively and quantitatively. Qualitative analysis involved content analysis of the responses obtained through interviews and quantitative analysis involved generation of tables, frequencies and percentages. The results revealed that there were shortages of trained teachers, lack of proficiency in the language of instruction (English) and major facilities like laboratories and books. These led to poor delivery of subject matter and consequently resulting in poor performance. Based on the findings, this study recommends that provision of trained, competent, and effective teachers as vital aspects to be considered. Government through Ministry of Education should put effort to stalk libraries and equip laboratories with modern books and instruments. In addition, the ministry should strengthen teachers’ training and encourage use of instructional media in class and make conducive learning environment to both teachers and students. Keywords—Zanzibar, secondary schools, chemistry, science, performance and factors.
Universal Grammar and Lexis for Quick Ramp-Up of MT Systems

This paper introduces Boas, a semi-automatic knowledge elicitation system that guides a team of two people through the process of developing the static knowledge sources for a moderate-quality, broad-coverage MT system from any "low-density" language into English in about six months. The paper focuses on some issues in the elicitation of descriptive knowledge in Boas and also the issue of the principled reuse of pre-existing resources, such as a lexicon, an ontology, and an English generation module, among others, made possible by the fact that the client MT system is developed for a single target language.
Hydroxylation of the eukaryotic ribosomal decoding center affects translational accuracy

Significance The processing of DNA sequences into proteins is fine-tuned to meet the conflicting demands of accuracy and speed. DNA mutations can introduce premature stop codons, leading to inactive proteins. We report that oxygen-dependent posttranslational modification of the ribosomal decoding center affects stop codon readthrough in an mRNA sequence-dependent manner. Our work demonstrates that oxygenases catalyzing RPS23 hydroxylation are conserved in eukaryotes, including yeasts, flies, and humans. In basal eukaryotes, RPS23 undergoes two hydroxylations, whereas in animals we only observe one hydroxylation. Yeast ribosomes lacking hydroxylation manifest altered stop codon readthrough up to ∼10-fold. The results reveal oxygen-dependent modifications that regulate translational accuracy and suggest unprecedented approaches to modulating ribosomal accuracy for medicinal application. The mechanisms by which gene expression is regulated by oxygen are of considerable interest from basic science and therapeutic perspectives. Using mass spectrometric analyses of Saccharomyces cerevisiae ribosomes, we found that the amino acid residue in closest proximity to the decoding center, Pro-64 of the 40S subunit ribosomal protein Rps23p (RPS23 Pro-62 in humans) undergoes posttranslational hydroxylation. We identify RPS23 hydroxylases as a highly conserved eukaryotic subfamily of Fe(II) and 2-oxoglutarate dependent oxygenases; their catalytic domain is closely related to transcription factor prolyl trans-4-hydroxylases that act as oxygen sensors in the hypoxic response in animals. The RPS23 hydroxylases in S. cerevisiae (Tpa1p), Schizosaccharomyces pombe and green algae catalyze an unprecedented dihydroxylation modification. This observation contrasts with higher eukaryotes, where RPS23 is monohydroxylated; the human Tpa1p homolog OGFOD1 catalyzes prolyl trans-3-hydroxylation. TPA1 deletion modulates termination efficiency up to ∼10-fold, including of pathophysiologically relevant sequences; we reveal Rps23p hydroxylation as its molecular basis. In contrast to most previously characterized accuracy modulators, including antibiotics and the prion state of the S. cerevisiae translation termination factor eRF3, Rps23p hydroxylation can either increase or decrease translational accuracy in a stop codon context-dependent manner. We identify conditions where Rps23p hydroxylation status determines viability as a consequence of nonsense codon suppression. The results reveal a direct link between oxygenase catalysis and the regulation of gene expression at the translational level. They will also aid in the development of small molecules altering translational accuracy for the treatment of genetic diseases linked to nonsense mutations.
Visual Dialog

We introduce the task of Visual Dialog, which requires an AI agent to hold a meaningful dialog with humans in natural, conversational language about visual content. Specifically, given an image, a dialog history, and a question about the image, the agent has to ground the question in image, infer context from history, and answer the question accurately. Visual Dialog is disentangled enough from a specific downstream task so as to serve as a general test of machine intelligence, while being grounded in vision enough to allow objective evaluation of individual responses and benchmark progress. We develop a novel two-person chat data-collection protocol to curate a large-scale Visual Dialog dataset (VisDial). VisDial contains 1 dialog (10 question-answer pairs) on ~140k images from the COCO dataset, with a total of ~1.4M dialog question-answer pairs. We introduce a family of neural encoder-decoder models for Visual Dialog with 3 encoders (Late Fusion, Hierarchical Recurrent Encoder and Memory Network) and 2 decoders (generative and discriminative), which outperform a number of sophisticated baselines. We propose a retrieval-based evaluation protocol for Visual Dialog where the AI agent is asked to sort a set of candidate answers and evaluated on metrics such as mean-reciprocal-rank of human response. We quantify gap between machine and human performance on the Visual Dialog task via human studies. Our dataset, code, and trained models will be released publicly at https://visualdialog.org. Putting it all together, we demonstrate the first visual chatbot!
Coexpression of the High Molecular Weight Glutenin Subunit 1Ax1 and Puroindoline Improves Dough Mixing Properties in Durum Wheat (Triticum turgidum L. ssp. durum)

Wheat end-use quality mainly derives from two interrelated characteristics: the compositions of gluten proteins and grain hardness. The composition of gluten proteins determines dough rheological properties and thus confers the unique viscoelastic property on dough. One group of gluten proteins, high molecular weight glutenin subunits (HMW-GS), plays an important role in dough functional properties. On the other hand, grain hardness, which influences the milling process of flour, is controlled by Puroindoline a (Pina) and Puroindoline b (Pinb) genes. However, little is known about the combined effects of HMW-GS and PINs on dough functional properties. In this study, we crossed a Pina-expressing transgenic line with a 1Ax1-expressing line of durum wheat and screened out lines coexpressing 1Ax1 and Pina or lines expressing either 1Ax1 or Pina. Dough mixing analysis of these lines demonstrated that expression of 1Ax1 improved both dough strength and over-mixing tolerance, while expression of PINA detrimentally affected the dough resistance to extension. In lines coexpressing 1Ax1 and Pina, faster hydration of flour during mixing was observed possibly due to the lower water absorption and damaged starch caused by PINA expression. In addition, expression of 1Ax1 appeared to compensate the detrimental effect of PINA on dough resistance to extension. Consequently, coexpression of 1Ax1 and PINA in durum wheat had combined effects on dough mixing behaviors with a better dough strength and resistance to extension than those from lines expressing either 1Ax1 or Pina. The results in our study suggest that simultaneous modulation of dough strength and grain hardness in durum wheat could significantly improve its breadmaking quality and may not even impair its pastamaking potential. Therefore, coexpression of 1Ax1 and PINA in durum wheat has useful implications for breeding durum wheat with dual functionality (for pasta and bread) and may improve the economic values of durum wheat.