Miracle-dz/UniFAR-FTUs huggingface dataset:
Reproduction and morphology of Polydorella (Polychaeta: Spionidae), including the description of a new species from the Philippines

A new spionid polychaete, Polydorella kamakamai, associated with sponges is described from the Philippines. Polydorella kamakamai is characterized by acicular neurosetae in segments 2–7, a fifth segment containing a ventral row of spines with digitiform bosses, and lack of branchiae. As in all members of the genus, P. kamakamai undergoes asexual reproduction via paratomy; the process of paratomy is examined through scanning electron and light microscopy. This species exhibits a growth zone following segment 10, leading to the production of stolon individuals budding from the stock individual; five or more individuals can thus be formed in a single chain. Paratomic division typically occurs in chains containing four to five individuals and as a result colonies are dominated by chains of two individuals. Sexual reproduction is documented for only the second time in the genus; P. kamakamai produces eggs in segments 13–15. Asexual reproduction and fine morphological structure of the ventral spines of the fifth segment are examined by SEM in P. dawydoffi and P. stolonifera. Polydorella dawydoffi is recorded for the first time from the Philippines and the Red Sea and these are compared to type specimens from Vietnam. The ventral spines of P. dawydoffi contain eight or nine rounded or pointed teeth along the apical end and a capillary extension not previously observed with light microscopy. Notes on feeding biology, parasitism by copepods, and a discussion of the evolutionary relationships of Polydorella and other polydorids are provided.
Neoadjuvant rectal score as individual-level surrogate for disease-free survival in rectal cancer in the CAO/ARO/AIO-04 randomized phase III trial

Background Surrogate end points in rectal cancer after preoperative chemoradiation are lacking as their statistical validation poses major challenges, including confirmation based on large phase III trials. We examined the prognostic role and individual-level surrogacy of neoadjuvant rectal (NAR) score that incorporates weighted cT, ypT and ypN categories for disease-free survival (DFS) in 1191 patients with rectal carcinoma treated within the CAO/ARO/AIO-04 phase III trial. Patients and methods Cox regression models adjusted for treatment arm, resection status, and NAR score were used in multivariable analysis. The four Prentice criteria (PC1-4) were used to assess individual-level surrogacy of NAR for DFS. Results After a median follow-up of 50 months, the addition of oxaliplatin to fluorouracil-based chemoradiotherapy (CRT) significantly improved 3-year DFS [75.9% (95% confidence interval [CI] 72.30% to 79.50%) versus 71.3% (95% CI 67.60% to 74.90%); P = 0.034; PC 1) and resulted in a shift toward lower NAR groups (P = 0.034, PC 2) compared with fluorouracil-only CRT. The 3-year DFS was 91.7% (95% CI 88.2% to 95.2%), 81.8% (95% CI 78.4% to 85.1%), and 58.1% (95% CI 52.4% to 63.9%) for low, intermediate, and high NAR score, respectively (P < 0.001; PC 3). NAR score remained an independent prognostic factor for DFS [low versus high NAR: hazard ratio (HR) 4.670; 95% CI 3.106-7.020; P < 0.001; low versus intermediate NAR: HR 1.971; 95% CI 1.303-2.98; P = 0.001] in multivariable analysis. Notwithstanding the inherent methodological difficulty in interpretation of PC 4 to establish surrogacy, the treatment effect on DFS was captured by NAR, supporting satisfaction of individual-level PC 4. Conclusion Our study validates the prognostic role and individual-level surrogacy of NAR score for DFS within a large randomized phase III trial. NAR score could help oncologists to speed up response-adapted therapeutic decision, and further large phase III trial data sets should aim to confirm trial-level surrogacy.
A Closer Look at Weak Label Learning for Audio Events

Audio content analysis in terms of sound events is an important research problem for a variety of applications. Recently, the development of weak labeling approaches for audio or sound event detection (AED) and availability of large scale weakly labeled dataset have finally opened up the possibility of large scale AED. However, a deeper understanding of how weak labels affect the learning for sound events is still missing from literature. In this work, we first describe a CNN based approach for weakly supervised training of audio events. The approach follows some basic design principle desirable in a learning method relying on weakly labeled audio. We then describe important characteristics, which naturally arise in weakly supervised learning of sound events. We show how these aspects of weak labels affect the generalization of models. More specifically, we study how characteristics such as label density and corruption of labels affects weakly supervised training for audio events. We also study the feasibility of directly obtaining weak labeled data from the web without any manual label and compare it with a dataset which has been manually labeled. The analysis and understanding of these factors should be taken into picture in the development of future weak label learning methods. Audioset, a large scale weakly labeled dataset for sound events is used in our experiments.
Antibody expression stability in CHO clonally derived cell lines and their subclones: Role of methylation in phenotypic and epigenetic heterogeneity

Routine CHO cell line development practices involve a lengthy process of iteratively screening clonally derived cell lines to identify a single line suitable for IND filing and clinical manufacture. Paramount in this process is development of a stable production cell line having consistent growth, productivity and product quality for the entire generational length of the manufacturing process. Scale‐down stability models used to screen clones for consistency are time consuming and often a rate‐limiting step in clone selection. To investigate CHEF1 production stability in CHO cells we analyzed genotypic and phenotypic attributes of monoclonal primary clones and their respective subclones over time in standard antibody production models. The main finding of this work indicates that monoclonal cell lines derived from single cell progenitors grow into populations of cells with varied phenotypic heterogeneity, as revealed in their subclones, from either stable or unstable cell lines. Investigation of the subclones demonstrates that clonally derived cell lines grow out into populations with variable phenotypes and genotypes, even if the primary clone shows consistency in both over many generations in a stability study. Phenotypic and genotypic heterogeneity mostly did not correlate, but growth and productivity appear driven in part by cytosine methylation heterogeneity in both primary and secondary clones. This work presents evidence that epigenetic analysis may be useful for early detection of stability traits, but emphasizes the continued importance of rigorous cell line stability screening to identify primary clones that have consistent phenotypic characteristics, especially growth and productivity, throughout the in vitro lifecycle of the cells. © 2018 American Institute of Chemical Engineers Biotechnol. Prog. , 34:635–649, 2018
Interaction between propofol and thiopental: Isobolographic analysis using dose, central compartment and effect compartment concentrations

Background: Giving a benzodiazepine or opioid with an intravenous anaesthetic agent generally result in synergism. However, few studies so far have detailed the relationship when two intravenous anaesthetics are given simultaneously. The aim of this study is to investigate the interaction between propofol and thiopental when given in fixed and variable dose ratios. Methods: Ninety patients were given propofol and / or thiopental for induction of anaesthesia. Twenty patients received an infusion of either drug while 30 patients received an infusion of an admixture of both drugs. Another 40 patients received a bolus of one drug followed by an infusion of the other. Isobolographic analysis was used to determine the interaction between the two drugs. Results: Both fixed and variable drug dose ratios resulted in an additive interaction between propofol and thiopental. The average dose of propofol at loss of the eyelash reflex was 1.14 mg kg-1. The corresponding average thiopental dose of 2.49 mg kg-1. Conclusions: Propofol and thiopental interact in an additive fashion when given at induction of anaesthesia.
Simultaneously Extracted Metals/Acid-Volatile Sulfide and Total Metals in Surface Sediment from the Hanford Reach of the Columbia River and the Lower Snake River

Metals have been identified as contaminants of concern for the Hanford Reach because of upriver mining, industrial activities, and past nuclear material production at the US Department of Energy's Hanford Site. This study was undertaken to better understand the occurrence and fate of metals in sediment disposition areas in the Columbia and Snake Rivers.
School and workplace meals promote healthy food habits

Abstract Objective The present study is to describe, on the basis of recent Finnish population surveys, (i) the frequencies of school and worksite canteen use, (ii) the determinants of having a hot lunch during school or working hours and (iii) the associations of lunch eating patterns with food habits. Setting The study summarises mainly basic reports and studies concerning catering services conducted in Finland based on nationally representative population surveys. Design and subjects Cross-sectional study. The most important surveys cited in this paper are the School Health Promotion Study, the Work and the Working Conditions survey, the National FINDIET 2002 Study, and the Health Behavior and Health among Finnish Adult Population survey. Results School lunch is eaten by on average 70–90 % of children aged 9–18 years. Of all employees, 30 % eat at a worksite canteen daily, whereas 30 % of men and 45 % of women eat packed lunches. Nationally representative cross-sectional population surveys show that the use of catering services is associated with more healthy food habits; schoolchildren eating school meals and employees eating lunch at a worksite canteen tend to make food choices closer to nutritional recommendations as compared to those not using catering services to the same degree. Conclusions Some evidence exists that catering services in schools and worksites contribute to healthy eating habits in the population. In order to verify the positive role of catering services more scientific research with prospective and intervention design studies will be needed.
Synthesis of Programs from Multimodal Datasets

We describe MultiSynth, a framework for synthesizing domain-specific programs from a multimodal dataset of examples. Given a domain-specific language (DSL), a dataset is multimodal if there is no single program in the DSL that generalizes over all the examples. Further, even if the examples in the dataset were generalized in terms of a set of programs, the domains of these programs may not be disjoint, thereby leading to ambiguity in synthesis. MultiSynth is a framework that incorporates concepts of synthesizing programs with minimum generality, while addressing the need of accurate prediction. We show how these can be achieved through (i) transformation driven partitioning of the dataset, (ii) least general generalization, for a generalized specification of the input and the output, and (iii) learning to rank, for estimating feature weights in order to map an input to the most appropriate mode in case of ambiguity. We show the effectiveness of our framework in two domains: in the first case, we extend an existing approach for synthesizing programs for XML tree transformations to ambiguous multimodal datasets. In the second case, MultiSynth is used to preorder words for machine translation, by learning permutations of productions in the parse trees of the source side sentences. Our evaluations reflect the effectiveness of our approach.
Systematic review of the relationship between early introduction of solid foods to infants and the development of allergic disease.

OBJECTIVE To assess the evidence that early solid feeding (before age 4 months) increases the risk of allergic disease. DATA SOURCES MEDLINE, the Cochrane Library, and the Drugs and Pharmacology section of EMBASE with key words "infant," "food," and "allergy. " STUDY SELECTION We found 2719 article citations and reviewed references of relevant articles. We critically evaluated the methods and results of articles that met inclusion criteria. We identified 13 studies that met inclusion criteria. There was only 1 controlled trial. DATA EXTRACTION Allergic disease. DATA SYNTHESIS Five studies found a positive association between early solid feeding and eczema, with a persistence of the association for 10 years in 1 study. Four studies found no association. One study found an association between early solid feeding and pollen allergy. We found no strong evidence to support the association between early solid feeding and the development of persistent asthma, persistent food allergy, allergic rhinitis, or animal dander allergy. CONCLUSIONS Systematic review of available evidence suggests that early solid feeding may increase the risk of eczema. However, there are little data supporting an association between early solid feeding and other allergic conditions. Since many studies had problematic methods, additional controlled trials are needed to help guide physicians as they advise parents about the allergic risks of early introduction of solids.
Neural Knowledge Acquisition via Mutual Attention Between Knowledge Graph and Text

We propose a general joint representation learning framework for knowledge acquisition (KA) on two tasks, knowledge graph completion (KGC) and relation extraction (RE) from text. In this framework, we learn representations of knowledge graphs (KGs) and text within a unified parameter sharing semantic space. To achieve better fusion, we propose an effective mutual attention between KGs and text. The reciprocal attention mechanism enables us to highlight important features and perform better KGC and RE. Different from conventional joint models, no complicated linguistic analysis or strict alignments between KGs and text are required to train our models. Experiments on relation extraction and entity link prediction show that models trained under our joint framework are significantly improved in comparison with other baselines. Most existing methods for KGC and RE can be easily integrated into our framework due to its flexible architectures. The source code of this paper can be obtained from https://github.com/thunlp/JointNRE.
Obesity Prevention Interventions in US Public Schools: Are Schools Using Programs That Promote Weight Stigma?

Introduction Despite substantial research on school-based obesity prevention programs, it is unclear how widely they are disseminated. It is also unknown whether schools use obesity programs that inadvertently promote weight stigma or disordered weight-control behaviors. Methods In spring 2016, we distributed an online survey about school wellness programming to a simple random sample of US public school administrators (N = 247 respondents; 10.3% response rate). We analyzed survey responses and conducted immersion/crystallization analysis of written open-ended responses. Results Slightly less than half (n = 117, 47.4%) of schools offered any obesity prevention program. Only 17 (6.9%) reported using a predeveloped program, and 7 (2.8%) reported using a program with evidence for effectiveness. Thirty-seven schools (15.0%) reported developing intervention programs that focused primarily on individual students’ or staff members’ weight rather than nutrition or physical activity; 28 schools (11.3% of overall) used staff weight-loss competitions. School administrators who reported implementing a program were more likely to describe having a program champion and adequate buy-in from staff, families, and students. Lack of funding, training, and time were widely reported as barriers to implementation. Few administrators used educational (n = 12, 10.3%) or scientific (n = 6, 5.1%) literature for wellness program decision making. Conclusion Evidence-based obesity prevention programs appear to be rarely implemented in US schools. Schools may be implementing programs lacking evidence and programs that may unintentionally exacerbate student weight stigma by focusing on student weight rather than healthy habits. Public health practitioners and researchers should focus on improving support for schools to implement evidence-based programs.
Norm-Product Belief Propagation: Primal-Dual Message-Passing for Approximate Inference

Inference problems in graphical models can be represented as a constrained optimization of a free-energy function. In this paper, we treat both forms of probabilistic inference, estimating marginal probabilities of the joint distribution and finding the most probable assignment, through a unified message-passing algorithm architecture. In particular we generalize the belief propagation (BP) algorithms of sum-product and max-product and tree-reweighted (TRW) sum and max product algorithms (TRBP) and introduce a new set of convergent algorithms based on “convex-free-energy” and linear-programming (LP) relaxation as a zero-temperature of a convex-free-energy. The main idea of this work arises from taking a general perspective on the existing BP and TRBP algorithms while observing that they all are reductions from the basic optimization formula of f +Σihi where the function f is an extended-valued, strictly convex but nonsmooth and the functions hi are extended-valued functions (not necessarily convex). We use tools from convex duality to present the “primal-dual ascent” algorithm which is an extension of the Bregman successive projection scheme and is designed to handle optimization of the general type f + Σihi. We then map the fractional-free-energy variational principle for approximate inference onto the optimization formula above and introduce the “norm-product” message-passing algorithm. Special cases of the norm-product include sum-product and max-product (BP algorithms), TRBP and NMPLP algorithms. When the fractional-free-energy is set to be convex (convex-free-energy) the norm-product is globally convergent for the estimation of marginal probabilities and for approximating the LP-relaxation. We also introduce another branch of the norm-product which arises as the “zero-temperature” of the convex-free-energy which we refer to as the “convex-max-product”. The convex-max-product is convergent (unlike max-product) and aims at solving the LP- relaxation.
Zur prädiktiven Validität von Berufswahlreifeinstrumenten.

In the first part of the paper the current status of criterion-related validity research in the field of career development assessment is analyzed. The results of long-term predictive studies provide only minor evidence for the assumption that career maturity in school has substantial impact for future career adjustment. In the second part the results of a follow-up study conducted three years after graduation from high school are discussed.
On Being More Amenable to Threatening Risk Messages Concerning Close Others (vis-à-vis the Self)

People often respond defensively to risk messages impugning their own behavior. We explored whether people are more amenable to risk messages impugning a close other’s behavior. In two experiments, participants learned how being overweight could influence their own cancer risk or that of an opposite-sex close other. As predicted, participants expressed higher affective risk perceptions (i.e., worry) and experiential risk perceptions for their close others than for themselves. Participants in the close other condition also reported greater interest in diagnostic testing and additional information (Experiment 1) and greater interest in consulting a provider and more plans for remediation (Experiment 2). These effects were mediated by a combination of worry and experiential risk perceptions. The self/other difference emerged even though participants endorsed the messages as believable and relevant; participants were simply more willing to extrapolate from the message to their close other’s risk than to their own risk.
Economic Growth and Income Inequality in Resource Countries: Theory and Evidence

While much ink has been spilled over the study of income inequality and economic growth, little attention has been paid to investigate the interaction between these variables of interest in resource-dependent economies. The present paper develops a two-sector small open economy model including two groups of households (the rich and the poor). The mechanism is derived by two forces: 1) a composition of productivity growth with Learning by Doing (LBD) and capital accumulation with absorptive capacity constraints on the supply-side 2) a change in the relative demand of the non-traded to the traded goods on the demand-side. Applying a panel data approach for a sample database of 40 countries over the period 1975-2015, I evaluate the predictions of my theory. The main findings are fourfold. In response to a windfall income, first, the natural resource curse (i.e. the Dutch disease and Deindustrialization) appears. Second, income inequality rises if the non-traded sector is relatively capital-intensive while income inequality falls if the non-traded sector is relatively labor-intensive. Third, rising (falling) income inequality tends to deepen (moderate) the natural resource curse. Fourth, natural resource curse and income inequality change are relatively more intensive in a democratic country than in a non-democratic country.
BaCelLo: a balanced subcellular localization predictor

MOTIVATION The knowledge of the subcellular localization of a protein is fundamental for elucidating its function. It is difficult to determine the subcellular location for eukaryotic cells with experimental high-throughput procedures. Computational procedures are then needed for annotating the subcellular location of proteins in large scale genomic projects. RESULTS BaCelLo is a predictor for five classes of subcellular localization (secretory pathway, cytoplasm, nucleus, mitochondrion and chloroplast) and it is based on different SVMs organized in a decision tree. The system exploits the information derived from the residue sequence and from the evolutionary information contained in alignment profiles. It analyzes the whole sequence composition and the compositions of both the N- and C-termini. The training set is curated in order to avoid redundancy. For the first time a balancing procedure is introduced in order to mitigate the effect of biased training sets. Three kingdom-specific predictors are implemented: for animals, plants and fungi, respectively. When distributing the proteins from animals and fungi into four classes, accuracy of BaCelLo reach 74% and 76%, respectively; a score of 67% is obtained when proteins from plants are distributed into five classes. BaCelLo outperforms the other presently available methods for the same task and gives more balanced accuracy and coverage values for each class. We also predict the subcellular localization of five whole proteomes, Homo sapiens, Mus musculus, Caenorhabditis elegans, Saccharomyces cerevisiae and Arabidopsis thaliana, comparing the protein content in each different compartment. AVAILABILITY BaCelLo can be accessed at http://www.biocomp. unibo.it/bacello/.