LLukas22/scidocs huggingface dataset:
An Immunochip-based interaction study of contrasting interaction effects with smoking in ACPA-positive versus ACPA-negative rheumatoid arthritis.

OBJECTIVE
To investigate the gene-environment interaction between smoking and single nucleotide polymorphisms (SNPs), using Immunochip material, on the risk of developing either of two serologically defined subsets of RA.


METHODS
Interaction between smoking and 133,648 genetic markers from the Immunochip was examined for two RA subsets, defined by the presence or absence of ACPA. A total of 1590 ACPA-positive and 891 ACPA-negative cases were compared with 1856 controls in the Swedish Epidemiological Investigation of RA (EIRA) case-control study. Logistic regression models were used to determine the presence of interaction. The proportion attributable to interaction was calculated for each smoking-SNP pair. Replication was carried out in an independent dataset from northern Sweden. To further validate and extend the results, interaction analysis was also performed using genome-wide association studies data on EIRA individuals.


RESULTS
In ACPA-positive RA, 102 SNPs interacted significantly with smoking, after Bonferroni correction. All 102 SNPs were located in the HLA region, mainly within the HLA class II region, 51 of which were replicated. No additional loci outside chromosome 6 were identified in the genome-wide association studies validation. After adjusting for HLA-DRB1 shared epitope, 15 smoking-SNP pairs remained significant for ACPA-positive RA, with 8 of these replicated (loci: BTNL2, HLA-DRA, HLA-DRB5, HLA-DQA1, HLA-DOB and TAP2). For ACPA-negative RA, no smoking-SNP pairs passed the threshold for significance.


CONCLUSION
Our study presents extended gene variation patterns involved in gene-smoking interaction in ACPA-positive, but not ACPA-negative, RA. Notably, variants in HLA-DRB1 and those in additional genes within the MHC class II region, but not in any other gene regions, showed interaction with smoking.
Schizophrenia Subjects Show Intact Success-Related Neural Activation but Impaired Uncertainty Processing during Decision-Making

Decision-making is a complex process that is important for everyday life. This study examined the effect of the degree of success, and outcome uncertainty, on decision-making and associated neural substrate activation in schizophrenia subjects (SZS) and normal comparison subjects (NCS). A total of 15 subjects with a diagnosis of schizophrenia and 15 age- and education-matched NCS participated in this study. These subjects completed the two-choice prediction task during functional magnetic resonance imaging. Decision-making characteristics and activation of neural substrates were obtained at 20, 50, or 80% error rate. Success and uncertainty influenced the behavioral characteristics on the two-choice prediction task, and the task-related activation in SZS and NCS. Neither success nor uncertainty differentially affected the behavioral characteristics of SZS relative to NCS during the two-choice prediction task. Nonetheless, there was a significant interaction between group and error rate in bilateral parietal cortex. The activation in NCS was the highest when the outcome was most uncertain. In contrast, task-related activation in SZS was not modulated by the degree of uncertainty. Thus, SZS failed to utilize the parietal cortex to process decision-making situations with highly uncertain outcomes.
Favorable outcome of pregnancy with an elective use of epoprostenol and sildenafil in women with severe pulmonary hypertension.

BACKGROUND
Pulmonary hypertension carries significant maternal and fetal risk during pregnancy and the postpartum period. As maternal mortality is high, specific targeted therapy for pulmonary hypertension may be required during pregnancy.


CASES
We describe 2 pregnant patients who presented with severe secondary pulmonary arterial hypertension during their last trimester. They were electively treated in the late antepartum and early postpartum periods with sildenafil and intravenous epoprostenol and successfully delivered healthy infants via cesarean section without postpartum complications.


CONCLUSION
Although pulmonary hypertension is associated with a risk of maternal mortality and most women are advised against pregnancy, new therapies may improve the outcome of pregnancy in patients with pulmonary hypertension.
Smoothed marginal distribution constraints for language modeling

We present an algorithm for re-estimating parameters of backoff n-gram language models so as to preserve given marginal distributions, along the lines of wellknown Kneser-Ney (1995) smoothing. Unlike Kneser-Ney, our approach is designed to be applied to any given smoothed backoff model, including models that have already been heavily pruned. As a result, the algorithm avoids issues observed when pruning Kneser-Ney models (Siivola et al., 2007; Chelba et al., 2010), while retaining the benefits of such marginal distribution constraints. We present experimental results for heavily pruned backoff ngram models, and demonstrate perplexity and word error rate reductions when used with various baseline smoothing methods. An open-source version of the algorithm has been released as part of the OpenGrm ngram library.1
Parental eating behaviours, home food environment and adolescent intakes of fruits, vegetables and dairy foods: longitudinal findings from Project EAT.

OBJECTIVE
To examine longitudinal associations of parental report of household food availability and parent intakes of fruits, vegetables and dairy foods with adolescent intakes of the same foods. This study expands upon the limited research of longitudinal studies examining the role of parents and household food availability in adolescent dietary intakes.


DESIGN
Longitudinal study. Project EAT-II followed an ethnically and socio-economically diverse sample of adolescents from 1999 (time 1) to 2004 (time 2). In addition to the Project EAT survey, adolescents completed the Youth Adolescent Food-Frequency Questionnaire in both time periods, and parents of adolescents completed a telephone survey at time 1. General linear modelling was used to examine the relationship between parent intake and home availability and adolescent intake, adjusting for time 1 adolescent intakes. Associations were examined separately for the high school and young adult cohorts and separately for males and females in combined cohorts.


SUBJECTS/SETTING
The sample included 509 pairs of parents/guardians and adolescents.


RESULTS
Vegetables served at dinner significantly predicted adolescent intakes of vegetables for males (P = 0.037), females (P = 0.009), high school (P = 0.033) and young adults (P = 0.05) at 5-year follow-up. Among young adults, serving milk at dinner predicted dairy intake (P = 0.002). Time 1 parental intakes significantly predicted intakes of young adults for fruit (P = 0.044), vegetables (P = 0.041) and dairy foods (P = 0.008). Parental intake predicted intake of dairy for females (P = 0.02).


CONCLUSIONS
The findings suggest the importance of providing parents of adolescents with knowledge and skills to enhance the home food environment and improve their own eating behaviours.
Risk factors for poor iron status in British toddlers: further analysis of data from the National Diet and Nutrition Survey of children aged 1.5-4.5 years.

OBJECTIVE
: To examine risk factors for poor iron status in British toddlers.


DESIGN
: National Diet and Nutrition Survey (NDNS) of children aged 1.5-4.5 years.


SETTING
: Mainland Britain, 1992/93.


SUBJECTS
: Of the 1859 children whose parents or guardians were interviewed, a weighed dietary intake was provided for 1675, and a blood sample obtained from 1003.


RESULTS
: Mean haemoglobin (Hb) and ferritin levels were significantly lower in younger (1.5-2.5 years) than in older (3.5-4.5 years) children, with boys having significantly lower ferritin levels than girls. Poor iron status ferritin <10 microg l-1, or low values for both indices) was associated with lower socioeconomic and employment status. Iron status was directly associated with meat and fruit consumption and inversely with that of milk and milk products, after adjustment for age and gender. The latter association remained significant after further adjustment for sociodemographic variables, energy intake and body weight. Children consuming >400 g day-1 of milk and cream were less likely to consume foods in other groups, with those also consuming little meat, fish, fruit and nuts at greatest risk of poor iron status. Few associations were observed between poor iron status and individual nutrient intakes, and iron status was not associated with either iron intake or with consumption of a vegetarian diet.


CONCLUSIONS
: Overdependence on milk, where it displaces iron-rich or iron-enhancing foods, may put toddlers at increased risk of poor iron status. However, this becomes non-significant when moderate-to-high amounts of foods known to enhance iron status (e.g. meat and/or fruit) are also consumed. Milk consumption in this age group should ideally be part of a mixed and balanced diet including all food groups, and particularly lean meat (or other iron-rich or fortified foods) and fruit. This is particularly relevant for households of lower socioeconomic and employment status.
Methylation Linear Discriminant Analysis (MLDA) for identifying differentially methylated CpG islands

Hypermethylation of promoter CpG islands is strongly correlated to transcriptional gene silencing and epigenetic maintenance of the silenced state. As well as its role in tumor development, CpG island methylation contributes to the acquisition of resistance to chemotherapy. Differential Methylation Hybridisation (DMH) is one technique used for genome-wide DNA methylation analysis. The study of such microarray data sets should ideally account for the specific biological features of DNA methylation and the non-symmetrical distribution of the ratios of unmethylated and methylated sequences hybridised on the array. We have therefore developed a novel algorithm tailored to this type of data, Methylation Linear Discriminant Analysis (MLDA). MLDA was programmed in R (version 2.7.0) and the package is available at CRAN [1]. This approach utilizes linear regression models of non-normalised hybridisation data to define methylation status. Log-transformed signal intensities of unmethylated controls on the microarray are used as a reference. The signal intensities of DNA samples digested with methylation sensitive restriction enzymes and mock digested are then transformed to the likelihood of a locus being methylated using this reference. We tested the ability of MLDA to identify loci differentially methylated as analysed by DMH between cisplatin sensitive and resistant ovarian cancer cell lines. MLDA identified 115 differentially methylated loci and 23 out of 26 of these loci have been independently validated by Methylation Specific PCR and/or bisulphite pyrosequencing. MLDA has advantages for analyzing methylation data from CpG island microarrays, since there is a clear rational for the definition of methylation status, it uses DMH data without between-group normalisation and is less influenced by cross-hybridisation of loci. The MLDA algorithm successfully identified differentially methylated loci between two classes of samples analysed by DMH using CpG island microarrays.
Cross-Platform Emoji Interpretation: Analysis, a Solution, and Applications

Most social media platforms are largely based on text, and users oen write posts to describe where they are, what they are seeing, and how they are feeling. Because wrien text lacks the emotional cues of spoken and face-to-face dialogue, ambiguities are common in wrien language. is problem is exacerbated in the short, informal nature of many social media posts. To bypass this issue, a suite of special characters called “emojis,” which are small pictograms, are embedded within the text. Many emojis are small depictions of facial expressions designed to help disambiguate the emotional meaning of the text. However, a new ambiguity arises in the way that emojis are rendered. Every platform (Windows, Mac, and Android, to name a few) renders emojis according to their own style. In fact, it has been shown that some emojis can be rendered so dierently that they look “happy” on some platforms, and “sad” on others. In this work, we use real-world data to verify the existence of this problem. We verify that the usage of the same emoji can be signicantly dierent across platforms, with some emojis exhibiting dierent sentiment polarities on dierent platforms. We propose a solution to identify the intended emoji based on the platform-specic nature of the emoji used by the author of a social media post. We apply our solution to sentiment analysis, a task that can benet from the emoji calibration technique we use in this work. We conduct experiments to evaluate the eectiveness of the mapping in this task. ACM Reference format: Fred Morstaer, Kai Shu, Suhang Wang, and Huan Liu. 2016. Cross-Platform Emoji Interpretation: Analysis, a Solution, and Applications. In Proceedings of ACM Conference, Washington, DC, USA, July 2017 (Conference’17), 9 pages. DOI: 10.1145/nnnnnnn.nnnnnnn Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for prot or commercial advantage and that copies bear this notice and the full citation on the rst page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permied. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specic permission and/or a fee. Request permissions from permissions@acm.org. Conference’17, Washington, DC, USA © 2016 ACM. 978-x-xxxx-xxxx-x/YY/MM. . .$15.00 DOI: 10.1145/nnnnnnn.nnnnnnn
Screening Twitter Users for Depression and PTSD with Lexical Decision Lists

This paper describes various systems from the University of Minnesota, Duluth that participated in the CLPsych 2015 shared task. These systems learned decision lists based on lexical features found in training data. These systems typically had average precision in the range of .70 – .76, whereas a random baseline attained .47 – .49.
Repetitive transcranial magnetic stimulation is as effective as electroconvulsive therapy in the treatment of nondelusional major depressive disorder: an open study

BACKGROUND
Repetitive transcranial magnetic stimulation (rTMS), a new method for the stimulation of the central nervous system, is being proposed as a potential new treatment in patients with major depressive disorder (MDD). We tested the hypothesis that rTMS would be as effective as electroconvulsive therapy (ECT) in patients with MDD.


METHODS
Forty patients with MDD referred for ECT were randomly assigned to either ECT or rTMS. Repetitive transcranial magnetic stimulation was performed at 90% power of the motor threshold. The stimulation frequency was 10 Hz for either 2 sec (first eight patients) or 6 sec (final 12 patients) for 20 trains. Patients were treated for up to 20 treatment days. Electroconvulsive therapy was performed according to standard protocols.


RESULTS
Overall patients responded best to ECT (chi(2) = 3.8, p <.05). Patients with MDD and psychosis responded significantly better to ECT (chi(2) = 9.2, p <. 01), whereas MDD patients without psychosis responded similarly to both treatments (chi(2) = 0.0, ns). The analysis of variance with repeated measures of clinical variables for the whole sample revealed significant treatment effects for both groups; however, interaction between group and treatment was seen only for the Global Assessment of Function and the Sleep assessment. When the psychosis-nonpsychosis grouping was considered, patients with psychosis responded dramatically better to ECT in all assessments, whereas those without psychosis responded similarly to both treatments.


CONCLUSIONS
Overall ECT was a more potent treatment for patients with MDD, this being particularly evident in patients with MDD and psychosis; however, in patients with MDD without psychosis the effects of rTMS were similar to those of ECT. The results we report are encouraging and support an important role for rTMS in the treatment of severe MDD; however, additional blinded studies are needed to precisely define this role.
Is biosorption suitable for decontamination of metal-bearing wastewaters? A critical review on the state-of-the-art of biosorption processes and future directions.

For the past few decades, biosorption has been widely investigated for the removal of different contaminants in aqueous media. A number of biomasses of different genre have been identified to possess good biosorption capacity. Insights into biosorption mechanisms have been provided by various researchers in order to develop a fundamental scientific understanding of the biosorption process. However, biosorption has not been employed widely for its large-scale commercial applications. The key factors that affect the growth and evolution of biosorption as a practical technology for decontamination of wastewaters include, (1) lack of investigations on multi-component solutions and wastewaters with complex matrix effects, (2) incomplete understanding of physico-chemical characteristics of biomasses of different types, (3) lack of studies to improve the performance of biosorbents through surface functionalization, and (4) non-integration of biosorption in wastewater/water treatment plants. This critical review aims to identify and discuss the practical limitations of biosorption and provide future research directions to make biosorption a technologically viable process with emphasis on selection and modification of biomasses to suit desired treatment applications, identify appropriate operation modes for large-scale applications of biosorption, and perform techno-economic evaluation of overall biosorption processes.
A correlated topic model of Science

Topic models, such as latent Dirichlet allocation (LDA), can be useful tools for the statistical analysis of document collections and other discrete data. The LDA model assumes that the words of each document arise from a mixture of topics, each of which is a distribution over the vocabulary. A limitation of LDA is the inability to model topic correlation even though, for example, a document about genetics is more likely to also be about disease than X-ray astronomy. This limitation stems from the use of the Dirichlet distribution to model the variability among the topic proportions. In this paper we develop the correlated topic model (CTM), where the topic proportions exhibit correlation via the logistic normal distribution [J. Roy. Statist. Soc. Ser. B 44 (1982) 139–177]. We derive a fast variational inference algorithm for approximate posterior inference in this model, which is complicated by the fact that the logistic normal is not conjugate to the multinomial. We apply the CTM to the articles from Science published from 1990–1999, a data set that comprises 57M words. The CTM gives a better fit of the data than LDA, and we demonstrate its use as an exploratory tool of large document collections.
Factors Affecting the Citizen ’ s Intention to Adopt E-government in Saudi Arabia

This paper discusses E-government, in particular the challenges that face its development and widespread adoption in Saudi Arabia. E-government can be defined based on an existing set of requirements. E-government has been implemented for a considerable time in developed countries. However, E-government services still face many challenges in their implementation and general adoption in Saudi Arabia. In addition, the literature review and the discussion identify the influential factors, such as quality of service, diffusion of innovation, computer and information literacy, culture, lack of awareness, technical infrastructure, website design, and security, that affect the citizens’ intention to adopt E-government services in Saudi Arabia. Consequently, these factors have been integrated in a new model that would influence citizen to adopt Egovernment services. Therefore, this research presents an integrated model for ascertaining the intention to adopt E-government services and thereby aiding governments in accessing what is required to increase adoption. Keywords—Adoption, citizens’ intention, E-government, G2C, influential factors.
Occupational stress, job satisfaction and job performance among hospital nurses in Kampala, Uganda.

AIMS
To assess levels of occupational stress, job satisfaction and job performance among hospital nurses in Kampala, Uganda; and how they are influenced by work and personal characteristics.


BACKGROUND
Occupational stress is reported to affect job satisfaction and job performance among nurses, thus compromising nursing care and placing patients' lives at risk. Although these factors have been studied extensively in the US and Europe, there was a need to explore them from the Ugandan perspective.


METHODS
A correlational study was conducted with 333 nurses from four hospitals in Kampala, Uganda. A questionnaire measuring occupational stress, job satisfaction and job performance was used. Data were analysed using descriptive statistics and anova.


RESULTS
There were significant differences in levels of occupational stress, job satisfaction and job performance between public and private not-for-profit hospitals, nursing experience and number of children.


CONCLUSIONS
Organizational differences between public and private not-for-profit hospitals influence the study variables.


IMPLICATIONS FOR NURSING MANAGEMENT
On-the-job training for nurse managers in human resource management to increase understanding and advocacy for organizational support policies was recommended. Research to identify organizational, family or social factors which contribute to reduction of perceived occupational stress and increase job satisfaction and job performance was recommended.