LLukas22/scidocs huggingface dataset:
Delivering phonological and phonics training within whole-class teaching.

BACKGROUND
Early, intensive phonological awareness and phonics training is widely held to be beneficial for children with poor phonological awareness. However, most studies have delivered this training separately from children's normal whole-class reading lessons.


AIMS
We examined whether integrating this training into whole class, mixed-ability reading lessons could impact on children with poor phonological awareness, whilst also benefiting normally developing readers.


SAMPLE
Teachers delivered the training within a broad reading programme to whole classes of children from Reception to the end of Year 1 (N=251). A comparison group of children received standard teaching methods (N=213).


METHOD
Children's literacy was assessed at the beginning of Reception, and then at the end of each year until 1 year post-intervention.


RESULTS
The strategy significantly impacted on reading performance for normally developing readers and those with poor phonological awareness, vastly reducing the incidence of reading difficulties from 20% in comparison schools to 5% in intervention schools.


CONCLUSIONS
Phonological and phonics training is highly effective for children with poor phonological awareness, even when incorporated into whole-class teaching.
Cognitive insight and delusion proneness: An investigation using the Beck Cognitive Insight Scale

The present study investigated the relationship between delusion proneness, as assessed using the Peters et al. Delusions Inventory [Peters, E.R., Joseph, S.A., Garety, P.A., 1999. The measurement of delusional ideation in the normal population: Introducing the PDI (Peters et al. Delusions Inventory). Schizophr. Bull. 25 553-576], and cognitive insight, as assessed using the Beck Cognitive Insight Scale (BCIS; [Beck, A.T., Baruch, E., Balter, J.M., Steer, R.A., Warman, D.M., 2004. A new instrument for measuring insight: The Beck Cognitive Insight Scale. Schizophr. Res. 68, 319-329]. Two hundred undergraduate students with no history of psychotic disorder participated. Results indicated that, consistent with hypotheses, those higher in delusion proneness endorsed more certainty in their beliefs and judgment than those who were lower in delusion proneness (Self-Certainty subscale of the BCIS; p = .007). Contrary to hypotheses, however, those who were higher in delusion proneness were more open to external feedback and were more willing to acknowledge fallibility than those who were lower in delusion proneness (Self-Reflectiveness subscale of the BCIS; p = .002). The results are discussed in relation to theories of delusion formation.
Prospective, double-blind, randomized, placebo-controlled comparison of acetazolamide versus ibuprofen for prophylaxis against high altitude headache: the Headache Evaluation at Altitude Trial (HEAT).

OBJECTIVE
High altitude headache (HAH) is the most common neurological complaint at altitude and the defining component of acute mountain sickness (AMS). However, there is a paucity of literature concerning its prevention. Toward this end, we initiated a prospective, double-blind, randomized, placebo-controlled trial in the Nepal Himalaya designed to compare the effectiveness of ibuprofen and acetazolamide for the prevention of HAH.


METHODS
Three hundred forty-three healthy western trekkers were recruited at altitudes of 4280 m and 4358 m and assigned to receive ibuprofen 600 mg, acetazolamide 85 mg, or placebo 3 times daily before continued ascent to 4928 m. Outcome measures included headache incidence and severity, AMS incidence and severity on the Lake Louise AMS Questionnaire (LLQ), and visual analog scale (VAS).


RESULTS
Two hundred sixty-five of 343 subjects completed the trial. HAH incidence was similar when treated with acetazolamide (27.1%) or ibuprofen (27.5%; P = .95), and both agents were significantly more effective than placebo (45.3%; P = .01). AMS incidence was similar when treated with acetazolamide (18.8%) or ibuprofen (13.7%; P = .34), and both agents were significantly more effective than placebo (28.6%; P = .03). In fully compliant participants, moderate or severe headache incidence was similar when treated with acetazolamide (3.8%) or ibuprofen (4.7%; P = .79), and both agents were significantly more effective than placebo (13.5%; P = .03).


CONCLUSIONS
Ibuprofen and acetazolamide were similarly effective in preventing HAH. Ibuprofen was similar to acetazolamide in preventing symptoms of AMS, an interesting finding that implies a potentially new approach to prevention of cerebral forms of acute altitude illness.
Oriented tooth localization for periapical dental X-ray images via convolutional neural network

In studies using dental X-ray images, tooth localization is essential to produce accurate results. In this paper, we propose a tooth localization method that tightly localize diverse teeth in periapical dental X-ray images. Oriented tooth proposals are generated by using teeth separation lines (TSLs) and a tooth top line, which are reliable and tight to teeth. To classify each tooth proposal into either a tooth or a non-tooth, we utilize a convolutional neural network (CNN). Our CNN model is trained with three classes, i.e., one negative and two positives, for better classification. In addition, we propose scale based non-maximum suppression by integrating scale confidence with non-maximum suppression to efficiently eliminate multiple tooth localizations.
Alemtuzumab for patients with relapsing multiple sclerosis after disease-modifying therapy: a randomised controlled phase 3 trial

BACKGROUND
The anti-CD52 monoclonal antibody alemtuzumab reduces disease activity in previously untreated patients with relapsing-remitting multiple sclerosis. We aimed to assess efficacy and safety of alemtuzumab compared with interferon beta 1a in patients who have relapsed despite first-line treatment.


METHODS
In our 2 year, rater-masked, randomised controlled phase 3 trial, we enrolled adults aged 18-55 years with relapsing-remitting multiple sclerosis and at least one relapse on interferon beta or glatiramer. Eligible participants were randomly allocated in a 1:2:2 ratio by an interactive voice response system, stratified by site, to receive subcutaneous interferon beta 1a 44 μg, intravenous alemtuzumab 12 mg per day, or intravenous alemtuzumab 24 mg per day. Interferon beta 1a was given three-times per week and alemtuzumab was given once per day for 5 days at baseline and for 3 days at 12 months. The 24 mg per day group was discontinued to aid recruitment, but data are included for safety assessments. Coprimary endpoints were relapse rate and time to 6 month sustained accumulation of disability, comparing alemtuzumab 12 mg and interferon beta 1a in all patients who received at least one dose of study drug. This study is registered with ClinicalTrials.gov, number NCT00548405.


FINDINGS
202 (87%) of 231 patients randomly allocated interferon beta 1a and 426 (98%) of 436 patients randomly allocated alemtuzumab 12 mg were included in the primary analyses. 104 (51%) patients in the interferon beta 1a group relapsed (201 events) compared with 147 (35%) patients in the alemtuzumab group (236 events; rate ratio 0·51 [95% CI 0·39-0·65]; p<0·0001), corresponding to a 49·4% improvement with alemtuzumab. 94 (47%) patients in the interferon beta 1a group were relapse-free at 2 years compared with 278 (65%) patients in the alemtuzumab group (p<0·0001). 40 (20%) patients in the interferon beta 1a group had sustained accumulation of disability compared with 54 (13%) in the alemtuzumab group (hazard ratio 0·58 [95% CI 0·38-0·87]; p=0·008), corresponding to a 42% improvement in the alemtuzumab group. For 435 patients allocated alemtuzumab 12 mg, 393 (90%) had infusion-associated reactions, 334 (77%) had infections (compared with 134 [66%] of 202 patients in the interferon beta 1a group) that were mostly mild-moderate with none fatal, 69 (16%) had thyroid disorders, and three (1%) had immune thrombocytopenia.


INTERPRETATION
For patients with first-line treatment-refractory relapsing-remitting multiple sclerosis, alemtuzumab could be used to reduce relapse rates and sustained accumulation of disability. Suitable risk management strategies allow for early identification of alemtuzumab's main adverse effect of secondary autoimmunity.


FUNDING
Genzyme (Sanofi) and Bayer Schering Pharma.
Investigation of the effects of Chlorella vulgaris supplementation in patients with non-alcoholic fatty liver disease: a randomized clinical trial.

BACKGROUND/AIMS
To investigate the advantage of Chlorella vulgaris supplementation as an adjunctive therapy in patients with non-alcoholic fatty liver disease (NAFLD).


METHODOLOGY
In a randomized, open-label clinical trial, 76 individuals with NAFLD were randomly assigned to: 1) Chlorella group (n=33), receiving C. vulgaris extract (1200 mg/day) + metformin (750 mg/ day) + vitamin E (200 mg/day) for 3 months, or 2) Metformin group (n=43), receiving metformin (1250 mg/ day) + vitamin E (200 mg/day) for 3 months. Weight, body mass index (BMI), homeostasis model assessment of insulin resistance (HOMA-IR) index as well as serum levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), insulin, total and direct bilirubin, fasting blood sugar (FBS), glycated hemoglobin (HbA1c), uric acid, albumin and lipid profile were evaluated at baseline and at the end of trial.


RESULTS
Weight and BMI were decreased in both groups. Serum ALT, AST, triglycerides, uric acid, HbA1c and HOMA-IR index were reduced only in the Chlorella group whereas significant changes in total cholesterol, LDL, HDL and FBS were only observed in the metformin group. There were also borderline significant reductions in insulin and FBS in the Chlorella group.


CONCLUSIONS
The findings of the present trial indicated that addition of C. vulgaris extract to the therapeutic regimen of NAFLD including metformin and vitamin E, is associated with favorable effects on serum levels of transaminases, triglycerides as well as insulin sensitivity. Therefore, C. vulgaris extract might be a promising hepatoprotective supplement for patients with NAFLD.
Geochemistry and Geochronology of the Society Islands: New Evidence for Deep Mantle Recycling

We report new K-Ar ages, Sr, Nd, and Pb isotope ratios and concentrations of 34 trace elements in volcanic rocks from the Society Islands. Maximum ages of volcanism at Mehetia, Tahiti, and Maupiti indicate that volcanism in the Society Islands progresses southeastward at a rate of 11 cm/yr, which is consistent with current estimates of Pacific Plate motion. Tahaa has the largest range in ages, 2.3 million years. This large range reflects the eruption of highly undersaturated lavas during a posterosional phase that followed a volcanic hiatus of 1.2 million years. The entire range of isotope ratios observed in the Society Islands is nearly encompassed by the range observed on Tahaa: the two posterosional lavas have among the most depleted isotopic signatures while the shield series lavas have the most enriched isotopic signatures. The isotopic and chemical evolution of Tahaa thus follows the Hawaiian pattern. There is a strong correlation between Sr and Nd isotope ratios and weaker correlations involving Pb isotope ratios. Compared to other oceanic islands, Sr and Nd ratios range to extremely high and low values respectively, but Pb isotope ratios are intermediate. The isotope correlations indicate the Society plume can be approximately modeled as consisting of two slightly heterogeneous end members. All magmas are moderately to strongly enriched in light rare earth elements as well as other incompatible elements. After exclusion of weathered (as indicated by anomalous Ba/Rb ratios) and differentiated lavas, there are strong correlations between Hf/Sm, Pb/Ce, Zr/Nb, Nb/U, and Rb/Sr and 87Sr/86Sr (and εNd and 207Pb/204Pb) and weaker correlations between Nb/La and La/ Sm and 87Sr/86Sr (and εNd and 207Pb/204Pb). This indicates the variation in Hf/Sm, Pb/Ce, Zr/Nb, Nb/ U, and Rb/Sr is largely due to variations in the composition of the source. This inference is confirmed by factor analysis. On the other hand, variance in the La/Sm ratio appears dominated by varying degrees of partial melting, perhaps because differences between the two end members in La/Sm are small. The high 87Sr/86Sr component in the plume has high 207Pb/204Pb and Pb/Ce and low Nb/U. These characteristics are consistent with this component consisting partly of sediment that has been subducted into the deep mantle. The low 87Sr/86Sr component in the Society plume appears to be also richer in incompatible elements than depleted mantle and is isotopically similar to the common component of plumes postulated by others. This component is most prevalent in late and very early stage Society magmas and thus probably constitutes the sheath of the Society plume. This sheath was most likely viscously entrained in the deep mantle during ascent of the plume.
A randomised controlled trial of postal versus interviewer administration of a questionnaire measuring satisfaction with, and use of, services received in the year before death.

STUDY OBJECTIVES
To develop a short form of an interview schedule used successfully in previous national surveys of care for the dying, and to investigate the effect of administering it by post on response rate, response bias and on the nature of responses to questions.


DESIGN
Randomised controlled trial.


SETTING
An inner London health authority.


PARTICIPANTS
Informants (person registering death) of random sample of cancer deaths between June 1995 and July 1996.


MAIN RESULTS
The shortened questionnaire (VOICES) has 158 questions. Response rate did not differ significantly between postal and interview groups (interview; 56% (69 of 123), postal: 52% (161 of 308). Responders in the two groups did not differ in terms of their sociodemographic characteristics. Postal questionnaires had significantly more missing data, particularly on questions about service provision and satisfaction with services. Responses to questions differed between the groups on 11 of 158 questions. Interview group respondents were more likely to give top ranking responses to questions on service satisfaction and symptom control.


CONCLUSIONS
Postal questionnaires are an acceptable alternative to interviews in retrospective post-bereavement surveys of care for the dying, at least in terms of response rate and response bias. However, the increased costs of interview surveys need to be balanced against the fact that postal questionnaires result in more missing data, and possibly less reliable answers to some questions. Caution is needed in combining results from the two data collection methods as interview respondents gave more positive answers to some questions.
Shoaling transformation of wave frequency-directional spectra

[1] A Boussinesq model for the nonlinear transformation of the frequency-directional spectrum and bispectrum of surface gravity waves propagating over a gently sloping, alongshore uniform beach is compared with field and laboratory observations. Outside the surf zone the model predicts the observed spectral evolution, including energy transfers to harmonic components traveling in the direction of the dominant waves, and the crossinteractions of waves traveling in different directions that transfer energy to components with the vector sum wavenumber. The sea surface elevation skewness and asymmetry, third-order moments believed to be important for sediment transport, also are predicted well. Effects of surf zone wave breaking are incorporated with a heuristic frequencydependent dissipation term in the spectral energy balance equation and an empirical relaxation of the bispectrum to Gaussian statistics. The associated coefficients are calibrated with observations that span a wide range of surf zone conditions. With calibrated coefficients, the model predicts observed surf zone frequency spectra well and surf zone skewness and asymmetry fairly well. The observed directional spectra inside the surf zone are broader than the predicted spectra, suggesting that neglected scattering effects associated with the random onset of wave breaking or with higher-order nonlinearity may be important.
The expression of CYP2W1: a prognostic marker in colon cancer.

AIM
The enzyme Cytochrome P450 2W1 (CYP2W1) is found in fetal colon tissue and is also detected in colorectal cancer but not in non-transformed tissue. In a pilot study, we reported that the immunohistochemically-detected expression of CYP2W1 might be of prognostic value since high expression of CYP2W1 was indicative of a worse prognosis. The aim of this study was to validate the pilot study's results using a larger, independent group of patients with colon cancer.


MATERIALS AND METHODS
Immunohistochemical detection of CYP2W1 in 235 malignant colon tumors of stage II and III, was carried out using a polyclonal antibody. Grading of staining was carried out by two independent readers. The highest grade that involved more than 5% of the tumor area on each slide was used for the classification of CYP2W1 expression.


RESULTS
CYP2W1 was expressed at high levels in 30% of the tumors. In the entire colon cancer group it was an independent prognostic factor in multivariate analysis (p=0.04), where high expression (grade 3) correlated with worse outcome. CYP2W1 expression was an independent prognostic factor in the subgroup of patients with colon cancer stage III (p=0.003), but not for those with stage II. In 107 cases, two slices from different areas of the same tumor were available, and no significant difference in CYP2W1 expression between the slices was observed (r=0.53, p<0.001).


CONCLUSION
The results of the current study were in agreement with those of the previous pilot study and show that higher expression of CYP2W1 seems to be of prognostic value in colon cancer. Furthermore, we found equal expression in slices from two different areas of the same tumor. Since the CYP2W1 enzyme has been shown to catalytically activate compounds to cytotoxic products, the enzyme might be used as a novel drug target for the treatment of colon cancer.
Knowledge Discovery in Databases: An Overview

After a decade of fundamental interdisciplinary research in machine learning, the spadework in this field has been done; the 1990s should see the widespread exploitation of knowledge discovery as an aid to assembling knowledge bases. The contributors to the AAAI Press book Knowledge Discovery in Databases were excited at the potential benefits of this research. The editors hope that some of this excitement will communicate itself to "AI Magazine readers of this article.
A novel adaptive unscented Kalman filter for nonlinear estimation

The normal unscented Kalman filter (UKF) suffers from performance degradation and even divergence while mismatch between the noise distribution assumed to be known as a priori by UKF and the true ones in a real system. In this paper, a novel adaptive UKF (AUKF) is developed and applied to nonlinear joint estimation of both time-varying states and parameters. A cost function is built based on the error between the covariance matrices of innovation and their corresponding estimations. An adaptive algorithm is then designed to online update the covariance of the process noise by minimizing the cost function. The updated covariance is further fed back into the normal UKF. As a result of using such an adaptive mechanism, the robustness of conventional UKF is substantially improved with respect to the uncertain and time-varying noise covariance in the real system. To illustrate this mechanism, simulations are conducted on the dynamics of an unmanned helicopter by jointly estimating both the states and model errors. The improvements of the proposed AUKF are demonstrated by comparing the results with and without the adaptive mechanism.
Effect of yoga on arrhythmia burden, anxiety, depression, and quality of life in paroxysmal atrial fibrillation: the YOGA My Heart Study.

OBJECTIVES
The purpose of this study was to examine the impact of yoga on atrial fibrillation (AF) burden, quality of life (QoL), depression, and anxiety scores.


BACKGROUND
Yoga is known to have significant benefit on cardiovascular health. The effect of yoga in reducing AF burden is unknown.


METHODS
This single-center, pre-post study enrolled patients with symptomatic paroxysmal AF with an initial 3-month noninterventional observation period followed by twice-weekly 60-min yoga training for next 3 months. AF episodes during the control and study periods as well as SF-36, Zung self-rated anxiety, and Zung self-rated depression scores at baseline, before, and after the study phase were assessed.


RESULTS
Yoga training reduced symptomatic AF episodes (3.8 ± 3 vs. 2.1 ± 2.6, p < 0.001), symptomatic non-AF episodes (2.9 ± 3.4 vs. 1.4 ± 2.0; p < 0.001), asymptomatic AF episodes (0.12 ± 0.44 vs. 0.04 ± 0.20; p < 0.001), and depression and anxiety (p < 0.001), and improved the QoL parameters of physical functioning, general health, vitality, social functioning, and mental health domains on SF-36 (p = 0.017, p < 0.001, p < 0.001, p = 0.019, and p < 0.001, respectively). There was significant decrease in heart rate, and systolic and diastolic blood pressure before and after yoga (p < 0.001).


CONCLUSIONS
In patients with paroxysmal AF, yoga improves symptoms, arrhythmia burden, heart rate, blood pressure, anxiety and depression scores, and several domains of QoL.
Oncoproteomic Analysis Reveals Co-Upregulation of RELA and STAT5 in Carboplatin Resistant Ovarian Carcinoma

BACKGROUND
Ovarian cancer is one of the most lethal types of female malignancy. Although most patients are initially responsive to platinum-based chemotherapy, almost all develop recurrent chemoresistant tumors and succumb to their diseases. Elucidating the pathogenesis underlying drug resistance is fundamental to the development of new therapeutics, leading to improved clinical outcomes in these patients.


METHODS AND FINDINGS
We compared the proteomes of paired primary and recurrent post-chemotherapy ovarian high-grade serous carcinomas from nine ovarian cancer patients using CIEF/Nano-RPLC coupled with ESI-Tandem MS. As compared to their primary tumors, more than half of the recurrent tumors expressed higher levels of several proteins including CP, FN1, SYK, CD97, AIF1, WNK1, SERPINA3, APOD, URP2, STAT5B and RELA (NF-kappaB p65), which were also validated by quantitative RT-PCR. Based on shRNA screening for the upregulated genes in in vitro carboplatin-resistant cells, we found that simultaneous knockdown of RELA and STAT5B was most effective in sensitizing tumor cells for carboplatin treatment. Similarly, the NF-kappaB inhibitor, BMS-345541, and the STAT5 inhibitor, Dasatinib, significantly enhanced cell sensitivity to carboplatin. Moreover, both RELA and STAT5 are known to bind to the promoter region of Bcl-X, regulating its promoter activity. In this regard, augmented Bcl-xL expression was detected in carboplatin-resistant cells. Combined ectopic expression of RELA and STAT5B enhanced Bcl-xL promoter activity while treatment with BMS-345541 and Dasatinib decreased it. Chromatin immunoprecipitation of the Bcl-X promoter region using a STAT5 antibody showed induction of RELA and STAT5 DNA-binding segments both in naïve cells treated with a high concentration of carboplatin as well as in carboplatin-resistant cells.


CONCLUSIONS
Proteomic analysis identified RELA and STAT5 as two major proteins associated with carboplatin resistance in ovarian tumors. Our results further showed that NF-kappaB and STAT5 inhibitor could sensitize carboplatin-resistant cells and suggest that such inhibitors can be used to benefit patients with carboplatin-resistant recurrent ovarian cancer.