LLukas22/scidocs huggingface dataset:
Metabolomics in nutritional epidemiology: identifying metabolites associated with diet and quantifying their potential to uncover diet-disease relations in populations.

BACKGROUND
Metabolomics is an emerging field with the potential to advance nutritional epidemiology; however, it has not yet been applied to large cohort studies.


OBJECTIVES
Our first aim was to identify metabolites that are biomarkers of usual dietary intake. Second, among serum metabolites correlated with diet, we evaluated metabolite reproducibility and required sample sizes to determine the potential for metabolomics in epidemiologic studies.


DESIGN
Baseline serum from 502 participants in the Prostate, Lung, Colorectal, and Ovarian (PLCO) Cancer Screening Trial was analyzed by using ultra-high-performance liquid-phase chromatography with tandem mass spectrometry and gas chromatography-mass spectrometry. Usual intakes of 36 dietary groups were estimated by using a food-frequency questionnaire. Dietary biomarkers were identified by using partial Pearson's correlations with Bonferroni correction for multiple comparisons. Intraclass correlation coefficients (ICCs) between samples collected 1 y apart in a subset of 30 individuals were calculated to evaluate intraindividual metabolite variability.


RESULTS
We detected 412 known metabolites. Citrus, green vegetables, red meat, shellfish, fish, peanuts, rice, butter, coffee, beer, liquor, total alcohol, and multivitamins were each correlated with at least one metabolite (P < 1.093 × 10(-6); r = -0.312 to 0.398); in total, 39 dietary biomarkers were identified. Some correlations (citrus intake with stachydrine) replicated previous studies; others, such as peanuts and tryptophan betaine, were novel findings. Other strong associations included coffee (with trigonelline-N-methylnicotinate and quinate) and alcohol (with ethyl glucuronide). Intraindividual variability in metabolite levels (1-y ICCs) ranged from 0.27 to 0.89. Large, but attainable, sample sizes are required to detect associations between metabolites and disease in epidemiologic studies, further emphasizing the usefulness of metabolomics in nutritional epidemiology.


CONCLUSIONS
We identified dietary biomarkers by using metabolomics in an epidemiologic data set. Given the strength of the associations observed, we expect that some of these metabolites will be validated in future studies and later used as biomarkers in large cohorts to study diet-disease associations. The PLCO trial was registered at clinicaltrials.gov as NCT00002540.
A layered software architecture for quantum computing design tools

Compilers and computer-aided design tools are essential for fine-grained control of nanoscale quantum-mechanical systems. A proposed four-phase design flow assists with computations by transforming a quantum algorithm from a high-level language program into precisely scheduled physical actions.
Doped aromatic derivatives wide-gap crystalline semiconductor structured layers for electronic application

Abstract We present some investigations on the electrical conductivity of two benzene substituted derivatives (m-DNB, benzil) emphasizing the correlation between the molecular structure, purity, structural defects and the particularities of the conduction mechanisms. The influence of inorganic/organic doping on the I – V plots of silicon/wide-gap organic semiconductor/silicon heterostructures has been analysed. The most significant increase in the conductance has been obtained for organic crystalline films of benzil doped with 3 wt.% m-DNB and m-DNB films doped with 1 wt.% oxine or 10 wt.% resorcinol. The influence of the silicon wafer's properties as resistivity, conduction type and surface processing on the carrier transport properties in these structures has been studied. We have remarked an increase in the conductance of the organic films of m-DNB doped with oxine or resorcinol in heterostructures realized with chemically polished, “n” type single crystal silicon wafers, compared to lapped ones. A special type of conduction mechanism given by a Poole–Frenkel dependence was evidenced in resorcinol doped m-DNB in the low voltages range.
Gaussian belief propagation solver for systems of linear equations

The canonical problem of solving a system of linear equations arises in numerous contexts in information theory, communication theory, and related fields. In this contribution, we develop a solution based upon Gaussian belief propagation (GaBP) that does not involve direct matrix inversion. The iterative nature of our approach allows for a distributed message-passing implementation of the solution algorithm. We also address some properties of the GaBP solver, including convergence, exactness, its max-product version and relation to classical solution methods. The application example of decorrelation in CDMA is used to demonstrate the faster convergence rate of the proposed solver in comparison to conventional linear-algebraic iterative solution methods.
Students' attitudes toward playing games and using games in education: Comparing Scotland and the Netherlands

Games-based learning has captured the interest of educationalists and industrialists who seek to exploit the characteristics of computer games as they are perceived by some to be a potentially effective approach for teaching and learning. Despite this interest in using games-based learning there is a dearth of empirical evidence supporting the validity of the approach covering the wider context of gaming and education. This study presents a large scale gaming survey, involving 887 students from 13 different Higher Education (HE) institutes in Scotland and the Netherlands, which examines students’ characteristics related to their gaming preferences, game playing habits, and their perceptions and thoughts on the use of games in education. It presents a comparison of three separate groups of students: a group in regular education in a Scottish university, a group in regular education in universities in the Netherlands and a distance learning group from a university in the Netherlands. This study addresses an overall research question of: Can computer games be used for educational purposes at HE level in regular and distance education in different countries? The study then addresses four sub-research questions related to the overall research question: What are the different game playing habits of the three groups? What are the different motivations for playing games across the three groups? What are the different reasons for using games in HE across the three groups? What are the different attitudes towards games across the three groups? To our knowledge this is the first in-depth cross-national survey on gaming and education. We found that a large number of participants believed that computer games could be used at HE level for educational purposes and that further research in the area of game playing habits, motivations for playing computer games and motivations for playing computer games in education are worthy of extensive further investigation. We also found a clear distinction between the views of students in regular education and those in distance education. Regular education students in both countries rated all motivations for playing computer games as significantly more important than distance education students. Also the results suggest that Scottish students aim to enhance their social experience with regards to competition and cooperation, while Dutch students aim to enhance their leisurely experience with regards to leisure, feeling good, preventing boredom and excitement. 2013 Elsevier Ltd. All rights reserved. Hainey), wim.westera@ou.nl (W. Westera), thomas.connolly@uws.ac.uk (T.M. Connolly), gavin.baxter@uws.ac.uk
Types of study in medical research: part 3 of a series on evaluation of scientific publications.

BACKGROUND
The choice of study type is an important aspect of the design of medical studies. The study design and consequent study type are major determinants of a study's scientific quality and clinical value.


METHODS
This article describes the structured classification of studies into two types, primary and secondary, as well as a further subclassification of studies of primary type. This is done on the basis of a selective literature search concerning study types in medical research, in addition to the authors' own experience.


RESULTS
Three main areas of medical research can be distinguished by study type: basic (experimental), clinical, and epidemiological research. Furthermore, clinical and epidemiological studies can be further subclassified as either interventional or noninterventional.


CONCLUSIONS
The study type that can best answer the particular research question at hand must be determined not only on a purely scientific basis, but also in view of the available financial resources, staffing, and practical feasibility (organization, medical prerequisites, number of patients, etc.).
Effects of functional electrical stimulation on the joints of adolescents with spinal cord injury

Nineteen adolescent subjects with complete spinal cord injuries resulting in paraplegia or tetraplegia participated in a functional electrical stimulation (FES) program consisting of computerized, controlled exercise and/or weight bearing. The effects of stimulated exercise and standing/ walking on the lower extremity joints were prospectively studied. Plain radiographs and MRIs were obtained prior to and following completion of the exercise and standing and walking stages. In addition, the joints of five subjects were studied with synovial biopsies, arthroscopy, and the analysis of serum and synovial fluid for a 550 000 dalton cartilage matrix glycoprotein (CMGP). Pre-exercise joint abnormalities secondary to the spinal cord injury improved following the stimulation program. None of the subjects developed Charcot joint changes. Upon standing with FES, one subject with poor hip coverage prior to participation developed hip subluxation which required surgical repair. No other detrimental clinical effects occured in the lower extremity joints of subjects participating in an FES program over a 1-year period.
A nonlocking end screw can decrease fracture risk caused by locked plating in the osteoporotic diaphysis.

BACKGROUND
Locking plates transmit load through fixed-angle locking screws instead of relying on plate-to-bone compression. Therefore, locking screws may induce higher stress at the screw-bone interface than that seen with conventional nonlocked plating. This study investigated whether locked plating in osteoporotic diaphyseal bone causes a greater periprosthetic fracture risk than conventional plating because of stress concentrations at the plate end. It further investigated the effect of replacing the locked end screw with a conventional screw on the strength of the fixation construct.


METHODS
Three different bridge-plate constructs were applied to a validated surrogate of the osteoporotic femoral diaphysis. Constructs were tested dynamically to failure in bending, torsion, and axial loading to determine failure loads and failure modes. A locked plating construct was compared with a nonlocked conventional plating construct. Subsequently, the outermost locking screw in locked plating constructs was replaced with a conventional screw to reduce stress concentrations at the plate end.


RESULTS
Compared with the conventional plating construct, the locked plating construct was 22% weaker in bending (p = 0.013), comparably strong in torsion (p = 0.05), and 15% stronger in axial compression (p = 0.017). Substituting the locked end screw with a conventional screw increased the construct strength by 40% in bending (p = 0.001) but had no significant effect on construct strength under torsion (p = 0.22) and compressive loading (p = 0.53) compared with the locked plating construct. Under bending, all constructs failed by periprosthetic fracture.


CONCLUSIONS
Under bending loads, the focused load transfer of locking plates through fixed-angle screws can increase the periprosthetic fracture risk in the osteoporotic diaphysis compared with conventional plates. Replacing the outermost locking screw with a conventional screw reduced the stress concentration at the plate end and significantly increased the bending strength of the plating construct compared with an all-locked construct (p = 0.001).
Does silent myocardial infarction add prognostic value in ST-elevation myocardial infarction patients without a history of prior myocardial infarction? Insights from the Assessment of Pexelizumab in Acute Myocardial Infarction (APEX-AMI) Trial.

BACKGROUND
ST-elevation myocardial infarction (STEMI) patients with a prior MI history have worse outcomes. The prognostic significance of silent MI (pathologic Q waves outside the ST-elevation territory) in STEMI is unclear.


METHODS
A total of 5,733 STEMI patients from 296 clinical centers in 17 countries were classified as (1) silent MI-baseline Q waves outside the infarct-related artery territory and no history of prior MI, (2) history of prior MI (HxMI), or (3) no prior MI.


RESULTS
Of 5,733 STEMI patients, 419 (7.3%) had silent MI, 693 (12.1%) had HxMI, and 4,621 (80.6%) had no prior MI. Ninety-day death and death/congestive heart failure/shock were higher in patients with HxMI (8.4% and 15.3%, respectively) and silent MI (6.7% and 13.9%, respectively) compared with patients with no prior MI (4.0% and 9.1%, respectively) (P ≤ .001 for all). After baseline adjustment, patients with HxMI were at increased risk for 90-day death (adjusted hazard ratio [HR] 1.62, 95% CI 1.18-2.21), whereas both those with HxMI and those with silent MI had increased risk of 90-day death/congestive heart failure/shock compared with those with no prior MI (adjusted HR 1.54, 95% CI 1.23-1.93 and adjusted HR 1.46, 95% CI 1.10-1.93, respectively).


CONCLUSIONS
Seven percent of STEMI patients had a silent MI. They represent a novel subgroup at increased risk comparable to those with known prior MI. Hence, in future studies, acquiring baseline Q wave data outside the distribution of acute injury should broaden the prognostic insights from STEMI patients with a prior MI.
Treatment of heart failure in real-world clinical practice: findings from the REFLECT-HF registry in patients with NYHA class II symptoms and a reduced ejection fraction.

BACKGROUND
Optimal medical therapy (OMT) for patients with chronic heart failure and a reduced ejection fraction (HF-REF) includes angiotensin-converting enzyme inhibitors/angiotensin receptor blockers, β-blockers, and mineralocorticoid receptor antagonists, plus a diuretic.


HYPOTHESIS
We hypothesized that OMT is less often prescribed in HF-REF patients (≤35%) with New York Heart Association (NYHA) class II symptoms compared with those with NYHA class III/IV symptoms.


METHODS
This was a cross-sectional, observational, multicenter survey of hospital-based cardiologists, office-based cardiologists, and general practitioners in Germany.


RESULTS
Out of a total of 384 patients enrolled, 144 had REF ≤35%. Patients with REF had NYHA class II symptoms in 39.6% (n = 57) and NYHA class III/IV symptoms in 60.4% (n = 87). The REF/NYHA class II group had a higher proportion of males than the REF/NYHA class III/IV group. For angiotensin-converting enzyme inhibitors/angiotensin receptor blockers and β-blockers, prescription rates were high and comparable between groups. However, prescription rates for mineralocorticoid receptor antagonists were lower compared with other guideline-recommended treatments. Multivariate analyses indicated that OMT prescription was reduced for older patients and increased for patients cared for by an office-based cardiologist.


CONCLUSIONS
Given the high proportion of patients with reduced left ventricular systolic function but only minor symptoms, HF-REF appears to be underdiagnosed, and a higher proportion of patients than are currently recognized could potentially be candidates for OMT.
Prediction of antidepressant response to venlafaxine by a combination of early response assessment and therapeutic drug monitoring.

INTRODUCTION
Early assessment of a therapeutic response is a central goal in antidepressant treatment. The present study examined the potential for therapeutic drug monitoring and symptom rating to predict venlafaxine treatment efficacy (measured by overall patient response and remission).


METHODS
88 patients were uptitrated homogenously to 225 mg/day venlafaxine. Serum concentrations of venlafaxine (VEN) and its active metabolite O-desmethylvenlafaxine (ODV) were measured at week 2. Continuous psychopathometric ratings were measured for up to 6 weeks by independent study raters.


RESULTS
An early improvement was significantly more common in venlafaxine responders than non-responders (χ(2); p=0.007). While ODV serum levels were significantly higher in responders (t test; p=0.006), VEN serum levels, sum level of VEN+ODV and the ratio of ODV/VEN levels were not. Moreover, patients who showed an early response combined with an ODV serum level above the median of 222 ng/mL were significantly more likely to achieve full response (binary logistic model; p<0.01). Sensitivity (84% for early response) and specificity (81% for combination of early response and therapeutic drug monitoring) were sufficient to qualify as a reasonable screening instrument.


CONCLUSION
Our results indicate that early improvement and ODV serum concentration are predictive of therapeutic outcome and can thus be used to guide use of the antidepressant venlafaxine.
Weapon Bias Split-Second Decisions and Unintended Stereotyping

Race stereotypes can lead people to claim to see a weapon where there is none. Split-second decisions magnify the bias by limiting people’s ability to control responses. Such a bias could have important consequences for decision making by police officers and other authorities interacting with racial minorities. The bias requires no intentional racial animus, occurring even for those who are actively trying to avoid it. This research thus raises difficult questions about intent and responsibility for racially biased errors. KEYWORDS—implicit; attitude; stereotyping; prejudice; weapon The trouble with split-second decisions is that they seem to make themselves. It is not simply that snap decisions are less accurate than ‘‘snail’’ decisions; it is easy to understand why people might make random errors when thinking fast. If you only have 30 seconds, it is probably a bad idea to do your taxes, pick a stock, or solve any problem beginning with ‘‘Two trains leave the station . . .’’ The real puzzle is when snap judgments show systematic biases that differ from our considered decisions. Should I consider those decisions my decisions if they differ from my intentions? Who is responsible? These questions are asked most loudly when decisions have immense consequences, as when a split-second decision has to be made by a surgeon, a soldier, or a police officer. Four New York City police officers had to make that kind of decision while patrolling the Bronx on a February night in 1999. When the officers ordered Amadou Diallo to stop because he matched a suspect’s description, Diallo reacted unexpectedly. Rather than raising his hands, he reached for his pocket. The Ghanaian immigrant may have misunderstood the order, or maybe he meant to show his identification. The misunderstanding was mutual: One officer shouted, ‘‘Gun!’’ and the rest opened fire. Only after the shooting stopped was it clear that Diallo held only his wallet. Many in the public were outraged. Some accused the NYPD of racial bias. Congress introduced legislation. Protests followed the officers’ acquittal, in which the defense successfully argued that at the moment of decision, the officers believed their lives were in danger and that they therefore did not have the conscious intent, the mens rae (literally, ‘‘guilty mind’’) to commit a crime. The court did not consider the mechanisms that might produce such a belief. The death of Amadou Diallo dragged into the spotlight some of the disquieting questions that have run through implicit social cognition research for some time. Can stereotypes about race influence such split-second decisions? And can that kind of race bias take place without intent to discriminate? To answer these questions, it is necessary to move away from the particulars of the Diallo case and toward controlled studies in which causes and mechanisms can be identified. What are the psychological factors that would lead a person, in the crucial moment, to shout, ‘‘Gun’’?
Clinical performance of serum prostate-specific antigen isoform [-2]proPSA (p2PSA) and its derivatives, %p2PSA and the prostate health index (PHI), in men with a family history of prostate cancer: results from a multicentre European study, the PROMEtheuS project.

OBJECTIVES
To test the sensitivity, specificity and accuracy of serum prostate-specific antigen isoform [-2]proPSA (p2PSA), %p2PSA and the prostate health index (PHI), in men with a family history of prostate cancer (PCa) undergoing prostate biopsy for suspected PCa. To evaluate the potential reduction in unnecessary biopsies and the characteristics of potentially missed cases of PCa that would result from using serum p2PSA, %p2PSA and PHI.


PATIENTS AND METHODS
The analysis consisted of a nested case-control study from the PRO-PSA Multicentric European Study, the PROMEtheuS project. All patients had a first-degree relative (father, brother, son) with PCa. Multivariable logistic regression models were complemented by predictive accuracy analysis and decision-curve analysis.


RESULTS
Of the 1026 patients included in the PROMEtheuS cohort, 158 (15.4%) had a first-degree relative with PCa. p2PSA, %p2PSA and PHI values were significantly higher (P < 0.001), and free/total PSA (%fPSA) values significantly lower (P < 0.001) in the 71 patients with PCa (44.9%) than in patients without PCa. Univariable accuracy analysis showed %p2PSA (area under the receiver-operating characteristic curve [AUC]: 0.733) and PHI (AUC: 0.733) to be the most accurate predictors of PCa at biopsy, significantly outperforming total PSA ([tPSA] AUC: 0.549), free PSA ([fPSA] AUC: 0.489) and %fPSA (AUC: 0.600) (P ≤ 0.001). For %p2PSA a threshold of 1.66 was found to have the best balance between sensitivity and specificity (70.4 and 70.1%; 95% confidence interval [CI]: 58.4-80.7 and 59.4-79.5 respectively). A PHI threshold of 40 was found to have the best balance between sensitivity and specificity (64.8 and 71.3%, respectively; 95% CI 52.5-75.8 and 60.6-80.5). At 90% sensitivity, the thresholds for %p2PSA and PHI were 1.20 and 25.5, with a specificity of 37.9 and 25.5%, respectively. At a %p2PSA threshold of 1.20, a total of 39 (24.8%) biopsies could have been avoided, but two cancers with a Gleason score (GS) of 7 would have been missed. At a PHI threshold of 25.5 a total of 27 (17.2%) biopsies could have been avoided and two (3.8%) cancers with a GS of 7 would have been missed. In multivariable logistic regression models, %p2PSA and PHI achieved independent predictor status and significantly increased the accuracy of multivariable models including PSA and prostate volume by 8.7 and 10%, respectively (P ≤ 0.001). p2PSA, %p2PSA and PHI were directly correlated with Gleason score (ρ: 0.247, P = 0.038; ρ: 0.366, P = 0.002; ρ: 0.464, P < 0.001, respectively).


CONCLUSIONS
%p2PSA and PHI are more accurate than tPSA, fPSA and %fPSA in predicting PCa in men with a family history of PCa. Consideration of %p2PSA and PHI results in the avoidance of several unnecessary biopsies. p2PSA, %p2PSA and PHI correlate with cancer aggressiveness.