LLukas22/scidocs huggingface dataset:
DeepSurv: personalized treatment recommender system using a Cox proportional hazards deep neural network

BACKGROUND
Medical practitioners use survival models to explore and understand the relationships between patients' covariates (e.g. clinical and genetic features) and the effectiveness of various treatment options. Standard survival models like the linear Cox proportional hazards model require extensive feature engineering or prior medical knowledge to model treatment interaction at an individual level. While nonlinear survival methods, such as neural networks and survival forests, can inherently model these high-level interaction terms, they have yet to be shown as effective treatment recommender systems.


METHODS
We introduce DeepSurv, a Cox proportional hazards deep neural network and state-of-the-art survival method for modeling interactions between a patient's covariates and treatment effectiveness in order to provide personalized treatment recommendations.


RESULTS
We perform a number of experiments training DeepSurv on simulated and real survival data. We demonstrate that DeepSurv performs as well as or better than other state-of-the-art survival models and validate that DeepSurv successfully models increasingly complex relationships between a patient's covariates and their risk of failure. We then show how DeepSurv models the relationship between a patient's features and effectiveness of different treatment options to show how DeepSurv can be used to provide individual treatment recommendations. Finally, we train DeepSurv on real clinical studies to demonstrate how it's personalized treatment recommendations would increase the survival time of a set of patients.


CONCLUSIONS
The predictive and modeling capabilities of DeepSurv will enable medical researchers to use deep neural networks as a tool in their exploration, understanding, and prediction of the effects of a patient's characteristics on their risk of failure.
Coronary computed tomography angiography for early triage of patients with acute chest pain: the ROMICAT (Rule Out Myocardial Infarction using Computer Assisted Tomography) trial.

OBJECTIVES
This study was designed to determine the usefulness of coronary computed tomography angiography (CTA) in patients with acute chest pain.


BACKGROUND
Triage of chest pain patients in the emergency department remains challenging.


METHODS
We used an observational cohort study in chest pain patients with normal initial troponin and nonischemic electrocardiogram. A 64-slice coronary CTA was performed before admission to detect coronary plaque and stenosis (>50% luminal narrowing). Results were not disclosed. End points were acute coronary syndrome (ACS) during index hospitalization and major adverse cardiac events during 6-month follow-up.


RESULTS
Among 368 patients (mean age 53 +/- 12 years, 61% men), 31 had ACS (8%). By coronary CTA, 50% of these patients were free of coronary artery disease (CAD), 31% had nonobstructive disease, and 19% had inconclusive or positive computed tomography for significant stenosis. Sensitivity and negative predictive value for ACS were 100% (n = 183 of 368; 95% confidence interval [CI]: 98% to 100%) and 100% (95% CI: 89% to 100%), respectively, with the absence of CAD and 77% (95% CI: 59% to 90%) and 98% (n = 300 of 368, 95% CI: 95% to 99%), respectively, with significant stenosis by coronary CTA. Specificity of presence of plaque and stenosis for ACS were 54% (95% CI: 49% to 60%) and 87% (95% CI: 83% to 90%), respectively. Only 1 ACS occurred in the absence of calcified plaque. Both the extent of coronary plaque and presence of stenosis predicted ACS independently and incrementally to Thrombolysis In Myocardial Infarction risk score (area under curve: 0.88, 0.82, vs. 0.63, respectively; all p < 0.0001).


CONCLUSIONS
Fifty percent of patients with acute chest pain and low to intermediate likelihood of ACS were free of CAD by computed tomography and had no ACS. Given the large number of such patients, early coronary CTA may significantly improve patient management in the emergency department.
A Discrete Differential Forms Framework for Computational Electromagnetism

In this article, we present a computational framework for solving problems arising in electromagnetism. The framework is derived from a modern geometrical approach and is based on differential forms (or p-forms). These geometrical entities provide a natural framework for modeling of physical quantities such as electric potentials, electric and magnetic fields, electric and magnetic fluxes, etc. We have implemented an object oriented class library, called FEMSTER. The library is designed for high order finite element approximations. In addition, it can be expanded by including user-defined data types or by deriving new classes. Finally, the versatility of the software is shown through different simulations. keyword: High order finite element, H (div) and H (curl) conforming methods, Computational electromagnetism, Object oriented programming.
Proton magnetic resonance techniques for characterization of water in wood: application to white spruce

Two new proton magnetic resonance techniques, relaxation spectra and relaxation selective imaging, have been used to investigate the distribution of water in samples of normal white spruce sapwood, heartwood, and juvenile wood as well as two rehydrated heartwood samples containing incipient decay and compression wood respectively. It is demonstrated that the spin-spin (T2) relaxation behavior in wood is best presented as a continuous spectrum of relaxation times. Spectra of T2 for white spruce show separate peaks corresponding to the different water environments. Bound water gives a peak with an T2 time of about 1 ms and lumen water gives a distribution of T2 times in the range of 10 to 100 ms. The lumen water T2 time is a function of the wood cell radius. Consequently, the different cell lumen radii distributions for spruce sapwood, juvenile wood, and compression wood are readily distinguishable by the shape of their T2 spectra. Water environments which are separable on a T2 spectrum may be imaged separately. Imaging has been carried out in one dimension for bound water and lumen water of a spruce sapwood sample at four different moisture contents ranging from 100% to 17%. For the first time, we demonstrate that above the fibre saturation point the moisture density profile of the bound water is largely independent of moisture content. The feasibility and utility of using these techniques for internal scanning of logs and lumber is discussed. These techniques should provide new insights into the wood drying process.
Lung cancer detectability by test, histology, stage, and gender: estimates from the NLST and the PLCO trials.

BACKGROUND
Implementing optimal lung cancer screening programs requires knowledge of the natural history and detectability of lung cancer. This information can be derived from the results of clinical trials with the aid of microsimulation models.


METHODS
Data from the Surveillance, Epidemiology, and End Results (SEER) program and individual-level data from the National Lung Screening Trial (NLST) and the Prostate, Lung, Colon, and Ovarian Cancer Screening trial (PLCO) were used to investigate the sensitivity (by histology and stage) of CT and chest radiography (CXR) and the mean preclinical sojourn time (MPST) of lung cancer (by gender, histology, and stage). The MISCAN-Lung model was used to reproduce the lung cancer incidence by method of detection (clinically or screen-detected), gender, histology, and stage in both trials and SEER, by calibrating CT and CXR sensitivity and natural history parameters.


RESULTS
CT sensitivity ranges from 8.83% to 99.35% and CXR sensitivity from 2.51% to 97.31%, depending on histology and stage. CT sensitivity for stage IA is more than 3-fold higher compared with CXR, for all histologies. The total MPST estimates for lung cancer progressing through preclinical stages IA to IV range from 3.09 to 5.32 years for men and 3.35 to 6.01 years for women. The largest difference in total MPST between genders was estimated for adenocarcinoma.


CONCLUSIONS
We estimate longer MPSTs for lung cancer compared with previous research, suggesting a greater window of opportunity for lung cancer screening.


IMPACT
This study provides detailed insights into the natural history of lung cancer and CT screening effectiveness.
Real-life effectiveness of budesonide/formoterol maintenance and reliever therapy in asthma patients across Asia: SMARTASIA study

BACKGROUND
The use of budesonide/formoterol in a single inhaler for both maintenance and reliever therapy is a recommended option for treatment of persistent asthma not responding well to inhaled corticosteroid (ICS) alone.


METHODS
This was a multi-centre open-label study on patients whose asthma condition remained inadequately controlled by various asthma treatments other than budesonide/formoterol. After a 2-week run-in period, eligible patients underwent a 12-week treatment period with budesonide/formoterol (Symbicort SMART(®), 160/4.5 μg) twice daily plus as needed. Patient's asthma control and quality of life were assessed using the 5-item Asthma Control Questionnaire (ACQ-5) and the standardized Asthma Quality of Life Questionnaire (AQLQ-S), respectively.


RESULTS
A total of 862 eligible asthma patients who have had asthma for a mean duration of 10.73 ± 12.03 years entered a 12-week treatment with budesonide/formoterol maintenance and reliever therapy. During treatment, ACQ-5 score improved significantly by 0.58 ± 0.93 (95% CI, 0.51 to 0.64, P < 0.0001) from the baseline level of 1.62 ± 1.00. AQLQ(S) score improved by 0.70 ± 0.89 (95% CI, 0.64 to 0.76, P < 0.0001) from baseline. Asthma symptom score was also reduced significantly (P < 0.0001); between run-in and treatment periods, night- and day-time symptom scores were reduced by 0.32 ± 0.54 (95% CI, 0.28 to 0.35) and 0.30 ± 0.52 (95% CI, 0.27 to 0.34), respectively. The percentage of nights with awakenings due to asthma symptoms was reduced by 11.09 ± 26.13% (95% CI, 9.34 to 12.85%), while the percentage of asthma-control and symptom-free days increased by 20.90 ± 34.40% (95% CI, 18.59 to 23.21%) and 23.89 ± 34.62% (95% CI, 21.56 to 26.21%), respectively (P < 0.0001). Together with the improvement in asthma control, the number of night- and day-time inhalations of as-needed reliever medication decreased by 0.30 ± 0.82 (95% CI, 0.24 to 0.35) inhalations and 0.30 ± 0.97 (95% CI, 0.23 to 0.36) inhalations, respectively (P < 0.0001). No unexpected adverse events were reported.


CONCLUSION
During treatment of inadequately controlled asthmatic patients with budesonide/formoterol maintenance and reliever therapy, significant improvement in patients' asthma control and reductions in asthma symptoms and as-needed medication use was observed. Patients' quality of life was improved and the treatment was well tolerated.


TRIAL REGISTRATION
ClinicalTrial.gov: (NCT00939341).
Constrained Model Predictive Control Implementation for a Heavy-Duty Gas Turbine Power Plant

In this paper, model predictive control (MPC) strategy is implemented to a GE9001E gas turbine power plant. A linear model is developed for the gas turbine using conventional mathematical models and ARX identification procedure. Also a process control model is identified for system outputs prediction. The controller is designed in order to adjust the exhaust gas temperature and the rotor speed by compressor inlet guide vane (IGV) position and fuel signals. The proposed system is simulated under load demand disturbances. It is shown that MPC controller can maintain the rotor speed and exhaust gas temperature more accurately in comprehension with both SpeedTronicTM control system and conventional PID control. Key-words: Gas turbine, Identification, ARX, Predictive control, Power plant, Modeling, Multivariable control, PID
A practical tool for maximal information coefficient analysis

Background
The ability of finding complex associations in large omics datasets, assessing their significance, and prioritizing them according to their strength can be of great help in the data exploration phase. Mutual information-based measures of association are particularly promising, in particular after the recent introduction of the TICe and MICe estimators, which combine computational efficiency with superior bias/variance properties. An open-source software implementation of these two measures providing a complete procedure to test their significance would be extremely useful.


Findings
Here, we present MICtools, a comprehensive and effective pipeline that combines TICe and MICe into a multistep procedure that allows the identification of relationships of various degrees of complexity. MICtools calculates their strength assessing statistical significance using a permutation-based strategy. The performances of the proposed approach are assessed by an extensive investigation in synthetic datasets and an example of a potential application on a metagenomic dataset is also illustrated.


Conclusions
We show that MICtools, combining TICe and MICe, is able to highlight associations that would not be captured by conventional strategies.
A study of relationship between managers' leadership style and employees' job satisfaction.

PURPOSE
The purpose of this descriptive and cross-sectional study is to explore the relationships between managers' leadership styles and employees' job satisfaction in Isfahan University Hospitals, Isfahan, Iran, 2004.


DESIGN/METHODOLOGY/APPROACH
The data were collected through the distribution of two questionnaires among the 814 employees, first line, middle and senior managers of these hospitals through a stratified random sampling.


FINDINGS
The dominant leadership style of managers was participative. The mean score of employee-oriented dimension of leadership style in first line, middle and senior managers were 52, 54, and 54 (from 75 credit) respectively. The mean score of task-oriented dimension of leadership style in first line, middle and senior managers were 68, 69, and 70 (from 100 credit) respectively. The mean score of employee's job satisfaction was 3.26 +/- 0.56 on a 6 scale (moderate satisfaction), 1.9, 26.1, 64.7, and 7.3 percent of hospital employees had respectively very low, low, moderate, and high satisfaction with their job. Employees demonstrated less satisfaction with salaries, benefits, work conditions, promotion and communication as satisfier factors and more satisfaction with factors such as the nature of the job, co-workers and supervision type factors. There was significant correlation (p < 0.001) between the use of leadership behaviors and employees and job satisfaction.


RESEARCH LIMITATIONS/IMPLICATIONS
Employee job satisfaction depends upon the leadership style of managers. Nevertheless, participative management is not always a good management style. Managers should select the best leadership style according to the organizational culture and employees' organizational maturity.


ORIGINALITY/VALUE
Although this study conducted in Iran, it is anticipated that the findings may have relevance on a broader scale. By replicating this study in different countries and contexts the results of could be very helpful for developing a new model of leadership with new implementation techniques that can be implemented easily and successfully in a cross cultural context.
Development of patterned carbon nanotubes on a 3D polymer substrate for the flexible tactile sensor application

We present a design methodology and manufacturing process for the construction of articulated three-dimensional microstructures with features on the micron to centimeter scale. Flexure mechanisms and assembly folds result from the bulk machining and lamination of alternating rigid and compliant layers, similar to rigid-flex printed circuit board construction. Pop-up books and other forms of paper engineering inspire designs consisting of one complex part with a single assembly degree of freedom. Like an unopened pop-up book, mechanism links reside on multiple interconnected layers, reducing interference and allowing folding mechanisms of greater complexity than achievable with a single folding layer. Machined layers are aligned using dowel pins and bonded in parallel. Using mechanical alignment that persists during bonding allows device layers to be anisotropically pre-strained, a feature we exploit to create self-assembling structures. These methods and three example devices are presented.
Mechanical and water barrier properties of agar/κ-carrageenan/konjac glucomannan ternary blend biohydrogel films.

Multicomponent hydrogel films composed of agar, κ-carrageenan, konjac glucomannan powder, and nanoclay (Cloisite(®) 30B) were prepared and their mechanical and water barrier properties such as water vapor permeability (WVP), water contact angle (CA), water solubility (WS), water uptake ratio (WUR), water vapor uptake ratio (WVUR) were determined. Mechanical, water vapor barrier, and water resistance properties of the ternary blend film exhibited middle range of individual component films, however, they increased significantly after formation of nanocomposite with the clay. Especially, the water holding capacity of the ternary blend biopolymer films increased tremendously, from 800% to 1681% of WUR for agar and κ-carrageenan films up to 5118% and 5488% of WUR for the ternary blend and ternary blend nanocomposite films, respectively. Water vapor adsorption behavior of films was also tested by water vapor adsorption kinetics and water vapor adsorption isotherms test. Preliminary test result for fresh spinach packaging revealed that the ternary blend biohydrogel films had a high potential for the use as an antifogging film for packaging highly respiring agricultural produce. In addition, the ternary blend nanocomposite film showed an antimicrobial activity against Gram-positive bacteria, Listeria monocytogenes.
The Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI): a completed reference database of lung nodules on CT scans.

PURPOSE
The development of computer-aided diagnostic (CAD) methods for lung nodule detection, classification, and quantitative assessment can be facilitated through a well-characterized repository of computed tomography (CT) scans. The Lung Image Database Consortium (LIDC) and Image Database Resource Initiative (IDRI) completed such a database, establishing a publicly available reference for the medical imaging research community. Initiated by the National Cancer Institute (NCI), further advanced by the Foundation for the National Institutes of Health (FNIH), and accompanied by the Food and Drug Administration (FDA) through active participation, this public-private partnership demonstrates the success of a consortium founded on a consensus-based process.


METHODS
Seven academic centers and eight medical imaging companies collaborated to identify, address, and resolve challenging organizational, technical, and clinical issues to provide a solid foundation for a robust database. The LIDC/IDRI Database contains 1018 cases, each of which includes images from a clinical thoracic CT scan and an associated XML file that records the results of a two-phase image annotation process performed by four experienced thoracic radiologists. In the initial blinded-read phase, each radiologist independently reviewed each CT scan and marked lesions belonging to one of three categories ("nodule > or =3 mm," "nodule <3 mm," and "non-nodule > or =3 mm"). In the subsequent unblinded-read phase, each radiologist independently reviewed their own marks along with the anonymized marks of the three other radiologists to render a final opinion. The goal of this process was to identify as completely as possible all lung nodules in each CT scan without requiring forced consensus.


RESULTS
The Database contains 7371 lesions marked "nodule" by at least one radiologist. 2669 of these lesions were marked "nodule > or =3 mm" by at least one radiologist, of which 928 (34.7%) received such marks from all four radiologists. These 2669 lesions include nodule outlines and subjective nodule characteristic ratings.


CONCLUSIONS
The LIDC/IDRI Database is expected to provide an essential medical imaging research resource to spur CAD development, validation, and dissemination in clinical practice.
Cue-based oral feeding clinical pathway results in earlier attainment of full oral feeding in premature infants

Objective:To study whether a cue-based clinical pathway for oral feeding initiation and advancement of premature infants would result in earlier achievement of full oral feeding.Study Design:Age of achievement of full oral intake was compared for two groups of preterm infants; a prospective study group vs historic cohort controls. Study infants had oral feedings managed by nurses using a clinical pathway that relied on infant behavioral readiness signs to initiate and advance oral feedings. Controls had oral feedings managed by physician orders.Result:Fifty-one infants (n=28 study and n=23 control) were studied. Gender distribution, gestational age, birth weight and ventilator days were not different between groups. Study infants reached full oral feedings 6 days earlier than controls (36±1 3/7 weeks of postmenstrual age (PMA) vs 36 6/7±1 4/7 weeks of PMA, P=0.02).Conclusion:The cue-based clinical pathway for oral feeding initiation and advancement of premature infants resulted in earlier achievement of full oral feeding.
Respiratory Filter Reduces the Cardiovascular Effects Associated With Diesel Exhaust Exposure: A Randomized, Prospective, Double-Blind, Controlled Study of Heart Failure: The FILTER-HF Trial.

OBJECTIVES
The goal of this study was to test the effects of a respiratory filter intervention (filter) during controlled pollution exposure.


BACKGROUND
Air pollution is considered a risk factor for heart failure (HF) decompensation and mortality.


METHODS
This study was a double-blind, randomized to order, controlled, 3-way crossover, single-center clinical trial. It enrolled 26 patients with HF and 15 control volunteers. Participants were exposed in 3 separate sessions to clean air, unfiltered diesel exhaust exposure (DE), or filtered DE. Endpoints were endothelial function assessed by using the reactive hyperemia index (RHi), arterial stiffness, serum biomarkers, 6-min walking distance, and heart rate variability.


RESULTS
In patients with HF, DE was associated with a worsening in RHi from 2.17 (interquartile range [IQR]: 1.8 to 2.5) to 1.72 (IQR: 1.5 to 2.2; p = 0.002) and an increase in B-type natriuretic peptide (BNP) from 47.0 pg/ml (IQR: 17.3 to 118.0 pg/ml) to 66.5 pg/ml (IQR: 26.5 to 155.5 pg/ml; p = 0.004). Filtration reduced the particulate concentration (325 ± 31 μg/m(3) vs. 25 ± 6 μg/m(3); p < 0.001); in the group with HF, filter was associated with an improvement in RHi from 1.72 (IQR: 1.5 to 2.2) to 2.06 (IQR: 1.5 to 2.6; p = 0.019) and a decrease in BNP from 66.5 pg/ml (IQR: 26.5 to 155.5 pg/ml) to 44.0 pg/ml (IQR: 20.0 to 110.0 pg/ml; p = 0.015) compared with DE. In both groups, DE decreased the 6-min walking distance and arterial stiffness, although filter did not change these responses. DE had no effect on heart rate variability or exercise testing.


CONCLUSIONS
To our knowledge, this trial is the first to show that a filter can reduce both endothelial dysfunction and BNP increases in patients with HF during DE. Given these potential benefits, the widespread use of filters in patients with HF exposed to traffic-derived air pollution may have beneficial public health effects and reduce the burden of HF. (Effects of Air Pollution Exposure Reduction by Filter Mask on Heart Failure; NCT01960920).