LLukas22/scidocs huggingface dataset:
Digital health for the End TB Strategy: developing priority products and making them work

In 2014, the World Health Organization (WHO) developed the End TB Strategy in response to a World Health Assembly Resolution requesting Member States to end the worldwide epidemic of tuberculosis (TB) by 2035. For the strategy's objectives to be realised, the next 20 years will need novel solutions to address the challenges posed by TB to health professionals, and to affected people and communities. Information and communication technology presents opportunities for innovative approaches to support TB efforts in patient care, surveillance, programme management and electronic learning. The effective application of digital health products at a large scale and their continued development need the engagement of TB patients and their caregivers, innovators, funders, policy-makers, advocacy groups, and affected communities.In April 2015, WHO established its Global Task Force on Digital Health for TB to advocate and support the development of digital health innovations in global efforts to improve TB care and prevention. We outline the group's approach to stewarding this process in alignment with the three pillars of the End TB Strategy. The supplementary material of this article includes target product profiles, as developed by early 2016, defining nine priority digital health concepts and products that are strategically positioned to enhance TB action at the country level.
Deep Learning as Feature Encoding for Emotion Recognition

Deep learning is popular as an end-to-end framework extracting the prominent features and performing the classification also. In this paper, we extensively investigate deep networks as an alternate to feature encoding technique of lowlevel descriptors for emotion recognition on the benchmark EmoDB dataset. Fusion performance with such obtained encoded features with other available features is also investigated. Highest performance to date in the literature is observed.
Effectiveness of hip muscle strengthening in patellofemoral pain syndrome
patients: a systematic review

INTRODUCTION
Patellofemoral pain syndrome (PFPS) is characterized by anterior knee pain, which may limit the performance of functional activities. The influence of hip joint motion on the development of this syndrome has already been documented in the literature. In this regard, studies have investigated the effectiveness of hip muscle strengthening in patients with PFPS.


OBJECTIVES
The aims of this systematic review were (1) to summarize the literature related to the effects of hip muscle strengthening on pain intensity, muscle strength, and function in individuals with PFPS and (2) to evaluate the methodological quality of the selected studies.


METHOD
A search for randomized controlled clinical trials was conducted using the following databases: Google Scholar, MEDLINE, PEDro, LILACS, and SciELO. The selected studies had to distinguish the effects of hip muscle strengthening in a group of patients with PFPS, as compared to non-intervention or other kinds of intervention, and had to investigate the following outcomes: pain, muscle strength, and function. The methodological quality of the selected studies was analyzed by means of the PEDro scale.


RESULTS
Seven studies were selected. These studies demonstrated that hip muscle strengthening was effective in reducing pain. However, the studies disagreed regarding the treatments' ability to improve muscle strength. Improvement in functional capabilities after hip muscle strengthening was found in five studies.


CONCLUSION
Hip muscle strengthening is effective in reducing the intensity of pain and improving functional capabilities in patients with PFPS, despite the lack of evidence for its ability to increase muscle strength.
A COMSOL Multiphysics ® Model of Droplet Formation at a Flow Focusing Device

Introduction The manipulation of droplets in microfluidic channels is an immensely useful technological platform for applications in many scientific fields such as biology, biomedical studies, chemical synthesis and drug discovery. Therefore a numerical study of microdroplet generation can play a crucial role in providing a model for predicting the effect of different parameters on a droplet generation module. These models may be able to forecast the performance of a module precisely in terms of droplet size and frequency, as well as the functionality of the entire system. Moreover, this will lead to a better understanding of the phenomenon of droplet generation. Use of COMSOL Multiphysics® In this work, we numerically investigated the process of droplet generation using water as the dispersed phase and FC-40 oil as the continuous phase in a microfluidic device. We used a twophase level set method in COMSOL Multiphysics® for our study. The simulations were carried out in a two dimensional domain through a flow-focusing droplet generator which is illustrated in Figure 1 along with the geometric dimensions and the computational mesh. All simulations were fulfilled through the laminar two-phase flow physics module with the channel walls specified as wetted walls with a constant contact angle of 0.349 radian. The effect of the velocity ratio between the aqueous and oil phases on droplet size was studied using two sets of simulations, one with a varying oil velocity at constant water velocity and the other with a constant oil velocity and varying water velocity (the velocity ratios were same in both cases). For the first set of simulations, the oil inlet velocity was varied between 0.0449 m/s to 0.12 m/s in six steps while the water inlet velocity was kept constant at 0.04 m/s. Figure 2 represents the results of this set of simulations. For the second set of simulations, the oil inlet velocity was held constant at 0.09 m/s and the water inlet velocity was varied between 0.03 m/s and 0.08 m/s in six stages. Figure 3 depicts all the simulations in this set. Droplet size was measured based on 34 measurements in each case and the standard deviation was calculated. All the measurements of both sets of simulations were later plotted on one graph representing the effect of the ratio of water to oil input velocities on droplet size (Figure 4). The results demonstrate that the velocity ratio of the two phases directly determine the size of the droplets. Both sets of simulations indicate similar droplet sizes for same ratio of input velocities. Additional simulations with different oil and water input velocity ranges are in progress. Moreover, this work could be extended to investigate the polydispersity of droplets and the effect of varying the device geometry, with for example different expansion angles near the nozzle. We will also endeavor to generate experimental results for this nozzle design for comparison with the simulation results.
Low levels of 1,5-anhydro-D-glucitol are associated with vascular endothelial dysfunction in type 2 diabetes

BACKGROUND
Vascular endothelial dysfunction is involved in macrovascular disease progression in type 2 diabetes mellitus (T2DM). We reported previously that blood glucose fluctuations, as evaluated by continuous glucose monitoring (CGM), correlate with vascular endothelial function, serving as a marker of vascular endothelial function. However, the use of CGM is limited, suggesting the need for another marker of vascular endothelial function. Here, we investigated the relationship between vascular endothelial dysfunction and blood levels of 1,5-anhydro-D-glucitol (1,5-AG), a marker of both postprandial hyperglycemia and fluctuations in blood glucose.


METHODS
In 32 inpatients with T2DM and HbA1c less than 8.0%, the reactive hyperemia index (RHI), an index of vascular endothelial function, was determined by peripheral arterial tonometry. The relationships between RHI and 1,5-AG, blood glucose, lipid metabolism markers, and blood pressure, were examined.


RESULTS
There was a strong correlation between 1,5-AG and natural logarithmic-scaled RHI (L_RHI) (r = 0.55; P = 0.001). However, there was no correlation between L_RHI and HbA1c, fasting blood glucose, IRI, LDL-C, HDL-C, TG, systolic blood pressure, or diastolic blood pressure. Multivariate analysis identified blood 1,5-AG levels to be the only significant and independent determinant of L_RHI.


CONCLUSIONS
In T2DM with HbA1c <8.0%, low 1,5-AG levels were associated with vascular endothelial dysfunction, suggesting it is a potentially useful marker for vascular endothelial dysfunction.


TRIAL REGISTRATION
UMIN000015317.
Relationship between pulmonary matrix metalloproteinases and quantitative CT markers of small airways disease and emphysema in COPD.

BACKGROUND
Matrix metalloproteinases (MMPs) are proteolytic enzymes that can degrade the extracellular matrix and drive tissue remodelling, key processes in the pathogenesis of COPD. The development of small airway disease has been identified as a critical mechanism in the early development of airflow obstruction but the contribution of MMPs in human disease is poorly characterised.


OBJECTIVES
We investigated the role of MMPs and inflammatory cytokines in the lung by quantifying levels and determining relationships with the key pathological components of COPD in patients and healthy controls.


METHODS
We analysed levels of MMPs and inflammatory cytokines in bronchoalveolar lavage from 24 COPD and 8 control subjects. Each subject underwent spirometry and high-resolution CT. Image analysis quantitatively assessed emphysema, bronchial wall thickening and small airways disease.


RESULTS
Multiple MMPs (MMP-1, -2, -3, -8, -9 and -10) and cytokines (interleukin (IL) 6 and IL-8) were elevated in lungs of subjects with COPD. MMP-3, -7, -8, -9, -10 and -12 concentrations closely associated with CT markers of small airways disease. Emphysema severity was also associated with MMP-3, -7 and -10. However, there were no strong relationships between MMPs and bronchial wall thickness of the larger airways.


CONCLUSIONS
Pulmonary MMP concentrations are directly associated with the extent of gas trapping and small airways disease identified on CT scan. This study suggests that MMPs play a significant role in small airways remodelling, a key feature in the pathogenesis of COPD.


TRIAL REGISTRATION NUMBER
NCT01701869.
Bias Field Effects on Microwave Frequency Behavior of PZT/YIG Magnetoelectric Bilayer

Magnetoelectric behavior of a yttrium iron garnet (YIG)/zirconate titanate (PZT) magnetoelectric bilayer composite was studied over 1-7 GHz under different bias magnetic fields and electric fields by using a broadband air-gap microstrip with the PZT/YIG loaded in the air gap. Electrostatically induced ferrimagnetic resonance (FMR) frequency shifts of the YIG/PZT bilayer composite were studied. The FMR frequency shift was negligible at bias fields when the YIG was not saturated. After saturation, the FMR frequency increased nearly linearly from 15 MHz at a bias field of 100 Oe to 30 MHz at 1200 Oe and dropped suddenly at a field of 1300 Oe to about 20 MHz. This nonlinear bias magnetic held dependence was due to magnetic domain activities when the YIG was not saturated and due to the interference between the uniform mode and other magnetostatic spin waves after saturation. An electrostatically tunable band-reject filter device was demonstrated which has a peak attenuation of greater than 50 dB, 40 dB rejection band of 10 MHz, and pass band insertion loss of <5 dB at ~4.6 GHz.
Firmware modification attacks on programmable logic controllers

Recent attacks on industrial control systems, such as the highly publicized Stuxnet malware, have intensified a “race to the bottom” where lower-level attacks have a tactical advantage. Programmable logic controller (PLC) firmware, which provides a softwaredriven interface between system inputs and physical outputs, can be easily modified at the user level. Efforts directed at protecting against firmware modification are hindered by the lack of foundational research about attack development and implementation. This paper examines the vulnerability of PLCs to intentional firmware modifications in order to obtain a better understanding of the threats posed by PLC firmware modification attacks and the feasibility of these attacks. A general firmware analysis methodology is presented, and a proof-of-concept experiment is used to demonstrate how legitimate firmware can be updated and uploaded to an Allen-Bradley ControlLogix L61 PLC. Published by Elsevier B.V.
Comparison of the liver function and hepatic specific genes expression in cultured mesenchymal stem cells and hepatocytes

OBJECTIVE(S)
Stem cell therapy is believed to be as a promising treatment strategy for tissue repair and regeneration. The plasticity specification of the adult stem cells, such as MSCs, has enabled that these cells to be used in the treatment of a broad spectrum of diseases like liver disorders. In this study, the production of urea and Albumin (Alb), glycogen storage, and expression of some liver genes including α-fetoprotein (AFP), Alb, cytokeratin18 (CK18) and cytokeratin19 (CK19) was compared between mesenchymal stem cells (MSCs) and isolated rat hepatocytes.


MATERIALS AND METHODS
The MSCs were isolated from rat femurs and tibias and cultured in α-MEM, DMEM and RPMI mediums supplemented with serum. Hepatocytes were isolated from Rat livers and cultured in DMEM with serum. The expression of AFP, Alb, CK18, and CK19 genes was evaluated using the reverse transcription-polymerase chain reaction (RT-PCR). Furthermore, the synthesis of albumin and urea of the cells was measured.


RESULTS
In vitro conditions, MSCs and hepatocytes exhibited the characteristic functions of the liver such as capacity to synthesize Alb, urea, the storage of glycogen. In this study, the expression of some liver genes such as AFP, Alb, CK18 and CK19 at mRNA levels was also shown.


CONCLUSION
The results showed that MSCs exhibited some liver functions, and may be considered as an alternative source for adult stem cell transplantation in liver repair due to the excellent proliferation and differentiation capacities.
MNE software for processing MEG and EEG data

Magnetoencephalography and electroencephalography (M/EEG) measure the weak electromagnetic signals originating from neural currents in the brain. Using these signals to characterize and locate brain activity is a challenging task, as evidenced by several decades of methodological contributions. MNE, whose name stems from its capability to compute cortically-constrained minimum-norm current estimates from M/EEG data, is a software package that provides comprehensive analysis tools and workflows including preprocessing, source estimation, time-frequency analysis, statistical analysis, and several methods to estimate functional connectivity between distributed brain regions. The present paper gives detailed information about the MNE package and describes typical use cases while also warning about potential caveats in analysis. The MNE package is a collaborative effort of multiple institutes striving to implement and share best methods and to facilitate distribution of analysis pipelines to advance reproducibility of research. Full documentation is available at http://martinos.org/mne.
Computer-assisted quantification of interstitial lung disease associated with rheumatoid arthritis: preliminary technical validation.

PURPOSE
To validate a threshold-based prototype software application (MeVis PULMO 3D) for quantification of chronic interstitial lung disease (ILD) in patients with rheumatoid arthritis (RA) using variable threshold settings for segmentation of diseased lung areas.


METHODS
Twenty-two patients with rheumatoid arthritis were included and underwent thin-section CT (4x1.25mm collimation). CT scans were assessed by two observers for extent of ILD (EoILD), and twice by MeVis PULMO 3D for each protocol. MeVis PULMO 3D used four segmentation threshold (ST) settings (ST=-740, -780, -800 and -840HU). Pulmonary function tests were obtained in all patients. Statistical evaluation used 95% limits of agreement (LoA) and linear regression analysis.


RESULTS
There was total concordance between the software measurements. Interobserver agreement was good (LoA=-28.36 to 17.58%). EoILD by readers correlated strongly with DL(CO) (r=-0.702, p<0.0001) and moderately with FVC (r=-0.523, p=0.018). There was close correlation between readers and MeVis PULMO 3D with best results for ST <780HU (EoILD vs. MeVis PULMO 3D: r=0.650 for ST=-800 and -840HU, respectively; p=0.002). MeVis PULMO 3D correlated best with DL(CO) at ST of -800HU (r=-0.44, -0.49, -0.58 and -0.57 for ST=-740, -780, -800 and -840, respectively; p=0.007-0.05) and moderately with FVC (r=-0.44, -0.51, -0.59 and -0.45 for ST=-740, -780, -800 and -840), respectively; p=0.007-0.05).


CONCLUSION
The MeVis PULMO 3D system used holds promise to become a valuable instrument for quantification of chronic ILD in patients with RA when using the threshold value of -800HU, with evidence of the closest correlations, both with human observers and physiologic impairment.
Synergy, Redundancy and Common Information

We consider the problem of decomposing the total mutual information conveyed by a pair of predictor random variables about a target random variable into redundant, uniqueand synergistic contributions. We focus on the relationship be tween “redundant information” and the more familiar information theoretic notions of “common information.” Our main contri bution is an impossibility result. We show that for independent predictor random variables, any common information based measure of redundancy cannot induce a nonnegative decompositi on of the total mutual information. Interestingly, this entai ls that any reasonable measure of redundant information cannot be deri ved by optimization over a single random variable. Keywords—common and private information, synergy, redundancy, information lattice, sufficient statistic, partial information decomposition
FILIPINO PHILOSOPHY : A WESTERN TRADITION IN AN EASTERN SETTING

[This paper is the third revised version (2013). It was originally presented in a philosophical conference in Athens, Greece on 6 June 2006, Athens Institute of Education and Research. It was first published as Chapter 28 in The philosophical landscape. Third edition. Edited by Rolando M. Gripaldo. Manila: Philippine National Philosophical Research Society, 2007. Other editions appeared in Philosophia: International Journal of Philosophy 36/8 (1): January 2007 and in The making of a Filipino philosopher and other essays. [A collection of Gripaldo’s essays.] Chapter 2. Mandaluyong City: National Book Store, 2009.]
Non-eligibility for reperfusion therapy in patients presenting with ST-segment elevation myocardial infarction: Contemporary insights from the National Cardiovascular Data Registry (NCDR).

BACKGROUND
Reperfusion therapy is lifesaving in patients presenting with ST-segment elevation myocardial infarction (STEMI). Contemporary data describing the characteristics and outcomes of patients presenting with STEMI not receiving reperfusion therapy are lacking.


METHODS
Using the ACTION Registry-GWTG database, we examined 219,726 STEMI patients (January 2007-December 2013) at 721 percutaneous coronary intervention (PCI)-capable hospitals in United States. Clinical characteristics and in-hospital outcomes were stratified by those who underwent reperfusion (n = 188,200; 86%), those who did not undergo reperfusion with a reason for ineligibility (n = 27,179; 12%), and those without reperfusion but had no reason for ineligibility (n = 4,347; 2%).


RESULTS
Compared with STEMI patients receiving reperfusion therapy, the nonreperfusion groups were older, were more often female, and had higher rates of hypertension, diabetes, prior myocardial infarction, prior stroke, atrial fibrillation, and left bundle-branch block and heart failure on presentation. The major reason for reperfusion noneligibility was coronary anatomy not suitable for PCI (33%). Presence of 3-vessel coronary disease was more common in the nonreperfusion groups (with or without a documented reason) compared with reperfusion group (38% and 36% vs 26%, P < .001, respectively). In-hospital mortality was higher in patients not receiving reperfusion therapy with or without a documented reason compared with the reperfusion group (adjusted odds ratio [95% CI] 1.88 [1.78-1.99] and 1.37 [1.21-1.57], respectively).


CONCLUSION
Most patients with STEMI not receiving reperfusion therapy had a documented reason. Coronary anatomy not suitable for PCI was the major contributor to ineligibility. In-hospital mortality was higher in patients not receiving reperfusion therapy.
Semantic structure from motion

Conventional rigid structure from motion (SFM) addresses the problem of recovering the camera parameters (motion) and the 3D locations (structure) of scene points, given observed 2D image feature points. In this paper, we propose a new formulation called Semantic Structure From Motion (SSFM). In addition to the geometrical constraints provided by SFM, SSFM takes advantage of both semantic and geometrical properties associated with objects in the scene (Fig. 1). These properties allow us to recover not only the structure and motion but also the 3D locations, poses, and categories of objects in the scene. We cast this problem as a max-likelihood problem where geometry (cameras, points, objects) and semantic information (object classes) are simultaneously estimated. The key intuition is that, in addition to image features, the measurements of objects across views provide additional geometrical constraints that relate cameras and scene parameters. These constraints make the geometry estimation process more robust and, in turn, make object detection more accurate. Our framework has the unique ability to: i) estimate camera poses only from object detections, ii) enhance camera pose estimation, compared to feature-point-based SFM algorithms, iii) improve object detections given multiple un-calibrated images, compared to independently detecting objects in single images. Extensive quantitative results on three datasets–LiDAR cars, street-view pedestrians, and Kinect office desktop–verify our theoretical claims.