Miracle-dz/UniFAR-FTUs huggingface dataset:
Precision cosmology in muddy waters: Cosmological constraints and N-body codes

Future large-scale structure surveys of the Universe will aim to constrain the cosmological model and the true nature of dark energy with unprecedented accuracy. In order for these surveys to achieve their designed goals, they will require predictions for the non-linear matter power spectrum to sub-percent accuracy. Through the use of a large ensemble of cosmological N-body simulations, we demonstrate that if we do not understand the uncertainties associated with simulating structure formation, i.e. knowledge of the `optimal' simulation parameters, and simply seek to marginalize over them, then the constraining power of such future surveys can be significantly reduced. However, for the parameters {ns, h, Ωb, Ωm}, this effect can be largely mitigated by adding the information from a cosmic microwave background experiment, like Planck. In contrast, for the amplitude of fluctuations σ8 and the time-evolving equation of state of dark energy {w0, wa}, the mitigation is mild. On marginalizing over the simulation parameters, we find that the dark-energy figure of merit can be degraded by ˜2. This is likely an optimistic assessment, since we do not take into account other important simulation parameters. A caveat is our assumption that the Hessian of the likelihood function does not vary significantly when moving from our adopted to the optimal simulation parameter set. This paper therefore provides strong motivation for rigorous convergence testing of N-body codes to meet the future challenges of precision cosmology.
Investigation of the Summer Climate of the Contiguous United States and Mexico Using the Regional Atmospheric Modeling System ( RAMS ) . Part II : Model Climate Variability

Summer simulations over the contiguous United States and Mexico with the Regional Atmospheric Modeling System (RAMS) dynamically downscaling the NCEP–NCAR Reanalysis I for the period 1950– 2002 (described in Part I of the study) are evaluated with respect to the three dominant modes of global SST. Two of these modes are associated with the statistically significant, naturally occurring interannual and interdecadal variability in the Pacific. The remaining mode corresponds to the recent warming of tropical sea surface temperatures. Time-evolving teleconnections associated with Pacific SSTs delay or accelerate the evolution of the North American monsoon. At the period of maximum teleconnectivity in late June and early July, there is an opposite relationship between precipitation in the core monsoon region and the central United States. Use of a regional climate model (RCM) is essential to capture this variability because of its representation of the diurnal cycle of convective rainfall. The RCM also captures the observed long-term changes in Mexican summer rainfall and suggests that these changes are due in part to the recent increase in eastern Pacific SST off the Mexican coast. To establish the physical linkage to remote SST forcing, additional RAMS seasonal weather prediction mode simulations were performed and these results are briefly discussed. In order for RCMs to be successful in a seasonal weather prediction mode for the summer season, it is required that the GCM provide a reasonable representation of the teleconnections and have a climatology that is comparable to a global atmospheric reanalysis.
Joint-sparse dictionary learning: Denoising multiple measurement vectors

This work addresses the problem of denoising multiple measurement vectors having a common sparse support. Such problems arise in a variety of imaging problems, e.g. color imaging, multi-spectral and hyper-spectral imaging, multi-echo and multi-channel magnetic resonance imaging, etc. For such cases, denoising them piecemeal, one channel at a time, is not optimal; since it does not exploit the full structure (joint sparsity) of the problem. Joint-sparsity based methods have been used for solving such problems when the sparsifying transform is assumed to be fixed. In this work, we learn the sparsifying basis following the dictionary learning paradigm. Results on multi-spectral denoising and multi-echo MRI denoising demonstrates the superiority of our method over existing ones based on KSVD and BM4D.
Blinded Contractility Analysis in hiPSC-Cardiomyocytes in Engineered Heart Tissue Format: Comparison With Human Atrial Trabeculae

Abstract Human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) may serve as a new assay for drug testing in a human context, but their validity particularly for the evaluation of inotropic drug effects remains unclear. In this blinded analysis, we compared the effects of 10 indicator compounds with known inotropic effects in electrically stimulated (1.5 Hz) hiPSC-CM-derived 3-dimensional engineered heart tissue (EHT) and human atrial trabeculae (hAT). Human EHTs were prepared from iCell hiPSC-CM, hAT obtained at routine heart surgery. Mean intra-batch variation coefficient in baseline force measurement was 17% for EHT and 49% for hAT. The PDE-inhibitor milrinone did not affect EHT contraction force, but increased force in hAT. Citalopram (selective serotonin reuptake inhibitor), nifedipine (LTCC-blocker) and lidocaine (Na+ channel-blocker) had negative inotropic effects on EHT and hAT. Formoterol (beta-2 agonist) had positive lusitropic but no inotropic effect in EHT, and positive clinotropic, lusitropic, and inotropic effects in hAT. Tacrolimus (calcineurin-inhibitor) had a negative inotropic effect in EHTs, but no effect in hAT. Digoxin (Na+-K+-ATPase-inhibitor) showed a positive inotropic effect only in EHTs, but no effect in hAT probably due to short incubation time. Ryanodine (ryanodine receptor-inhibitor) reduced contraction force in both models. Rolipram and acetylsalicylic acid showed noninterpretable results in hAT. Contraction amplitude and kinetics were more stable over time and less variable in hiPSC-EHTs than hAT. HiPSC-EHT faithfully detected cAMP-dependent and -independent positive and negative inotropic effects, but limited beta-2 adrenergic or PDE3 effects, compatible with an immature CM phenotype.
Cortical activation patterns to spatially presented pure tone stimuli with different intensities measured by functional near‐infrared spectroscopy

Functional near‐infrared spectroscopy (fNIRS) is an emerging technique for the assessment of functional activity of the cerebral cortex. Recently fNIRS was also envisaged as a novel neuroimaging approach for measuring the auditory cortex activity in the field of in auditory diagnostics. This study aimed to investigate differences in brain activity related to spatially presented sounds with different intensities in 10 subjects by means of functional near‐infrared spectroscopy (fNIRS). We found pronounced cortical activation patterns in the temporal and frontal regions of both hemispheres. In contrast to these activation patterns, we found deactivation patterns in central and parietal regions of both hemispheres. Furthermore our results showed an influence of spatial presentation and intensity of the presented sounds on brain activity in related regions of interest. These findings are in line with previous fMRI studies which also reported systematic changes of activation in temporal and frontal areas with increasing sound intensity. Although clear evidence for contralaterality effects and hemispheric asymmetries were absent in the group data, these effects were partially visible on the single subject level. Concluding, fNIRS is sensitive enough to capture differences in brain responses during the spatial presentation of sounds with different intensities in several cortical regions. Our results may serve as a valuable contribution for further basic research and the future use of fNIRS in the area of central auditory diagnostics.
Computed tomography-based quantitative assessment of lower extremity lymphedema following treatment for gynecologic cancer

Objective To develop an algorithmic quantitative skin and subcutaneous tissue volume measurement protocol for lower extremity lymphedema (LEL) patients using computed tomography (CT), to verify the usefulness of the measurement techniques in LEL patients, and to observe the structural characteristics of subcutaneous tissue according to the progression of LEL in gynecologic cancer. Methods A program for algorithmic quantitative analysis of lower extremity CT scans has been developed to measure the skin and subcutaneous volume, muscle compartment volume, and the extent of the peculiar trabecular area with a honeycombed pattern. The CT venographies of 50 lower extremities from 25 subjects were reviewed in two groups (acute and chronic lymphedema). Results A significant increase in the total volume, subcutaneous volume, and extent of peculiar trabecular area with a honeycombed pattern except quantitative muscle volume was identified in the more-affected limb. The correlation of CT-based total volume and subcutaneous volume measurements with volumetry measurement was strong (correlation coefficient: 0.747 and 0.749, respectively). The larger extent of peculiar trabecular area with a honeycombed pattern in the subcutaneous tissue was identified in the more-affected limb of chronic lymphedema group. Conclusion CT-based quantitative assessments could provide objective volume measurements and information about the structural characteristics of subcutaneous tissue in women with LEL following treatment for gynecologic cancer.
Bicycle injuries and helmet use: a systematic review and meta-analysis.

Background The research literature was systematically reviewed and results were summarized from studies assessing bicycle helmet effectiveness to mitigate head, serious head, face, neck and fatal head injury in a crash or fall. Methods Four electronic databases (MEDLINE, EMBASE, COMPENDEX and SCOPUS) were searched for relevant, peer-reviewed articles in English. Included studies reported medically diagnosed head, face and neck injuries where helmet use was known. Non-approved helmets were excluded where possible. Summary odds ratios (OR) were obtained using multivariate meta-regression models stratified by injury type and severity. Time trends and publication bias were assessed. Results A total of 43 studies met inclusion criteria and 40 studies were included in the meta-analysis with data from over 64 000 injured cyclists. For cyclists involved in a crash or fall, helmet use was associated with odds reductions for head (OR = 0.49, 95% confidence interval (CI): 0.42-0.57), serious head (OR = 0.31, 95% CI: 0.25-0.37), face (OR = 0.67, 95% CI: 0.56-0.81) and fatal head injury (OR = 0.35, 95% CI: 0.14-0.88). No clear evidence of an association between helmet use and neck injury was found (OR = 0.96, 95% CI: 0.74-1.25). There was no evidence of time trends or publication bias. Conclusions Bicycle helmet use was associated with reduced odds of head injury, serious head injury, facial injury and fatal head injury. The reduction was greater for serious or fatal head injury. Neck injury was rare and not associated with helmet use. These results support the use of strategies to increase the uptake of bicycle helmets as part of a comprehensive cycling safety plan.
Mobile Functional Reach Test in People Who Suffer Stroke: A Pilot Study

Background Postural instability is one of the major complications found in people who survive a stroke. Parameterizing the Functional Reach Test (FRT) could be useful in clinical practice and basic research, as this test is a clinically accepted tool (for its simplicity, reliability, economy, and portability) to measure the semistatic balance of a subject. Objective The aim of this study is to analyze the reliability in the FRT parameterization using inertial sensor within mobile phones (mobile sensors) for recording kinematic variables in patients who have suffered a stroke. Our hypothesis is that the sensors in mobile phones will be reliable instruments for kinematic study of the FRT. Methods This is a cross-sectional study of 7 subjects over 65 years of age who suffered a stroke. During the execution of FRT, the subjects carried two mobile phones: one placed in the lumbar region and the other one on the trunk. After analyzing the data obtained in the kinematic registration by the mobile sensors, a number of direct and indirect variables were obtained. The variables extracted directly from FRT through the mobile sensors were distance, maximum angular lumbosacral/thoracic displacement, time for maximum angular lumbosacral/thoracic displacement, time of return to the initial position, and total time. Using these data, we calculated speed and acceleration of each. A descriptive analysis of all kinematic outcomes recorded by the two mobile sensors (trunk and lumbar) was developed and the average range achieved in the FRT. Reliability measures were calculated by analyzing the internal consistency of the measures with 95% confidence interval of each outcome variable. We calculated the reliability of mobile sensors in the measurement of the kinematic variables during the execution of the FRT. Results The values in the FRT obtained in this study (2.49 cm, SD 13.15) are similar to those found in other studies with this population and with the same age range. Intrasubject reliability values observed in the use of mobile phones are all located above 0.831, ranging from 0.831 (time B_C trunk area) and 0.894 (displacement A_B trunk area). Likewise, the observed intersubject values range from 0.835 (time B_C trunk area) and 0.882 (displacement A_C trunk area). On the other hand, the reliability of the FRT was 0.989 (0.981-0.996) and 0.978 (0.970-0.985), intrasubject and intersubject respectively. Conclusions We found that mobile sensors in mobile phones could be reliable tools in the parameterization of the Functional Reach Test in people who have had a stroke.
A Buck and Boost Based Grid Connected PV Inverter Maximizing Power Yield From Two PV Arrays in Mismatched Environmental Conditions

A single phase grid connected transformerless photovoltaic (PV) inverter, which can operate either in buck or in boost mode, and can extract maximum power simultaneously from two serially connected subarrays while each of the subarray is facing different environmental conditions, is presented in this paper. As the inverter can operate in buck as well as in boost mode, depending on the requirement, the constraint on the minimum number of serially connected solar PV modules that is required to form a subarray is greatly reduced. As a result, power yield from each of the subarray increases when they are exposed to different environmental conditions. The topological configuration of the inverter and its control strategy are designed so that the high-frequency components are not present in the common mode voltage, thereby restricting the magnitude of the leakage current associated with the PV arrays within the specified limit. Further, high operating efficiency is achieved throughout its operating range. A detailed analysis of the system leading to the development of its mathematical model is carried out. The viability of the scheme is confirmed by performing detailed simulation studies. A 1.5 kW laboratory prototype is developed, and detailed experimental studies are carried out to corroborate the validity of the scheme.
Outcome of Critically ill Patients Undergoing Mandatory Insulin Therapy Compared to Usual Care Insulin Therapy: Protocol for a Pilot Randomized Controlled Trial

Background Observational and interventional studies in patients with both acute medical conditions and long-standing diabetes have shown that improved blood glucose control confers a survival advantage or reduces complication rates. Policies of “tight” glycaemic control were rapidly adopted by many general intensive care units (ICUs) worldwide in the mid 00’s, even though the results of the studies were not generalizable to mixed medical/surgical ICUs with different intravenous feeding policies. Objective The primary objective of the study is to assess the safety of mandatory insulin infusion in critically ill patients in a general ICU setting. Methods This protocol summarizes the rationale and design of a randomized, controlled, single-center trial investigating the effect of mandatory insulin therapy versus usual care insulin therapy for those patients admitted for a stay of longer than 48 hours. In total, 109 critically ill adults predicted to stay in intensive care for longer than 48 hours consented. The primary outcome is to determine the safety of mandatory insulin therapy in critically ill patients using the number of episodes of hypoglycaemia and hypokalaemia per unit length of stay in intensive care. Secondary outcomes include the duration of mechanical ventilation, duration of ICU and hospital stay, hospital mortality, and measures of renal, hepatic, and haematological dysfunction. Results The project was funded in 2005 and enrolment was completed 2007. Data analysis is currently underway and the first results are expected to be submitted for publication in 2018. Conclusions This protocol for a randomized controlled trial investigating the effect of mandatory insulin therapy should provide an answer to a key question for the management of patients in the ICU and ultimately improving outcome. Trial Registration International Standard Randomized Controlled Trial Number ISRCTN00550641; http://www.isrctn. com/ISRCTN00550641 (Archived at WebCite: http://www.webcitation.org/6xk8NXxNv).
Evaluating the performance of tools used to call minority variants from whole genome short-read data

Background: High-throughput whole genome sequencing facilitates investigation of minority virus sub-populations from virus positive samples. Minority variants are useful in understanding within and between host diversity, population dynamics and can potentially assist in elucidating person-person transmission pathways. Several minority variant callers have been developed to describe low frequency sub-populations from whole genome sequence data. These callers differ based on bioinformatics and statistical methods used to discriminate sequencing errors from low-frequency variants. Methods: We evaluated the diagnostic performance and concordance between published minority variant callers used in identifying minority variants from whole-genome sequence data from virus samples. We used the ART-Illumina read simulation tool to generate three artificial short-read datasets of varying coverage and error profiles from an RSV reference genome. The datasets were spiked with nucleotide variants at predetermined positions and frequencies. Variants were called using FreeBayes, LoFreq, Vardict, and VarScan2. The variant callers’ agreement in identifying known variants was quantified using two measures; concordance accuracy and the inter-caller concordance. Results: The variant callers reported differences in identifying minority variants from the datasets. Concordance accuracy and inter-caller concordance were positively correlated with sample coverage. FreeBayes identified the majority of variants although it was characterised by variable sensitivity and precision in addition to a high false positive rate relative to the other minority variant callers and which varied with sample coverage. LoFreq was the most conservative caller. Conclusions: We conducted a performance and concordance evaluation of four minority variant calling tools used to identify and quantify low frequency variants. Inconsistency in the quality of sequenced samples impacts on sensitivity and accuracy of minority variant callers. Our study suggests that combining at least three tools when identifying minority variants is useful in filtering errors when calling low frequency variants.
Strength and Density of Geopolymer Mortar Cured at Ambient Temperature for Use as Repair Material

Geopolymers produced by synthesizing aluminosilicate source materials with an alkaline activator solution promised an excellent properties akin to the existing construction material. This study focused on the effect of various binder to sand ratio on geopolymer mortar properties. Mix design of geopolymer mortar was produced using NaOH concentration of 12 molars, ratio of fly ash/alkaline activator and ratio Na2SiO3/NaOH of 2.0 and 2.5 respectively. Samples subsequently ware cured at ambient temperature. The properties of geopolymer mortar were analysed in term of compressive strength and density at different period which are on the 3rd and 7th day of curing. Experimental results revealed that the addition of sand slightly increase the compressive strength of geopolymer. The optimum compressive strength obtained was up to 31.39 MPa on the 7th day. The density of geopolymer mortar was in the range between 2.0 g/cm3 to 2.23 g/cm3. Based on this findings, the special properties promoted by geopolymer mortar display high potential to be implemented in the field of concrete patch repair.
A Combination of Fecal Immunochemical Test Results and Iron Deficiency Anemia for Detection of Advanced Colorectal Neoplasia in Asymptomatic Men

Purpose A substantial proportion of patients with colorectal cancer (CRC) present with iron deficiency anemia (IDA), and fecal immunochemical test (FIT) has proven to be an effective method for detecting the majority of CRC cases. A combination strategy of FIT results and IDA may be useful for risk stratification for detecting advanced colorectal neoplasia (ACRN). We compared the prevalence of ACRN among four groups stratified by FIT results and the presence of IDA. Materials and Methods A cross-sectional study was performed on asymptomatic male participants who underwent both FIT and colonoscopy between 2010 and 2014 as part of a comprehensive health screening program in Korea. Results Of 17236 participants, 522 (3.0%) showed positive FIT results and 26 (0.2%) had IDA. The mean age of the study participants was 40.8 years. The participants were classified into four groups: positive FIT result/IDA (G1, n=7), positive FIT result/no IDA (G2, n=515), negative FIT result/IDA (G3, n=19), and negative FIT result/no IDA (G4, n=16695). The prevalences of ACRN in G1, G2, G3, and G4 were 28.6, 13.4, 5.3, and 1.5%, respectively (p<0.001) and those of CRC were 28.6, 1.6, 0.0, and 0.01%, respectively (p<0.001). Subjects with positive FIT results and IDA had an increased risk of ACRN and CRC in both group aged <50 and ≥50 years. Conclusion Subjects with positive FIT results and IDA had an increased risk of ACRN. Our results suggest that a combination strategy of FIT and IDA may be helpful in selecting and prioritizing asymptomatic men for colonoscopy.
The heat shock response plays an important role in TDP-43 clearance: evidence for dysfunction in amyotrophic lateral sclerosis

Insoluble TDP-43 inclusions are the pathological hallmark of ALS and tau-negative frontotemporal lobar degeneration. Chen et al. show that the heat shock response (HSR), which regulates chaperone expression, is compromised in an ALS mouse model and in patients. Activation of the HSR clears insoluble TDP-43 and increases cell survival.