Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting the effects of climate change on avian life-history traits

Across North America, tree swallows have advanced their mean date of clutch initiation (lay date) by ≈9 days over the past 30 years, apparently in response to climate change. In a sample of 2,881 nest records collected by the lay public from 1959 to 1991, we examined whether clutch size has also responded to climate change. We found that clutch size is strongly related to lay date, both within and among years, and there has been no significant temporal variation in the slopes or intercepts of the clutch-size/lay-date regressions. As a consequence, we expected increases in clutch size with advancement in lay date; however, we detected no such trend over time. The distributions of egg-laying dates were more constricted in the warmest (and earliest) years, suggesting that changes in mean clutch size might be constrained by changes in the distribution of laying dates. If spring temperatures continue to increase, we predict further reductions of variance in laying dates and relatively small increases in clutch size. Such constraints on life-history variation probably are common and need to be considered when modeling the effects of climate change on reproduction in natural populations. Predicting the long-term effects of constraints and interpreting changes in life-history traits require a better understanding of both adaptive and demographic effects of climate change.
An evaluation of EEG scanner's dependence on the imaging technique, forward model computation method, and array dimensionality

EEG source reconstruction involves solving an inverse problem that is highly ill-posed and dependent on a generally fixed forward propagation model. In this contribution we compare a low and high density EEG setup's dependence on correct forward modeling. Specifically, we examine how different forward models affect the source estimates obtained using four inverse solvers Minimum-Norm, LORETA, Minimum-Variance Adaptive Beamformer, and Sparse Bayesian Learning.
Changes in Glomerular Filtration Rate and Impact on Long-Term Survival among Adults after Hematopoietic Cell Transplantation: A Prospective Cohort Study.

BACKGROUND AND OBJECTIVES Kidney injury is a significant complication for patients undergoing hematopoietic cell transplantation (HCT), but few studies have prospectively examined changes in GFR in long-term survivors of HCT. We described the association between changes in GFR and all-cause mortality in patients up to 10 years after HCT. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS We conducted a prospective, observational cohort study of adult patients undergoing HCT at the Fred Hutchinson Cancer Center in Seattle, Washington from 2003 to 2015. Patients were followed from baseline, before conditioning therapy, until a maximum of 10 years after transplant. We used Cox proportional hazard models to examine the association between creatinine eGFR and all-cause mortality. We used time-dependent generalized estimating equations to examine risk factors for decreases in eGFR. RESULTS A total of 434 patients (median age, 52 years; range, 18-76 years; 64% were men; 87% were white) were followed for a median 5.3 years after HCT. The largest decreases in eGFR occurred within the first year post-transplant, with the eGFR decreasing from a median of 98 ml/min per 1.73 m2 at baseline to 78 ml/min per 1.73 m2 by 1 year post-HCT. Two thirds of patients had an eGFR<90 ml/min per 1.73 m2 at 1 year after transplant. When modeled as a continuous variable, as eGFR declined from approximately 60 ml/min per 1.73 m2, the hazard of mortality progressively increased relative to a normal eGFR of 90 ml/min per 1.73 m2 (P<0.001). For example, when compared with an eGFR of 90 ml/min per 1.73 m2, the hazard ratios for eGFR of 60, 50, and 40 ml/min per 1.73 m2 are 1.15 (95% confidence interval, 0.87 to 1.53), 1.68 (95% confidence interval, 1.26 to 2.24), and 2.67 (95% confidence interval, 1.99 to 3.60), respectively. Diabetes, hypertension, acute graft versus host disease, and cytomegalovirus infection were independently associated with a decline in GFR, whereas calcineurin inhibitor levels, chronic graft versus host disease, and albuminuria were not. CONCLUSIONS Adult HCT recipients have a high risk of decreased eGFR by 1 year after HCT. Although eGFR remains fairly stable thereafter, a decreased eGFR is significantly associated with higher risk of mortality, with a progressively increased risk as eGFR declines.
NeuroImage: Clinical

A B S T R A C T Alzheimer's disease (AD) is marked by cognitive dysfunction emerging from neuropathological processes impacting brain function. AD a ﬀ ects brain dynamics at the local level, such as changes in the balance of inhibitory and excitatory neuronal populations, as well as long-range changes to the global network. Individual di ﬀ erences in these changes as they relate to behaviour are poorly understood. Here, we use a multi-scale neurophysiological model, “ The Virtual Brain (TVB) ” , based on empirical multi-modal neuroimaging data, to study how local and global dynamics correlate with individual di ﬀ erences in cognition. In particular, we modeled individual resting-state functional activity of 124 individuals across the behavioural spectrum from healthy aging, to amnesic Mild Cognitive Impairment (MCI), to AD. The model parameters required to accurately simulate empirical functional brain imaging data correlated signi ﬁ cantly with cognition, and exceeded the predictive capacity of empirical connectomes.
A Bayesian Model for Cross-Study Differential Gene Expression

In this article we define a hierarchical Bayesian model for microarray expression data collected from several studies and use it to identify genes that show differential expression between two conditions. Key features include shrinkage across both genes and studies, and flexible modeling that allows for interactions between platforms and the estimated effect, as well as concordant and discordant differential expression across studies. We evaluate the performance of our model in a comprehensive fashion, using both artificial data, and a “split-study” validation approach that provides an agnostic assessment of the model’s behavior under both the null hypothesis and a realistic alternative. The simulation results from the artificial data demonstrate the advantages of the Bayesian model. Furthermore, the simulations provide guidelines for when the Bayesian model is most likely to be useful. Most notably, in small studies the Bayesian model generally outperforms other methods when evaluated based on several performance measures across a range of simulation parameters, with the differences diminishing for larger sample sizes in the individual studies. The split-study validation illustrates appropriate shrinkage of the Bayesian model in the absence of platform, sample, and annotation differences that otherwise complicate experimental data analyses. Finally, we fit our model to four breast cancer studies using different technologies (cDNA and Affymetrix) to estimate differential expression in estrogen receptor– positive tumors versus estrogen receptor–negative tumors. Software and data for reproducing our analysis are available publicly.
Lattice dynamics in GaN and AlN probed with first- and second-order Raman spectroscopy

We present a selection of our contributions to basic research on the lattice dynamical properties of groupIII nitrides and their alloys. We used first-order Raman scattering to determine the zone-center phonons and their dependence on structural attributes such as stress, chemical composition, impurities, and doping. Results on the angular dispersion of the polar modes, strain distribution, coupled LO-phonon plasmon modes, multi-mode behavior in AlxGa1–xN, and the quantitative determination of the phase purity of cubic and hexagonal GaN are shown. Second-order Raman-scattering experiments on GaN and AlN provide information on the vibrational states throughout the entire Brillouin zone. Based on a comparison of experimental data and calculated phonon-dispersion curves we assigned the observed structures to particular phonon branches and points in the Brillouin zone. We also discuss the behavior of the optical modes under large hydrostatic pressure.
EURASIAN JOURNAL OF ECONOMICS AND FINANCE

It is well known that level of banks‟ credit plays an important role in economic developments. Indian banking sector has played a seminal role in supporting economic growth in India. Recently, Indian banks are experiencing consistent increase in non-performing assets (NPA). In this perspective, this paper investigates the trends in NPA in Indian banks and its determinants. The panel regressions, fixed effect allows evaluating the impact of selected macroeconomic variables on the NPA. The Panel regression result indicates that the GDP growth, change in exchange rate and global volatility have major effects on the NPA level of Indian banking sector.
Microglial Cells Prevent Hemorrhage in Neonatal Focal Arterial Stroke

Perinatal stroke leads to significant morbidity and long-term neurological and cognitive deficits. The pathophysiological mechanisms of brain damage depend on brain maturation at the time of stroke. To understand whether microglial cells limit injury after neonatal stroke by preserving neurovascular integrity, we subjected postnatal day 7 (P7) rats depleted of microglial cells, rats with inhibited microglial TGFbr2/ALK5 signaling, and corresponding controls, to transient middle cerebral artery occlusion (tMCAO). Microglial depletion by intracerebral injection of liposome-encapsulated clodronate at P5 significantly reduced vessel coverage and triggered hemorrhages in injured regions 24 h after tMCAO. Lack of microglia did not alter expression or intracellular redistribution of several tight junction proteins, did not affect degradation of collagen IV induced by the tMCAO, but altered cell types producing TGFβ1 and the phosphorylation and intracellular distribution of SMAD2/3. Selective inhibition of TGFbr2/ALK5 signaling in microglia via intracerebral liposome-encapsulated SB-431542 delivery triggered hemorrhages after tMCAO, demonstrating that TGFβ1/TGFbr2/ALK5 signaling in microglia protects from hemorrhages. Consistent with observations in neonatal rats, depletion of microglia before tMCAO in P9 Cx3cr1GFP/+/Ccr2RFP/+ mice exacerbated injury and induced hemorrhages at 24 h. The effects were independent of infiltration of Ccr2RFP/+ monocytes into injured regions. Cumulatively, in two species, we show that microglial cells protect neonatal brain from hemorrhage after acute ischemic stroke. SIGNIFICANCE STATEMENT The pathophysiological mechanisms of brain damage depend on brain maturation at the time of stroke. We assessed whether microglial cells preserve neurovascular integrity after neonatal stroke. In neonatal rats, microglial depletion or pharmacological inhibition of TGFbr2/ALK5 signaling in microglia triggered hemorrhages in injured regions. The effect was not associated with additional changes in expression or intracellular redistribution of several tight junction proteins or collagen IV degradation induced by stroke. Consistent with observations in neonatal rats, microglial depletion in neonatal mice exacerbated stroke injury and induced hemorrhages. The effects were independent of infiltration of monocytes into injured regions. Thus, microglia protect neonatal brain from ischemia-induced hemorrhages, and this effect is consistent across two species.
Amount and pattern of physical activity and sedentary behavior are associated with kidney function and kidney damage: The Maastricht Study

Background Chronic kidney disease, which is defined as having a reduced kidney function (estimated glomerular filtration rate (eGFR)) and/or signs of kidney damage (albuminuria), is highly prevalent in Western society and is associated with adverse health outcomes, such as cardiovascular disease. This warrants a search for risk factors of lower eGFR and higher albuminuria. Physical activity and sedentary behavior may be such risk factors. Objective To examine associations of physical activity (total, high, low), sedentary time and sedentary behavior patterns (breaks, prolonged bouts, average bout duration) with eGFR and albuminuria. Methods We examined these associations in 2,258 participants of the Maastricht Study (average age 60.1±8.1 years; 51.3% men), who wore an accelerometer 24h/day on 7 consecutive days. Associations with continuous eGFR and categories of urinary albumin excretion (UAE; <15 [reference category], 15-<30, ≥30 mg/24h) were evaluated with linear regression analyses and multinomial logistic regression analyses, respectively. Results After adjustment for potential confounders, each extra hour of total physical activity was associated with a more favorable kidney function (betaeGFR = 2.30 (95%CI = 1.46; 3.14)), whereas each extra hour of sedentary behavior was associated with a more adverse kidney function (betaeGFR = -0.71 (-1.08; -0.35)). Also, compared to individuals with the lowest levels of total physical activity, individuals with the highest levels had less kidney damage (OR15-<30mg/24h = 0.63 (0.41; 0.96), OR≥30mg/24h = 0.84 (0.53; 1.35). An extra hour of sedentary behavior was associated with more kidney damage (OR15-<30 mg/24h = 1.11 (1.01; 1.22), OR≥30 mg/24h = 1.10 (0.99; 1.22)). Further, a highly sedentary pattern was associated with a more adverse kidney function, but no association was seen with kidney damage. Conclusions Physical activity and sedentary behavior were associated with kidney function and kidney damage. Additionally, sedentary behavior patterns were associated with kidney function. Causal studies are required to examine whether this indeed implicates that prevention strategies should focus not only on increasing physical activity, but on reducing sedentary behavior as well.
Usability of a Patient Education and Motivation Tool Using Heuristic Evaluation

Background Computer-mediated educational applications can provide a self-paced, interactive environment to deliver educational content to individuals about their health condition. These programs have been used to deliver health-related information about a variety of topics, including breast cancer screening, asthma management, and injury prevention. We have designed the Patient Education and Motivation Tool (PEMT), an interactive computer-based educational program based on behavioral, cognitive, and humanistic learning theories. The tool is designed to educate users and has three key components: screening, learning, and evaluation. Objective The objective of this tutorial is to illustrate a heuristic evaluation using a computer-based patient education program (PEMT) as a case study. The aims were to improve the usability of PEMT through heuristic evaluation of the interface; to report the results of these usability evaluations; to make changes based on the findings of the usability experts; and to describe the benefits and limitations of applying usability evaluations to PEMT. Methods PEMT was evaluated by three usability experts using Nielsen’s usability heuristics while reviewing the interface to produce a list of heuristic violations with severity ratings. The violations were sorted by heuristic and ordered from most to least severe within each heuristic. Results A total of 127 violations were identified with a median severity of 3 (range 0 to 4 with 0 = no problem to 4 = catastrophic problem). Results showed 13 violations for visibility (median severity = 2), 38 violations for match between system and real world (median severity = 2), 6 violations for user control and freedom (median severity = 3), 34 violations for consistency and standards (median severity = 2), 11 violations for error severity (median severity = 3), 1 violation for recognition and control (median severity = 3), 7 violations for flexibility and efficiency (median severity = 2), 9 violations for aesthetic and minimalist design (median severity = 2), 4 violations for help users recognize, diagnose, and recover from errors (median severity = 3), and 4 violations for help and documentation (median severity = 4). Conclusion We describe the heuristic evaluation method employed to assess the usability of PEMT, a method which uncovers heuristic violations in the interface design in a quick and efficient manner. Bringing together usability experts and health professionals to evaluate a computer-mediated patient education program can help to identify problems in a timely manner. This makes this method particularly well suited to the iterative design process when developing other computer-mediated health education programs. Heuristic evaluations provided a means to assess the user interface of PEMT.
Genetic variation in Trillium erectum (Melanthiaceae), a widespread forest herb in eastern North America

Trillium erectum L. is an insect-pollinated understory herb widespread in forests of eastern North America. Marker gene studies indicate that the species has a mixed mating system, but aspects of population genetic structure have not been investigated. Using 10 allozyme loci, we measured genetic variation within and among 23 populations sampled from throughout the species' range. Overall, T. erectum displayed moderate levels of genetic diversity in comparison with other herbaceous plants. The percentage of loci that were polymorphic was 52%, with average values (±SE) of 1.20 ± 0.02, 0.08 ± 0.01, and 0.13 ± 0.01 for the number of alleles per locus (A), observed heterozygosity (Ho), and expected heterozygosity (He), respectively. There was evidence of inbreeding within populations (Fis = 0.39, 95% CI 0.260.55) and significant population differentiation (Fst = 0.16, 0.050.24). Analysis of genetic data provided no evidence of isolation by distance, and together with the occurrence of population subdivision,.
Finite element study of effective width in steel-concrete composite beams under long-term service loads

In this work, a finite element-based approach is presented to study the effective width variation in non-pre-stressed steel-concrete beams under the serviceability stage, including time dependent effects such as concrete creep, shrinkage and cracking. For this purpose, the viscoelasticity theory in conjunction with a nonlinear cracking monitoring algorithm is used to trace the nonlinear viscoelastic response of the structure along time. The present numerical model is fully three-dimensional and permits the inclusion of partial interaction at the slab-beam interface. A comprehensive study is carried out on the long-term response of a composite girder bridge previously studied by other researches. Then, previous results are revised and extended herein. Potential shortcomings of some standard codes related to the effective width evaluation are also investigated. It is demonstrated that the slab effective width varies sharply along the beam axis in the short-term, while it approaches to the actual slab width in the long-term. For the studied example, the common assumption of using only the middle layer of the reinforced concrete (RC) slab for the effective width calculation is revised with a through-thickness integration procedure. The influence of some creep and shrinkage models as well as the ultimate tensile concrete strain on the effective width response is also assessed. Finally, a simple formula is proposed to evaluate the short-term slab effective width for the studied example.
Cell culture-derived flu vaccine: Present and future

ABSTRACT The benefit of influenza vaccines is difficult to estimate due to the complexity of accurately assessing the burden of influenza. To improve the efficacy of influenza vaccines, vaccine manufacturers have developed quadrivalent influenza vaccine (QIV) formulations for seasonal vaccination by including both influenza B lineages. Three parallel approaches for producing influenza vaccines are attracting the interest of many vaccine manufacturing companies. The first and oldest is the conventional egg-derived influenza vaccine, which is used by the current licensed influenza vaccines. The second approach is a cell culture-derived influenza vaccine, and the third and most recent is synthetic vaccines. Here, we analyze the difficulties with vaccines production in eggs and compare this to cell culture-derived influenza vaccines and discuss the future of cell culture-derived QIVs.Keywords: Influenza vaccine, cell culture-derived, quadrivalent.
Nonlinear system modeling based on constrained Volterra series estimates

A simple non-linear system modelling algorithm designed to work with limited a priori knowledge and short data records, is examined. It creates an empirical Volterra series-based model of a system using an l q -constrained least squares algorithm with q ≥ 1 . If the system m ⋅ is a continuous and bounded map with a finite memory no longer than some known τ , then (for a D parameter model and for a number of measurements N) the difference between the resulting model of the system and the best possible theoretical one is guaranteed to be of order N − 1 ln ⁡ D , even for D ≥ N . The performance of models obtained for q = 1 , 1.5 and 2 is tested on the Wiener–Hammerstein benchmark system. The results suggest that the models obtained for q > 1 are better suited to characterise the nature of the system, while the sparse solutions obtained for q = 1 yield smaller error values in terms of input-output behaviour.
Title Survival following laparoscopic versus open resection forcolorectal cancer

Background This study aimed to compare the overall and disease specific survivals of patients who underwent laparoscopic and open resection of colorectal cancer in a high volume tertiary center. Methods Consecutive patients who underwent elective resection for colorectal cancer (open resection, n01,197; laparoscopic resection, n0814) from January 2000 to December 2009were included. The operative details, postoperative complications, postoperative outcomes, and survival data were collected prospectively. Comparison was made between patients who had laparoscopic and open surgery. Results The age, gender, medical morbidity, and American Society of Anesthesiologists status were similar in the two groups. Laparoscopic resection was associated with significantly less blood loss and a shorter hospital stay. The operating mortality and morbidity were significantly lower in the laparoscopic group. The qualities of the specimens in terms of the distal resection margin and the number of lymph nodes examined were not inferior in the laparoscopic group. With the median follow-up of 40.3 months, the 5-year overall survival (74.1% vs. 65.5%, p<0.001) and disease specific survival (81.9% vs. 75.2%, p00.002) were significantly better in patients with non-disseminated disease in the laparoscopic group. The operative approach was an independent prognostic factor in the overall (risk ratio 1.36, 95% CI 1.093–1.700, p0 0.006) and disease specific (risk ratio 1.32, 95% CI 1.005– 1.738, p00.048) survivals in multivariate analysis. Conclusion Laparoscopic resection for colorectal cancer is associated with more favorable overall and disease specific survivals when compared with open resection in a high volume tertiary center.