Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling an Innovation Ecosystem with Adaptive Agents

Agent-based modeling has proven effective in increasing the understanding of complex systems, including social-economical systems. A goal of modeling complex systems is to distill the system into simple agents with phenotypes guided by simple rules. The model then displays the emergent behavior of these agents interacting with each other and their environment. An agent-based model of innovation and its place in a global economy or ecosystem is presented. The model utilizes simple agents to represent innovating entities such as large corporations and small companies. The results produced by this model reveal the dynamics of innovation and its role in a global economy. The results indicate a large need for partnership in innovation for those entities working within rapidly changing domains. Domains, such as high technology, have constantly changing market expectations, which force innovating entities to seek external sources of assistance to meet these expectations in a timely enough fashion so as to incur benefit.
Abnormal Working Hours: Effect of Rapid Releases and Implications to Work Content

During the past years, overload at work leading to psychological diseases, such as burnouts, have drawn more public attention. This paper is a preliminary step toward an analysis of the work patterns and possible indicators of overload and time pressure on software developers with mining software repositories approach. We explore the working pattern of developers in the context of Mozilla Firefox, a large and long-lived open source project. To that end we investigate the impact of the move from traditional to rapid release cycle on work pattern. Moreover we compare Mozilla Firefox work pattern with another Mozilla product, Firefox OS, which has a different release cycle than Firefox. We find that both projects exhibit healthy working patterns, i.e. lower activity during the weekends and outside of office hours. Firefox experiences proportionally more activity on weekends than Firefox OS (Cohen's d = 0.94). We find that switching to rapid releases has reduced weekend work (Cohen's d = 1.43) and working during the night (Cohen's d = 0.45). This result holds even when we limit the analyzes on the hired resources, i.e. considering only individuals with Mozilla foundation email address, although, the effect sizes are smaller for weekends (Cohen's d = 0.64) and nights (Cohen's d = 0.23). Moreover, we use dissimilarity word clouds and find that work during the weekend is more technical while work during the week expresses more positive sentiment with words like "good" and "nice". Our results suggest that moving to rapid releases have positive impact on the work health and work-life-balance of software engineers. However, caution is needed as our results are based on a limited set of quantitative data from a single organization.
A Diagnostic Accuracy Study of Xpert®MTB/RIF in HIV-Positive Patients with High Clinical Suspicion of Pulmonary Tuberculosis in Lima, Peru

Background Diagnosis of pulmonary tuberculosis (TB) among human immunodeficiency virus (HIV) patients remains complex and demands easy to perform and accurate tests. Xpert®MTB/RIF (MTB/RIF) is a molecular TB diagnostic test which is rapid and convenient; the test requires minimal human resources and reports results within two hours. The majority of performance studies of MTB/RIF have been performed in high HIV burden settings, thus TB diagnostic studies among HIV patients in low HIV prevalence settings such as Peru are still needed. Methodology/Principal Findings From April 2010 to May 2011, HIV-positive patients with high clinical suspicion of TB were enrolled from two tertiary hospitals in Lima, Peru. Detection of TB by MTB/RIF was compared to a composite reference standard Löwenstein-Jensen (LJ) and liquid culture. Detection of rifampicin resistance was compared to the LJ proportion method. We included 131 patients, the median CD4 cell count was 154.5 cells/mm3 and 45 (34.4%) had TB. For TB detection among HIV patients, sensitivity of MTB/RIF was 97.8% (95% CI 88.4–99.6) (44/45); specificity was 97.7% (95% CI 91.9–99.4) (84/86); the positive predictive value was 95.7% (95% CI 85.5–98.8) (44/46); and the negative predictive value, 98.8% (95% CI 93.6–99.8) (84/85). MTB/RIF detected 13/14 smear-negative TB cases, outperforming smear microscopy [97.8% (44/45) vs. 68.9% (31/45); p = 0.0002]. For rifampicin resistance detection, sensitivity of MTB/RIF was 100% (95% CI 61.0–100.0) (6/6); specificity was 91.0% (95% CI 76.4–96.9) (30/33); the positive predictive value was 66.7% (95% CI 35.4–87.9) (6/9); and the negative predictive value was 100% (95% CI 88.7 –100.0) (30/30). Conclusions/Significance In HIV patients in our population with a high clinical suspicion of TB, MTB/RIF performed well for TB diagnosis and outperformed smear microscopy.
The induction and reversibility of cerebral acidosis in thiamine deficiency

Regional cerebral pH was determined autoradiographically using carbon 14‐labeled dimethyloxazolidinedione in normal rats, following various durations of thiamine deficiency and replenishment with thiamine when the clinical sequelae of the deficiency appeared. In our model the clinical sequelae of thiamine deficiency (opisthotonus) appeared on the average on day 18. Regional cerebral pH on day 12 was comparable to that in controls and ranged between 7.02 ± 0.03 and 7.09 ± 0.03 (mean ± SEM) in gray matter structures. On day 14 the pH in the inferior colliculus was 6.85 ± 0.08 and relative acidosis also appeared in thalamic structures. At opisthotonus the pH was 6.48 ± 0.17 in the mamillary body, 6.43 ± 0.14 in the vestibular nucleus, and 6.36 ± 0.14 in the medial dorsal nucleus of the thalamus (p < 0.01). One dose of thiamine replenishment at this stage transiently raised the pH in the inferior colliculus to 7.25 ± 0.19 and in the medial dorsal nucleus to 7.20 ± 0.13 (p < 0.01). Cerebral regions showing significant acidosis during thiamine deficiency coincided largely with those known to be histologically vulnerable and those previously reported to show a focal rise in local cerebral glucose utilization between days 11 and 14 of thiamine deficiency. This focal acidosis shown to occur in thiamine deficiency may be one mechanism contributing to the selective histological vulnerability in this model.
Insights into the bacterial community and its temporal succession during the fermentation of wine grapes

Grapes harbor complex microbial communities. It is well known that yeasts, typically Saccharomyces cerevisiae, and bacteria, commonly the lactic acid fermenting Oenococcus oeni, work sequentially during primary and secondary wine fermentation. In addition to these main players, several microbes, often with undesirable effects on wine quality, have been found in grapes and during wine fermentation. However, still little is known about the dynamics of the microbial community during the fermentation process. In previous studies culture dependent methods were applied to detect and identify microbial organisms associated with grapes and grape products, which resulted in a picture that neglected the non-culturable fraction of the microbes. To obtain a more complete picture of how microbial communities change during grape fermentation and how different fermentation techniques might affect the microbial community composition, we employed next-generation sequencing (NGS)—a culture-independent method. A better understanding of the microbial dynamics and their effect on the final product is of great importance to help winemakers produce wine styles of consistent and high quality. In this study, we focused on the bacterial community dynamics during wine vinification by amplifying and sequencing the hypervariable V1–V3 region of the 16S rRNA gene—a phylogenetic marker gene that is ubiquitous within prokaryotes. Bacterial communities and their temporal succession was observed for communities associated with organically and conventionally produced wines. In addition, we analyzed the chemical characteristics of the grape musts during the organic and conventional fermentation process. These analyses revealed distinct bacterial population with specific temporal changes as well as different chemical profiles for the organically and conventionally produced wines. In summary these results suggest a possible correlation between the temporal succession of the bacterial population and the chemical wine profiles.
Essential Oils as “A Cry for Help”. A Review

This work is an update of a recently published review and is consistently referred to this article and recent findings about plants’ indirect defense are added on. Herbivore induced plant volatiles (HIPVs) and their effects on the third trophic level that involves predators and parasitoids are discussed. The fact that plants are not passive individuals is confirmed on the basis of several studies. Plants can perceive and respond to cues in their environments with plastic morphological, physiological and behavioral traits. Plasticity allows plants to tailor their defenses to their current and expected risks caused by herbivores. The “cry for help” of plants is also observed from the carnivores’ point of view. The volatile mixture contains crucial information for decisions of carnivorous insects. Furthermore, the most important methods to examine the behavioral response of carnivorous insects to HIPVs are presented not only in laboratory set ups but also in the field. Manipulations of plants by silencing genes or over-expressing genes can help to understand mechanisms of indirect defense. Various interesting examples of indirect defense reveal the possibility to use HIPVs in biological control. Therefore, the application of synthetic pesticides, that pollute the environment, may be reduced in the future.
Mammary gland development: cell fate specification, stem cells and the microenvironment

The development of the mammary gland is unique: the final stages of development occur postnatally at puberty under the influence of hormonal cues. Furthermore, during the life of the female, the mammary gland can undergo many rounds of expansion and proliferation. The mammary gland thus provides an excellent model for studying the ‘stem/progenitor’ cells that allow this repeated expansion and renewal. In this Review, we provide an overview of the different cell types that constitute the mammary gland, and discuss how these cell types arise and differentiate. As cellular differentiation cannot occur without proper signals, we also describe how the tissue microenvironment influences mammary gland development. Summary: This Review discusses the various cell types that constitute the mammary gland, highlighting how they arise and differentiate, and how the microenvironment influences their development.
Prediction of Defibrillation Outcome by Ventricular Fibrillation Waveform Analysis: A Clinical Review

The most frequent initial rhythm in out-of-hospital witnessed cardiac arrest is ventricular fibrillation (VF) and electrical defibrillation is still the only effective therapy for the termination of this life-threatening cardiac arrhythmia. Even though earlier defibrillation is greatly emphasized during cardiopulmonary resuscitation (CPR), unnecessary or repetitive high energy defibrillations are associated with decreased post-resuscitation myocardial function. Optimizing the timing of defibrillation is of great importance in order to discriminate patients should receive immediate defibrillation versus alternate therapies such as CPR. Since characteristics of VF waveform changes over time and with CPR, which exhibit predictable ability of defibrillation success, quantitative analysis of VF waveform has the potential to guide defibrillation. This article reviewed methods developed for VF waveform analysis (including time domain, frequency domain, time-frequency domain, nonlinear analysis, and combination analysis techniques) and their performances for the prediction of defibrillation outcomes in clinical settings. The retrospective meta-analysis confirmed that VF waveform could predict the return of organized electrical activity, restoration of spontaneous circulation, and survival reliably. Additionally, predictors based on time-frequency and nonlinear methods were superior to other methods on the whole. However, no prospective studies have been performed to identify the optimal time of defibrillation utilizing VF waveform analysis until now. Therefore, the value of VF waveform analysis to guide clinical countershock management still needs further investigation.
A cautionary note on image downgrading

The results of an experiment that shows that it is very simple to contaminate digital images with information that can later be extracted are presented. This contamination cannot be detected when the image is displayed on a good quality graphics workstation. Based on these results, it is recommended that image downgrading based on visual display of the image to be downgraded not be performed if there is any threat of image contamination by Trojan horse programs. Potential Trojan horse programs may include untrusted image processing software. <<ETX>>
Global Tissue Revolutions in a Morphogenetic Movement Controlling Elongation

The ellipsoid shape of the Drosophila egg is controlled by global tissue revolutions that polarize the matrix. Polarized cell behaviors drive axis elongation in animal embryos, but the mechanisms underlying elongation of many tissues remain unknown. Eggs of Drosophila undergo elongation from a sphere to an ellipsoid during oogenesis. We used live imaging of follicles (developing eggs) to elucidate the cellular basis of egg elongation. We find that elongating follicles undergo repeated rounds of circumferential rotation around their long axes. Follicle epithelia mutant for integrin or collagen IV fail to rotate and elongate, which results in round eggs. We present evidence that polarized rotation is required to build a polarized, fibrillar extracellular matrix (ECM) that constrains tissue shape. Thus, global tissue rotation is a morphogenetic behavior that uses planar polarity information in the ECM to control tissue elongation.
Worst-case guarantees on a processor with temperature-based feedback control of speed

On-chip temperatures continue to rise, in spite of design efforts towards more efficient cooling and novel low-power technologies. Run-time thermal management techniques, such as speed scaling and system throttling, constitute a standard component in today's processors. One such technique is the feedback control of the processing speed based on the on-chip temperature. If suitably designed, such a controller can ensure that the temperature of the processor does not exceed a given bound, independent of the application. Such isolation of needs is encouraging. However, from the application's stand-point, such a processor must provide performance guarantees; in particular, the guarantee that real-time jobs do not have worst-case delays larger than their relative deadlines. For applications which exhibit variability, such as bursty arrival patterns, computing such guarantees is not apparent. As key enablers in such a computation, for the specific setting of First-Come-First-Serve (FCFS) scheduling, we (a) define and prove a monotonicity principle satisfied by the processor with the said controller, and (b) propose a thermally clipped processor model. We identify the worst-case trace simulating which on a suitably chosen thermally clipped processor provides the tight upper-bound on the worst-case delay. These results hold for general models of (a) the power consumption of the processor, (b) its thermal model, (c) the speed scaling law, and (d) the task model. For this modelling scope, we show that the same worst-case trace also leads to the worst-case temperature of the processor. This is useful to characterise tasks which do not load the processor sufficiently to hit the given peak temperature bound. We demonstrate the utility of this calculation by designing a shaper to delay the arrival times of jobs and thereby restrict the observed worst-case temperature while still meeting the task's deadlines.
Environmental Enrichment Promotes Plasticity and Visual Acuity Recovery in Adult Monocular Amblyopic Rats

Loss of visual acuity caused by abnormal visual experience during development (amblyopia) is an untreatable pathology in adults. In some occasions, amblyopic patients loose vision in their better eye owing to accidents or illnesses. While this condition is relevant both for its clinical importance and because it represents a case in which binocular interactions in the visual cortex are suppressed, it has scarcely been studied in animal models. We investigated whether exposure to environmental enrichment (EE) is effective in triggering recovery of vision in adult amblyopic rats rendered monocular by optic nerve dissection in their normal eye. By employing both electrophysiological and behavioral assessments, we found a full recovery of visual acuity in enriched rats compared to controls reared in standard conditions. Moreover, we report that EE modulates the expression of GAD67 and BDNF. The non invasive nature of EE renders this paradigm promising for amblyopia therapy in adult monocular people.
Multi-Functional Compression with Side Information

In this paper, we consider the problem of multifunctional compression with side information. The problem is how we can compress a source X so that the receiver is able to compute some deterministic functions f1(X, Y1), . , fm(X, Ym), where Yi, 1 ≤ i ≤ m, are available at the receiver as side information. In [1], Wyner and Ziv considered this problem for the special case of m = 1 and f1(X, Y1) = X and derived a rate-distortion function. Yamamoto extended this result in [2] to the case of having one general function f1(X, Y1). Both of these results were in terms of an auxiliary random variable. For the case of zero distortion, in [3], Orlitsky and Roche gave an interpretation of this variable in terms of properties of the characteristic graph which led to a particular coding scheme. This result was extended in [4] by providing an achievable scheme based on colorings of the characteristic graph. In a recent work, reference [5] has considered this problem for a general tree network where intermediate nodes are allowed to perform some computations. These previous works only considered the case where the receiver only wants to compute one function (m=1). Here, we want to consider the case in which the receiver wants to compute several functions with different side information random variables and zero distortion. Our results do not depend on the fact that all functions are desired in one receiver and one can apply them to the case of having several receivers with different desired functions (i.e., functions are separable). We define a new concept named the multi-functional graph entropy which is an extension of the graph entropy defined by Korner in [6]. We show that the minimum achievable rate for this problem is equal to the conditional multi-functional graph entropy of random variable X given side informations. We also propose a coding scheme based on graph colorings to achieve this rate.
Process‐based hydrological modelling: The potential of a bottom‐up approach for runoff predictions in ungauged catchments

Conceptual rainfall–runoff models are a valuable tool for predictions in ungauged catchments. However, most of them rely on calibration to determine parameter values. Improving the representation of runoff processes in models is an attractive alternative to calibration. Such an approach requires a straightforward, a priori parameter allocation procedure applicable on a wide range of spatial scales. However, such a procedure has not been developed yet.
Atmospheric CO2 observations at Finnish urban and rural sites

Four new ground-based atmospheric monitoring stations in Finland were examined for local and large-scale signals in carbon dioxide mole fraction, and the results were compared with the corresponding values obtained from WMO/GAW site Pallas, northern Finland and NOAA/ESRL marine boundary layer reference time series. The measurements were filtered with knowledge of local weather and air composition. Periods of a presumably well-mixed boundary layer and relatively pollutant-free air were close to the Pallas time series in mole fraction, particularly in the winter. Wintertime mole fractions were 5–10 ppm higher than the signal in the marine boundary layer at all stations. The seasonal amplitude was 18–24 ppm, and diurnal amplitude was 0–3 ppm in winter and 3–20 ppm in the summer months. All stations, with the possible exception of the urban site in Helsinki, showed potential for observing a large-scale carbon dioxide signal.
ATTACHMENT AND ATTENTIONAL BIASES FOR FACIAL ExPRESSIONS OF DISGUST

Research on biological and psychological functions of disgust is increasing, yet relatively little is known about how people react to facial displays of disgust. This study used the dot probe task to examine attachment-related biases for emotional faces. Anxiously-attached individuals exhibited a significant tendency both to attend away from closed-mouth disgust faces, which have been associated with social rejection (social-moral disgust), and to attend toward open-mouth disgust faces, which are associated with visceral or core disgust. Consistent with theoretical proposals that there are two distinct sub-types of disgust, we propose that attentional avoidance of closed-mouth disgust faces represents an emotion-regulatory response to perceived social threat among individuals high in attachment anxiety. Future research examining attentional biases to disgust in clinical populations may shed light on interpersonal functions of disgust in psychopathology.
Freeze-fracture appearance of the capillary endothelium in the cerebral cortex of mouse brain.

Extensive tight junctions are located between overlaps of plasma membranes of capillary endothelial cells. Micropinocytotic vesicles are few in number and are seen as invaginations on the A face and as protrusions on the B face. The freeze-fracture appearance of these cells is consistent with their thin section appearance and their role as the site of the blood-brain barrier.
Rationale and design of ARTS: a randomized, double‐blind study of BAY 94‐8862 in patients with chronic heart failure and mild or moderate chronic kidney disease

BAY 94‐8862 is a novel, non‐steroidal, mineralocorticoid receptor antagonist with greater selectivity than spironolactone and stronger mineralocorticoid receptor binding affinity than eplerenone. The aims of the MinerAlocorticoid Receptor Antagonist Tolerability Study (ARTS; NCT01345656) are to evaluate the safety and tolerability of BAY 94‐8862 in patients with heart failure associated with a reduced left ventricular ejection fraction (HFREF) and chronic kidney disease (CKD), and to examine the effects on biomarkers of cardiac and renal function.
The time course of steroid action on blood‐to‐brain and blood‐to‐tumor transport of 82Rb: A positron emission tomographic study

Blood‐to‐brain and blood‐to‐tumor transport rate constants for Rb (K1) and apparent tissue blood volume (Vb) were estimated in 8 patients with primary or metastatic brain tumors before and approximately 6 hours after a 100‐mg intravenous bolus injection of dexamethasone using 82Rb and positron emission tomography. Eight additional patients were studied to evaluate test‐retest variability and repositioning errors. Six hours following dexamethasone administration tumor K1 (but not Vb) was significantly reduced compared with contralateral control brain regions (p < 0.03). These data are consistent with our previously published 24‐hour‐postdexamethasone data and suggest that comparable effects of corticosteroids on brain/tumor capillaries may be observed at 5 to 6 and 24 hours. The time course of dexamethasone‐induced alterations in brain/tumor capillary permeability supports the view that these alterations may be responsible for at least some of the antiedema effects of corticosteroids.