Miracle-dz/UniFAR-FTUs huggingface dataset:
Recurrent Rearrangement during Adaptive Evolution in an Interspecific Yeast Hybrid Suggests a Model for Rapid Introgression

Genome rearrangements are associated with eukaryotic evolutionary processes ranging from tumorigenesis to speciation. Rearrangements are especially common following interspecific hybridization, and some of these could be expected to have strong selective value. To test this expectation we created de novo interspecific yeast hybrids between two diverged but largely syntenic Saccharomyces species, S. cerevisiae and S. uvarum, then experimentally evolved them under continuous ammonium limitation. We discovered that a characteristic interspecific genome rearrangement arose multiple times in independently evolved populations. We uncovered nine different breakpoints, all occurring in a narrow ∼1-kb region of chromosome 14, and all producing an “interspecific fusion junction” within the MEP2 gene coding sequence, such that the 5′ portion derives from S. cerevisiae and the 3′ portion derives from S. uvarum. In most cases the rearrangements altered both chromosomes, resulting in what can be considered to be an introgression of a several-kb region of S. uvarum into an otherwise intact S. cerevisiae chromosome 14, while the homeologous S. uvarum chromosome 14 experienced an interspecific reciprocal translocation at the same breakpoint within MEP2, yielding a chimaeric chromosome; these events result in the presence in the cell of two MEP2 fusion genes having identical breakpoints. Given that MEP2 encodes for a high-affinity ammonium permease, that MEP2 fusion genes arise repeatedly under ammonium-limitation, and that three independent evolved isolates carrying MEP2 fusion genes are each more fit than their common ancestor, the novel MEP2 fusion genes are very likely adaptive under ammonium limitation. Our results suggest that, when homoploid hybrids form, the admixture of two genomes enables swift and otherwise unavailable evolutionary innovations. Furthermore, the architecture of the MEP2 rearrangement suggests a model for rapid introgression, a phenomenon seen in numerous eukaryotic phyla, that does not require repeated backcrossing to one of the parental species.
SeLINQ

The root cause for confidentiality and integrity attacks against computing systems is insecure information flow. The complexity of modern systems poses a major challenge to secure end-to-end information flow, ensuring that the insecurity of a single component does not render the entire system insecure. While information flow in a variety of languages and settings has been thoroughly studied in isolation, the problem of tracking information across component boundaries has been largely out of reach of the work so far. This is unsatisfactory because tracking information across component boundaries is necessary for end-to-end security. This paper proposes a framework for uniform tracking of information flow through both the application and the underlying database. Key enabler of the uniform treatment is recent work by Cheney et al., which studies database manipulation via an embedded language-integrated query language (with Microsoft's LINQ on the backend). Because both the host language and the embedded query languages are functional F#-like languages, we are able to leverage information-flow enforcement for functional languages to obtain information-flow control for databases "for free", synergize it with information-flow control for applications and thus guarantee security across application-database boundaries. We develop the formal results in the form of a security type system that includes a treatment of algebraic data types and pattern matching, and establish its soundness. On the practical side, we implement the framework and demonstrate its usefulness in a case study with a realistic movie rental database.
Brain injury expands the numbers of neural stem cells and progenitors in the SVZ by enhancing their responsiveness to EGF

There is an increase in the numbers of neural precursors in the SVZ (subventricular zone) after moderate ischaemic injuries, but the extent of stem cell expansion and the resultant cell regeneration is modest. Therefore our studies have focused on understanding the signals that regulate these processes towards achieving a more robust amplification of the stem/progenitor cell pool. The goal of the present study was to evaluate the role of the EGFR [EGF (epidermal growth factor) receptor] in the regenerative response of the neonatal SVZ to hypoxic/ischaemic injury. We show that injury recruits quiescent cells in the SVZ to proliferate, that they divide more rapidly and that there is increased EGFR expression on both putative stem cells and progenitors. With the amplification of the precursors in the SVZ after injury there is enhanced sensitivity to EGF, but not to FGF (fibroblast growth factor)-2. EGF-dependent SVZ precursor expansion, as measured using the neurosphere assay, is lost when the EGFR is pharmacologically inhibited, and forced expression of a constitutively active EGFR is sufficient to recapitulate the exaggerated proliferation of the neural stem/progenitors that is induced by hypoxic/ischaemic brain injury. Cumulatively, our results reveal that increased EGFR signalling precedes that increase in the abundance of the putative neural stem cells and our studies implicate the EGFR as a key regulator of the expansion of SVZ precursors in response to brain injury. Thus modulating EGFR signalling represents a potential target for therapies to enhance brain repair from endogenous neural precursors following hypoxic/ischaemic and other brain injuries.
Long Run Risks, the Macroeconomy, and Asset Prices

Ravi Bansal and Amir Yaron (2004) developed the Long Run Risk (LRR) model which emphasizes the role of long run risks, that is, low-frequency movements in consumption growth rates and volatility, in accounting for a wide range of asset pricing puzzles. In this article we present a generalized LRR model, which allows us to study the role of cyclical fluctuations and macroeconomic crises on asset prices and expected returns. The Bansal and Yaron (2004) LRR model contains (i) a persistent expected consumption growth component, (ii) long-run variation in consumption volatility, and (iii) preference for early resolution of uncertainty. To evaluate the role of cyclical risks, we incorporate a cyclical component in consumption growth—this component is stationary in levels. To study financial market crises, we also entertain jumps in consumption growth and volatility. We find that the magnitude of risk compensation for cyclical risks in consumption critically depends on the magnitude of the intertemporal elasticity of substitution (IES). When the IES is larger than one, cyclical risks carry a very small risk premium. When IES is close to zero, the risk compensation for cyclical variations is large; however, in this case the risk-free rate is implausibly high (in excess of 10 percent). It is, therefore, unlikely that the compensation for cyclical risks is of economically significant magnitude. This implication is also consistent Long Run Risks and asset MaRkets †
Depressed levels of Ca2+-cycling proteins may underlie sarcoplasmic reticulum dysfunction in the diabetic heart.

In view of the depressed sarcoplasmic reticulum (SR) Ca2+-pump and Ca2+-release activities in the diabetic heart and the critical role of phosphorylation in regulating the SR function, we examined the status of Ca2+-calmodulin-dependent protein kinase (CaMK) and cAMP-dependent protein kinase (PKA)-mediated phosphorylations in the diabetic heart. Diabetes was induced in male Sprague-Dawley rats by an injection of streptozotocin (65 mg/kg i.v.), and the animals were killed 6 weeks later for assessment of the ventricular SR function. Depressed cardiac performance and SR Ca2+-uptake and -release activities in diabetic animals were accompanied by a significant decrease in the level of SR Ca2+-cycling proteins, such as ryanodine receptor, Ca2+-pump ATPase, and phospholamban. On the other hand, the CaMK- and PKA-mediated phosphorylations of these Ca2+-cycling proteins, the endogenous SR CaMK and PKA activities, and the endogenous SR and cytosolic phosphatase activities were increased in the diabetic heart. Treatment of 3-week diabetic animals with insulin partially or fully prevented the diabetes-induced changes in cardiac performance, SR Ca2+-uptake and -release activites, and SR protein content, whereas the diabetes-induced changes in SR CaMK- and PKA-mediated phosphorylations and activities, as well as phosphatase activities, were not significantly affected. These results suggest that the reduced content of the Ca2+-cycling proteins, unlike alterations in PKA and phosphatase activities, appear to be the major defect underlying SR dysfunction in the diabetic heart.
ISE01-4: Deployment Time Performance Optimization of Internet Services

This paper introduces a novel deployment time optimization (DTO) technology for Internet services. Using the configuration information collected from the target operation environment, the proposed optimization technology attempts to deploy only necessary and most performant components for a service in the target environment. To facilitate DTO, we have developed a framework called blue pencil, which consists of the following modules: configuration discovery module, optimization rule repository, deployment optimization module, proxy generation module, and code transformation module. We present how these modules enable DTO and show the performance benefit of DTP in a client-server binding selection scenario.
A new area-efficient 4-PAM 10 Gb/s CMOS serial link transmitter

A new area efficient CMOS current-mode 4-PAM 10 Gb/s serial link transmitter is presented. The pre-emphasis of the proposed transmitter is realized by employing a delay block for each pre-emphasis tap such that the degree of each pre-emphasis tap can be tuned individually and independent of the current symbol. The multiplexing-at-input approach of the serializer ensures that the transistors of the multiplexing branches are minimum sized. A differential output current is obtained from a class AB pre-amplifier and a push-pull configured current-symbol driver and pre-emphasis drivers. The proposed transmitter minimizes the noise injected to the power and ground rails by drawing a constant current from the power supply and electromagnetic interference exerted from the channel to neighboring devices by conveying an output current of the same amplitude but opposite polarities to the channel. Implemented in a 1.2V 0.13mum CMOS technology, the transmitter outputs a 3.5 mA peak-to-peak differential output current to the channel, consumes 19.2 mW DC power with inverter buffer chain. The current received at the far end of a 10-cm FR-4 cable has eye-width of 185 ps and eye-height of 1.21 mA
Seismic Random Noise Attenuation Using Synchrosqueezed Wavelet Transform and Low-Rank Signal Matrix Approximation

Random noise elimination acts as an important role in the seismic signal processing. Generally, noise in seismic data can be divided into two categories of coherent and incoherent or random noise. Suppression of wide-band noise which is characterized by random oscillation in seismic data over time is one of the challenging issues in the seismic data processing. This paper describes a new noise suppression algorithm for seismic data denoising. The seismic data, trace-by-trace are transformed into sparse subspace using the synchrosqueezed wavelet transform, then the obtained sparse time-frequency representation is decomposed into semilow-rank and sparse components using the Optshrink algorithm. Finally, the denoised seismic trace can be recovered by back-transforming the semilow-rank component to the time domain using inverse synchrosqueezed wavelet transform. The proposed method is assessed using a single synthetic seismic trace and a synthetic seismic section with two crossover linear and curve events with two discontinuities that are buried in the random noise. We have also evaluated the method using a prestack real seismic data set from an oil field in the southwest of Iran. A comparison is performed between the proposed method and the semisoft GoDec algorithm, classical f-x singular spectrum analysis, and prediction Wiener filter. The results visually and quantitatively confirmed the superiority of the proposed method in contrast to the other well-established noise reduction methods.
Composition and antifungal activity of Zhumeria majdae essential oil

Background and Purpose: Essential oils extracted from different plants are extensively used in perfume, beverage, and food industries and are reported to exhibit antimicrobial activities against a variety of fungi. Zhumeria majdae belonging to the Lamiaceae family is a rare and endemic medicinal plant species in Iran, with a strong and pleasant odor. The leaves of this plant have been used for many years as an antiseptic carminative agent for the treatment of stomachache (especially in infants) and dysmenorrhea. Materials and Methods: Gas chromatography/mass spectrometry (GC/MS) analysis was performed to determine the main constituents of the essential oil extracted from the aerial parts of Z. majdae. Also, the minimum inhibitory concentrations (MICs) were determined, using serial dilution method. Results: Based on the GC/MS analysis, 31 compounds representing 95.36% of the essential oil, extracted from the aerial parts of the plant, were identified, among which linalool (63.40%) and camphor (27.48%) were recognized as the major constituents. The total phenolic content was 42.74 GAE (mg)/DW (g). The hydro-distilled essential oil from the aerial part of the plant displayed potential antifungal activities against all the tested pathogenic fungal species (i.e., Candida albicans, Trichophyton mentagrophytes, Aspergillus flavus, Trichophyton rubrum, Microsporum canis, Microsporum gypseum, and Epidermophyton floccosum). Based on the inhibition zone (29 mm) and MIC value (0.015 μl/ml), all the tested strains were sensitive to Z. majdae essential oil. Conclusion: The present results support the traditional and possible use of Z. majdae essential oil in food, pharmaceutical, and cosmetic industries.
User interface specification and modeling in an object oriented environment for automatic software development

Nowadays, most of the research developed by industry and academia has led to several object-oriented methods that are highly adequate for the development of systems, but most of these methods do not include mechanisms (models) for identifying and specifying user needs and requirements, as well as testing and validating requirements with end users before, during and after development. These considerations are especially important in interactive systems, where the user interaction is very high and the user interface is a significant part of the system. As a result of this weakness, interactive systems developed using such methods can meet all technical requirements, be very robust, and yet be unusable by the end user. This problem explains a large part of the frequently-observed phenomenon whereby large numbers of change requests to modify the services of an application are made after its deployment. As a solution to this problem, we propose a method for integrating a user interface model into the software life-cycle, taking into account user needs and requirements. Also, this approach to the development process ensures the quality of the delivered applications from the end user's point of view.
Comprehensive Evaluation of Different T-Helper Cell Subsets Differentiation and Function in Rheumatoid Arthritis

Rheumatoid arthritis (RA) is the most common autoimmune disorder. Loss of Th1/Th2 and Th17/Treg balance has been reported in several inflammatory autoimmune diseases. This study was to investigate Th1, Th2, Th17, and Treg differentiation and related cytokines in RA patients. The frequencies of Th1, Th2, Th17, and Treg cells in peripheral blood of RA patients (n = 76) and healthy controls (n = 18) were determined by flow cytometry. Eight serum cytokines were analyzed using cytometric bead array. The results demonstrated that RA patients exhibited increased peripheral Th1/Th17 cells and Th1/Th17-related cytokines. However, Th1 cells only reached significant difference at advanced stage, but Th17 at all stages, suggesting more important roles in Th17 cells. For Th2 and Treg cells, there was a different function pattern in RA progression. Although with the increase of DAS28 score, Th2 cell experienced some degree of decrease in RA patients, no significant difference was observed. IL-4 and IL-10 showed a significant increase in RA patients. These indicated that Th2 cells might exert immunosuppression effects mainly by secreting cytokines. Treg cells were found significantly decreased in RA patients, but no difference was observed in TGF-β expression, indicating a cell-cell interaction pattern in Treg cell.
Perceptual enhancement as a result of a top-down attentional influence in a scene viewing task: Evidence from saccadic inhibition

Prior research has shown that task instructions influence the locations and durations of eye fixations during scene viewing. These task-related changes in gaze patterns are likely to be associated with a top-down influence of attention. Presently we applied a saccadic-inhibition manipulation in order to detect another expected manifestation of top-down attention: perceptual enhancement. Participants viewed eight-item arrays containing photographs from two categories of scenes. Four of the photos depicted natural landscapes (“nature”) and the other four depicted urban environments (“buildings”). Participants were instructed to memorize scenes from one of the categories in preparation for a later recognition memory test. During eye fixations the border around the fixated scene flickered briefly from black to white with a random interval between flickers ranging from 400 to 600 ms. We computed the likelihood of a saccade being initiated in the period following the flicker. Consistent with prior research, we found a strong saccadic inhibition effect with maximum saccadic inhibition occurring approximately 97 ms following the flicker. Importantly, the saccadic inhibition effect was stronger and longer lasting when the subject’s eyes were fixated on a relevant scene compared to an irrelevant scene. These findings are consistent with perceptual enhancement as a result of top-down attention.
Overarching framework for data-based modelling

One of the main modelling paradigms for complex physical systems are networks. When estimating the network structure from measured signals, typically several assumptions such as stationarity are made in the estimation process. Violating these assumptions renders standard analysis techniques fruitless. We here propose a framework to estimate the network structure from measurements of arbitrary non-linear, non-stationary, stochastic processes. To this end, we propose a rigorous mathematical theory that underlies this framework. Based on this theory, we present a highly efficient algorithm and the corresponding statistics that are immediately sensibly applicable to measured signals. We demonstrate its performance in a simulation study. In experiments of transitions between vigilance stages in rodents, we infer small network structures with complex, time-dependent interactions; this suggests biomarkers for such transitions, the key to understand and diagnose numerous diseases such as dementia. We argue that the suggested framework combines features that other approaches followed so far lack.
Insulin and body weight but not hyperandrogenism seem involved in seasonal serum 25-OH-vitamin D3 levels in subjects affected by PCOS

Abstract PCOS patients were frequently characterized by lower plasma vitamin D levels. The mechanisms involved in this dysfunction remains still debated, therefore we evaluated the role of androgen, insulin and body weight on the serum VitD levels in women with or without PCOS. Eighty one patients 18–42 yrs old were studied into “SUMMER” and “WINTER” seasonal period: thirty seven PCOS, seventeen no-ovarian hyperandrogenic (noPCOS), twelve functional hypothalamic amenorrhea (FHA) and finally fifteen healthy (Con). Patients were further divided into: lean (L), obese (O), normo- (nINS) and hyperinsulinemic (hINS). All hormonal and metabolic parameters were measured at 1-7 days of the menstrual cycle. Our results show that VitD levels were lower in PCOS and in noPCOS than in FHA and Con, in particular in (O) and (hINS) PCOSs. Both in summer and in winter, PCOSs had basal VitD levels significantly lower than FHA and Con, whereas they were similar to noPCOS. Yet, LhINS and OPCOS had VitD levels lower than Con and noPCOS. VitD levels were comparable in LnINS PCOS and Con. In conclusion, PCOSs had levels of VitD lower than controls. Weight and hyperinsulinemia had a significant influence on these values. Finally, over 70% of our healthy patients had VitD deficiency. Chinese abstract 多囊卵巢综合征（PCOS）患者常有的特征是较低的血浆维生素D3浓度。 这种功能异常的作用机制仍有争议，因此在伴或不伴PCOS妇女中，我们将雄激素、胰岛素及体重对血浆维生素D水平的影响进行了评估。 我们研究了81例年龄在18-42岁患者“夏季”和“冬季”的季节性周期：其中37例PCOS患者、17例无高雄激素血症的PCOS患者（noPCOS）、12例下丘脑性闭经（FHA）患者和15例健康患者（对照组）。 这些患者被进一步分为瘦型（L）、肥胖型（O）、胰岛素正常型（nINS）和高胰岛素型（hINS）。 所有激素和代谢参数都是在月经第1-7天测量。 结果显示与FHA和对照组相比，PCOS和noPCOS尤其是肥胖型和高胰岛素型维生素D水平较低。 在夏冬两季，PCOS患者基础维生素D水平明显低于FHA组和对照组而与noPCOS组相似，而肥胖型PCOS组和瘦型高胰岛素组维生素D水平明显低于对照组和无高雄激素血症的PCOS组。 瘦型胰岛素正常组与对照组维生素D水平相似。 结论：PCOS患者维生素D水平低于控制组。 体重和高胰岛素水平明显影响这些参数。 最终，有超过70%的健康患者存在维生素D缺乏。
Computer Vision and Image Understanding Deep-anomaly: Fully convolutional neural network for fast anomaly detection in crowded scenes

The detection of abnormal behaviour in crowded scenes has to deal with many challenges. This paper presents an e ﬃ cient method for detection and localization of anomalies in videos. Using fully convolutional neural networks (FCNs) and temporal data, a pre-trained supervised FCN is transferred into an unsupervised FCN ensuring the detection of (global) anomalies in scenes. High performance in terms of speed and accuracy is achieved by investigating the cascaded detection as a result of reducing computation complexities. This FCN-based archi- tecture addresses two main tasks, feature representation and cascaded outlier detection. Experimental results on two benchmarks suggest that the proposed method outperforms existing methods in terms of accuracy regarding detection and localization.