Miracle-dz/UniFAR-FTUs huggingface dataset:
Homogeneous Time Constants Promote Oscillations in Negative Feedback Loops

Biological oscillators are present in nearly all self-regulating systems, from individual cells to entire organisms. In any oscillator structure, a negative feedback loop is necessary, but not sufficient to guarantee the emergence of periodic behaviors. The likelihood of oscillations can be improved by careful tuning of the system time constants and by increasing the loop gain, yet it is unclear whether there is any general relationship between optimal time constants and loop gain. This issue is particularly relevant in genetic oscillators resulting from a chain of different subsequent biochemical events, each with distinct (and uncertain) kinetics. Using two families of genetic oscillators as model examples, we show that the loop gain required for oscillations is minimum when all elements in the loop have the same time constant. On the contrary, we show that homeostasis is ensured if a single element is considerably slower than the others.
Year : 2002 Technical terminology as a critical resource

Technical documentation is riddled with domain specic terminology which needs to be detected and properly organized in order to be meaningfully used. In this paper we describe how we coped with the problem of terminology detection for a specic type of document and how the extracted terminology was used within the context of our Answer Extraction System. Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-19096 Originally published at: Dowdall, J; Hess, M; Kahusk, N; Kaljurand, K; Koit, M; Rinaldi, Fabio; Vider, K (2002). Technical terminology as a critical resource. In: LREC-2002, Las Palmas, Spain, May 2002 May 2002. Technical Terminology as a Critical Resource James Dowdall , Michael Hess , Neeme Kahusk, Kaarel Kaljurand , Mare Koit , Fabio Rinaldi , Kadri Vider y University of Zürich, Institute of Computational Linguistics Winterthurerstrasse 190, CH-8057 Z ̈ urich, Switzerland fdowdall,hess,rinaldi g@ifi.unizh. ch Research Group of Computational Linguistics, University of Tartu J. Liivi 2, 50409 Tartu, Estonia fnkahusk, kaarel, koit, kvider g@psych.ut. ee
Sparse Latent Semantic Analysis

Latent semantic analysis (LSA), as one of the most popular unsupervised dimension reduction tools, has a wide range of applications in text mining and information retrieval. The key idea of LSA is to learn a projection matrix that maps the high dimensional vector space representations of documents to a lower dimensional latent space, i.e. so called latent topic space. In this paper, we propose a new model called Sparse LSA, which produces a sparse projection matrix via the `1 regularization. Compared to the traditional LSA, Sparse LSA selects only a small number of relevant words for each topic and hence provides a compact representation of topic-word relationships. Moreover, Sparse LSA is computationally very efficient with much less memory usage for storing the projection matrix. Furthermore, we propose two important extensions of Sparse LSA: group structured Sparse LSA and non-negative Sparse LSA. We conduct experiments on several benchmark datasets and compare Sparse LSA and its extensions with several widely used methods, e.g. LSA, Sparse Coding and LDA. Empirical results suggest that Sparse LSA achieves similar performance gains to LSA, but is more efficient in projection computation, storage, and also well explain the topic-word relationships.
An Approach for Hybrid-Memory Scaling Columnar In-Memory Databases

In-memory DBMS enable high query performance by keeping data in main memory instead of only using it as a buffer. A crucial enabler for this approach has been the major drop of DRAM prices in the market. However, storing large data sets in main memory DBMS is much more expensive than in disk-based systems because of three reasons. First, the price for DRAM per gigabyte is higher than the price for disk. Second, DRAM is a major cause for high energy consumption. Third, the maximum amount of DRAM within one server is limited to a few terabytes, which makes it necessary to distribute larger databases over multiple server nodes. This so called Scale-Out approach is a root cause for increasing total costs of ownership and introduces additional overhead to an in-memory database system landscape. Recent developments in the area of hardware technology have brought up memory solutions, known as Storage Class Memory, that are capable of offering much higher data density and reduced energy consumption than traditional DRAM. Of course these advantages come at a price: higher read and write latencies than DRAM. Hence, such solutions might not replace DRAM but can be thought of as an additional memory-tier. As those solutions are not available on the market today, we investigate the usage of an available bridge-technology combining high-end flash SSD and DRAM referred to as hybrid-memory. In this paper we present an approach for columnar inmemory DBMS to leverage hybrid-memory by vertically partitioning data depending on its access frequency. We outline in what way our approach is suited to scale columnar in-memory DBMS to overcome existing drawbacks of ScaleOut solutions for certain workloads.
Guard cells elongate: relationship of volume and surface area during stomatal movement.

Stomata in the epidermis of photosynthetically active plant organs are formed by pairs of guard cells, which create a pore, to facilitate CO2 and water exchange with the environment. To control this gas exchange, guard cells actively change their volume and, consequently, surface area to alter the aperture of the stomatal pore. Due to the limited elasticity of the plasma membrane, such changes in surface area require an exocytic addition or endocytic retrieval of membrane during stomatal movement. Using confocal microscopic data, we have reconstructed detailed three-dimensional models of open and closed stomata to precisely quantify the necessary area to be exo- and endocytosed by the guard cells. Images were obtained under a strong emphasis on a precise calibration of the method and by avoiding unphysiological osmotical imbalance, and hence osmocytosis. The data reveal that guard cells of Vicia faba L. , whose aperture increases by 111.89+/-22.39%, increase in volume and surface area by 24.82+/-6.26% and 14.99+/-2.62%, respectively. In addition, the precise volume to surface area relationship allows quantitative modeling of the three-dimensional changes. While the major volume change is caused by a slight increase in the cross section of the cells, an elongation of the guard cells achieves the main aperture change.
Hsp90 as a therapeutic target in endocrinology: current evidence

The ability of heat shock protein 90 (Hsp90) to modulate many growth and signal- ing pathways simultaneously makes it an attractive target in the field of cancer therapeutics and provided the initial impetus for significant efforts over the past decade to identify Hsp90 inhibitors, several of which are now showing promise in the clinic for cancer treatment. The four known human Hsp90 members are compartmentalized: Hsp90α and β in the cytoplasm, GRP94 in the endoplasmic reticulum, and TRAP1 in the mitochondrial matrix. While these isoforms share a similar N-terminal domain adenosine triphosphate-binding pocket, structural variations allow unique interactions for inhibitors targeting this binding site, providing an avenue for the development of paralog-selective drugs with different biological effects applicable therapeuti- cally to a wide range of diseases. At the same time, the conformational flexibility of the Hsp90 molecular chaperone has unveiled multiple small-molecule target sites within all subdomains of the protein, greatly expanding opportunities for viable drug development. This review summa- rizes the function, expression, and clinical significance of the Hsp90 isoforms and elaborates on the inhibitors and modulators that impact Hsp90 chaperone activity. Finally, the review focuses on the therapeutic utility of a range of Hsp90-modulating agents in the treatment of specific diseases associated with the endocrine system.
The efficacy of 37% phosphoric acid + Mi Paste Plus on remineralization of enamel white spot lesions

The efficacy of 37% phosphoric acid + Mi Paste Plus on remineralization of enamel white spot lesions. " MS ___________________________________ Fang Qian ii To my dear husband Nicholas, my loving mother Mary Jo, and my amazing grandmother Irene for their unconditional love and support. I would not have accomplished all I have without you encouraging me through this journey. To the countless others who have been there for me along the way…. Thank you! iii. Learn from yesterday, live for today, hope for tomorrow. -Albert Einstein. iv ACKNOWLEDGMENTS I would like to express my appreciation to Drs. Clayton Parks, and Fang Qian for all of their valuable advice and insight. In addition, I am very thankful to Jeff Harless and Maggie Hogan for their willingness to help at all times during this project. I would also like to express my deepest gratitude to Abbie Kershner, Clinton Ambroson, and Monica Popowski for their help and dedication to this project from start to finish and for being available to assist me when needed. I would also like to thank Dr. Tom Southard and the rest of the faculty at the University of Iowa Department of Orthodontics for allowing me the opportunity to further my education and pursue a career in orthodontics.
Delay Discounting and Frontostriatal Fiber Tracts: A Combined DTI and MTR Study on Impulsive Choices in Healthy Young Adults

Delay discounting, a measure of impulsive choice, has been associated with decreased control of the prefrontal cortex over striatum responses. The anatomical connectivity between both brain regions in delaying gratification remains unknown. Here, we investigate whether the quality of frontostriatal (FS) white matter tracts can predict individual differences in delay-discounting behavior. We use tract-based diffusion tensor imaging and magnetization transfer imaging to measure the microstructural properties of FS fiber tracts in 40 healthy young adults (from 18 to 25 years). We additionally explored whether internal sex hormone levels affect the integrity of FS tracts, based on the hypothesis that sex hormones modulate axonal density within prefrontal dopaminergic circuits. We calculated fractional anisotropy (FA), mean diffusivity (MD), longitudinal diffusivity, radial diffusivity (RD), and magnetization transfer ratio (MTR), a putative measure of myelination, for the FS tract. Results showed that lower integrity within the FS tract (higher MD and RD and lower FA), predicts faster discounting in both sexes. MTR was unrelated to delay-discounting performance. In addition, testosterone levels in males were associated with a lower integrity (higher RD) within the FS tract. Our study provides support for the hypothesis that enhanced structural integrity of white matter fiber bundles between prefrontal and striatal brain areas is associated with better impulse control.
Self-organized criticality as a fundamental property of neural systems

The neural criticality hypothesis states that the brain may be poised in a critical state at a boundary between different types of dynamics. Theoretical and experimental studies show that critical systems often exhibit optimal computational properties, suggesting the possibility that criticality has been evolutionarily selected as a useful trait for our nervous system. Evidence for criticality has been found in cell cultures, brain slices, and anesthetized animals. Yet, inconsistent results were reported for recordings in awake animals and humans, and current results point to open questions about the exact nature and mechanism of criticality, as well as its functional role. Therefore, the criticality hypothesis has remained a controversial proposition. Here, we provide an account of the mathematical and physical foundations of criticality. In the light of this conceptual framework, we then review and discuss recent experimental studies with the aim of identifying important next steps to be taken and connections to other fields that should be explored.
Transfer Learning with Human Corneal Tissues: An Analysis of Optimal Cut-Off Layer

Transfer learning is a powerful tool to adapt trained neural networks to new tasks. Depending on the similarity of the original task to the new task, the selection of the cut-off layer is critical. For medical applications like tissue classification, the last layers of an object classification network might not be optimal. We found that on real data of human corneal tissues the best feature representation can be found in the middle layers of the Inception-v3 and in the rear layers of the VGG-19 architecture.
a-Linolenic acid and risk of cardiovascular disease : a systematic review and meta-analysis 1 – 3

ABSTRACT Background: Prior studies of a-linolenic acid (ALA), a plant-derived omega-3 (n23) fatty acid, and cardiovascular disease (CVD) risk have generated inconsistent results. Objective: We conducted a meta-analysis to summarize the evidence regarding the relation of ALA and CVD risk. Design: We searched multiple electronic databases through January 2012 for studies that reported the association between ALA (assessed as dietary intake or as a biomarker in blood or adipose tissue) and CVD risk in prospective and retrospective studies. We pooled the multivariate-adjusted RRs comparing the top with the bottom tertile of ALA using random-effects meta-analysis, which allowed for between-study heterogeneity. Results: Twenty-seven original studies were identified, including 251,049 individuals and 15,327 CVD events. The overall pooled RR was 0.86 (95% CI: 0.77, 0.97; I = 71.3%). The association was significant in 13 comparisons that used dietary ALA as the exposure (pooled RR: 0.90; 95% CI: 0.81, 0.99; I = 49.0%), with similar but nonsignificant trends in 17 comparisons in which ALA biomarkers were used as the exposure (pooled RR: 0.80; 95% CI: 0.63, 1.03; I = 79.8%). An evaluation of mean participant age, study design (prospective compared with retrospective), exposure assessment (self-reported diet compared with biomarker), and outcome [fatal coronary heart disease (CHD), nonfatal CHD, total CHD, or stroke] showed that none were statistically significant sources of heterogeneity. Conclusions: In observational studies, higher ALA exposure is associated with a moderately lower risk of CVD. The results were generally consistent for dietary and biomarker studies but were not statistically significant for biomarker studies. However, the high unexplained heterogeneity highlights the need for additional welldesigned observational studies and large randomized clinical trials to evaluate the effects of ALA on CVD. Am J Clin Nutr 2012;96:1262–73.
Optical sensors for monitoring water uptake in plants

The monitoring of water uptake in plants is becoming increasingly important. Optical sensors offer considerable advantages over conventional methods and several sensors have been developed including an optical potometer that monitors water uptake from individual roots, the detection of xylem cavitation using audio acoustic emissions with an interferometric force feedback microphone, and an optical fiber displacement transducer that detects changes in leaf thickness in relation to leaf-water potential. >
Cognitive therapy for the prevention of psychosis in people at ultra-high risk

Background Advances in the ability to identify people at high risk of developing psychosis have generated interest in the possibility of preventing psychosis. Aims To evaluate the efficacy of cognitive therapy for the prevention of transition to psychosis. Method A randomised controlled trial compared cognitive therapy with treatment as usual in 58 patients at ultra-high risk of developing a first episode of psychosis. Therapy was provided over 6 months, and all patients were monitored on a monthly basis for 12 months. Results Logistic regression demonstrated that cognitive therapy significantly reduced the likelihood of making progression to psychosis as defined on the Positive and Negative Syndrome Scale over 12 months. In addition, it significantly reduced the likelihood of being prescribed antipsychotic medication and of meeting criteria for a DSM – IV diagnosis of a psychotic disorder. Analysis of covariance showed that the intervention also significantly improved positive symptoms of psychosis in this population over the 12-month period. Conclusions Cognitive therapy appears to be an acceptable and efficacious intervention for people at high risk of developing psychosis.
The Bone-Cardiovascular Axis: Mechanisms and Clinical Relevance

Department of Cardiology, Medical University of Graz, Graz, Austria Division of Endocrinology and Diabetology, Department of Internal Medicine, Medical University of Graz, Graz, Austria Department of Cardiology, Swiss Cardiovascular Center Bern, Bern University Hospital, University of Bern, Bern, Switzerland Hypertension Unit, Internal Medicine, Department of Experimental and Clinical Medical Sciences, University of Udine, Udine, Italy Department of Internal Medicine, Division of Endocrinology and Diabetology, Medical University of Graz, Graz, Austria Department of Health Sciences, Vrije Universiteit Amsterdam and the Amsterdam Public Health Research Institute, Amsterdam, Netherlands
Bloomfield Model Based Signal Process for Networks

This paper proposes a novel speech signal analysis approach based on the Bloomfield (<inline-formula> <tex-math notation="LaTeX">$BF$ </tex-math></inline-formula>) model, and provides a formulation of a time-domain <inline-formula> <tex-math notation="LaTeX">$BF$ </tex-math></inline-formula> model for speech signals with which speech signals can be reconstructed and the relevant characteristic parameters analyzed. The relationship between the parameters of the <inline-formula> <tex-math notation="LaTeX">$BF$ </tex-math></inline-formula> model and those of the linear prediction (<inline-formula> <tex-math notation="LaTeX">$LP$ </tex-math></inline-formula>) model are derived, and the speech feature sets derived via the <inline-formula> <tex-math notation="LaTeX">$LP$ </tex-math></inline-formula> and <inline-formula> <tex-math notation="LaTeX">$BF$ </tex-math></inline-formula> models are compared. A new algorithm is proposed for the recognition of isolated digit speech that utilizes a vector quantization approach and is based on the <inline-formula> <tex-math notation="LaTeX">$BF$ </tex-math></inline-formula> Model. The result is obtained with this <inline-formula> <tex-math notation="LaTeX">$BF$ </tex-math></inline-formula> approach that provides better results than those of the <inline-formula> <tex-math notation="LaTeX">$LP$ </tex-math></inline-formula> model when predicting speech signals. In particular, the <inline-formula> <tex-math notation="LaTeX">$BF$ </tex-math></inline-formula> approach has several advantages, including fewer parameters, a lower computational complexity, and accurate characterization of speakers. These advantages ensure the utility of the <inline-formula> <tex-math notation="LaTeX">$BF$ </tex-math></inline-formula> model in speech processing applications.
Source/Drain Engineered Charge-Plasma Junctionless Transistor for the Immune of Line Edge Roughness Effect

In this paper, the charge-plasma structure over the source/drain region is incorporated into a dopingless junctionless transistor for obtaining the superior immunity of line edge roughness (LER). An optimized on/off current ratio is observed by using numerical simulations. It is also demonstrated that the proposed charge-plasma junctionless transistor (CP-JLT) is insensitive to the variation of LER magnitude. We further reveal the physics that LER affects the electrical characteristics of CP-JLT. Channel minimal width position variation and channel width variation are put forward to explore the impact of LER for the first time. It is observed that the LER affects the <inline-formula> <tex-math notation="LaTeX">${I}_{\text {ON}}$ </tex-math></inline-formula> of CP-JLT due to the changes of the source width caused by channel minimal width position variation, whereas the LER affects the <inline-formula> <tex-math notation="LaTeX">${I}_{\text {OFF}}$ </tex-math></inline-formula>, SS, and <inline-formula> <tex-math notation="LaTeX">${V}_{\text {th}}$ </tex-math></inline-formula> mainly through channel width variation. It is thus proved to be a helpful guide to suppress the LER variation of CP-JLT.
The pharmacological role of histone demethylase JMJD3 inhibitor GSK-J4 on glioma cells

Glioma is regarded as the most prevalent malignant carcinoma of the central nervous system, and lack of effective treatment. Thus, the development of new therapeutic strategies targeting glioma is of significant clinical importance. In the present study, histone H3K27 demethylase jumonji domain-containing protein 3 (JMJD3) was investigated as target for glioma treatment. The mRNA of JMJD3 was overexpressed in glioblastoma tissues compared to normal brain tissues (P<0.05). The content of JMJD3 was also higher in glioma cells than in human brain microvascular endothelial cell (hCMEC), and the corresponding level of H3K27me3 was decreased (P<0.05). The treatment with JMJD3 specific inhibitor GSK-J4 can increase the content of H3K27me3 in glioma cells, which means the activity of JMJD3 was inhibited. GSK-J4 can inhibit glioma cell proliferation in a concentration dependent and time-dependent manner (P<0.05). GSK-J4 also induced glioma cell apoptosis and inhibited cell migration (P<0.05). But there was no obvious effect of GSK-J4 on hCMEC cells. All together, these data suggest that GSK-J4 has important potential in the gliomas treatment.
Fast Lookups for In-Memory Column Stores: Group-Key Indices, Lookup and Maintenance

In-memory column-oriented databases have become a major topic of interest in academia and commercial applications. The demand for analytics on up-to-the-minute data and the availability of systems with hundreds of gigabytes of main memory led to the proposal of combined systems, which provide a single database for operational processing and adhoc analytical queries on current data. Recent research has identified In-Memory Column-Stores as a possible database architecture to meet these requirements. They are claimed to be capable of delivering the analytical insights while providing sufficient transactional performance. Data therein is typically split up into a write-optimized partition, which gains speed from its small size and tree-structured indices, and a larger read-only partition. To enable fast transactional and analytical performance, an index on the large, read-only partition is advisable in many cases. In this paper we present an index structure for the read-only partition, describe its advantage over the column scan and present an algorithm for the maintenance of the index. The index drastically reduces the memory traffic during query execution, leading to faster lookups and joins, thereby providing benefits to transactional and analytical processing. We analyze the memory traffic of index lookups in comparison with full column scans and the maintenance of the index structure. We develop formulas to determine the viability of an index lookup over a column scan at query runtime. While other research claimed that an index for in-memory systems should just be rebuild after every bulk-load, we show that a substantial performance increase can be achieved by reusing the former index to create an updated index. Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise, to republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. This article was presented at: The Third International Workshop on Accelerating Data Management Systems using Modern Processor and Storage Architectures (ADMS’12). Copyright 2012.