Miracle-dz/UniFAR-FTUs huggingface dataset:
Signal peptide peptidase functions in ERAD to cleave the unfolded protein response regulator XBP1u

Signal peptide peptidase (SPP) catalyzes intramembrane proteolysis of signal peptides at the endoplasmic reticulum (ER), but has also been suggested to play a role in ER‐associated degradation (ERAD). Here, we show that SPP forms a complex with the ERAD factor Derlin1 and the E3 ubiquitin ligase TRC8 to cleave the unfolded protein response (UPR) regulator XBP1u. Cleavage occurs within a so far unrecognized type II transmembrane domain, which renders XBP1u as an SPP substrate through specific sequence features. Additionally, Derlin1 acts in the complex as a substrate receptor by recognizing the luminal tail of XBP1u. Remarkably, this interaction of Derlin1 with XBP1u obviates the need for ectodomain shedding prior to SPP cleavage, commonly required for intramembrane cuts. Furthermore, we show that XBP1u inhibits the UPR transcription factor XBP1s by targeting it toward proteasomal degradation. Thus, we identify an ERAD complex that controls the abundance of XBP1u and thereby tunes signaling through the UPR.
Phenolics composition in lettuce upon ultraviolet radiation and temperature effects

Book – 18th Alps-Adria Scientific Workshop 144 Phenolics composition in lettuce upon ultraviolet radiation and temperature effects Oksana SYTAR1,2 – Marek ZIVCAK1 – Marian BRESTIC1 – Cornelia RAUH3 – Ivan SIMKO4 1: Department of Plant Physiology, Slovak University of Agriculture, Nitra, A. Hlinku 2, 94976 Nitra, Slovak Republic 2: Departement of Plant Biology, Educational and Scientific Center ‘Institute of Biology’, TarasShevchenko National University of Kyiv, Kyiv, Ukraine 3: Department of Food Biotechnology and Food Process Engineering, Institute of Food Technology and Food Chemistry TU Berlin, Königin-Luise-Str. , 22, 14195 Berlin, Germany 4: U.S. Department of Agriculture, Agricultural Research Service, U.S. Agricultural Research Station, Crop Improvement and Protection Research Unit, 1636 E. Alisal St., Salinas, CA 93905, USA
Can needle nitrogen content explain the interspecific difference in ozone sensitivities of photosynthesis between Japanese larch (Larix kaempferi) and Sakhalin fir (Abies sachalinensis)?

Although deciduous and evergreen conifers are expected to utilize needle nitrogen differently, their interspecific differences in the ozone sensitivity remain unclear. We compared the growth and physiological responses to elevated O3 concentrations in deciduous Japanese larch (Larix kaempferi) and evergreen Sakhalin fir (Abies sachalinensis) seedlings. Seedlings of both species were exposed to 62.5 ± 1.95 nmol(O3) mol-1 during the day time in open-top chambers. Elevated O3 had no effect on height or diameter growth in either of the species but suppressed photosynthetic parameters. A decline in photosynthetic nitrogen-use efficiency was observed in both species. However, needle N content in larch was decreased by O3, whereas it was not decreased in fir. Needle N responses to O3 were different between larch and fir seedlings, indicating that the O3 sensitivity of photosynthesis could vary depending on needle N dynamics. We also observed a higher correlation between photosynthesis and needle N even under O3 exposure, particularly in the mass-based relationship with higher accuracy. The result indicated that mass-based needle N could explain difference in O3 sensitivity of photosynthesis between the different leaf habits in larch and fir seedlings.
Limitations of magnetic resonance imaging in measurement of hepatic iron.

To evaluate the usefulness of magnetic resonance imaging for the quantitative determination of hepatic iron, we examined 43 patients with thalassemia major and assessed the influence of pathologic changes in the liver on the precision of estimates of the hepatic iron concentration. Tissue signal intensities were measured from magnetic resonance T1-weighted images derived from gradient-echo (GE) pulse sequences and the ratio of the signal intensity of liver to muscle calculated. By excluding patients (n = 9) having a signal intensity ratio (SIR) less than or equal to 0.2, a linear relationship with hepatic iron was found and subsequent analyses were limited to these 34 patients. In 27 patients with hepatic fibrosis, an overall correlation of -0.848 was found between hepatic iron and SIR. By contrast, in the seven patients with no fibrosis, the correlation coefficient (-0.993) was significantly greater (P < .0001). Despite the differences in correlation, the regression line between hepatic iron and SIR for the patients with no fibrosis did not differ significantly with respect to either slope or intercept from that of the patients with fibrosis. Thus, the presence of fibrosis did not seem to affect the pattern of the relationship between hepatic iron and the SIR, but rather to increase the variability of the relationship. Clinically, the presence of fibrosis makes estimates of hepatic iron derived from magnetic resonance imaging so variable as to be of little practical use in the management of transfusional iron overload.
Rate-based vs delay-based control for DVFS in NoC

Minimization of power via DVFS in an NoC is possible, but may result in an intolerable increase of network delay. We examined two DVFS policies, a rate-based policy that scales down frequency and voltage to the minimum value that allows to sustain the injection rate without reaching saturation, and a delay-based policy in which a closed-loop control tunes frequency and voltage such that the NoC average delay tracks a target value. We evaluated the power-delay trade-off by means of network simulations and accurate power estimations after synthesis on a 28-nm FDSOI CMOS technology. Our results over synthetic and multimedia traffic patterns show that the first policy largely pays the better saving in power (20%-50% less than the second policy) with a large network delay increase (up to 3×). We then conclude that the delay-based policy offers a better power-delay trade-off.
Sparsity Score: A new filter feature selection method based on graph

Recently, l1 graph based analysis using sparse representation has received much attention in pattern recognition and related communities. In this paper, motivated by the success of l1 graph in dimensionality reduction, we extend it to feature selection and propose a novel filter-type method called Sparsity Score (SS) which ranks features according to their respective sparsity preserving capability. For that aim, a l1 graph is constructed based on sparse representationon samples, where a l1-norm based optimization is used to simultaneously determine the graph adjacency structure and corresponding graph weights of the l1 graph. Experimental results on a series of benchmark data sets show that the proposed SS method achieves better performance than conventional feature selection methods.
A hybrid algorithm to reduce energy consumption management in cloud data centers

There are several physical data centers in cloud environment with hundreds or thousands of computers. Virtualization is the key technology to make cloud computing feasible. It separates virtual machines in a way that each of these so-called virtualized machines can be configured on a number of hosts according to the type of user application. It is also possible to dynamically alter the allocated resources of a virtual machine. Different methods of energy saving in data centers can be divided into three general categories: 1) methods based on load balancing of resources; 2) using hardware facilities for scheduling; 3) considering thermal characteristics of the environment. This paper focuses on load balancing methods as they act dynamically because of their dependence on the current behavior of system. By taking a detailed look on previous methods, we provide a hybrid method which enables us to save energy through finding a suitable configuration for virtual machines placement and considering special features of virtual environments for scheduling and balancing dynamic loads by live migration method.
Pharos: accurate and decentralised network coordinate system

Network coordinates (NC) system is an efficient mechanism for Internet distance prediction with scalable measurements. The intrinsical cause for the unsatisfactory accuracy of the simulation-based NC algorithms has been identified. Then Pharos, a fully decentralised and hierarchical scheme, is proposed to solve this problem. Pharos leverages multiple coordinate sets at different distance scales, with the right scale being chosen for prediction each time. We evaluate the performance of Pharos system with the King data set and latency data from PlanetLab, and compare it with the representative NC system, Vivaldi. The experimental results show that Pharos greatly outperforms Vivaldi in Internet distance prediction without adding any significant overhead. Our extensive evaluation results also demonstrate that Pharos can significantly improve the performance in distributed Internet applications, such as overlay multicast and server selection.
Towards Universal Web Parsebanks

Recently, there has been great interest both in the development of cross-linguistically applicable annotation schemes and in the application of syntactic parsers at web scale to create parsebanks of online texts. The combination of these two trends to create massive, consistently annotated parsebanks in many languages holds enormous potential for the quantitative study of many linguistic phenomena, but these opportunities have been only partially realized in previous work. In this work, we take a key step toward universal web parsebanks through a single-language case study introducing the first retrainable parser applied to the Universal Dependencies representation and its application to create a Finnish web-scale parsebank. We further integrate this data into an online dependency search system and demonstrate its applicability by showing linguistically motivated search examples and by using the dependency syntax information to analyze the language of the web corpus. We conclude with a discussion of the requirements of extending from this case study on Finnish to create consistently annotated web-scale parsebanks for a large number of languages.
High‐order sliding‐mode observer–based input‐output linearization

The problem of output control in multiple‐input–multiple‐output nonlinear systems is addressed. A high‐order sliding‐mode observer is used to estimate the states of the system and identify the discrepancy between the nominal model and the real plant. The exact and finite‐time estimation may be tackled as long as the system presents the algebraic strong observability property. Thus, a continuous robust input‐output linearization strategy can be obtained with respect to a prescribed output. As a consequence, the closed‐loop dynamics performs robustly to uncertainties/perturbations. To illustrate the advantages of the proposed method, we introduce a study case that demands a robust linear system behavior: the self‐oscillations induced in an underactuated mechanical system through a two‐relay controller. Experiments with an inertial wheel pendulum illustrate the feasibility of the proposed approach.
APPROXIMATION TO THE ORIGIN OF FALSE MILDEW IN SAFFLOWER

An approximation of the origin of the “false mildew” in safflower was proposed from a phylogenetic tree obtained by the Maximum Likelihood method with the genomic alignment of a nucleotide sequence of Ramularia cercosporelloides isolated from safflower lesions. The approximation is the origin of the disease known as "false mildew" in the safflower may be due to new host adaptations of Mycosphaerella graminicola.
Knowledge Management for a LAN design and operations using multi-agent systems

The department of Computer Science, at Chiba Institute of Technology has been using LANs since 1988. Its own LAN, CS-LAN, is steadily expanding, becoming very complex and reaching now a spaghetti state. Next April 2011, the department of Computer Science will move to another building on the same campus. We need to design a new LAN to be installed in the future building. It will be provided by new vendors, use new technologies complying with the constraints of the new building. However, our department has no full time network manager, one of our colleague professors working as a network manager on his spare time. Therefore, all the knowledge about the CS-LAN is scattered among users, mainly professors and is not recorded. Indeed, the changes in configuration of the CS-LAN were often reported by e-mail only. In this paper, we try to propose a design plan working with multi agent systems in order to compare the design parts of the new CS-LAN, and capture design and operational knowledge semi-automatically for future use.
Encoding Prior Knowledge with Eigenword Embeddings

Canonical correlation analysis (CCA) is a method for reducing the dimension of data represented using two views. It has been previously used to derive word embeddings, where one view indicates a word, and the other view indicates its context. We describe a way to incorporate prior knowledge into CCA, give a theoretical justification for it, and test it by deriving word embeddings and evaluating them on a myriad of datasets.
CCR5 and CXCR4 expression correlated with X4 and R5 HIV-1 infection yet not sustained replication in Th1 and Th2 cells

ObjectiveTo investigate the infectivity of T-helper (Th)1 and Th2 cells (derived from ccr5 wild-type and homozygous ccr5 Δ32) to R5 and X4 HIV-1. DesignIt remains unclear whether infection of Th1 and Th2 CD4 cells by R5 and X4 viruses mirrors their co-receptor expression profile as no direct quantitation of coreceptor levels and infection has been performed. In addition, it is unknown whether the lack of CCR5 expression affects the degree of Th1/Th2 polarization. MethodsSurface expression of CCR5 and CXCR4 was determined by quantitative fluorescence activated cell sorter analysis on in vitro differentiated Th1 and Th2 cells. R5 (Ba-L) and X4 (IIIB) HIV-1 isolates were used for infection studies and the efficiency of viral entry was determined by quantitative real time polymerase chain reaction detection of reverse transcribed proviral DNA. ResultsCell surface density of CCR5 molecules was eight-fold higher in Th1 versus Th2 subsets (P = 0.005) whereas CXCR4 surface density was four-fold higher in Th2 versus Th1 subsets (P = 0.006). Preferential infection and entry of Th1 cells by R5 HIV-1 was not associated with preferential replication, as eventually the R5-virus replicated to a higher level in Th2 cells in spite of lower initial viral infection/entry. By contrast, Th2 cells preferentially supported X4-virus infection and replication. High beta chemokine secretion by Th1 cells was associated with a lower R5 replication rate. ConclusionsTh1 and Th2 cells differ in their infection efficiency for R5 and X4 HIV-1. ccr 5Δ32-homozygous individuals maintain the ability for Th1/Th2 polarization, i.e., the expression of CCR5 is not required for Th1/Th2 polarization.
BitVisor: a thin hypervisor for enforcing i/o device security

Virtual machine monitors (VMMs), including hypervisors, are a popular platform for implementing various security functionalities. However, traditional VMMs require numerous components for providing virtual hardware devices and for sharing and protecting system resources among virtual machines (VMs), enlarging the code size of and reducing the reliability of the VMMs. This paper introduces a hypervisor architecture, called parapass-through, designed to minimize the code size of hypervisors by allowing most of the I/O access from the guest operating system (OS) to pass-through the hypervisor, while the minimum access necessary to implement security functionalities is completely mediated by the hypervisor. This architecture uses device drivers of the guest OS to handle devices, thereby reducing the size of components in the hypervisor to provide virtual devices. This architecture also allows to run only single VM on it, eliminating the components for sharing and protecting system resources among VMs. We implemented a hypervisor called BitVisor and a parapass-through driver for enforcing storage encryption of ATA devices based on the parapass-through architecture. The experimental result reveals that the hypervisor and ATA driver require approximately 20 kilo lines of code (KLOC) and 1.4 KLOC respectively.
Predicting and Parsing Language in Time and Space

viii LIST OF FIGURES.xii LIST OF TABLES. xiv Chapter 1 Introduction . 1 1.1 The syntax-first puzzle and prediction . 2 1.2 Part 1: Are early effects of linguistic violati ons sensory in nature? 6 1.3 Part 2: Can early sensory effects of linguistic violations be explained in terms of predictive processing? 10 Chapter 2 Early effects of linguistic violations:. 12 The sensory hypothesis . 12 2.1 A puzzle: the ELAN . 12 2.2 The Sensory Hypothesis . 15 2.3 Potential generators of early effects . 24
An eGovernment Platform for Improving Communication among Municipalities and Citizens in the North of Chile

Government and its further development has been increasingly associated with the use of IT and communication. This interconnection is also happening in developing countries such as Chile. This study is designed to assess the e-government infrastructure and the use of IT and communication among some municipalities in Chile in order to implement a platform that allows government to government (G2G), government to employees and government to citizens (G2C) communication. The proposed platform will allow these municipalities to share information about citizens and corporations in the region. This study is conducted in second region of Chile and considered eight municipal governments. The findings suggest that while all the municipalities are highly interested in e-government initiatives, their infrastructure are different and in a very early stage of development. Thus, the study suggested e-government platform highly flexible to incorporate the differences in infrastructure among the municipalities, as secure as possible to allows government interactions, and implemented using an Application Service Provider (ASP) solution. As a result a distributed system using a Java system (J2EE) was the technology chosen e implemented for the ARM2 e-government platform.
Albumin and Amino Acid Levels as Markers of Adequacy in Continuous Ambulatory Peritoneal Dialysis

Similar to previous findings in HD patients, a markedly decreased serum albumin level has been found to be a strong predictor of morbidity and mortality in CAPD patients. However, a slight decrease in serum albumin levels (to about 30 g/L if measured with nephelometry or the bromcresol purple method) does not always seem to reflect impaired nutritional status or to be associated with an increased morbidity or mortality in CAPD patients. A low serum albumin level among CAPD patients is related to dialysate albumin loss, comorbidity, age, and a low dietary protein intake. The possible relation between the dialysis dose (as assessed by small solute clearances) and serum albumin levels among CAPD patients is much less established and needs further study, although serum albumin tends to increase in prospective studies of increased peritoneal dialysis dose. Although the plasma levels of amino acids seem to be lower in CAPD patients compared to HD patients, this does not reflect the intracellular amino acid pattern in muscle which is less abnormal in CAPD patients, possibly because of the sustained hyperinsulinemia during CAPD, resulting in an in creased intracellular to extracellular gradient. It is at present not established to what extent the amino acid abnormalities are related to the dialysis dose. Malnourished and hypoalbuminemic CAPD patients should be recommended to increase the protein intake, and if this is not effective, the dialysis dose should be increased. Furthermore, the use of amino acid-based peritoneal dialysis solutions is a promising new tool for the treatment of malnourished CAPD patients and may become an important component of CAPD therapy in the future. On the other hand, if the nutritional status deteriorates in spite of these efforts, the patient should be transferred to hemodialysis if possible.
Gain and Fan-Out in a Current-Field Driven Spin Transistor With an Assisting AC Magnetic Field

We investigated gain and fan-out in a current-field driven spin transistor that is driven by a current-induced magnetic field. The basic structure of the transistor consisted of a coplanar waveguide for magnetic field application and an MgO-based magnetic tunnel junction with high magnetoresistance and low resistance area product. Under an assisting ac magnetic field and a dc bias voltage of 0.4 V, we demonstrated substantial power gain of 130, current gain of 4.9, and a fan-out value of 5.7. The scaling of the fan-out value in this device is discussed in detail. The current-field driven spin transistor is proven to be a promising candidate as a basic component of a nonvolatile logic device.
Exploring Mobile Phone Data for Urban Activity Analysis: Applications from Individual Activity Pattern to Group Activity Regularity

Data collected from mobile phones have potential knowledge to provide background information of users, which are quite valuable to many location-aware applications. In the current research, there is relatively few commercial software or application systems to fully meet the requirements of effectively analyzing these characteristics of urban activity. In the paper, we provide with a complete framework for the applications of urban activity analysis from mobile phone location data, including individual behavioral pattern, comparison among individuals, and group activity. We use actual mobile phone data to implement these functions of discovering pattern and regularity of urban activity to show our rich applications related to mobile phone under our framework.
The effect of salinity stress on survival percentage and physiological characteristics in three varieties of pistachio (Pistacia vera)

Abstract Greenhouse pot experiments were conducted to investigate the effect of salinity stress on survival percentage and physiological parameters in three varieties of Pistacia vera L. ; including ‘Sarakhs’, ‘Badami’ and ‘Akbari’. To impose salinity stress, the plants were watered with NaCl solution (250 mM). The physiological characters were investigated at 3rd, 6th and 9th days of salinity induction. Based on our results, Badami showed a greater survival percentage among the other varieties. The highest level of proline, soluble sugar, anthocyanin and glycine-betaine contents and the lowest amount of H2O2 and MDA were also detected in Badami. Large quantities of H2O2, MDA and phenolic compounds were detected in Sarakhs. The highest level of superoxide dismutase (SOD) and catalase (CAT) activity was detected in Badami, while the highest activity of polyphenol oxidase (PPO) was seen in Sarakhs. All physiological characters increased during 3rd to 9th days of salinity induction, except CAT and SOD. In conclusion, Badami was more tolerant to salinity stress in comparison with other varieties due to it’s high capacity for osmotic adjustment and antioxidant protection. The physiological parameters including proline and H2O2 contents, besides the activity of CAT can be used as biochemical markers for identification of tolerant varieties of Pistacia vera.