Miracle-dz/UniFAR-FTUs huggingface dataset:
Alpha/Beta Interferons Regulate Murine Gammaherpesvirus Latent Gene Expression and Reactivation from Latency

ABSTRACT Alpha/beta interferon (IFN-α/β) protects the host from virus infection by inhibition of lytic virus replication in infected cells and modulation of the antiviral cell-mediated immune response. To determine whether IFN-α/β also modulates the virus-host interaction during latent virus infection, we infected mice lacking the IFN-α/β receptor (IFN-α/βR−/−) and wild-type (wt; 129S2/SvPas) mice with murine gammaherpesvirus 68 (γHV68), a lymphotropic gamma-2-herpesvirus that establishes latent infection in B cells, macrophages, and dendritic cells. IFN-α/βR−/− mice cleared low-dose intranasal γHV68 infection with wt kinetics and harbored essentially wt frequencies of latently infected cells in both peritoneum and spleen by 28 days postinfection. However, latent virus in peritoneal cells and splenocytes from IFN-α/βR−/− mice reactivated ex vivo with >40-fold- and 5-fold-enhanced efficiency, respectively, compared to wt cells. Depletion of IFN-α/β from wt mice during viral latency also significantly increased viral reactivation, demonstrating an antiviral function of IFN-α/β during latency. Viral reactivation efficiency was temporally regulated in both wt and IFN-α/βR−/− mice. The mechanism of IFN-α/βR action was distinct from that of IFN-γR, since IFN-α/βR−/− mice did not display persistent virus replication in vivo. Analysis of viral latent gene expression in vivo demonstrated specific upregulation of the latency-associated gene M2, which is required for efficient reactivation from latency, in IFN-α/βR−/− splenocytes. These data demonstrate that an IFN-α/β-induced pathway regulates γHV68 gene expression patterns during latent viral infection in vivo and that IFN-α/β plays a critical role in inhibiting viral reactivation during latency.
Expression Profiles of the Trehalose-6-Phosphate Synthase Gene Associated With Thermal Stress in Ostrinia furnacalis (Lepidoptera: Crambidae)

Abstract Trehalose is the major blood sugar in insects. Physiological significance of this compound has been extensively reported. Trehalose-6-phosphate synthase (TPS) is an important enzyme in the trehalose biosynthesis pathway. Full-length cDNAs of TPS (Of tps) and its alternative splicing isoform (Of tps_isoformI) were cloned from the Asian corn borer (ACB), Ostrinia furnacalis (Guenée; Lepidoptera: Crambidae) larvae. The Of tps and Of tps_isoformI transcripts were 2913 and 1689 bp long, contained 2529 and 1293 bp open reading frames encoding proteins of 842 and 430 amino acids with a molecular mass of 94.4 and 48.6 kDa, respectively. Transcriptional profiling and response to thermal stress of Of tps gene were determined by quantitative real-time PCR showing that the Of tps was predominantly expressed in the larval fat body, significantly enhanced during molting and transformation; and thermal stress also induced Of tps expression. Gene structure analysis is indicating that one TPS domain and one trehalose-6-phosphate phosphatase (TPP) domain were located at the N- and C-termini of Of TPS, respectively, while only the TPS domain was detected in OfTPS_isoformI. Three-dimensional modeling and heterologous expression were developed to predict the putative functions of OfTPS and Of TPS_isoformI. We infer that the expression of Of tps gene is thermally induced and might be crucial for larvae survival.
Creepy Tracker Toolkit for Context-aware Interfaces

Context-aware pervasive applications can improve user experiences by tracking people in their surroundings. Such systems use multiple sensors to gather information regarding people and devices. However, when developing novel user experiences, researchers are left to building foundation code to support multiple network-connected sensors, a major hurdle to rapidly developing and testing new ideas. We introduce Creepy Tracker, an open-source toolkit to ease prototyping with multiple commodity depth cameras. It automatically selects the best sensor to follow each person, handling occlusions and maximizing interaction space, while providing full-body tracking in scalable and extensible manners. It also keeps position and orientation of stationary interactive surfaces while offering continuously updated point-cloud user representations combining both depth and color data. Our performance evaluation shows that, although slightly less precise than marker-based optical systems, Creepy Tracker provides reliable multi-joint tracking without any wearable markers or special devices. Furthermore, implemented representative scenarios show that Creepy Tracker is well suited for deploying spatial and context-aware interactive experiences.
Wavelength-dependent UV photodesorption of pure N2 and O2 ices

Context. Ultraviolet photodesorption of molecules from icy interstellar grains can explain observations of cold gas in regions where thermal desorption is negligible. This non-thermal desorption mechanism should be especially important where UV fluxes are high. Aims: N$_{2}$ and O$_{2}$ are expected to play key roles in astrochemical reaction networks, both in the solid state and in the gas phase. Measurements of the wavelength-dependent photodesorption rates of these two infrared-inactive molecules provide astronomical and physical-chemical insights into the conditions required for their photodesorption. Methods: Tunable radiation from the DESIRS beamline at the SOLEIL synchrotron in the astrophysically relevant 7 to 13.6 eV range is used to irradiate pure N$_{2}$ and O$_{2}$ thin ice films. Photodesorption of molecules is monitored through quadrupole mass spectrometry. Absolute rates are calculated by using the well-calibrated CO photodesorption rates. Strategic N$_{2}$ and O$_{2}$ isotopolog mixtures are used to investigate the importance of dissociation upon irradiation. Results: N$_{2}$ photodesorption mainly occurs through excitation of the b$^{1}${$Pi$}$_u$ state and subsequent desorption of surface molecules. The observed vibronic structure in the N$_{2}$ photodesorption spectrum, together with the absence of N$_{3}$ formation, supports that the photodesorption mechanism of N$_{2}$ is similar to CO, i.e., an indirect DIET (Desorption Induced by Electronic Transition) process without dissociation of the desorbing molecule. In contrast, O$_{2}$ photodesorption in the 7-13.6 eV range occurs through dissociation and presents no vibrational structure. Conclusions: Photodesorption rates of N$_{2}$ and O$_{2}$ integrated over the far-UV field from various star-forming environments are lower than for CO. Rates vary between 10$^{-3}$ and 10$^{-2}$ photodesorbed molecules per incoming photon.
Immature truncated O-glycophenotype of cancer directly induces oncogenic features

Significance Cancer cells characteristically express proteins with immature O-glycosylation, but how and why cancer cells express immature O-glycans has remained poorly understood. Here, we report that one prevalent mechanism in pancreatic cancer is epigenetic silencing, rather than somatic mutations in a key chaperone, core 1 β3-Gal-T-specific molecular chaperone (COSMC), required for mature elongated O-glycosylation. We also demonstrate, with the use of well-defined cell systems generated by precise gene editing, that the aberrant O-glycophenotype by itself induces oncogenic features with enhanced growth and invasion. Our study suggests that the characteristic aberrant O-glycophenotype is critical for the development and behavior of cancer and further provides support for immunotherapeutic strategies that target aberrant O-glycans. Aberrant expression of immature truncated O-glycans is a characteristic feature observed on virtually all epithelial cancer cells, and a very high frequency is observed in early epithelial premalignant lesions that precede the development of adenocarcinomas. Expression of the truncated O-glycan structures Tn and sialyl-Tn is strongly associated with poor prognosis and overall low survival. The genetic and biosynthetic mechanisms leading to accumulation of truncated O-glycans are not fully understood and include mutation or dysregulation of glycosyltransferases involved in elongation of O-glycans, as well as relocation of glycosyltransferases controlling initiation of O-glycosylation from Golgi to endoplasmic reticulum. Truncated O-glycans have been proposed to play functional roles for cancer-cell invasiveness, but our understanding of the biological functions of aberrant glycosylation in cancer is still highly limited. Here, we used exome sequencing of most glycosyltransferases in a large series of primary and metastatic pancreatic cancers to rule out somatic mutations as a cause of expression of truncated O-glycans. Instead, we found hypermethylation of core 1 β3-Gal-T-specific molecular chaperone, a key chaperone for O-glycan elongation, as the most prevalent cause. We next used gene editing to produce isogenic cell systems with and without homogenous truncated O-glycans that enabled, to our knowledge, the first polyomic and side-by-side evaluation of the cancer O-glycophenotype in an organotypic tissue model and in xenografts. The results strongly suggest that truncation of O-glycans directly induces oncogenic features of cell growth and invasion. The study provides support for targeting cancer-specific truncated O-glycans with immunotherapeutic measures.
Development and validation of an HPLC-UV method for the simultaneous determination of the antipsychotics clozapine, olanzapine and quetiapine, several beta-blockers and their metabolites.

A simple, accurate and selective column-switching high-performance liquid chromatography (HPLC) method was developed and validated for simultaneous quantification of six beta-blockers (metoprolol, timolol, bisoprolol, propranolol, carvedilol and nebivolol), three of their metabolites (α-hydroxy metoprolol, N-desisopropyl propranolol and 4'-hydroxy carvedilol 4-HCAR), three antipsychotics (olanzapine, clozapine and quetiapine) and three of their metabolites (N-desmethyl olanzapine, N-desmethyl clozapine and N-desalkyl quetiapine) in human serum. After pretreatment on a Merck LiChrospher RP-4 ADS column (25 μm), drugs were separated on a Phenomenex Gemini Phenyl Hexyl 110 A column (250 × 4.6 mm, 5 μm) using a gradient mixture of acetonitrile and potassium dihydrogen phosphate buffer pH 3.1 (containing 10% methanol) as a mobile phase at a flow rate of 1 mL/min. The total analysis time was 40 min. For detection of the analytes, four different UV wavelengths were used: 215, 226, 242 and 299 nm. The method was validated according to the guidelines of the Society of Toxicology and Forensic Chemistry in terms of selectivity, linearity, accuracy, precision and stability and successfully applied for the analysis of the 15 described analytes in human serum.
Vertical alignment of liquid crystals with zinc oxide nanorods

The alignment of liquid crystals (LCs) on zinc oxide (ZnO) nanorods grown vertically on an indium tin oxide (ITO) layer has been investigated as an alternative alignment layer for the vertical alignment of LCs. We found that the degree of vertical alignment strongly depends on the length and density of the vertically aligned ZnO nanorods on the ITO layer and also that a uniform vertical alignment using the proposed structure can be achieved. Finally, vertically aligned LC cells with ZnO nanorods were fabricated and their electro-optical properties were evaluated and compared with those of a conventional vertically aligned LC cell with a polymer alignment layer.
Graph-based Entity Linking using Shortest Path

Entity Linking (EL) is a technique to link named entities in a given context to relevant entities in a given knowledge base. Generally, EL consists of two important task. But, there are limitations of these tasks. To overcome these limitations, we tried to solve the problem of EL through the interdependencies between not only named entities but also common nouns and verbs appearing in the context. The second approach is that the words appeared in context are more closely related and the distance between those is closer. In this paper, we proposed the approaches to overcome these limitations.
Generalized output synchronization of heterogeneous linear multi-agent systems

This paper investigates output synchronization of heterogeneous linear time-invariant systems. Agents distributively communicate measured outputs and synchronize on regulated outputs. Necessary structure of single-agents' drift dynamics is used. Relations between single-agent dynamics, measured outputs and regulated outputs are investigated. Cooperative stability conditions reduce to requirements depending separately on single-agents' structure and interconnecting graph topology, allowing for a distributed control design. Sufficient condition is given based on coordinate transformations which reveal the effects of distributed control on single-agents. It is shown that identical subsystem state synchronization and robustness to interconnections guarantee regulated output synchronization.
A 30μW, 3.3dB NF CMOS LNA for wearable WSN applications

To meet the requirements of wearable wireless sensor networks (W-WSN), the power dissipation of the RF transceiver has to be drastically reduced. This paper presents an ultra-low power LNA with RF performance exceeding the requirement of the intended application. By reusing the current several times and employing passive gm boosting, the LNA input impedance is reduced by a factor of 24 compared to a single transistor using the same current. The resulting power consumption is only 30μW from a 0.8V supply. Simulation results in 40nm TSMC CMOS technology show NF of 3.3dB and gain of 14.2dB at 2.4GHz. Using a widely accepted FOM for LNAs, the proposed circuit is two times better than the best previously published one.
Bit-rate flexible high-speed OTDM add/drop multiplexing

In this paper, we have performed numerical investigations on the ADM performance from an aggregate bit stream of 160Gbit/s to 10Gbit/s and 40Gbit/s data rates. A validated SOA model based on was used in our investigations. The input pulses are sech/sub 2/ shaped with a pulse width of 1.5ps. The delay between control pulses was set to /spl Delta/T=6ps and the average data power was assumed to be -15dBm while the control power was varied. In the present work we assume that the data signal does not saturate the amplifier, i.e., the gain and phase dynamics are determined only by the control signal.
Optical music recognition based on locality-constrained linear coding and double distribution support vector machine

Optical Music Recognition (OMR) has received increasing attention in recent years. In this paper, we adopt the descriptor of Locality-constrained Linear Coding (LLC) and Double Distribution Support Vector Machine (DDSVM) to address music symbol classification in OMR. LLC can obtain stronger feature representation ability compared with original music symbol. Recently, DDSVM is presented to obtain stronger robustness and generalization performance. Therefore, DDSVM is adopted to improve the classification performance in OMR. Moreover, One Versus Rest Double Distribution Support Vector Machine (OVR-DDSVM) is proposed for multi-class music symbol classification. OVR-DDSVM can obtain high accuracy only using linear kernel due to LLC descriptor, and this speeds the classification process. OVR-DDSVM is tested on more than 10000 music symbol images of 20 classes, and experimental results verify the superiority of LLC+DDSVM to other algorithms.
Exploiting sequential Low-Rank Factorization for multilingual DNNS

DNNs have shown remarkable performance in multilingual scenarios; however, these models are often too large in size that adaptation to a target language with relatively small amount of data cannot be well accomplished. In our previous work, we utilized Low-Rank Factorization (LRF) using singular value decomposition for multilingual DNNs to learn compact models which can be adapted more successfully. In this paper, we address two problems associated with that LRF scheme and we propose a compellingly simple methodology to overcome them. First, factorizing all layers results in a huge drop in performance and consequently a long recovery process is required which is not practically efficient. Secondly, LRF can be viewed as a regularization by which some noise is added to weight layers; however, factorizing all layers together equates to adding too much noise which results in bad performance. To mitigate these problems, we propose to apply LRF sequentially. We demonstrate that the lost information after factorizing one layer is small and can be rapidly retrieved; hence, sequential factorization is more efficient. Moreover, the sequential LRF adds only a small amount of noise sequentially which is a better regularization. Our experiments are conducted on five languages from the GlobalPhone dataset.
Geschichte der Flora in der Regio Basiliensis seit 7500 Jahren : Ergebnisse von Untersuchungen pflanzlicher Makroreste aus archäologischen Ausgrabungen

Seit rund 30 Jahren werden im Institut fur prahistorische und naturwissenschaftliche Archaologie (vor 2003 im Botanischen Institut) der Universitat Basel Pflanzenreste von archaologischen Ausgrabungen, auch aus der Basler Region, untersucht. Seit Ende der 80er Jahre werden diese in einer relationalen Datenbank erfasst. Die Menge und Qualitat der Daten hat nun ein Niveau erreicht, das es erlaubt, erstmals eine ubergreifende Auswertung aller in der erweiterten Regio Basiliensis gesammelten archaobotanischen Daten anzugehen. Der in dieser Arbeit behandelte Zeitraum umfasst die Zeit seit den fruhesten grosseren aktiven Eingriffen des Menschen in der Jungsteinzeit (ab 5500 v. Chr.; Einfuhrung von Ackerbau und Viehzucht) bis hin in die Neuzeit (18. Jh. n. Chr.). Unsere Datenbasis ist die Untersuchung von uber 3400 Bodenproben mit einem Gesamtvolumen von uber 12'200 Litern Bodenmaterial und einer Gesamtzahl von uber 1 Million Pflanzenresten. Im Ganzen haben wir 550 Taxa in den total 131 untersuchten Fundstellen nachgewiesen. Die Ergebnisse zeigen, dass der Mensch die Landschaft und damit die Pflanzenwelt in den letzten 7500 Jahren nachhaltig gepragt und verandert hat. Es gibt 2 Zeitraume mit besonders grossen Veranderungen: Die Spatbronzezeit (um 1000 v. Chr.) sowie die Romerzeit (um Chr. Geb.). Die vorliegende Arbeit bezweckt, einen ersten groben Uberblick uber die Veranderungen der (vor allem) synanthropen Pflanzenwelt in den letzten gut 7500 Jahren zu geben. Solche Kenntnisse sind die unabdingbare Voraussetzung fur eine nachhaltige Nutzung der Landschaft und die Erhaltung von Biotopen.
Diffusion tensor imaging the medial longitudinal fasciculus in INO: opportunities and challenges

The medial longitudinal fasciculus (MLF) is a white matter pathway in the brainstem that plays a key role in coordinating eye movements. Injury to the MLF leads to abnormalities in eye movements that can be measured with high precision by oculography, making it an ideal eloquent pathway to study imaging/function correlates. Tractography is an emerging method for identifying white matter pathways and offers the tantalizing promise of noninvasive, quantitative characterization of tissue integrity underlying functional deficits. However, the small caliber of the MLF and partial volume averaging with signal from nearby cerebrospinal fluid pose severe technical challenges to tractography‐based delineation of the MLF. We discuss progress toward the goal of imaging the MLF and potential benefits of achieving this goal. Initial work suggests that ultra‐high field (7 tesla) may complement tractography for characterizing the MLF.
Blocked autophagy enhances radiosensitivity of nasopharyngeal carcinoma cell line CNE-2 in vitro

Abstract Conclusion: Autophagy was involved in the radiation treatment of CNE-2 cells, and blocked autophagy enhances the radiosensitivity of nasopharyngeal carcinoma cell line CNE-2 in vitro. Objective: To determine whether autophagy induced by radiation therapy contributes to tumor cell death or represents a mechanism of resistance to therapy-mediated cell death. Methods: Autophagy in the CNE-2 nasopharyngeal carcinoma cells after radiation treatment was determined by quantitative GFP-LC3 analysis, electron microscopy, and autophagy-related molecules analysis by Western blotting. The contribution of autophagy to the cell viability was determined by MTT assay and clonogenic assay. Results: Autophagy was involved in CNE-2 cells post radiation treatment, and autophagy could ameliorate the cell viability post radiation. On the other hand, inhibition of autophagy could reduce cell viability and decrease the cell survival.
A novel dimensional scaling bilateral control for realization of mobile-hapto

This paper proposes a novel dimensional scaling bilateral control for mobile-hapto. The dimensional scaling bilateral control realizes force feedback between the master and the slave with different motion areas. By this system, an operator can manipulate velocity of the slave, and feel reaction force at the slave. For realizing this system, force and position responses of the master and the slave are transformed to a modal space. And force and position controllers are constructed in the modal space. In the conventional method, however, a precise bilateral controller is not achieved because the dynamics in the modal space is not considered. Therefore, in this paper, the dynamic behaviors in the modal space is described, and a decoupling control system with the disturbance observer in the modal space is realized by the proposed method. Finally, the validity of the proposal is verified by simulation and experimental results.
Seamless Automation and Integration of Machine Learning Capabilities for Big Data Analytics

The paper aims at proposing a solution for designing and developing a seamless automation and integration of machine learning capabilities for Big Data with the following requirements: 1) the ability to seamlessly handle and scale very large amount of unstructured and structured data from diversified and heterogeneous sources; 2) the ability to systematically determine the steps and procedures needed for analyzing Big Data datasets based on data characteristics, domain expert inputs, and data pre-processing component; 3) the ability to automatically select the most appropriate libraries and tools to compute and accelerate the machine learning computations; and 4) the ability to perform Big Data analytics with high learning performance, but with minimal human intervention and supervision. The whole focus is to provide a seamless automated and integrated solution which can be effectively used to analyze Big Data with high-frequency and high-dimensional features from different types of data characteristics and different application problem domains, with high accuracy, robustness, and scalability. This paper highlights the research methodologies and research activities that we propose to be conducted by the Big Data researchers and practitioners in order to develop and support seamless automation and integration of machine learning capabilities for Big Data analytics.
Developing Web services

Web based application developers are attempting to move towards Web services as a mechanism for developing component based Web applications. Unfortunately, traditional tools and development models are inadequately architected to meet the rapidly evolving needs for the future of scalable Web services. Today's Web services development model is mired with complexity as traditional tools and technologies, focused on client-server application development, are ill suited. The author examines the challenges of today's Web service development model.
Somatic mutations of calreticulin in myeloproliferative neoplasms and myelodysplastic/myeloproliferative neoplasms

According to the World Health Organization (WHO) classification of tumors of hematopoietic and lymphoid tissues, myeloproliferative neoplasms (MPN) include chronic myeloid leukemia and the so-called Philadelphia-negative myeloproliferative neoplasms, i.e. essential thrombocythemia, polycythemia vera