Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcription of the human cytomegalovirus genome in productively infected cells.

Nuclear and cytoplasmic RNAs, synthesized in cells productively infected with human cytomegalovirus (HCMV) were analysed at various times after infection by liquid and filter DNA-RNA hybridization. Results of these experiments have revealed that: (i) the fraction of the genome transcribed increased as infection progressed. In the nucleus, transcripts represented approx. 20% of the virus DNA sequences at both 2 and 4 h post-infection (p.i.) and 36% of the virus DNA at 40 h p.i; (ii) the increase in virus sequences among nuclear transcripts at late times was prevented by the DNA synthesis inhibitor, 2'-deoxyfluorouridine; (iii) early virus RNA transcripts were subset of those represented in late RNA; (iv) two classes of early RNA were identified by competition hybridization; (v) approx. 10% of the late nuclear transcripts were symmetrical. Results of filter hybridization at DNA excess indicated that virus-specific RNA represented 0.6% of RNA labelled from 0 to 2 h p.i. , and 1.8% of RNA labelled from 28 to 30 h. Polyadenylated RNA isolated from cytoplasm represented 1.2% and 10% of labelled mRNA at 2 h and 30 h respectively. Our data show that during productive infection of human cells by HCMV, gene expression is under temporal, quantitative and post-transcriptional control.
Endobronchial ultrasound for the diagnosis of pulmonary sarcoidosis.

BACKGROUND The diagnosis of pulmonary sarcoidosis can be established by a variety of techniques. Transbronchial lung biopsy is often the preferred approach, but it is frequently nondiagnostic and carries a risk of pneumothorax and bleeding. Mediastinoscopy is often suggested as the next diagnostic step but entails significant cost and associated morbidity. Endobronchial ultrasound (EBUS) with transbronchial needle aspiration (TBNA) is emerging as a safe, minimally invasive tool for the primary diagnosis of mediastinal and hilar lymphadenopathy. The purpose of this study was to assess the utility of EBUS-TBNA for pulmonary sarcoidosis. METHODS Fifty consecutive patients who had been referred for EBUS-TBNA for suspected pulmonary sarcoidosis were included in the study. On-site cytology was used to assess the adequacy of the samples. The presence of noncaseating granulomas without necrosis in the appropriate clinical setting was deemed to be adequate for the diagnosis of pulmonary sarcoidosis. Patients with a negative EBUS-TBNA underwent further histologic biopsy or clinical follow-up to determine the final diagnosis. RESULTS Eighty-two lymph nodes with a median size of 16 mm (range, 4 to 40 mm) were punctured. EBUS-TBNA demonstrated noncaseating granulomas without necrosis in 41 of 48 patients (85%) with a final diagnosis of sarcoidosis. EBUS-TBNA, therefore, has a sensitivity of 85% for the primary diagnosis of pulmonary sarcoidosis. CONCLUSIONS EBUS-TBNA is a safe, minimally invasive tool for the primary diagnosis of pulmonary sarcoidosis that has a high diagnostic yield. EBUS-TBNA should be considered an appropriate alternative diagnostic technique for patients with suspected pulmonary sarcoidosis.
Mining building metadata by data stream comparison

Improving at scale the energy performance of buildings requires that applications are portable among buildings (i.e. the same application in two different buildings). One challenge in enabling portable applications is metadata about building instrumentation. The problem is that there are multiple ways to annotate sensor and actuation points. This makes it difficult to create intuitive queries for retrieving data streams from points. Another problem is the amount of insufficient or missing metadata. We introduce Metafier, a tool for extracting metadata from comparing data streams. Metafier enables a semi-automatic labeling of metadata to building instrumentation. Metafier annotates points with metadata by comparing the data from a set of validated points with unvalidated points. Metafier has three different algorithms to compare points with based on their data. The three algorithms are Dynamic Time Warping (DTW), Empirical Mode Decomposition (EMD), and the differential coefficient. Two of the algorithms compare the slope of the data stream in the values. EMD finds similarities based on the frequency bands among the data stream. By using several algorithms the system is robust enough to handle data streams with only slightly similar patterns. We have evaluated Metafier with points and data from one building located in Denmark. We have evaluated Metafier with 903 points, and the overall accuracy, with only 3 known examples, was 94.71%. Furthermore we found that using DTW for mining points with the point type of room temperature achieved an accuracy as high as 98.13%.
Comparative genetic studies on the APRR5 and APRR7 genes belonging to the APRR1/TOC1 quintet implicated in circadian rhythm, control of flowering time, and early photomorphogenesis.

In Arabidopsis thaliana, a number of circadian-associated factors have been identified. Among those, TOC1 (TIMING OF CAB EXPRESSION 1) is believed to be a component of the central oscillator. TOC1 is a member of a small family of proteins, designated as Arabidopsis PSEUDO-RESPONSE REGULATORS (APRR1/TOC1, APRR3, APRR5, APRR7, and APRR9). Nonetheless, it is not very clear whether or not the APRR family members other than APRR1/TOC1 are also implicated in the mechanisms underlying the circadian rhythm. To address this issue further, here we characterized a set of T-DNA insertion mutants, each of which is assumed to have a severe lesion in each one of the quintet genes (i.e. APRR5 and APRR7). For each of these mutants (aprr5-11 and aprr7-11) we demonstrate that a given mutation singly, if not directly, affects the circadian-associated biological events simultaneously: (i) flowering time in the long-day photoperiod conditions, (ii) red light sensitivity of seedlings during the early photomorphogenesis, and (iii) the period of free-running rhythms of certain clock-controlled genes including CCA1 and APRR1/TOC1 in constant white light. These results suggest that, although the quintet members other than APRR1/TOC1 may not be directly integrated into the framework of the central oscillator, they are crucial for a better understanding of the molecular mechanisms underlying the Arabidopsis circadian clock.
A Comparison of Hard-State and Soft-State Signaling Protocols

One of the key infrastructure components in all telecommunication networks, ranging from the telephone network to VC-oriented data networks to the Internet, is its signaling system. Two broad approaches towards signaling can be identified: so-called hard-state and soft-state approaches. Despite the fundamental importance of signaling, our understanding of these approaches-their pros and cons and the circumstances in which they might best be employed-is mostly anecdotal (and, occasionally, religious). In this paper, we compare and contrast a variety of signaling approaches ranging from "pure" soft state to soft-state approaches augmented with explicit state removal and/or reliable signaling, to a "pure" hard state approach. We develop an analytic model that allows us to quantify state inconsistency in singleand multiple-hop signaling scenarios, and the "cost" (both in terms of signaling overhead and application-specific costs resulting from state inconsistency) associated with a given signaling approach and its parameters (e.g., state refresh and removal timers). Among the class of soft-state approaches, we find that a soft-state approach coupled with explicit removal substantially improves the degree of state consistency while introducing little additional signaling message overhead. The addition of reliable explicit setup/update/removal allows the soft-state approach to achieve comparable (and sometimes better) consistency than that of the hard-state approach
Phosphorylation and disruption of intermediate filament proteins in oligodendrocyte precursor cultures treated with calyculin A

Treatment of primary cultures of oligodendrocyte precursors with calyculin A, a potent inhibitor of protein phosphatases 1 and 2A, caused the phosphorylation of two intermediate filament components, nestin and vimentin. Phosphoamino acid analysis demonstrated that phosphorylation took place mainly on serine and to a lesser extent on threonine residues. In addition, calyculin A treatment caused a shift in the distribution of the two proteins from the Triton‐X‐100 insolube fraction to the detergent soluble fraction as demonstrated by immunoblotting. This redistribution, which was evident within 15 min after treatment and was nearly completed by 90 min, was accompanied by a disruption of the intermediate filament network. Thus, both nestin and vimentin retracted from the cytoplasmic processes to form a large perikaryal ring as shown by immunocytochemical analysis. Both morphological and biochemical changes were reversed 2–5 hr after removal of calyculin A from the culture medium. © 1993 Wiley‐Liss, Inc.
Pseudoanalytical modeling of electromagnetic well-logging sensors inside directional wells

Logging-while-drilling (LWD) electromagnetic sensors provide real-time resistivity data of the geophysical Earth formation for oilfield exploration. Proactive geosteering allows the exploration of deviated and horizontal wells by means of real-time adjustments in the drilling direction to steer the well towards a target region. In this paper, we describe a new pseudoanalytical technique to analyze LWD tools inside directional wells by using sections of toroidal structures, where axial bending is present. Preliminary results demonstrate the ability of our method to accurately modeling LWD tools in deviated drilling conditions.
Changes to Its Peptidoglycan-Remodeling Enzyme Repertoire Modulate β-Lactam Resistance in Pseudomonas aeruginosa

ABSTRACT Pseudomonas aeruginosa is a leading cause of hospital-acquired infections and is resistant to many antibiotics. Among its primary mechanisms of resistance is expression of a chromosomally encoded AmpC β-lactamase that inactivates β-lactams. The mechanisms leading to AmpC expression in P. aeruginosa remain incompletely understood but are intricately linked to cell wall metabolism. To better understand the roles of peptidoglycan-active enzymes in AmpC expression—and consequent β-lactam resistance—a phenotypic screen of P. aeruginosa mutants lacking such enzymes was performed. Mutants lacking one of four lytic transglycosylases (LTs) or the nonessential penicillin-binding protein PBP4 (dacB) had altered β-lactam resistance. mltF and slt mutants with reduced β-lactam resistance were designated WIMPs (wall-impaired mutant phenotypes), while highly resistant dacB, sltB1, and mltB mutants were designated HARMs (high-level AmpC resistant mutants). Double mutants lacking dacB and sltB1 had extreme piperacillin resistance (>256 μg/ml) compared to either of the single knockouts (64 μg/ml for a dacB mutant and 12 μg/ml for an sltB1 mutant). Inactivation of ampC reverted these mutants to wild-type susceptibility, confirming that AmpC expression underlies resistance. dacB mutants had constitutively elevated AmpC expression, but the LT mutants had wild-type levels of AmpC in the absence of antibiotic exposure. These data suggest that there are at least two different pathways leading to AmpC expression in P. aeruginosa and that their simultaneous activation leads to extreme β-lactam resistance.
Elementary Functions Hardware Implementation Using Constrained Piecewise-Polynomial Approximations

A novel technique for designing piecewise-polynomial interpolators for hardware implementation of elementary functions is investigated in this paper. In the proposed approach, the interval where the function is approximated is subdivided in equal length segments and two adjacent segments are grouped in a segment pair. Suitable constraints are then imposed between the coefficients of the two interpolating polynomials in each segment pair. This allows reducing the total number of stored coefficients. It is found that the increase in the approximation error due to constraints between polynomial coefficients can easily be overcome by increasing the fractional bits of the coefficients. Overall, compared with standard unconstrained piecewise-polynomial approximation having the same accuracy, the proposed method results in a considerable advantage in terms of the size of the lookup table needed to store polynomial coefficients. The calculus of the coefficients of constrained polynomials and the optimization of coefficients bit width is also investigated in this paper. Results for several elementary functions and target precision ranging from 12 to 42 bits are presented. The paper also presents VLSI implementation results, targeting a 90 nm CMOS technology, and using both direct and Horner architectures for constrained degree-1, degree-2, and degree-3 approximations.
Mining in Latvian Text Using Semantic Polarity Analysis and Machine Learning Approach

In this paper we demonstrate approaches for opinion mining in Latvian text. Authors have applied, combined and extended results of several previous studies and public resources to perform opinion mining in Latvian text using two approaches, namely, semantic polarity analysis and machine learning. One of the most significant constraints that make application of opinion mining for written content classification in Latvian text challenging is the limited publicly available text corpora for classifier training. We have joined several sources and created a publically available extended lexicon. Our results are comparable to or outperform current achievements in opinion mining in Latvian. Experiments show that lexicon-based methods provide more accurate opinion mining than the application of Naive Bayes machine learning classifier on Latvian tweets. Methods used during this study could be further extended using human annotators, unsupervised machine learning and bootstrapping to create larger corpora of classified text.
Effects of extraction solvent, morphological parts and ripening stage on antioxidative activity of Solanum anguivi fruit.

Effects of extraction solvent namely ethanol, diethylether-chloroform mixture, morphological matrix namely fruit pericarp seed and three ripening stages namely green, yellow and red on antioxidative activity of S. anguivi fruit were studied. Phytochemical screening and assessment of some antioxidative markers were evaluated. Result showed that all samples were endowed with variable amounts of reductones, phenolics, alkaloids and saponins. Quantitative (mg ascorbic acid activity equivalent/ mg sample) assessment showed that antioxidative activity of ethanolic derived extracts were high in terms of total phenolic content (TPC) (75.00196.88), relative reducing power (RRP) (165.00-889.29) and radical scavenging activity (RSA, %) (64.00-85.50) in comparison to low antioxidative activity in terms of TPC (2.81-45.00), RRP (18.21-25.71) and RSA (14.10-40.00) of diethyl ether derived extracts. With respect to morphological matrix, antioxidative activity was in the order : seed fruit pericarp. Stage of ripeness conferred no significant increase on antioxidative activity.
Zinc transport across an endothelium includes vesicular cotransport with albumin

Bovine pulmonary arterial endothelial cells (BPAEC) were grown on permeable polycarbonate membrane filters suspended between two compartments representing the blood vessel lumen and the interstitium. This in vitro model of an endothelium was subjected to a battery of tests to unravel the mechanisms of zinc transport from the blood into peripheral tissues. Transport of 65Zn across BPAEC from media containing zinc concentrations up to 50 μmol/L exhibited both saturable and nonsaturable kinetics. Vmax of the saturable component was 246 ± 43 pmol/(h × cm2) and Km was 2.3 ± 1.3 μmol/L. Transport was pH and temperature sensitive and substantially influenced by albumin and histidine concentrations, but not influenced by analogous minerals or metabolic inhibitors. Inhibition of coated vesicle formation by depletion of intracellular potassium reduced 65Zn transport. Albumin carrying a zinc ion crossed the endothelium more rapidly than zinc‐free albumin. When evaluated together, this body of evidence supports the existence of two major pathways of zinc transport across the pulmonary endothelium, but neither involves entry into the endothelial cells. One pathway involves receptor‐mediated cotransport with albumin by transcytotic vesicles. The other is nonsaturable and involves cotransport with albumin and low molecular weight ligands, principally histidine, through intercellular junctions and nonselective, bulk‐fluid transcytosis. © 1996 Wiley‐Liss, Inc.
Study of large-scale traveling ionospheric disturbances using the data of SuperDARN Hokkaido radar and Russian chirp sounding network

In the paper a study of the large-scale traveling ionospheric disturbances observed on March 17, 2007 is presented. The TIDs main parameters were estimated using the data of SuperDARN Hokkaido radar and Russian chirp sounding network separately. The comparison of the estimations shows some discrepancies in propagation direction that can be explained by convex shape of the TID's front.
Using an ultrasonic vibration microfluidic chip to generate alginate microcapsule

This study managed to generate UV-crosslinking microparticles and wraped in the microcapsules by using an ultrasonic vibration microfluidic chip, and we had demonstrated that the UV-crosslinking microparticles is real wraped in the microcapsule and the microcapsules size was able to be controlled by altering the flow rate of the wraped and sheath phase. Through control this experiment conditions we had successfully generated microcapsules and its size distribution is from 89 µm to 248 µm. The proposed ultrasonic vibration microfluidic chip was easy to fabricate and capable of high throughput and low cost.
Modular Semi-automatic Formal Verification of Critical Systems Software ; Modulaire halfautomatische formele verificatie van kritische systeemsoftware

In the first part of this thesis, we present a case study on successfully verifying the Linux USB BP keyboard driver. Our verification approach is (a) sound, (b) takes into account dynamic memory allocation, complex API rules and concurrency, and (c) is applied on a real kernel driver which was not written with verification in mind. We employ VeriFast, a software verifier based on separation logic. Besides showing that it is possible to verify this device driver, we identify the parts where the verification went smoothly and the parts where the verification approach requires further research to be carried out. In the second part of this thesis, we present a program verification approach that uses an input/output style of reasoning. It can be applied both to programs that perform input/output, and programs that do not but instead manipulate memory. The approach is sound, modular, compositional (I/O actions can be defined on top of other actions) and supports concurrency. It uses Petri nets and separation logic. We have implemented the approach, both for programs that do and do not perform I/O, in the VeriFast verifier and sketched how it can be implemented in the Iris framework for programs that perform I/O.
Melatonin for Treatment of Sleep Disorders: Summary

Studies suggest that sleep disorders affect 50 to 70 million Americans, representing approximately 20 percent of the population. A sleep disorder exists whenever a lower quality of sleep results in impaired functioning or excessive sleepiness. Insomnia, literally “inability to sleep,” has various etiologies and is the most common sleep disorder, affecting between 6 to 12 percent of the adult population. In addition to the adult population, difficulties initiating and maintaining sleep are very common in children, affecting about 15 to 25 percent of this population.
GOL-A Language to Define Tactics in Robot Soccer

Humanoid soccer serves as a suitable benchmark problem for research in artificial intelligence and robotics, and has seen impressive progress in recent years. Thus, many teams participating in the Standard Platform League (SPL) of the RoboCup competition were focusing on improving basic skills for many years. But flexible and fast behavior engineering incorporating team tactics still remains as a challenge, albeit the application of sophisticated team play, consisting of tactics and strategies are still evolving, especially on the robot hardware. In this paper, we introduce the novel language GOL (Group Organizing Language) to design tactical instructions in robot soccer. In addition, we show how the visual editor TOR (Tactic Organizer for Robots) facilitates behavior engineering. Finally, we evaluate the developed components by suitable experiments.
Secure Telemedicine: Biometrics for Remote and Continuous Patient Verification

The technological advancements in the field of remote sensing have resulted in substantial growth of the telemedicine industry. While health care practitioners may now monitor their patients’ well-being from a distance and deliver their services remotely, the lack of physical presence introduces security risks, primarily with regard to the identity of the involved parties. The sensing apparatus, that a patient may employ at home, collects and transmits vital signals to medical centres which respond with treatment decisions despite the lack of solid authentication of the transmitter’s identity. In essence, remote monitoring increases the risks of identity fraud in health care. This paper proposes a biometric identification solution suitable for continuous monitoring environments. The system uses the electrocardiogram (ECG) signal in order to extract unique characteristics which allow to discriminate users. In security, ECG falls under the category of medical biometrics, a relatively young but promising field of biometric security solutions. In this work, the authors investigate the idiosyncratic properties of home telemonitoring that may affect the ECG signal and compromise security. The effects of psychological changes on the ECG waveform are taken into consideration for the design of a robust biometric system that can identify users based on cardiac signals despite physical or emotional variations.
A time-domain block equalization scheme on SIMO frequency selective channels

In recent years, high speed, high-capacity and reliable wireless communications are very demanding. To achieve those requests, it is necessary to solve both time and frequency selective fadings caused by multi-path propagation on wireless channels. Up to now, OFDM as a frequency domain equalization scheme has been mainly considered for the frequency selective fading, but OFDM suffers from its long symbol duration under the time selective fading. On the other hand, single carrier transmission with time domain equalizer does not suffer from the time selective fading because of the very short symbol duration. In this paper, we have proposed the novel time domain equalization schemes for single carrier transmission using block processing on SIMO (single-input multiple-output) frequency selective fading channels, i.e., block linear equalizer (BLE), block equalizer by QRD and M algorithm (QRD-M), etc. They have low complexities and excellent BER performances derived from the path-diversity and the zero padding for IBI (inter-block interference) cancellation.
Sparse array of dielectric resonator antennas for ultra-wide band applications

We present our latest advances in antenna miniaturization using dielectric resonators and design of sparse arrays for ultra-wide band applications without the need for non-linear numerical optimization. We experimentally demonstrate a dual-feed, low-profile, stacked dielectric resonator antenna for the C band with wide bandwidth and high gain, as well as a bio-inspired sparse array design for ultra-wide band applications. We show that the results presented can be successfully extended to other frequency windows, in particular the near-infrared range, where specific issues prevent the use of more conventional antenna and antenna array designs.