Miracle-dz/UniFAR-FTUs huggingface dataset:
Exact probabilities for the indeterminacy of complex networks as perceived through press perturbations

We consider the goal of predicting how complex networks respond to chronic (press) perturbations when characterizations of their network topology and interaction strengths are associated with uncertainty. Our primary result is the derivation of exact formulas for the expected number and probability of qualitatively incorrect predictions about a system’s responses under uncertainties drawn form arbitrary distributions of error. Additional indices provide new tools for identifying which links in a network are most qualitatively and quantitatively sensitive to error, and for determining the volume of errors within which predictions will remain qualitatively determinate (i.e. sign insensitive). Together with recent advances in the empirical characterization of uncertainty in networks, these tools bridge a way towards probabilistic predictions of network dynamics.
Recent developments of genetically encoded optical sensors for cell biology

Optical sensors are powerful tools for live cell research as they permit to follow the location, concentration changes or activities of key cellular players such as lipids, ions and enzymes. Most of the current sensor probes are based on fluorescence which provides great spatial and temporal precision provided that high‐end microscopy is used and that the timescale of the event of interest fits the response time of the sensor. Many of the sensors developed in the past 20 years are genetically encoded. There is a diversity of designs leading to simple or sometimes complicated applications for the use in live cells. Genetically encoded sensors began to emerge after the discovery of fluorescent proteins, engineering of their improved optical properties and the manipulation of their structure through application of circular permutation. In this review, we will describe a variety of genetically encoded biosensor concepts, including those for intensiometric and ratiometric sensors based on single fluorescent proteins, Forster resonance energy transfer‐based sensors, sensors utilising bioluminescence, sensors using self‐labelling SNAP‐ and CLIP‐tags, and finally tetracysteine‐based sensors. We focus on the newer developments and discuss the current approaches and techniques for design and application. This will demonstrate the power of using optical sensors in cell biology and will help opening the field to more systematic applications in the future.
Push-pull constraint graph for efficient points-to analysis

We present techniques for efficient computation of points-to information for C programs. Pointer analysis is an important phase in the compilation process. The computed points-to information and the alias information is useful for client analyses from varied domains such as bug finding, data-flow analysis, identifying security vulnerabilities, and parallelization, to name a few. Former research on pointer analysis has indicated that the main bottleneck towards scalability is manifested by the presence of complex constraints (load p = *q and store *p = q constraints) in the program. Complex constraints add edges to the constraint graph in an unpredictable manner and are responsible for initiating propagation of large amounts of points-to information across edges. We identify that the root cause to this issue is in the homogeneous structure in the constraint graph, due to which existing analyses treat loads and stores in a uniform manner. To address these issues, we present two techniques. First, we represent a constraint graph in a non-homogeneous manner, treat loads and stores in different ways, and employ a push-pull model for non-uniform propagation. Second, we propose lazy propagation which propagates information in the constraint graph only when necessary. We illustrate the effectiveness of our techniques using six large open-source programs and show that they improve the analysis time over a state-of-the-art BDD-based analysis by 33% and over Deep Propagation by 21%.
Exploring the Potential of Wearables to Support Employment for People with Mild Cognitive Impairment

We interviewed adults with mild cognitive impairment working in a sheltered workshop and three support professionals about competitive employment in the community, and what concerns or barriers they may have. While individuals were most concerned about managing their health, professionals also described personal safety and productivity challenges. Families' worries about the safety of their family members were reported to be a barrier to competitive employment. Using a smart watch as a technology probe, we identified three potential applications of wearable technology in tackling these challenges: health support, family support, and productivity support.
Efficient implementation of video post-processing algorithms on the BOPS parallel architecture

Deblocking and deringing are two video post-processing techniques largely used to remove coding artifacts and improve the visual quality when rendering low bit rate coded video. The algorithms used to achieve these tasks are computationally intensive and usually require high speed processors to be able to run in real time. Efficient implementations of signal adaptive filters for video post-processing can be obtained using the specialized features of the parallel BOPS(R) DSP cores. The performance achieved by deblocking and deringing CIF and SDTV size video sequences on the MANTA/sup TM/ prototype chip are illustrated. It is shown that such complex tasks may be executed at low clock rates using the BOPS ManArray/sup TM/ technology.
The Mobility of Carbon Atoms in Graphitic Nanoparticles Studied by the Relaxation of Strain in Carbon Onions

The migration of carbon atoms in graphitic lattices is of great importance in the technology of carbon nanomaterials. Of particular interest is the ability of carbon atoms to jump between the graphitic layers of a nanoparticle, for example, in a carbon nanotube. The thermally induced exchange of atoms between the layers leads to a relaxation of the particle towards an equilibrium structure and determines its morphological or mechanical stability at high temperature. Thermal relaxation would lead to plastic ﬂow by diffusional creep and limit the applicability of graphitic structures. Therefore, a microscopic measurement of the diffusivity of carbon atoms between the layers of graphitic nanoparticles is highly desirable
The Effect of a Fish-oil Fraction on Plasma Lipids

Since the original report from this laboratory in 1952 many investigators have confirmed that the substitution in the diet of vegetable fats containing large amounts of linoleic acid (e.g., corn, cottonseed, safflower, soy oil) for fats containing predominantly saturated fatty acids (e.g., fat from meat, eggs, and dairy products) will result in a marked fall in plasma lipids in most human subjects. It has further been demonstrated that the addition of sufficient amounts of polyunsaturated fats to (a) fat-free diets or (b) diets containing significant amounts of saturated fats will result in a significant fall in the level of plasma lipids. The amount of vegetable fat required under the latter set of conditions is of considerable magnitude and from a clinical standpoint is unfeasible because of the increase in dietary calories. Recently, Ahrens and his associates reported that menhaden oil, a fish oil with an iodine value in excess of 150, had at least as great an effect upon plasma lipids as an equal amount of vegetable oil containing more than 50 per cent of linoleic acid. On the basis of existing information there is some reason to believe that the efficacy of a fat in lowering plasma lipids may be in a measure proportional to the total number of double bonds present in its fatty acids. Conceivably, a highly unsaturated fat containing fatty acids of proper molecular configuration would be capable of lowering plasma lipids when added in relatively small quantities to a diet containing considerable quantities of saturated fat. Accordingly, the ethyl esters of menhaden oil were fractionated by appropriate methods with the yield of the fish oil fraction shown in figure 1. The gas-liquid chromatographic pattern of menhaden oil fatty acids is shown at the top of this figure, the menhaden ethyl ester fraction in the center, and a standard fatty acid mixture is shown at the bottom for orientation purposes. It is apparent that the fractionated material contains very much larger amounts of long-chain highly unsaturated material than the original menhaden oil. The
Phenotypic Plasticity in Uveal Melanoma Is Not Restricted to a Tumor Subpopulation and Is Unrelated to Cancer Stem Cell Characteristics.

Purpose Uveal melanoma (UM) is the most common primary intraocular malignancy in adults and approximately half of those diagnosed will die of metastasis. This study investigates whether UM progression is driven by a subpopulation of stem-like cells, termed "cancer stem cells" (CSCs). Methods Expression of postulated stem cell markers aldehyde dehydrogenase (ALDH), CD44, and CD133 was analyzed in UM cell lines and primary UM short-term cultures (STCs) established from tumor samples. Additionally, the notion of a "cellular hierarchy" within UM was investigated. Finally, the phenomenon of phenotypic plasticity in response to environmental factors was explored. Results We demonstrate that expression of ALDH, CD44, and CD133 does not select for a subpopulation of stem-like cells in either UM cell lines or UM STCs. Furthermore, there is an absence of a cellular hierarchy in cell lines and all cells in culture are able to drive tumor progression. Last, we show that established UM cell lines and UM STCs are plastic in nature and switch their phenotype in response to environmental stimuli. Conclusions We hypothesize that this capacity to undergo phenotypic plasticity may be a consequence of neural crest lineage and renders the exploration of the CSC hypothesis extremely challenging in UM.
Improved classification of breast cancer by analysis of genetic alterations and gene expression profiling

Doel van het onderzoek was betere classificatie van borsttumoren. Hugo Horlings analyseerde genetische veranderingen, zoals het aantal DNA-kopieen of het voorkomen van bepaalde mutaties, en genexpressieprofielen. Normaal borstweefsel onderscheidt zich van invasieve tumoren door verhoogde expressie van microRNA-21. Horlings gebruikte grootschalige RNA-interferentiescreening om genen op te sporen die misschien betrokken zijn bij resistentie tegen Trastuzumab (een middel gebruikt voor de behandeling van borstkanker) en ontdekte een biomarker. Wellicht kan die op termijn gebruikt worden voor identificatie van patienten die niet reageren op Trastuzumab.
Context-Dependency Relation Extraction Based on Web Mining

Entity relation extraction is the task of finding semantic relations between two entities from text. In this paper, we propose a novel Web-mining-based Chinese entity relation extraction approach. This approach explicitly defines and explores the Web mining process and relation feature words for entity relation extraction. The results of the research indicate this method is promising.
Process Mining Methodology for Health Process Tracking Using Real-Time Indoor Location Systems

The definition of efficient and accurate health processes in hospitals is crucial for ensuring an adequate quality of service. Knowing and improving the behavior of the surgical processes in a hospital can improve the number of patients that can be operated on using the same resources. However, the measure of this process is usually made in an obtrusive way, forcing nurses to get information and time data, affecting the proper process and generating inaccurate data due to human errors during the stressful journey of health staff in the operating theater. The use of indoor location systems can take time information about the process in an unobtrusive way, freeing nurses, allowing them to engage in purely welfare work. However, it is necessary to present these data in a understandable way for health professionals, who cannot deal with large amounts of historical localization log data. The use of process mining techniques can deal with this problem, offering an easily understandable view of the process. In this paper, we present a tool and a process mining-based methodology that, using indoor location systems, enables health staff not only to represent the process, but to know precise information about the deployment of the process in an unobtrusive and transparent way. We have successfully tested this tool in a real surgical area with 3613 patients during February, March and April of 2015.
Immunopathogenic and Antibacterial Effects of H3N2 Influenza A Virus PB1-F2 Map to Amino Acid Residues 62, 75, 79, and 82

ABSTRACT The influenza A virus protein PB1-F2 has been linked to the pathogenesis of both primary viral and secondary bacterial infections. H3N2 viruses have historically expressed full-length PB1-F2 proteins with either proinflammatory (e.g., from influenza A/Hong Kong/1/1968 virus) or noninflammatory (e.g., from influenza A/Wuhan/359/1995 virus) properties. Using synthetic peptides derived from the active C-terminal portion of the PB1-F2 protein from those two viruses, we mapped the proinflammatory domain to amino acid residues L62, R75, R79, and L82 and then determined the role of that domain in H3N2 influenza virus pathogenicity. PB1-F2-derived peptides containing that proinflammatory motif caused significant morbidity, mortality, and pulmonary inflammation in mice, manifesting as increased acute lung injury and the presence of proinflammatory cytokines and inflammatory cells in the lungs compared to peptides lacking this motif, and better supported bacterial infection with Streptococcus pneumoniae. Infections of mice with an otherwise isogenic virus engineered to contain this proinflammatory sequence in PB1-F2 demonstrated increased morbidity resulting from primary viral infections and enhanced development of secondary bacterial pneumonia. The presence of the PB1-F2 noninflammatory (P62, H75, Q79, and S82) sequence in the wild-type virus mediated an antibacterial effect. These data suggest that loss of the inflammatory PB1-F2 phenotype that supports bacterial superinfection during adaptation of H3N2 viruses to humans, coupled with acquisition of antibacterial activity, contributes to the relatively diminished frequency of severe infections seen with seasonal H3N2 influenza viruses in recent decades compared to their first 2 decades of circulation.
A microthread technique for studying the viability of microbes in a simulated airborne state.

SUMMARY: A technique is described in which airborne micro-organisms are captured on ultra-fine spider threads. In this state the organisms may be subjected to any environment of interest for extended periods of time, during which their loss of viability may be assayed. Experiments are described which show that the loss of viability is quantitatively similar to that in the true airborne state, provided that the microthread and aerosol environments are identical and that certain other precautions are observed.
MMDB and VAST+: tracking structural similarities between macromolecular complexes

The computational detection of similarities between protein 3D structures has become an indispensable tool for the detection of homologous relationships, the classification of protein families and functional inference. Consequently, numerous algorithms have been developed that facilitate structure comparison, including rapid searches against a steadily growing collection of protein structures. To this end, NCBI’s Molecular Modeling Database (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-date archive of protein structure similarities computed with the Vector Alignment Search Tool (VAST). These similarities have been recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pairwise alignments. Here we present VAST+, an extension to the existing VAST service, which summarizes and presents structural similarity on the level of biological assemblies or macromolecular complexes. VAST+ simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity. VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI’s Entrez query and retrieval system. MMDB and VAST+ can be accessed via http://www.ncbi. nlm.nih. gov/Structure.
Hierarchical pitch target model for Mandarin speech

In this study, a hierarchical pitch target model is proposed to analyze the underlying factors of tones and intonation in Mandarin pitch, which can be applied in speech synthesis systems. This model assumes that the surface pitch contour is produced by approximating the sequential pitch targets assigned to the syllables in an utterance, and each pitch target possesses a hierarchical structure. Moreover, the pitch target associated with each syllable can be generated by adding up the tonal pattern of the syllable and the stepped intonation biases contributed by higher level prosodic units, including prosodic words, prosodic phrases, intonation phrases and utterances. The parameters of these factors can be learned from a speech corpus by a gradient method. Finally, the learned tonal patterns of syllables and the intonation patterns from different prosodic layers are illustrated, and the synthesis experiments show the effectiveness of the presented model.
Recent trends in the epidemiology of non-typhoid Salmonella and antimicrobial resistance: the Israeli experience and worldwide review

Purpose of review The epidemiology of non-typhoid Salmonella has changed significantly since the turn of the century. Interestingly, non-typhoid Salmonella epidemiology in Israel mirrors some important global trends, and these new trends are reviewed. Recent research that has shed more light on the true toll of non-typhoid Salmonella epidemic and resistance is also summarized. Recent findings After more than three decades of a persistent rise, reports from Israel, the US, and the UK indicate that the trend may be reversed and the incidence of NTS illnesses is starting to decline. In contrast, the rates of resistance and multidrug resistance are increasing and expanding worldwide. Of major concern are the increasing rates of multidrug resistance in Salmonella typhimurium, particularly definitive phage-type 104, the alarming increase in low-level ciprofloxacin resistance among several non-typhoid Salmonella serotypes, and the upsurge of high-level ciprofloxacin resistance, mainly in Taiwan. In Israel, high rates of resistance were reported for Salmonella virchow, which accounts for 16% of non-typhoid Salmonella illnesses, and is highly invasive in children. The true burden of Salmonella illnesses in the US was calculated as 520 cases per 100 000, compared with an annual incidence of 13.4 per 100 000 of laboratory confirmed cases. Hospitalization and death rates were 20% and 0.6%, respectively. Infection with resistant non-typhoid Salmonella isolates, and particularly S. typhimurium, increases the likelihood of hospitalization and death. Summary Many important trends of non-typhoid Salmonella epidemiology are not restricted to a single geographic location, but spread worldwide, reflecting the global nature of the epidemic. This epidemic imposes a heavy burden worldwide.
MR imaging-related heating of deep brain stimulation electrodes: in vitro study.

BACKGROUND AND PURPOSE Recent work has shown a potential for excessive heating of deep brain stimulation electrodes during MR imaging. This in vitro study investigates the relationship between electrode heating and the specific absorption rate (SAR) of several MR images. METHODS In vitro testing was performed by using a 1.5-T MR imaging system and a head transmit-receive coil, with bilateral deep brain stimulation systems positioned in a gel saline-filled phantom, and temperature monitoring with a fluoroptic thermometry system. Standardized fast spin-echo sequences were performed over a range of high, medium, and low SAR values. Several additional, clinically important MR imaging techniques, including 3D magnetization prepared rapid acquisition gradient-echo imaging, echo-planar imaging, quantitative magnetization transfer imaging, and magnetization transfer-suppressed MR angiography, were also tested by using typical parameters. RESULTS A significant, highly linear relationship between SAR and electrode heating was found, with the temperature elevation being approximately 0.9 times the local SAR value. Minor temperature elevations, <1 degrees C, were found with the fast spin-echo, magnetization prepared rapid acquisition gradient-echo, and echo-planar clinical imaging sequences. The high dB/dt echo-planar imaging sequence had no significant heating independent of SAR considerations. Sequences with magnetization transfer pulses produced temperature elevations in the 1.0 to 2.0 degrees C range, which was less than theoretically predicted for the relatively high SAR values. CONCLUSION A potential exists for excessive MR imaging-related heating in patients with deep brain stimulation electrodes; however, the temperature increases are linearly related to SAR values. Clinical imaging sequences that are associated with tolerable temperature elevations in the <or=2.0 degrees C range at the electrode tips can be performed safely within an SAR range <2.4 W/kg local (0.9 W/kg whole body averaged).
Plasma treatment of polymers: the effect of the plasma parameters on the chemical, physical, and morphological states of the polymer surface and on the metal-polymer interface

The results of the characterization of plasma-treated polypropylene (PP) and polymethylmethacrylate (PMMA) by X-ray photoelectron spectroscopic, atomic force microscopic (AFM), and surface resistivity measurements are presented. Chemical, physical, and morphological modifications of the polymer surface were investigated. The importance of the neutral gas of the electron cyclotron resonance-radio frequency (ECR-RF) plasma treatment is principally demonstrated. Large differences between the effects of noble and reactive gas plasmas were observed by AFM and surface resistivity measurements. However, the maximum sticking coefficient of evaporated Mg on PP is similar for both Ar and N2 plasma treatments.
ON THE EFFECTIVENESS OF FISCAL DEVALUATIONS IN A MONETARY UNION

This paper examines the effects of fiscal devaluations in a model of a monetary union characterized by national fiscal policies and supranational monetary policy. We show that a revenue-neutral permanent tax shift in one country, which raises its consumption tax to finance a cut to labor taxes, increases welfare of the monetary union in the long run. The distribution of gains among countries depends on their degree of financial integration. We also document that price rigidities result in short-run welfare costs.
A Logical Framework for Identifying and Explaining Unexpected News

The number of news reports published online is now so great that it is impossible for any person to read all of them. Not all of these reports are equally interesting. Automating the identification and evaluation of interest in news is therefore a potentially valuable goal. Traditional methods of information management such as information filtering, information retrieval and collaborative filtering are unsuited to the task of filtering news. This abstract presents a framework that permits the identification of interesting news by means of the identification of violated expectations. Facts derived from news reports, expectations and related background knowledge can be used to (i) justify the decision to rate news as interesting, (ii) explain why the information in the report is unexpected and, (iii) explain the context in which the report appears.