Miracle-dz/UniFAR-FTUs huggingface dataset:
Statistical inference for censored bivariate normal distributions based on induced order statistics

SUMMARY For a censored sample from a bivariate normal distribution consisting of the first k of n order statistics of one variable and the induced order statistics of the other variable, the maximum likelihood estimators of the parameters and the associated large sample covariance matrix are derived. The likelihood ratio test for independence is also given and its power properties studied. These methods are useful in selection problems or in life testing situations in which concomitant variates are observable only for the uncensored primary variates.
Improving Quality of Follow-Up Imaging Recommendations in Radiology

Failure of timely follow-up imaging recommendations can result in suboptimal patient care. Evidence suggests that the use of conditional language in follow-up recommendations is associated with changes to follow-up compliance. Assuming that referring physicians prefer explicit guidance for follow-up recommendations, we develop algorithms to extract recommended modality and interval from follow-up imaging recommendations related to lung, thyroid and adrenal findings. Using a production dataset of 417,451 radiology reports, we observed that on average, follow-up interval was not mentioned in 79.4% of reports, and modality was missing in 47.4% of reports (4,819 reports contained a follow-up imaging recommendation for one of the three findings). We also developed an interactive dashboard to be used to monitor compliance rates. Recognizing the importance of increasing precision of follow-up recommendations, a quality improvement pilot study is underway with the goal of achieving a target where follow-up modality and interval are both explicitly specified.
Transfer of Voltage Independence from a Rat Olfactory Channel to the Drosophila Ether-à-go-go K+ Channel

The S4 segment is an important part of the voltage sensor in voltage-gated ion channels. Cyclic nucleotide-gated channels, which are members of the superfamily of voltage-gated channels, have little inherent sensitivity to voltage despite the presence of an S4 segment. We made chimeras between a voltage-independent rat olfactory channel (rolf) and the voltage-dependent ether-à-go-go K+ channel (eag) to determine the basis of their divergent gating properties. We found that the rolf S4 segment can support a voltage-dependent mechanism of activation in eag, suggesting that rolf has a potentially functional voltage sensor that is silent during gating. In addition, we found that the S3-S4 loop of rolf increases the relative stability of the open conformation of eag, effectively converting eag into a voltage-independent channel. A single charged residue in the loop makes a significant contribution to the relative stabilization of the open state in eag. Our data suggest that cyclic nucleotide-gated channels such as rolf contain a voltage sensor which, in the physiological voltage range, is stabilized in an activated conformation that is permissive for pore opening.
Widespread Neonatal Brain Damage following Calcium Channel Blockade

An abundance of evidence exists that shows calcium channel blockade promotes injury in cultured neurons. However, few studies have addressed the in vivo toxicity of such agents. We now show that the L-type calcium channel antagonist nimodipine promotes widespread and robust injury throughout the neonatal rat brain, in an age-dependent manner. Using both isolated neuronal as well as brain slice approaches, we address mechanisms behind such injury. These expanded studies show a consistent pattern of injury using a variety of agents that lower intracellular calcium. Collectively, these observations indicate that postnatal brain development represents a transitional period for still developing neurons, from being highly sensitive to reductions in intracellular calcium to being less vulnerable to such changes. These observations directly relate to current therapeutic strategies targeting neonatal brain injury.
Power-Efficient and Path-Stable Broadcasting Scheme for Wireless Ad Hoc Networks

The simplest broadcasting scheme in the mobile ad hoc networks (MANETs) uses flooding which may result in the broadcast storm problem. The Multipoint Relays (MPR) is another broadcasting scheme for solving the broadcast storm problem. In MPR, the mobile hosts (MHs) use a greedy algorithm to find a connected dominating set (CDS) by the exchange of 2-hop neighbor information. In order to reduce the size of CDS, the greedy algorithm used by MPR usually selects the farthest nodes from the source called the border nodes as the forwarding nodes. Since the border nodes have a higher probability of moving out the transmission range, the routing paths in MPR from the source to some destinations may be unstable. In this paper, we propose a broadcasting scheme called dynamic power-aware and stability-aware multipoint relays (DPS-MPR) which avoids selecting the border nodes as the forwarding nodes. As a result, the transmission range of MHs can be reduced for saving energy and the negative impact of unstable forwarding nodes can also be reduced. In addition, we use a range buffer to further enhance the stability of the forwarding nodes. We evaluate the performance of the proposed DPS-MPR by using NS2 and compared it with the existing schemes. The experimental result shows that DPS-MPR saves 20%~25% of energy and increases the lifetime of forwarding nodes by several seconds.
Novel Avian Influenza A (H7N9) Virus Induces Impaired Interferon Responses in Human Dendritic Cells

In March 2013 a new avian influenza A(H7N9) virus emerged in China and infected humans with a case fatality rate of over 30%. Like the highly pathogenic H5N1 virus, H7N9 virus is causing severe respiratory distress syndrome in most patients. Based on genetic analysis this avian influenza A virus shows to some extent adaptation to mammalian host. In the present study, we analyzed the activation of innate immune responses by this novel H7N9 influenza A virus and compared these responses to those induced by the avian H5N1 and seasonal H3N2 viruses in human monocyte-derived dendritic cells (moDCs). We observed that in H7N9 virus-infected cells, interferon (IFN) responses were weak although the virus replicated as well as the H5N1 and H3N2 viruses in moDCs. H7N9 virus-induced expression of pro-inflammatory cytokines remained at a significantly lower level as compared to H5N1 virus-induced “cytokine storm” seen in human moDCs. However, the H7N9 virus was extremely sensitive to the antiviral effects of IFN-α and IFN-β in pretreated cells. Our data indicates that different highly pathogenic avian viruses may show considerable differences in their ability to induce host antiviral responses in human primary cell models such as moDCs. The unexpected appearance of the novel H7N9 virus clearly emphasizes the importance of the global influenza surveillance system. It is, however, equally important to systematically characterize in normal human cells the replication capacity of the new viruses and their ability to induce and respond to natural antiviral substances such as IFNs.
SKIN FRICTION RESISTANCE FOR PILES IN COHESIONLESS SOILS

Compression tension and torsion tests have been carried out on model steel piles for the purpose of evaluating the major factors affecting the skin friction resistance of piles driven into or placed in cohesionless soils of various relative densities. A review of available data from tests carried out elsewhere has also been made. The test data obtained by the authors and by others have been compared with the skin friction resistance as calculated by a method first proposed by Dorr.
Study of the airflow through in-vitro oscillating pathological vocal folds

and introduction We present in this study experimental and theoretical results concerning the behaviour of the airflow through the glottis during phonation. This work follows our previous study on the behaviour of the flow in asymmetric models of vocal folds modelling pathologies ([6]). For sake of better control of the parameters, the vocal folds models were rigid but supplied with oscillating airflow. The measurements are now carried out on a more realistic set-up that reproduces the selfsustained oscillations of the vocal folds. It is inspired by previous works on brass player lips oscillations ([2]). By modifying asymmetricaly the mechanical properties of the vocal folds models we can simulate pathologies. We then try to reproduce the measured phenomena by use of numerical simulation with a two-mass model inspired by Lous et all. ([3]). In the first section, we describe the experimental set-up we use in this study, then we look at measurements with a special care to ‘pathological’ cases. Finally, after a brief description of the numerical model, we present numerical simulations that fit our experimental data. 1. Experimental set-up As proposed by Gilbert et all. ([2]), the vocal folds are modelled by two rubber tubes of thickness 0.2 mm filled with pressurised water and mounted on cylindrical brass holders of diameter 11 mm in which half of the metal has been removed over a length Lg = 30 mm (see figure 1). The mechanical model is thus 3 times larger than in ‘real life’. The water pressure in each vocal fold i is imposed by a water column of variable height i w H . In our experiment, i w H ranges between 0.8 and 1.6 meter of water (7.8 10 and 15.7 10 Pa). We define Q as the ratio between water pressures in both vocal folds: 2 1
The internet and information retrieval research: a brief review

The Internet and related information services attract increasing interest from information retrieval researchers. A survey of recent publications show that frequent topics are the effectiveness of search engines, information validation and quality, user studies, design of user interfaces, data structures and metadata, classification and vocabulary based aids, and indexing and search agents. Current research in these areas is briefly discussed. The changing balance between CD‐ROM sources and traditional online searching is quite important and is noted.
Explorer Neurokinin B Receptor Antagonism in Women with Polycystic Ovary Syndrome : A Randomized , Placebo-Controlled Trial

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Cockpit Displays of Traffic and Weather Information: Effects of 3D Perspective Versus 2D Coplanar Rendering and Database Integration

ABSTRACT Objective: The objectives were to evaluate the viability of 3-dimensional (3D) perspective aircraft hazard displays for traffic and weather, in isolation, and when the two were integrated into a single display panel. Background: Prior research identified the costs of such 3D perspective hazard displays, presented from an exocentric perspective, because of their ambiguity in presenting spatial relations in an unstructured 3D space. Research also supported the advantage of display overlay, particularly when both databases (traffic and weather) need to be integrated to make hazard avoidance judgments. The two variables had not been examined in conjunction. Method: Seventeen certified flight instructors flew a series of hazard avoidance maneuvers in a part-task simulator, with four displays, created by the combination of 3D versus 2-dimensional (2D) perspective and separate versus overlay hazard formats. Positioning of traffic and weather that would make it necessary to avoid hazards was designed to allow the study of both the strengths of overlay and weaknesses of 3D integration. Results: The data clearly indicated that hazard avoidance was worse with the 3D perspective display, for both traffic and weather hazards, and pointed to ambiguity as the cause. Display overlay was better than separation, but only when the task required consulting both databases. Conclusion: 3D perspective displays are not advised for hazard presentation on the flight deck. Overlays can be helpful, as long as clutter issues are addressed.
Ranking Query Results using Context-Aware Preferences

To belter serve users' information needs without requiring comprehensive queries from users, a simple yet effective technique is to explore the preferences of users. Since these preferences can differ for each context of the user, we introduce context-aware preferences. To anchor the semantics of context-aware preferences in a traditional probabilistic model of information retrieval, we present a semantics for context-aware preferences based on the history of the user. An advantage of this approach is that the inherent uncertainty of context information, due to the fact that context information is often acquired through sensors, can be easily integrated in the model. To demonstrate the feasibility of our approach and current bottlenecks we provide a naive implementation of our technique based on database views.
A Family of Human Zinc Finger Proteins That Bind Methylated DNA and Repress Transcription

ABSTRACT In vertebrates, densely methylated DNA is associated with inactive transcription. Actors in this process include proteins of the MBD family that can recognize methylated CpGs and repress transcription. Kaiso, a structurally unrelated protein, has also been shown to bind methylated CGCGs through its three Krüppel-like C2H2 zinc fingers. The human genome contains two uncharacterized proteins, ZBTB4 and ZBTB38, that contain Kaiso-like zinc fingers. We report that ZBTB4 and ZBTB38 bind methylated DNA in vitro and in vivo. Unlike Kaiso, they can bind single methylated CpGs. When transfected in mouse cells, the proteins colocalize with foci of heavily methylated satellite DNA and become delocalized upon loss of DNA methylation. Chromatin immunoprecipitation suggests that both of these proteins specifically bind to the methylated allele of the H19/Igf2 differentially methylated region. ZBTB4 and ZBTB38 repress the transcription of methylated templates in transfection assays. The two genes have distinct tissue-specific expression patterns, but both are highly expressed in the brain. Our results reveal the existence of a family of Kaiso-like proteins that bind methylated CpGs. Like proteins of the MBD family, they are able to repress transcription in a methyl-dependent manner, yet their tissue-specific expression pattern suggests nonoverlapping functions.
Mlc regulation of Salmonella pathogenicity island I gene expression via hilE repression

The global regulator Mlc is a repressor of several genes and operons that are involved in sugar uptake and metabolism. A Salmonella enterica serovar Typhimurium mlc mutant showed reduced levels of invasion and cytotoxicity compared to the wild-type, and exhibited reduced expression levels of hilD, hilA and invF, which are regulatory genes in the Salmonella pathogenicity island 1 (SPI1). However, the effects of Mlc on hilD expression and bacterial invasiveness were not seen in the hilE mutant, and hilE expression was increased in the mlc mutant, which suggests that Mlc exerts positive effects on the expression of SPI1 genes by reducing the expression of HilE, which is known to down-regulate the expression of SPI1 genes through direct interaction with HilD. We found that the two known promoters of hilE were not modulated by Mlc, and we identified a third promoter, designated P3, which was repressed by Mlc. The gel mobility shift assay and footprinting analysis revealed that Mlc repressed hilE in a direct manner by binding to two distinct sites in the hilE P3 promoter region. The specific down-regulation of hilD observed in the presence of Mlc regulon-inducible sugars, such as glucose and mannose, could not be detected in the mlc mutant. Based on these results, we propose that Mlc functions to sense the availability of sugars and is linked to virulence gene regulation by its ability to control hilE expression in Salmonella.
Secular and orbital variability of Cir X-1 observed in optical spectra

ABSTRA C T We have observed variations in the optical emission lines from the X-ray binary Circinus X-1. These variations may be attributed both to orbital variations and to long term secular changes in line strength. We have detected double-peaked Ha emission lines on two occasions, providing the first direct evidence for an accretion disc in the system. The separation of the peaks was different on the two occasions, suggesting that the disc might have a different size. The equivalent width of the emission lines dropped by more than a factor of three between 1999 and 2000; this continues the trend seen in earlier data, so that the Ha equivalent width has now declined by a factor of 20 since 1976. The emission lines do not appear to show signature of orbital motion, except for the data taken near phase 0, which show a significant velocity shift. We have observed an absorption component to the He I lines on one occasion. We suggest that, unlike the P Cygni profiles seen in X-ray spectra, this absorption does not arise in the accelerating zone of a radiatively driven wind. Instead, the absorption arises in material previously ejected from the system. It was only seen on this one occasion because the strength of the emission line had dropped dramatically.
What is preserved in the aeolian rock record? A Jurassic Entrada Sandstone case study at the Utah–Arizona border

Aeolian dune fields evolve from protodunes and small dunes into a pattern of progressively fewer, larger and more widely spaced dunes within limits defined by boundary conditions. However, the allogenic boundary conditions that promote aeolian dune‐field development, accumulation of strata and preservation of accumulated strata are not the same. Autogenic processes, such as dune interactions, scour‐depth variation along migrating dunes and substrate cannibalization by growing dunes, result in removal of the stratigraphic record. Moreover, dune‐field events may be collapsed into major erosional bounding surfaces. The question is what stages of evolving dune fields are represented in the rock record? This case study of ca 60 m of Jurassic Entrada Sandstone on the Utah/Arizona border (USA) defines stratigraphic intervals by gross architecture of bounding surfaces and sets of cross‐strata. The interpreted intervals in stratigraphic order consist of: (i) a lower sabkha bed that transitions upward into erosional remnants of small sets representing an initial wet aeolian system; (ii) large, compound cross‐strata representing a mature dune field; (iii) isolated scour‐fill representing negatively climbing dunes that produced ca 25 m of palaeo‐topographic relief; (iv) downlapping sets that fill the landscape‐scale relief; (v) four intervals of stacked climbing sets that each represent short periods of time; and (vi) an upper sabkha bed that again transitions into small sets representing a wet system. Accumulations appear to be associated with sediment pulses, a rising water table, and filling of scoured troughs and landscape‐scale depressions. Preservation of the accumulations is selective and associated with a rising water table, burial and subsidence. The preserved record appears remarkably incomplete. Speculation about missing strata gravitates towards cannibalization of the record of early dune‐field construction, and strata removed during the formation of bounding surfaces. This local Entrada record is thought to represent a point in the spectrum of preservation styles in the rock record.
Differences in infectivity between endosymbiotic Chlorella variabilis cultivated outside host Paramecium bursaria for 50 years and those immediately isolated from host cells after one year of reendosymbiosis

ABSTRACT Chlorella variabilis strain NC64A is an intracellular photobiont of the ciliate Paramecium bursaria. NC64A was isolated from P. bursaria nearly 50 years ago and was thereafter cultivated outside the host. This study was undertaken to detect changes in its infectivity to P. bursaria and its auxotrophy for growth outside the host induced during long-term cultivation. NC64A can grow in Modified Bold's Basal Medium but not in C medium, whereas another symbiotic Chlorella variabilis strain, 1N, that was recently isolated from the host grew in C medium but not in Modified Bold's Basal Medium. With regards infectivity, NC64A in the logarithmic phase of growth showed low infectivity to alga-removed P. bursaria cells, whereas those in the early stationary phase showed high infectivity of about 30%. Those in the decay phase of growth showed no infectivity. Results show that NC64A has infectivity, but the infection rate depends on their culture age in the growth curve. Furthermore, NC64A that had been re-infected to P. bursaria for more than one year and isolated from the host showed a nearly 100% infection rate, which indicates that NC64A can recover its infectivity by re-infection to P. bursaria. Summary: This study was undertaken to detect changes in infectivity induced during long-term cultivation of Chlorella variabilis to alga-free Paramecium bursaria, and its auxotrophy for growth outside the host.
Transcriptional analyses and mapping of the ospC gene in Lyme disease spirochetes

In Lyme disease spirochetes, the ospC gene encodes a 22.7-kDa protein referred to as either the pC or the OspC protein. Using a variety of electrophoretic approaches followed by Southern blotting and probing with oligonucleotide probes, we mapped the ospC gene to a circular 26-kb plasmid. The ospC gene represents the first gene to be mapped to a circular plasmid in Lyme disease spirochetes. The occurrence of this gene in isolates belonging to each of the three Lyme disease-associated species, Borrelia burgdorferi, Borrelia garinii, and the VS461 group, was evaluated. The ospC gene was found to occur in all 21 isolates tested from each of the three species. Differential hybridization with a series of ospC probes in both Northern (RNA) and Southern blot analyses demonstrated that there is sequence variability in the ospC gene among isolates. While the gene was found to be present in all isolates, not all actively transcribed the gene. Transcriptional start site analyses suggest that the gene may be under the control of multiple promoters that are highly similar in nucleotide sequence.
Inference in continuous-time change-point models

We consider the problem of Bayesian inference for continuous-time multi-stable stochastic systems which can change both their diffusion and drift parameters at discrete times. We propose exact inference and sampling methodologies for two specific cases where the discontinuous dynamics is given by a Poisson process and a two-state Markovian switch. We test the methodology on simulated data, and apply it to two real data sets in finance and systems biology. Our experimental results show that the approach leads to valid inferences and non-trivial insights.