Miracle-dz/UniFAR-FTUs huggingface dataset:
Crystal structures of Nipah and Hendra virus fusion core proteins

The Nipah and Hendra viruses are highly pathogenic paramyxoviruses that recently emerged from flying foxes to cause serious disease outbreaks in humans and livestock in Australia, Malaysia, Singapore and Bangladesh. Their unique genetic constitution, high virulence and wide host range set them apart from other paramyxoviruses. These characteristics have led to their classification into the new genus Henpavirus within the family Paramyxoviridae and to their designation as Biosafety Level 4 pathogens. The fusion protein, an enveloped glycoprotein essential for viral entry, belongs to the family of class I fusion proteins and is characterized by the presence of two heptad repeat (HR) regions, HR1 and HR2. These two regions associate to form a fusion‐active hairpin conformation that juxtaposes the viral and cellular membranes to facilitate membrane fusion and enable subsequent viral entry. The Hendra and Nipah virus fusion core proteins were crystallized and their structures determined to 2.2 Å resolution. The Nipah and Hendra fusion core structures are six‐helix bundles with three HR2 helices packed against the hydrophobic grooves on the surface of a central coiled coil formed by three parallel HR1 helices in an oblique antiparallel manner. Because of the high level of conservation in core regions, it is proposed that the Nipah and Hendra virus fusion cores can provide a model for membrane fusion in all paramyxoviruses. The relatively deep grooves on the surface of the central coiled coil represent a good target site for drug discovery strategies aimed at inhibiting viral entry by blocking hairpin formation.
Non-Uniform Graph Partitioning

We consider the problem of Non-Uniform Graph Partitioning, where the input is an edge-weighted undirected graph G = (V, E) and k capacities n1, . , nk, and the goal is to find a partition {S1, S2, . , Sk} of V satisfying |Sj| ≤ nj for all 1 ≤ j ≤ k, that minimizes the total weight of edges crossing between different parts. This natural graph partitioning problem arises in practical scenarios, and generalizes well-studied balanced partitioning problems such as Minimum Bisection, Minimum Balanced Cut, and Minimum k-Partitioning. Unlike these problems, Non-Uniform Graph Partitioning seems to be resistant to many of the known partitioning techniques, such as spreading metrics, recursive partitioning, and Racke's tree decomposition, because k can be a function of n and the capacities could be of different magnitudes. We present a bicriteria approximation algorithm for Non-Uniform Graph Partitioning that approximates the objective within O(log n) factor while deviating from the required capacities by at most a constant factor. Our approach is to apply stopping-time based concentration results to a simple randomized rounding of a configuration LP. These concentration bounds are needed as the commonly used techniques of bounded differences and bounded conditioned variances do not suffice.
Allele‐specific measurement of low‐density lipoprotein receptor transcript levels

We have developed an assay for allele‐specific determination of low‐density lipoprotein receptor (LDLR) mRNAs. Transcript levels are measured by reverse transcription (RT), PCR, and electrophoresis on an automatic DNA sequencer using fluorescence‐labeled primers and direct quantitation of the allele‐specific RT‐PCR products. The discrimination between the allelic products is based on the use of DNA polymorphisms located in the coding regions of the gene as markers for the individual alleles. Using this method on LDLR mRNA from heterozygous patients with familial hypercholesterolemia (FH) due to a defective LDLR protein, it is possible to relate the expression of the mutant allele directly to the expressed amounts of the normal allele, thus overcoming the problems of using artificial internal standards in the PCR. To validate the method we have measured (1) the range of normal LDLR allele transcript levels, and (2) the transcript levels in patients heterozygous for different types of mutant LDLR alleles associated with FH. The method is general in principle and can be applied in the allele‐specific analysis of transcripts from all enes harbouring DNA polymorphisms in their coding regions. © 1996 Wiley‐Liss, Inc.
A novel sensor system for 3D face scanning based on infrared coded light

In this paper we present a novel sensor system for three-dimensional face scanning applications. Its operating principle is based on active triangulation with a color coded light approach. As it is implemented in the near infrared band, the used light is invisible for human perception. Though the proposed sensor is primarily designed for face scanning and biometric applications, its performance characteristics are beneficial for technical applications as well. The acquisition of 3d data is real-time capable, provides accurate and high resolution depthmaps and shows high robustness against ambient light. Hence most of the limiting factors of other sensors for 3d and face scanning applications are eliminated, such as blinding and annoying light patterns, motion constraints and highly restricted scenarios due to ambient light constraints.
Na‐K‐Cl Cotransport in Chloride‐transporting Epithelia a

The elasmobranch rectal gland has served as a useful model to study features of Na-K-Cl cotransport that are common to many chloride-transporting epithelia. These include: (1) dependence on a Na+ gradient created by Na-K-ATPase; (2) high intracellular Cl- concentration; (3) characteristic inhibitor profile including inhibition by loop diuretics and barium but not by amiloride, SITS, DIDS, or carbonic anhydrase inhibitors; and (4) remarkable energy efficiency of transepithelial transport (25-30 NaCl/l 02). The mechanism by which this is accomplished is clarified by kinetic analysis of experiments with isolated perfused rectal glands of Squalus acanthias in which perfusate concentrations of Na and Cl are systematically varied. These show a Hill coefficient of one for Na+ and two for Cl-, suggesting that one Na+, one K+, and two Cl- interact with the cotransport carrier. Nitrate can substitute for Cl- to some extent, and it itself weakly transported. The loop diuretic bumetanide behaves like a competitive inhibitor of Cl-. The teleological significance of the neutral cotransport of two Cl- with one Na+ and one K+ is that it enables transporting epithelia like the rectal gland, cornea, salivary gland, and thick ascending limb of Henle's loop to double the efficiency of their Na-K-ATPase pump.
Bacteriophage WO Can Mediate Horizontal Gene Transfer in Endosymbiotic Wolbachia Genomes

Phage-mediated horizontal gene transfer (HGT) is common in free-living bacteria, and many transferred genes can play a significant role in their new bacterial hosts. However, there are few reports concerning phage-mediated HGT in endosymbionts (obligate intracellular bacteria within animal or plant hosts), such as Wolbachia. The Wolbachia-infecting temperate phage WO can actively shift among Wolbachia genomes and has the potential to mediate HGT between Wolbachia strains. In the present study, we extend previous findings by validating that the phage WO can mediate transfer of non-phage genes. To do so, we utilized bioinformatic, phylogenetic, and molecular analyses based on all sequenced Wolbachia and phage WO genomes. Our results show that the phage WO can mediate HGT between Wolbachia strains, regardless of whether the transferred genes originate from Wolbachia or other unrelated bacteria.
Cloud Computing infrastructure for latency sensitive applications

The emerging Cloud Computing shows an attractive vision. Cheap hardware takes over workload from expensive dedicated hardware. Easy to develop, deploy and pay as you use model accelerates application release cycle and saves overall cost. The march to All-IP network continues and more latency sensitive mission-critical operations migrate to the Cloud. But the current geographical distributed Cloud introduces unpredictable latencies caused by dispatching, network transmission and computation comparing with traditional computing model. It challenges Cloud Computing and hinders the effort to migrate applications to the Cloud. This paper analyzed the latency in current Cloud and presented an empirical taxonomy of latency with four classes, gave a Cloud Computing infrastructure for different classes of latency sensitive applications with high efficiency and a proof of concept prototype.
Efficacy of early anticoagulant therapy for venous thromboembolism in polytrauma patients in the acute phase.

OBJECTIVE To determine whether antithrombotic therapy with warfarin is effective and safe in patients who developed venous thromboembolism in the acute stage of polytrauma, which is associated with bleeding risk. METHOD A retrospective study of 11 patients (8 males, 3 females; mean age, 39.8 years; injury severity score, 30.1; no fatalities) with deep venous thromboembolism and/or pulmonary embolism who were medicated with heparin and warfarin during their iCU stay. RESULTS Thrombosis was diagnosed at an average of 11.8 days after admission. Thrombus formation was confirmed in pulmonary arteries in 5 cases and in deep veins in 9 cases. Diagnosis was based on Doppler ultrasound findings in 6 cases and on computed tomography findings in 5 cases. anticoagulant therapy was used in 10 cases, but not in 1 case with cerebral contusion. approximately 33 days after starting anticoagulant therapy, thrombi had disappeared or were reduced in size in 9 of 10 patients with no complications observed. CONCLUSIONS Heparin and warfarin therapy cleared deep vein and pulmonary artery thrombosis after polytrauma without any bleeding complications. Further studies are necessary to determine the safe anticoagulant dosage and duration for rapid thrombus removal.
Handling declared information leakage: extended abstract

We address the problem of controlling information leakage in a concurrent declarative programming setting. Our aim is to define formal tools in order to distinguish between authorized, or declared, information flows such as password testing (e.g., ATM, login processes, etc.) and non-authorized ones. We propose to define security policies as rewriting systems. Such policies define how the privacy levels of information evolve. A formal definition of secure processes with respect to a given security policy is given.
Gene selection using interaction information for microarray-based cancer classification

Gene selection is an important pre-processing step in microarray analysis and classification. While traditional gene selection algorithms focus on identifying relevant and irredundant genes, we present a new gene selection algorithm that chooses gene subsets based on their interaction information. Many individual genes may be irrelevant with the class, but when combined together, they can interact and provide information useful for classification. Our proposed gene selection algorithm is tested on four well-known cancer microarray datasets. Initial results show that our algorithm selects effective gene subsets and outperforms prior gene selection algorithm in terms of classification accuracy.
TrkA Expression Levels of Sympathetic Neurons Correlate with NGF‐dependent Survival During Development and After Treatment with Retinoic Acid

Sympathetic neurons depend on the classical neurotrophin nerve growth factor (NGF) for survival by the time they innervate their targets, but not before. The acquisition of NGF responsiveness is thought to be controlled by environmental cues in sympathetic neurons. We have investigated the expression of the signal transducing NGF receptor trkA on mRNA and protein level during development of chick sympathetic neurons obtained from lumbosacral, paravertebral chain ganglia between embryonic days (E) 6.5 and 10. We demonstrate that trkA mRNA levels increase between E6.5 and E10, whereas the levels of trkC and p75 do not change. We also observed a similar increase in trkA protein during this time period. This increase correlates with the increase in NGF‐dependent survival of sympathetic neurons from the corresponding stages in vitro. To define the correlation between trkA expression and NGF‐mediated survival in more detail, trkA expression was adjusted to different levels by treatment with increasing concentrations of retinoic acid. We observed that small changes of trkA mRNA expression levels, below one order of magnitude, are decisive for the ability of immature sympathetic neurons to survive in the presence of NGF. A small and transient increase in trkA mRNA expression was also elicited in vivo by application of retinoids. These data provide evidence that sympathetic neurons upregulate the NGF receptor trkA and in this way acquire NGF‐dependency.
Characterization of linker histone H1FOO during bovine in vitro embryo development

Linker histones H1 are involved in various mechanisms, such as chromatin organization and gene transcription. In different organisms, a unique subtype can be found in the oocyte, however its function remains unclear. To assess the potential involvement of this oocyte linker histone (H1FOO) in chromatin modulation, we have cloned and sequenced the bovine H1FOO cDNA and followed its mRNA profile by quantitative RT‐PCR in the oocyte and throughout bovine early embryo development. The highest level of mRNA was found in the germinal vesicle (GV) oocyte and diminished constantly throughout embryo development. In the 16‐cell embryo and blastocyst, respectively, the mRNA levels were 200 and 2,000 times lower than in the GV oocyte. A specific antibody raised against bovine H1FOO was used to establish protein distribution in the oocyte and preimplantation embryo by immunocytochemistry. In the GV and metaphase II (MII) oocyte, as well as in the 1‐, 2‐ and 4‐cell embryo, H1FOO was localized in the cytoplasm and nucleus. The protein was uniformly spread within the cytoplasm, while it was concentrated onto the chromatin in the nucleus. In the 8‐ to 16‐cell embryo, H1FOO's presence diminished in the cytoplasm, although it was still strongly expressed in nucleus. In the morula and blastocyst stages, the protein was totally lacking. By its position on chromatin, H1FOO could not only be involved in chromatin conformation but could also participate in activation or repression of genes during oogenesis and embryo development before embryonic genome activation. Mol. Reprod. Dev. © 2006 Wiley‐Liss, Inc.
Cultural Translation of Debate in Korean

Transformational processes of borrowed speech activities are addressed since the topic of debate. Debate is rooted in Western political discourse, and is now situated in Korean discourse. This study examines debate in order to understand the concept and rules of speaking which govern that activity. Considering the popularity of debate in Korean, particularly in educational domains, it seems only natural to see how Korean language/culture compares with and has modified a Western-oriented activity. The motivation of this current study is as a response to a prior lack of effort to look at language from a broader context. This study attempts to apply the ethnography of communication to debate proposed by Hymes (1964; 1972; 1974). From the ethnographic approach to communication, speaking is inseparable from the context in which it takes place. The need to examine contextual factors is taken into consideration, and a set of components are identified to study language in use (i.e. setting, participants, keys, and norms). In this view, debate is analyzed as a cultural product. Findings reveal certain diverse features of ‘Koreanized’ debate. The language of Korean debate in expressing disagreement tends to be indirect. While agreement is directly expressed, disagreement is likely to be realized by means of disarmers and prefacing statements. The expression of oppositional opinion also becomes longer. 36 Cultural translation of debate in Korean
Novel Wearable Seismocardiography and Machine Learning Algorithms Can Assess Clinical Status of Heart Failure Patients

Background: Remote monitoring of patients with heart failure (HF) using wearable devices can allow patient-specific adjustments to treatments and thereby potentially reduce hospitalizations. We aimed to assess HF state using wearable measurements of electrical and mechanical aspects of cardiac function in the context of exercise. Methods and Results: Patients with compensated (outpatient) and decompensated (hospitalized) HF were fitted with a wearable ECG and seismocardiogram sensing patch. Patients stood at rest for an initial recording, performed a 6-minute walk test, and then stood at rest for 5 minutes of recovery. The protocol was performed at the time of outpatient visit or at 2 time points (admission and discharge) during an HF hospitalization. To assess patient state, we devised a method based on comparing the similarity of the structure of seismocardiogram signals after exercise compared with rest using graph mining (graph similarity score). We found that graph similarity score can assess HF patient state and correlates to clinical improvement in 45 patients (13 decompensated, 32 compensated). A significant difference was found between the groups in the graph similarity score metric (44.4±4.9 [decompensated HF] versus 35.2±10.5 [compensated HF]; P<0.001). In the 6 decompensated patients with longitudinal data, we found a significant change in graph similarity score from admission (decompensated) to discharge (compensated; 44±4.1 [admitted] versus 35±3.9 [discharged]; P<0.05). Conclusions: Wearable technologies recording cardiac function and machine learning algorithms can assess compensated and decompensated HF states by analyzing cardiac response to submaximal exercise. These techniques can be tested in the future to track the clinical status of outpatients with HF and their response to pharmacological interventions.
Signals in chicken beta-globin DNA influence chromatin assembly in vitro

We have confirmed the result that chicken beta-globin gene chromatin, which possesses the characteristics of active chromatin in erythroid cells, has shortened internucleosome spacings compared with bulk chromatin or that of the ovalbumin gene, which is inactive. To understand how the short (approximately 180-bp) nucleosome repeat arises specifically on beta-globin DNA, we have studied chromatin assembly of cloned chicken beta-globin DNA in a defined in vitro system. With chicken erythrocyte core histones and linker histone H5 as the only cellular components, a cloned 6.2-kb chicken beta-globin DNA fragment assembled into chromatin possessing a regular 180 +/- 5-bp repeat, very similar to what is observed in erythroid cells. A 2-kb DNA subfragment containing the beta A gene and promoter region, but lacking the downstream intergenic region between the beta A and epsilon genes, failed to generate a regular nucleosome array in vitro, suggesting that the intergenic region facilitates linker histone-induced nucleosome alignment. When the beta A gene was placed on a plasmid that contained a known chromatin-organizing signal, nucleosome alignment with a 180-bp periodicity was restored, whereas nucleosomes on flanking plasmid sequences possessed a 210-bp spacing periodicity. Our results suggest that the shortened 180-bp nucleosome spacing periodicity observed in erythroid cells is encoded in the beta-globin DNA sequence and that nucleosome alignment by linker histones is facilitated by sequences in the beta A-epsilon intergenic region.
Comparative histochemical observations on the lipids in the immature and mature stages of Cotylophoron cotylophorum (Paramphistomatidae: Digenea)

Abstract Immature and mature stages of the sheep amphistome Cotylophoron cotylophorum have been analysed histochemically for their lipids. Excretory ducts of the immature worms were the common sites for the accumulation of neutral lipids (triglycerides) and phospholipids which showed very sparse distribution at the corresponding sites in the adult. Phospholipids and lipoproteins observed in the tegument of the adult could not be seen in the immature form. Intestinal caecae of both forms showed the presence of diffused and granular lipids which were relatively less in the immature. The possible physiological significance of these differences in the lipid contents of the immature and mature forms has been discussed.
Channel capacity behavior for simple models of optical fiber communication

We discuss the capacity of certain binary input, ternary output, memoryless communication channels that arise in optical fiber communication (OFC). By using the Kuhn-Tucker condition we provide analytic solutions for channel capacity, under certain conditions. Numerical capacity results are provided along with closed form approximations, which accurately mimic capacity behavior, under all conditions.
Long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia): survey methods, data management, and long-term population trends

Long-term observational studies conducted at large (regional) spatial scales contribute to better understanding of landscape effects on population and evolutionary dynamics, including the conditions that affect long-term viability of species, but large-scale studies are expensive and logistically challenging to keep running for a long time. Here, we describe the long-term metapopulation study of the Glanville fritillary butterfly (Melitaea cinxia) that has been conducted since 1991 in a large network of 4000 habitat patches (dry meadows) within a study area of 50 by 70 km in the Åland Islands in Finland. We explain how the landscape structure has been described, including definition, delimitation, and mapping of the habitat patches; methods of field survey, including the logistics, cost, and reliability of the survey; and data management using the EarthCape biodiversity platform. We describe the long-term metapopulation dynamics of the Glanville fritillary based on the survey. There has been no long-term change in the overall size of the metapopulation, but the level of spatial synchrony and hence the amplitude of fluctuations in year-to-year metapopulation dynamics have increased over the years, possibly due to increasing frequency of exceptional weather conditions. We discuss the added value of large-scale and long-term population studies, but also emphasize the need to integrate more targeted experimental studies in the context of long-term observational studies. For instance, in the case of the Glanville fritillary project, the long-term study has produced an opportunity to sample individuals for experiments from local populations with a known demographic history. These studies have demonstrated striking differences in dispersal rate and other life-history traits of individuals from newly established local populations (the offspring of colonizers) versus individuals from old, established local populations. The long-term observational study has stimulated the development of metapopulation models and provided an opportunity to test model predictions. This combination of empirical studies and modeling has facilitated the study of key phenomena in spatial dynamics, such as extinction threshold and extinction debt.