Miracle-dz/UniFAR-FTUs huggingface dataset:
Persistent Host Markers in Pandemic and H5N1 Influenza Viruses

ABSTRACT Avian influenza viruses have adapted to human hosts, causing pandemics in humans. The key host-specific amino acid mutations required for an avian influenza virus to function in humans are unknown. Through multiple-sequence alignment and statistical testing of each aligned amino acid, we identified markers that discriminate human influenza viruses from avian influenza viruses. We applied strict thresholds to select only markers which are highly preserved in human influenza virus isolates over time. We found that a subset of these persistent host markers exist in all human pandemic influenza virus sequences from 1918, 1957, and 1968, while others are acquired as the virus becomes a seasonal influenza virus. We also show that human H5N1 influenza viruses are significantly more likely to contain the amino acid predominant in human strains for a few persistent host markers than avian H5N1 influenza viruses. This sporadic enrichment of amino acids present in human-hosted viruses may indicate that some H5N1 viruses have made modest adaptations to their new hosts in the recent past. The markers reported here should be useful in monitoring potential pandemic influenza viruses.
First Scottish date from the last interglacial

SIRS At present, only three sites claimed to be of interglacial age are known from Scotland (Fitzpatrick 1965; Birks and Ransom 1969; Birks and Peglar 1979). The interglacial status of these sites—Teindland, Fugla Ness and Sel Ayre—is based on evidence from pollen analysis of organic lenses. Attempts to date two of these deposits by C-assay have produced finite dates of 40100 ± M B. P., 37 000 ± 1? 88 B. P., 34 000 ± g88 B.P. (all from Fugla Ness), and 36 800 ± M B.P. (Sel Ayre). Because the last interglacial is beyond the range of the radiocarbon dating method, these dates are widely regarded as incorrect, having been contaminated by younger material (Sissons 1981). The effective range of the 23oxh/U disequilibrium dating method is much greater. Application of this technique to a speleothem from a cave in Sutherland has provided the first radiometric interglacial date from Scotland. The cave, Uamh an Claonaite [NC 271
GoGetIt!: a tool for generating structure-driven web crawlers

We present GoGetIt! , a tool for generating structure-driven crawlers that requires a minimum effort from the users. The tool takes as input a sample page and an entry point to a Web site and generates a structure-driven crawler based on navigation patterns, sequences of patterns for the links a crawler has to follow to reach the pages structurally similar to the sample page. In the experiments we have performed, structure-driven crawlers generated by GoGetIt! were able to collect all pages that match the samples given, including those pages added after their generation.
Why the garden club couldn't save Youngstown

This paper seeks to understand how the structure of civic relationships shapes trajectories of economic change through an examination of two well-matched Rust Belt cities: Allentown, Pennsylvania and Youngstown, Ohio. Despite sharing very similar economic histories, Allentown and Youngstown have nevertheless taken dramatically different post-industrial paths since the 1970s. The paper analyses how the intersection of economic and civic social networks shapes the strategic choice and possibilities for mobilization of key organizational actors. The analysis shows that differences in the way that civic and economic relationships intersected facilitated collective action in one location and impeded it in the other. However, in contrast to much of the literature on "social capital", the results indicate the downsides of network density, particularly in times of acute economic crisis. More important than network density is that the structure of social relationships facilitate interaction--and mobilization--across social, political and economic divisions.
Slope Failure Hazard in the Atlantic Provinces: A Review

Slope failures present a common hazard throughout the world and have considerable impact on transportation, forestry, coastal and urban development, and other human activities. Although little recognized in much of Atlantic Canada, mass movements have resulted in as many as 71 fatalities in Newfoundland. Due to the high relief of Newfoundland, rockfalls have caused several fatalities and damage to property is frequent. In the Ferryland disaster of ca. 1823, 42 fishermen were reportedly killed when a cave roof collapsed onto them. Debris torrents and flows are widespread particularly in areas of higher relief in Newfoundland and Cape Breton Island, and tend to be most hazardous for highway engineering and community development. Typically, a thin cover of till or colluvium overlies a steeply sloping and polished bedrock substrate. Failure is generally triggered by rainfall events. Rotational slumps of glaciomarine clays are particularly evident along the major river valleys of Labrador and are an important consideration for hydroelectric development such as along the lower Churchill River. Numerous sackungs have been identified, notably in the ultramafic rocks of western Newfoundland. In other areas of Atlantic Canada, earthflows frequently affect transportation routes and commonly involve movement of saturated sediment during spring thaw. Along the Gulf of St. Lawrence and Northumberland Strait and the Bay of Fundy coastlines, the combination of friable Carboniferous and Permian sediments, glaciotectonic activity, frost wedging, and coastal erosion has resulted in numerous small failures, along with incremental retreat of coastal cliffs. Ongoing climate change will have an impact on slope failure activity. The pattern of increasing summer frequency and intensity of thunderstorms and hurricane events, increased winter precipitation in some locations, and more erratic freeze-thaw events during late winter and spring, will result in an increase in debris torrents triggered by precipitation, and rockfalls triggered by freeze-thaw. Human utilization of coastal areas for recreation and residential construction is also increasing both the frequency and hazard of slope failures across Atlantic Canada.
Cerebral Blood Flow Immediately Following Brief Circulatory Stasis

Cerebral blood flow was studied in rabbits immediately following complete circulatory stasis of varying duration. Systemic arterial pressure was measured continuously. The postischemic circulation was examined both by an infusion of carbon black and, in separate experiments, by injection of 14C-antipyrine into the blood. We examined the relationship between the duration of stasis, the postischemic arterial pressure, and the amount of cerebral reperfusion. As stasis increased from 5 to 30 min the pressure required to achieve reperfusion of the entire brain rose from 20 to 100 torr. Following even temporary exposure to arterial pressures above 110 torr all areas of the brain were generally reperfused. Blood flow in reperfused brain varied directly with arterial pressure, indicating failure of autoregulation. At normal (preischemic) arterial pressure, postischemic cortical flow was twice the normal rate. The data indicate that the pressure required to initiate flow in ischemic brain increases as the duration of stasis is lengthened and that once flow occurs there will be a significant hyperperfusion unless systemic arterial pressure is lowered to the low normal or hypotensive range.
Local Volumetric Hybrid-Map-Based Simultaneous Localization and Mapping With Moving Object Tracking

In this paper, we present a novel framework for solving two environmental perception tasks concurrently-simultaneous localization and mapping, and moving-object tracking-by using a Velodyne laser scanner. To extract proper input data for these tasks from the sensor, several sensor data preprocessing algorithms are first addressed. For the simultaneous localization and mapping problem, we propose a local volumetric hybrid-map-based approach using Rao-Blackwellized particle filters. We represent the static environments with the hybrid map consisting of feature and 3-D grid maps. This framework basically allows us to utilize the traditional approaches using a single map. In addition, we derive a new sampling formula by combining a feature measurement likelihood to the traditional grid-map-based approach, and this significantly improves the accuracy and efficiency of the algorithm. The proposed moving-object tracking algorithm is achieved based on the geometric and multiple motion models. We introduce a robust extraction and parameterization method of the geometric shape based on predefined contour models. Then, the geometric shape is inferred with a multiple-base-point method. We establish three motion models, which are utilized for tracking in an adaptive way by using the well-known interacting multiple model algorithm. The algorithms proposed are evaluated using the data sets collected from our test vehicle in the complex urban scenarios. The experimental results show that our approach works well even in real outdoor environments and outperforms traditional approaches.
Relevance and Loci of Odorant Features in the Rat Olfactory Bulb - Statistical Methods for Understanding Olfactory Codes in Glomerular Images

The relationship between physicochemical properties of odor molecules and perceived odor quality is arguably one of the most important issues in olfaction and the rules governing this re lationship remain unknown. Any given odor molecule will stimulate more than one type of receptor in the nose , perhaps hundreds, and this stimulation reflects itself in the neural code of the olfactory nervous system . We present a method to investigate neural coding at the glomerular level of the olfactory bulb, the first rela y for olfactory processing in the brain. Our results give insights into localization of coding sites, relevance of odor ant properties for information processing, and the size of coding zones.
Terminology extraction from text to build an ontology in surgical intensive care

In many medical fields, the maintenance of unabiguous terminologies, the comparison and aggregation of different terminologies go through the building of formal specialized clinical terminologies, the ontologies. In this paper, we describe the building of an ontology in the surgical intensive care medical domain. We considered textual reports as the main source of information and a natural language processing tool, the SYNTEX software, is used to build the ontology. We have tested the possibility for an expert to build a sizeable ontology in a reasonable time. The quality of the ontology has been evaluated according to its capacity to cover the ICD-10 terminology in the field. Examples of coding activity with the ontology are proposed and discussed.
Long-range memory in internal and forced dynamics of millennium-long climate model simulations

Abstract. Northern Hemisphere (NH) temperature records from a palaeoclimate reconstruction and a number of millennium-long climate model experiments are investigated for long-range memory (LRM). The models are two Earth system models and two atmosphere–ocean general circulation models. The periodogram, detrended fluctuation analysis and wavelet variance analysis are applied to examine scaling properties and to estimate a scaling exponent of the temperature records. A simple linear model for the climate response to external forcing is also applied to the reconstruction and the forced climate model runs, and then compared to unforced control runs to extract the LRM generated by internal dynamics of the climate system. The climate models show strong persistent scaling with power spectral densities of the form S(f) ~ f −β with 0.8
Sensitization rates of causative allergens for dogs with atopic dermatitis: detection of canine allergen-specific IgE

Allergen-specific IgE serology tests became commercially available in the 1980s. Since then these tests have been widely used to diagnose and treat allergic skin diseases. However, the relationship between a positive reaction and disease occurrence has been controversial. The purpose of this study was to evaluate allergens using a serologic allergy test in dogs with atopic dermatitis (AD). Dogs clinically diagnosed with AD (n=101) were tested using an allergen-specific IgE immunoassay. Among the total 92 environmental and food allergens, house dust and house dust mites were the most common. Several allergens including airborne pollens and molds produced positive reactions, and which was considered increasing allergens relating to the climate changes. The presence of antibodies against staphylococci and Malassezia in cases of canine AD was warranted in this study. Additionally, strong (chicken, turkey, brown rice, brewer's yeast, and soybean) and weakly (rabbit, vension, duck, and tuna) positive reactions to food allergens could be used for avoidance and limited-allergen trials.
C20 − T carbon: a novel superhard sp3 carbon allotrope with large cavities

Through first-principles calculations, we predict a new superhard carbon allotrope named C20 − T, which possesses a cubic T symmetry with space group No.198(P213). This new carbon allotrope has an all-sp3 hybridized bonding network with 20 atoms in its primitive unit cell. The dynamic, mechanical, and thermal stabilities of this new carbon phase at zero pressure are confirmed by using a variety of state-of-the-art theoretical calculations. Interestingly, despite the fact that C20 − T carbon has a porous structure with large cavities, our calculations identify its superhard properties with the Vickers hardness of 72.76 Gpa. The ideal tensile and shear strength of C20 − T carbon are calculated to be 71.1 and 55.2 GPa respectively, comparable to that of c-BN. Electronic band calculations reveal that this new carbon allotrope is a transparent insulator with an indirect band gap of 5.44 eV. These results broaden our understanding of superhard carbon allotropes.
Personalization of structural PDB files.

PDB format is most commonly applied by various programs to define three-dimensional structure of biomolecules. However, the programs often use different versions of the format. Thus far, no comprehensive solution for unifying the PDB formats has been developed. Here we present an open-source, Python-based tool called PDBinout for processing and conversion of various versions of PDB file format for biostructural applications. Moreover, PDBinout allows to create one's own PDB versions. PDBinout is freely available under the LGPL licence at http://pdbinout.ibch. poznan.pl.
Targeting brain, body and heart for cognitive health and dementia prevention

This report looks into the current research regarding dementia and Alzheimer's disease prevention and offers ideas for possible future solutions. Prevention of dementia is the ultimate aim of a large, albeit under resourced, international research effort. The success of this effort would have enormous benefits for millions of people and save billions of dollars in health care costs. Conversely, the status quo will see the number of Australians living with dementia soar in coming years. Many more people will experience and seek help for mild cognitive impairment. There are many different forms of dementia, a syndrome caused by brain disease and characterised by declining cognitive function that impairs daily activities. Dementia can affect memory, language, attention, judgement, planning, behaviour, mood and personality. Mild cognitive impairment does not significantly impair daily activities, but often represents an earlier stage of cognitive decline. There is no cure for the common forms of cognitive decline and dementia, including the most common, Alzheimer’s disease. A cure may only be achieved by prevention, because the diseases that cause dementia begin many years before symptoms become apparent and gradually damage the brain until it can no longer function normally. Intervening early to stop or slow disease progression, before cognitive impairment emerges, offers the best hope of preventing dementia. Is this achievable? It requires breakthroughs in early detection and intervention. New diagnostic technologies have been developed that can detect the presence of abnormal protein accumulations in the brain that characterise Alzheimer’s disease. The disease can now be detected by brain scans or cerebrospinal fluid tests in the preclinical stage, before any cognitive changes occur.
Multidirectional Asymmetrical Microlens-Array Light Control Films for High Performance Reflective Liquid Crystal Displays

The multidirectional asymmetrical microlens array light control film (MAMA-LCF) is developed to enhance the image brightness and contrast ratio of reflective liquid crystal displays. Through optimized designs and optical alignments, the MAMA-LCF which is constructed with asymmetrical microlens arrays, leads to a ~5x gain in brightness over the MgO standard white and 12:1 contrast ratio for color STN-LCDs, 10x gain and 11.5:1 contrast ratio for PDLC, and 9x gain over the conventional Ch-LCD. In each display, the light control film does not induce visible surface diffusion, moiré patterns and parallax.
Grating of perforated strips as a multi-rejection FSS

Simple grating of perforated strips is considered. Such a grating with one slot over the period, provides rejection frequency response. The grating with two different slots over the period provides frequency response with two rejection resonances. Simple and strict dependences of quality-factor and location of the resonance on the grating geometry are demonstrated. A numerical example for layered FSS forming quasi-elliptical frequency response is proposed as well.
Efficient hosted interpreters on the JVM

Many guest languages are implemented using the Java Virtual Machine (JVM) as a host environment. There are two major implementation choices: custom compilers and so-called hosted interpreters. Custom compilers are complex to build but offer good performance. Hosted interpreters are comparatively simpler to implement but until now have suffered from poor performance. We studied the performance of hosted interpreters and identified common bottlenecks preventing their efficient execution. First, similar to interpreters written in C/C++, instruction dispatch is expensive on the JVM. Second, Java’s semantics require expensive runtime exception checks that negatively affect array performance essential to interpreters. We present two optimizations targeting these bottlenecks and show that the performance of optimized interpreters increases dramatically: we report speedups by a factor of up to 2.45 over the Jython interpreter, 3.57 over the Rhino interpreter, and 2.52 over the JRuby interpreter, respectively. The resulting performance is comparable with that of custom compilers. Our optimizations are enabled by a few simple annotations that require only modest implementation effort; in return, performance increases substantially.
Characterization of a Novel Intramolecular Chaperone Domain Conserved in Endosialidases and Other Bacteriophage Tail Spike and Fiber Proteins*

Folding and assembly of endosialidases, the trimeric tail spike proteins of Escherichia coli K1-specific bacteriophages, crucially depend on their C-terminal domain (CTD). Homologous CTDs were identified in phage proteins belonging to three different protein families: neck appendage proteins of several Bacillus phages, L-shaped tail fibers of coliphage T5, and K5 lyases, the tail spike proteins of phages infecting E. coli K5. By analyzing a representative of each family, we show that in all cases, the CTD is cleaved off after a strictly conserved serine residue and alanine substitution prevented cleavage. Further structural and functional analyses revealed that (i) CTDs are autonomous domains with a high α-helical content; (ii) proteolytically released CTDs assemble into hexamers, which are most likely dimers of trimers; (iii) highly conserved amino acids within the CTD are indispensable for CTD-mediated folding and complex formation; (iv) CTDs can be exchanged between proteins of different families; and (v) proteolytic cleavage is essential to stabilize the native protein complex. Data obtained for full-length and proteolytically processed endosialidase variants suggest that release of the CTD increases the unfolding barrier, trapping the mature trimer in a kinetically stable conformation. In summary, we characterize the CTD as a novel C-terminal chaperone domain, which assists folding and assembly of unrelated phage proteins.
Mercury levels in Lake Powell. Bioamplification of mercury in man-made desert reservoir

Flameless atomic absorption analyses of samples from Lake Powell yield mean mercury levels in ppb of 0.01 in water, 30 in bottom sediments, 10 in shoreline substrates, 34 in plant leaves, 145 in plant debris, 28 in algae, 10 in crayfish, and 232 in fish muscle. Trout were unique in having lower concentrations in muscle than in highly vascularized blood tissues. Concentrations increased with increased body weight and higher levels on the food chain. Muscle of some large fish over 2 kg whole body weight exceeded 500 ppb. Bioamplification of mercury up the food chain and association of mercury with organic matter are demonstrated.
Strategies for handling ethical problems in end of life care: obstacles and possibilities

Background: In end of life care, ethical problems often come to the fore. Little research is performed on ways or strategies for handling those problems and even less on obstacles to and possibilities of using such strategies. A previous study illuminated stroke team members’ experiences of ethical problems and how the teams managed the situation when caring for patients faced with sudden and unexpected death from stroke. These findings have been further explored in this study. Objective: The aim of the study was to illuminate obstacles and possibilities perceived by stroke team members in using strategies for handling ethical problems when caring for patients afflicted by sudden and unexpected death caused by stroke. Research design: A qualitative method with combined deductive and inductive content analysis was utilized. Participants and research context: Data were collected through individual interviews with 15 stroke team members working in stroke units of two associated county hospitals in western Sweden. Ethical considerations: The study was approved by the Regional Ethics Review Board, Gothenburg, Sweden. Permission was also obtained from the director of each stroke unit. Findings: All the studied strategies for handling of ethical problems were found to have both obstacles and possibilities. Uncertainty is shown as a major obstacle and unanimity as a possibility in the use of the strategies. The findings also illuminate the value of the concept “the patient’s best interests” as a starting point for the carers’ ethical reasoning. Conclusion: The concept “the patient’s best interests” used as a starting point for ethical reasoning among the carers is not explicitly defined yet, which might make this value difficult to use both as a universal concept and as an argument for decisions. Carers therefore need to strengthen their argumentation and reflect on and use ethically grounded arguments and defined ethical values like dignity in their clinical work and decisions.