jimnoneill/paper-to-field-training huggingface dataset:
Faculty Opinions recommendation of Microarray-based detection and genotyping of viral pathogens.

The detection of viral pathogens is of critical importance in biology, medicine, and agriculture. Unfortunately, existing techniques to screen for a broad spectrum of viruses suffer from severe limitations. To facilitate the comprehensive and unbiased analysis of viral prevalence in a given biological setting, we have developed a genomic strategy for highly parallel viral screening. The cornerstone of this approach is a long oligonucleotide (70-mer) DNA microarray capable of simultaneously detecting hundreds of viruses. Using virally infected cell cultures, we were able to efficiently detect and identify many diverse viruses. Related viral serotypes could be distinguished by the unique pattern of hybridization generated by each virus. Furthermore, by selecting microarray elements derived from highly conserved regions within viral families, individual viruses that were not explicitly represented on the microarray were still detected, raising the possibility that this approach could be used for virus discovery. Finally, by using a random PCR amplification strategy in conjunction with the microarray, we were able to detect multiple viruses in human respiratory specimens without the use of sequence-specific or degenerate primers. This method is versatile and greatly expands the spectrum of detectable viruses in a single assay while simultaneously providing the capability to discriminate among viral subtypes. PMID: 12429852 Funding information This work was supported by: NHLBI NIH HHS, United States Grant ID: HL56385 NIAID NIH HHS, United States Grant ID: AI50496 NHLBI NIH HHS, United States Grant ID: P50 HL056385 NIAID NIH HHS, United States Grant ID: P01 AI050496

Topic: Bacteriophages and microbial interactions
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Alkaline Adjuvant Regulates Proteolytic Activity of Macrophages for Antigen Cross‐Presentation and Potentiates Radioimmunotherapy

Abstract Failures of radiotherapy (RT) in adaptive antitumor immunomodulation often associate with recruited tissue‐repairing macrophages. Although training these macrophages to phagocytose post‐RT cancer cells reverses their protumoral performance, engulfed tumor antigens are severely underrated. In fact, regulating the processing and presentation of tumor antigens, a key determinant of tumor immunogenicity, can fundamentally affect adaptive immune responses. Here it is reported that a simple Alum‐like adjuvant (MgAl‐based hydrotalcite, bLDH) improves radioimmunotherapy via inducing antigen cross‐presentation by macrophages, independent of phenotypes. It is identified that cytidine monophosphate guanosine oligodeoxynucleotide engenders macrophages to phagocytose irradiated cancer cells. However, as semiprofessional antigen‐presenting cells, macrophages possess powerful proteolytic function that is detrimental to antigen presentation. The administration of alkaline bLDH intriguingly relieves the activity of phagolysosomal proteases with acidic pH optima by preventing phagosomal acidification resulting from the vacuolar‐type ATPase proton pump. The adjuvant‐modulated phagolysosomes thus limit antigen degradation and enhance tumor antigen cross‐presentation over tenfold. To examine from an in vivo breast tumor model, trained macrophages successfully cross‐prime antigen‐specific CD8 + T cells and curb RT‐associated metastasis. The findings propose to pay close attention to the effect of adjuvants on precision immunotherapy and highlight the positive contribution of cross‐presenting macrophages in radioimmunotherapy.

Topic: Immune cells in cancer
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
An Algebra for Queueing Networks with Time-Varying Service and Its Application to the Analysis of Integrated Service Networks

We introduce a network model that allows us to capture the time-varying service delivered to a traffic stream due to the presence of random perturbations (e.g., cross-traffic in a communication network). We first present the model for a single network element and then describe how such elements may be interconnected using the operations of fork and join. Such networks may be seen as a generalization of stochastic event graphs and of the class of fork-join networks. The departure processes in such a network satisfy a system of equations along with the exogenous arrival processes and the service processes of the various network elements. This system can be seen as a general time-varying linear system in the (min, plus) semi-field. We obtain an explicit representation of the departure process in terms of the exogenous arrival processes and the service processes. Sufficient conditions are derived for this system to have a unique solution. We also study liveness and absence of explosion in this class of networks. Under appropriate stationarity and ergodicity assumptions, we establish stability theorems for such networks. To this end we first obtain a rate result for the departure process in terms of the rates of the exogenous arrival process and the throughput of a saturated system. We then use this result to show that in a network with a single exogenous arrival, all queue lengths are finite with probability one if the arrival rate is less than the throughput of the saturated system, and to give a representation of the queue-length process. This class of networks allows for a detailed description of controlled sessions in integrated service networks. We also show that it contains several earlier discrete event models of the literature pertaining to stochastic Petri nets, service curves, and fork-join networks and show how the present model unifies them in a single algebraic structure. This structure is that of a semi-ring of functions of two real variables, where the addition is the pointwise minimum and the multiplication a generalization of inf-convolution.

Topic: Advanced Queuing Theory Analysis
Subfield: Management Information Systems
Field: Business, Management and Accounting
Domain: Social Sciences
Differences in the genetic diversity and genome size between two ecotypes of <i>Imperata cylindrica</i> in <scp>Japan</scp>

Abstract Understanding genomic characteristics, such as genetic diversity and genome size, is important because they relate to species and ecotype performance. Imperata cylindrica has two ecotypes, the common type (C‐type) and the early‐flowering type (E‐type), which differ in their ecological characteristics and distribution ranges in Japan. This study aimed to elucidate the genetic diversity of the C‐type and E‐type ecotypes of I. cylindrica throughout Japan, using the multiplexed inter‐simple sequence repeat genotyping by sequencing (MIG‐seq) method. Genome‐wide single‐nucleotide polymorphism data analysis revealed that the C‐type had greater genetic diversity and clearer isolation by distance than the E‐type. Additionally, the C‐type exhibited clear genetic differentiation between the southern part of Amami Oshima and other populations, consistent with differences in its life history. The C‐type also had a smaller genome than the E‐type, which may contribute to faster plant growth and smaller seed mass, as compared with the larger genome of the E‐type. These phenomena were consistent with the characteristics of the C‐type. These results showed that the two ecotypes differ genetically, highlighting the necessity for different guidelines for each ecotype in their conservation and use for revegetation.

Topic: Flowering Plant Growth and Cultivation
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
On the Ekman divergence in an oceanic jet

When a steady wind stress acts on the rapidly northward-moving Gulf Stream, an intense Ekman divergence is produced at the axis of the Stream. This is primarily due to the fact that, at the axis, the effective Coriolis parameter, the sum of the earth's rotation and the shear of the Stream, changes by three-fold in a distance of 15 km. The magnitude of this divergence, when the wind is southerly, is two orders of magnitude larger than that in the regions outside the jet and results in intense upwelling.

Topic: Meteorological Phenomena and Simulations
Subfield: Atmospheric Science
Field: Earth and Planetary Sciences
Domain: Physical Sciences
Supplementary Data from ZNF677 Suppresses Akt Phosphorylation and Tumorigenesis in Thyroid Cancer

&lt;p&gt;1. Supplementary tables include: the relationship between promoter methylation of ZNF677 and clinical characteristics in PTCs, STR DNA profiling of cell lines, primers for PCR, qPCR, pyrosequencing and plasmid construction, the sequences of siRNAs and shRNAs, and informations of antibodies. 2. Supplementary figures include: methylation and expression of ZNF677; the inhibitory effect of ZNF677 on migration and invasion; the effect of ZNF677 on the activity of the MAPK/Erk signaling; the effect of CDKN3 or HSPB1 knockdown on tumor promoting role of ZNF677 depletion in thyroid cancer cells; dual-luciferase reporter assay in HEK293T cells, the effect of CDKN3 or HSPB1 overexpression on tumor inhibitory role of ZNF677 in lung, gastric and breast cancers; Ki-67 staining of xenograft tumors; quantitative illustration of the proteins in figures 3, 5 and 6. 3. Supplementary figure legends.&lt;/p&gt;

Topic: Nutrition, Genetics, and Disease
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Biocrusts modulate carbon losses under warming across global drylands: A bayesian meta-analysis

Biocrusts are critical biological components of drylands and play an important role in soil carbon (C) cycling. However, the effect of biocrusts on soil CO2 exchange across global gradients of temperature and moisture is poorly understood. Moreover, their response to climate change remains highly uncertain. Bayesian hierarchical meta-analyses were performed on 47 published studies to quantify the impact of biocrusts on net soil exchange (NSE) of carbon- the difference between respiration and photosynthesis. Meta-analyses were also used on 23 studies to examine the effects of experimental warming on NSE in biocrusts. Meta-regressions further explored the thermal and wetness sensitivities of biocrust NSE and potential adaptation of biocrust responses to climate change. The development of biocrusts in dryland soils significantly increased NSE by 66.5 [22.2, 112.2] g C m−2yr−1, despite seasonal fluctuations, indicating a net loss of carbon to the atmosphere. Experimental warming, on average, increased biocrust NSE by 22.9 [-0.1, 40.8] g C m−2yr−1 per °C. However, across the spatial climate gradient, aridity limited the effects of warming, while high temperature decreased the thermal sensitivity of biocrust NSE, thus supporting the thermal adaptation of biocrusts. These results emphasize the critical role of biocrusts in modulating soil carbon exchange in response to climate warming across drylands, with particularly high thermal sensitivity in cool and moist regions. This highlights the need to incorporate biocrusts into global carbon budgets and models for a comprehensive understanding of their impact on the carbon cycle.

Topic: Biocrusts and Microbial Ecology
Subfield: Ecology, Evolution, Behavior and Systematics
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Simulation study: emergency diesel-generator availability

The availability of the emergency diesel generator (EDG) standby system of a nuclear power plant is studied by computer simulation. Availability, or the probability that the EDG system is capable of supplying power on demand, is influenced by individual EDG failure and repair rates, system configuration (interconnections) and inspection and maintenance policies. A computer program has been developed that simulates the effects of these elements. Numerical illustrations are presented.

Topic: Power System Reliability and Maintenance
Subfield: Safety, Risk, Reliability and Quality
Field: Engineering
Domain: Physical Sciences
On the Measurement of Concordance Among Variables and Its Application

In educational testing problems, some natural restriction on the coefficients may arise in maximizing the correlation or variance of linear combinations of sets of variables. In this article, two statistics based on restricted principal component and restricted canonical correlation (Das &amp; Sen, 1994) are proposed to measure the intra- and inter-group concordance of variables. We also propose using these statistics as criteria for clustering variables. The analysis of encyclopedia data is provided as an illustration.

Topic: Advanced Statistical Methods and Models
Subfield: Statistics and Probability
Field: Mathematics
Domain: Physical Sciences
A method for fine mapping quantitative trait loci in outbred animal stocks

High-resolution mapping of quantitative trait loci (QTL) in animals has proved to be difficult because the large effect sizes detected in crosses between inbred strains are often caused by numerous linked QTLs, each of small effect. In a study of fearfulness in mice, we have shown it is possible to fine map small-effect QTLs in a genetically heterogeneous stock (HS). This strategy is a powerful general method of fine mapping QTLs, provided QTLs detected in crosses between inbred strains that formed the HS can be reliably detected in the HS. We show here that single-marker association analysis identifies only two of five QTLs expected to be segregating in the HS and apparently limits the strategy's usefulness for fine mapping. We solve this problem with a multipoint analysis that assigns the probability that an allele descends from each progenitor in the HS. The analysis does not use pedigrees but instead requires information about the HS founder haplotypes. With this method we mapped all three previously undetected loci [chromosome (Chr.) 1 logP 4.9, Chr. 10 logP 6.0, Chr. 15 logP 4.0]. We show that the reason for the failure of single-marker association to detect QTLs is its inability to distinguish opposing phenotypic effects when they occur on the same marker allele. We have developed a robust method of fine mapping QTLs in genetically heterogeneous animals and suggest it is now cost effective to undertake genomewide high-resolution analysis of complex traits in parallel on the same set of mice.

Topic: Genetic Mapping and Diversity in Plants and Animals
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Cardiorespiratory and metabolic effects in men on the South Polar Plateau

Dyspnea, anorexia, insomnia, and headaches are frequent symptoms in visitors to the South Pole. Intense cold, low humidity, altitude, and isolation are the major stresses. This study was undertaken to explore the mechanisms of symptoms and the physiological changes in man after arrival at the pole and during the course of one year there. Arterial hypoxia, hyperventilation, and erythrocytosis occurred as anticipated in the high-altitude environment. Exposure to intense cold resulted in little evidence of airway obstruction. Carboxyhemoglobin was present in significant amounts, even in nonsmokers, and may be related to inadequate ventilation of the underground living quarters. These factors and their relationship to isolation, dietary restriction, the sixmonth day-night cycle, and other stresses may be important in the production of symptoms at the pole.

Topic: High Altitude and Hypoxia
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Kelsen's Concept of Authority

The concept of authority is one which may be explicated in many ways—normatively, psychologically, sociologically, politically. That is to say, one may seek to show how it is used in the contexts of normative justifications or of assertions about psychological, sociological or political phenomena. As a normative concept, “authority” relates to situations in which there is given as a reason warranting that something should, must not, or may be done the fact that a particular individual or individuals has so laid it down.

Topic: Political Philosophy and Ethics
Subfield: Political Science and International Relations
Field: Social Sciences
Domain: Social Sciences
Tell Me Your Story: A Case Report on the Use of Occupational Storytelling in the Treatment of a Subject with an Upper Extremity Burn Injury and Complex Psychosocial Issues

Abstract Recovering from a burn can leave a burn survivor struggling to cope with the physical and psychological trauma of their injury. Finding new ways to encourage positive coping strategies and strengthen their sense of self-efficacy and occupational identity can help to encourage the burn survivor to actively participate in their recovery and thereby increase their resiliency after injury. Occupational storytelling is a treatment strategy that utilizes the client’s occupational history and experiences to form their life story. Utilizing this technique with the Kawa Model as the practice model and guide uses the image of life as a river to facilitate the formation of the survivor’s story. The survivor is able to form a narrative of their life story by using their past, present, and future occupational identities as a means cope and problem solve after their injury. This case report will illustrate how the subject “Ray,” a pseudonym, used occupational storytelling to create a narrative of his past strengths to aid in recovering from his burn injury. Through his story, Ray was able to connect to a new occupational identity as a burn survivor rather than victim.

Topic: Occupational Therapy Practice and Research
Subfield: Occupational Therapy
Field: Health Professions
Domain: Health Sciences
Tripartite plant microbe and nutrients interaction in the below ground soil ecosystems

Plants are the sole producers that support all the trophic levels and sustain life on earth. In their growth and development, plants interact with both biotic and abiotic factors. The major biotic factors are the below ground microbes though there also above grown microbes and other herbivores. The abiotic factors are mainly the soil nutrients, soil temperature, moisture and light intensity. This paper therefore aimed at reviewing the various interactions within the soil rhizosphere especially between the plant roots interaction with soil microbes and how they are affected by the soil nutrient availability. The review focussed on identifying the major soil microbes in the soil rhizosphere, interaction of the plant roots with these microbes and how the interactions bring about nutrient cycling as well as dynamics in the trophic levels. From the review it came out clearly that plants interact with both pathogenic and non-pathogenic microbes resulting to varied results. Symbiotic relationship among plant roots and nitrogen fixing bacteria and mycorrhizal fungi results in improved plant growth and yields while interaction with pathogenic soil microbes resulted in disease development and reduced yield. Plants react to soil microbes by producing defensive secondary metabolites like phenolics. From the interaction some of the pathogenic microbes have developed mechanisms of evading the effects of plant defensive compounds by modifying them into forms that are less toxic. The review also shows that plant microbe interaction affects nutrient cycling and is also affected by the nutrients availability. The tripartite interaction of soil microbes, soil abiotic factors and plant root affects the general trophic levels in almost the entire ecosystems.

Topic: Mycorrhizal Fungi and Plant Interactions
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Temporal Coverage Analysis of Router-Based Cloudlets Using Human Mobility Patterns

Responsive applications such as augmented reality require nearby computational offloading units with low latency. The concept of cloudlets is one promising approach that satisfies these requirements. However, due to their wireless range restrictions cloudlets have always been faced with deployment issues of achieving high spatial coverage. In this paper, we look at the coverage issue from an end-user's perspective instead of an established provider perspective: we first argue that temporal coverage of cloudlet accessibility is preferable to spatial coverage for an end- user's experience considering his daily mobility behavior. Next, we investigate what is necessary to achieve a high temporal coverage for an individual user and to what extent is temporal coverage realizable with concepts like router- based cloudlets. To show our hypothesis and understanding the temporal coverage aspect, we collected two comprehensive datasets, an access points dataset with estimated location information and a human mobility dataset consisting of mobility traces from 30 participants within a major city over 4 weeks. Our analysis results show that high temporal coverage can be achieved by a relatively small set of router-based cloudlets since students mainly stay at two places, their homes and university, which represent a large part of the temporal coverage. The remaining rate at which coverage increases heavily depends on the user's mobility patterns. Our findings can be used to place router-based cloudlets at the right locations and estimate the number needed to achieve a certain temporal coverage in urban environments.

Topic: Human Mobility and Location-Based Analysis
Subfield: Transportation
Field: Social Sciences
Domain: Social Sciences
Sir William Howe: A Study in Failed Strategic Leadership

Abstract : This paper examines the strategic leadership competencies of British General William Howe during the American Revolution (1775-1778). During the American War of Independence, General Howe displayed periodic tactical brilliance and operational competence but consistent strategic ineptitude. After arriving in America, Howe was quickly thrust into the position of Commander-in-Chief of British Forces and General of North America. Howe's lack of self awareness, ineptness in managing the personalities of his subordinate commanders, personal biases, and lack of political savvy resulted in the strategic failure of the British war effort. Howe's difficulty in transitioning from tactical, through operational to the strategic level provides a useful example as to the dramatically different challenges faced by current leaders as they prepare for and address similar challenges in our contemporary operational and strategic environment.

Topic: Military History and Strategy
Subfield: Political Science and International Relations
Field: Social Sciences
Domain: Social Sciences
Studies on Isolation and Identification of Yersinia enterocolitica from Cheese and Pasteurized Milk (Turkish with English Abstract)

In this study, dairy and dairy products have been investigated for Yersinia enterocolitica accepted as a human pathogen. For this purpose 66 cheese and 60 pasteurized milk samples were collected in different periods. 19 cheese (28.8%) and 4 pasteurized milk samples (2.4%) were found to be positive according to both biochemical tests and typical appearance of colonies on selective media. Five out of 19 isolated colonies obtained from cheese were atypical, whereas two out of 4 isolated colonies obtained from pasteurized milk were found to be atypical.

Topic: Yersinia bacterium, plague, ectoparasites research
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences