Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular Epidemiology of Two Fowl Cholera Outbreaks on a Free-Range Chicken Layer Farm

Two outbreaks of fowl cholera on a multiage free-range egg farm were investigated. The outbreaks occurred in 1994 and 2002. A total of 22 strains of Pasteurella multocida were available for study, 11 from the 1994 outbreak and 11 from the 2002 outbreak. Lesions typical of acute fowl cholera were seen in the 1994 outbreak, whereas both acute and chronic fowl cholera occurred in the 2002 outbreak. The isolates were examined in an extended phenotypic typing methodology, by a P. multocida–specific polymerase chain reaction (PCR), by the Heddleston somatic serotyping scheme, and by restriction endonuclease analysis (REA) typing using the enzyme HpaII. All 22 strains had the same phenotypic properties, all were confirmed as P. multocida by PCR, all were Heddleston serovar 4, and all had the same REA pattern. The results indicate that these 2 outbreaks were caused by the same clone of P. multocida–-despite the 8-year time period between the outbreaks.
Improving Decision Making about Genetic Testing in the Clinic: An Overview of Effective Knowledge Translation Interventions

Background Knowledge translation (KT) interventions are attempts to change behavior in keeping with scientific evidence. While genetic tests are increasingly available to healthcare consumers in the clinic, evidence about their benefits is unclear and decisions about genetic testing are thus difficult for all parties. Objective We sought to identify KT interventions that involved decisions about genetic testing in the clinical context and to assess their effectiveness for improving decision making in terms of behavior change, increased knowledge and wellbeing. Methods We searched for trials assessing KT interventions in the context of genetic testing up to March 2014 in all systematic reviews (n = 153) published by two Cochrane review groups: Effective Practice and Organisation of Care (EPOC) and Consumers and Communication. Results We retrieved 2473 unique trials of which we retained only 28 (1%). Two EPOC reviews yielded two trials of KT interventions: audit and feedback (n = 1) and educational outreach (n = 1). Both targeted health professionals and the KT intervention they assessed was found to be effective. Four Consumers and Communication reviews yielded 26 trials: decision aids (n = 15), communication of DNA-based disease risk estimates (n = 7), personalized risk communication (n = 3) and mobile phone messaging (n = 1). Among these, 25 trials targeted only health consumers or patients and the KT interventions were found to be effective in four trials, partly effective in seven, and ineffective in four. Lastly, only one trial targeted both physicians and patients and was found to be effective. Conclusions More research on the effectiveness of KT interventions regarding genetic testing in the clinical context may contribute to patients making informed value-based decisions and drawing the maximum benefit from clinical applications of genetic and genomic innovations.
Proresolution Lipid Mediators in Multiple Sclerosis — Differential, Disease Severity-Dependent Synthesis — A Clinical Pilot Trial

Background The severity and longevity of inflammation is controlled by endogenous counter-regulatory signals. Among them are long-chain polyunsaturated fatty acid (PUFA)-derived lipid mediators, which promote the resolution of inflammation, an active process for returning to tissue homeostasis. Objective To determine whether endogenous production of lipid-derived resolution agonists is regulated differentially in patients with highly active and less active multiple sclerosis (MS). Design Matched-pairs study in University hospital Neurology department. Patients Based on clinical (relapse frequency) and paraclinical (MRI lesions, contrast enhancement) criteria, 10 pairs of age- and sex-matched patients with relapsing-remitting MS were assigned either to a group with highly active or less active MS. Lipid mediators were quantified in serum and cerebrospinal fluid using LC-MS/MS-based lipidomics. Results Levels of the key arachidonic (ω-6) and docosahexaenoic acid (ω-6)-derived mediators prostaglandins (PG), leukotrienes, hydroxyeicosatetraenoic acids (HETE) and resolution agonists lipoxin A4 (LXA4), resolvin D1 (RvD1) and neuroprotectin D1 (NPD1) were quantified. In the patient group with highly active MS, 15-HETE and PGE2 were increased, which are products of the 15-lipoxygenase and cyclooxygenase pathways. The proresolution mediator RvD1 was significantly upregulated and NPD1 was detected in the highly active group only. LXA4 levels were not increased in patients with highly active MS. Conclusions Lipid mediator pathways are regulated differentially in the cerebrospinal fluid of MS patients, depending on disease severity. Non-exhaustive or possibly ‘delayed’ resolution pathways may suggest a defective resolution program in patients with highly active MS. Longitudinal analyses are required to hetero-typify this differential resolution capacity, which may be associated with disease progression, longevity and eventual termination.
Selection and Evaluation of Tissue Specific Reference Genes in Lucilia sericata during an Immune Challenge

The larvae of the common green bottle fly Lucilia sericata (Diptera: Calliphoridae) have been used for centuries to promote wound healing, but the molecular basis of their antimicrobial, debridement and healing functions remains largely unknown. The analysis of differential gene expression in specific larval tissues before and after immune challenge could be used to identify key molecular factors, but the most sensitive and reproducible method qRT-PCR requires validated reference genes. We therefore selected 10 candidate reference genes encoding products from different functional classes (18S rRNA, 28S rRNA, actin, β-tubulin, RPS3, RPLP0, EF1α, PKA, GAPDH and GST1). Two widely applied algorithms (GeNorm and Normfinder) were used to analyze reference gene candidates in different larval tissues associated with secretion, digestion, and antimicrobial activity (midgut, hindgut, salivary glands, crop and fat body). The Gram-negative bacterium Pseudomonas aeruginosa was then used to boost the larval immune system and the stability of reference gene expression was tested in comparison to three immune genes (lucimycin, defensin-1 and attacin-2), which target different pathogen classes. We observed no differential expression of the antifungal peptide lucimycin, whereas the representative targeting Gram-positive bacteria (defensin-1) was upregulated in salivary glands, crop, nerve ganglion and reached its maximum in fat body (up to 300-fold). The strongest upregulation in all immune challenged tissues (over 50,000-fold induction in the fat body) was monitored for attacin-2, the representative targeting Gram-negative bacteria. Here we identified and validated a set of reference genes that allows the accurate normalization of gene expression in specific tissues of L. sericata after immune challenge.
Subcellular localization and sequence of sea urchin kinesin heavy chain: evidence for its association with membranes in the mitotic apparatus and interphase cytoplasm [published erratum appears in J Cell Biol 1991 Aug;114(4):following 863]

Kinesin was previously immunolocalized to mitotic apparatuses (MAs) of early sea urchin blastomeres (Scholey, J.M., M.E. Porter, P.M. Grissom, and J.R. McIntosh. 1985. Nature [Lond.]. 318:483-486). Here we report evidence that this MA-associated motor protein is a conventional membrane-bound kinesin, rather than a kinesin-like protein. Our evidence includes the observation that the deduced amino acid sequence of this sea urchin kinesin heavy chain is characteristic of a conventional kinesin. In addition, immunolocalizations using antibodies that distinguish kinesin from kinesin-like proteins confirm that conventional kinesin is concentrated in MAs. Finally, our immunocytochemical data further suggest that conventional kinesin is associated with membranes which accumulate in MAs and interphase asters of early sea urchin embryos, and with vesicles that are distributed in the perinuclear region of coelomocytes. Thus kinesin may function as a microtubule-based vesicle motor in some MAs, as well as in the interphase cytoplasm.
Enactment and communicative competence in aphasia: A functional linguistic perspective

References Eggins, S. , & Slade, D. (2004). Analysing casual conversation. London: Equinox. Groenewold, R. , Bastiaanse, R. , Nickels, L. , & Huiskes, M. (2014). Perceived liveliness and speech comprehensibility in aphasia: the effects of direct speech in auditory narratives. Int J Lang Commun Disord, 49(4), 486-497. Holland,A. (1977). Some practical considerations in aphasia rehabilitation. In M. Sullivan & M. Kommers (Eds.), Rationale for Adult AphasiaTherapy (pp. 167-180). University of Nebraska, Lincoln: NB. Lind, M. (2002). The use of prosody in interaction: Observations from a case study of a Norwegian speaker with a non-fluent type of aphasia. In F.Windsor, M. L. Kelly, & N. Hewlett (Eds.), Investigations in clinical phonetics and linguistics (pp. 373-389). Mahwah, NJ: Lawrence ErlbaumAssociates Ind. MacWhinney, B. , Fromm,D. , Forbes, M. , & Holland,A. (2011). AphasiaBank: Methods for studying discourse. Aphasiology, 25(11), 1286-1307. Merrill, N. , Gallo, E. , & Fivush, R. (2015). Gender Differences in Family Dinnertime Conversations.Discourse Processes, 52(7), 533-558. Oelschlaeger, M. L. , & Damico, J. S. (1998). Joint productions as a conversational strategy in aphasia. Clinical Linguistics & Phonetics, 12(6), 459-480. Richmond,V. P., & McCroskey, J. C. (1985). Communication: apprehension, avoidance, and effectiveness. Scottsdale,Arizona: Gorsuch Scarisbrick. Wilkinson, R. , Beeke, S. , & Maxim, J. (2010). Formulating actions and events with limited linguistic resources: Enactment and iconicity in agrammatic aphasic talk. Research on Language and Social Interaction, 43(1), 57-84. PROCEDURES
Prior oropharyngeal colonization and ventilator-associated pneumonia

This study evaluated the relationship between previous colonization of the oropharynx and development of ventilator-associated pneumonia through the classification of genomic fingerprint pattern by pulsed-field gel electrophoresis of both oxacillin-resistant and oxacillin-susceptible Staphylococcus aureus isolates obtained from hospitalized patients in an intensive care unit.
The role of digital user feedback in a user-centred development process in citizen science

In citizen science, user-centred development is often emphasised for its potential to involve participants in the development of technology. We describe the development process of the mobile app “Naturblick” as an example of a user-centred design in citizen science and discuss digital user feedback with regard to the users' involvement. We have identified three types of digital user feedback using qualitative content analysis: general user feedback, contributory user feedback and co-creational user feedback. The results indicate that digital user feedback can link UCD techniques with more participatory design approaches.
Finding the Optimal Subspace for Clustering

The ability to simplify and categorize things is one of the most important elements of human thought, understanding, and learning. The corresponding explorative data analysis techniques -- dimensionality reduction and clustering -- have initially been studied by our community as two separate research topics. Later algorithms like CLIQUE, ORCLUS, 4C, etc. Performed clustering and dimensionality reduction in a joint, alternating process to find clusters residing in low-dimensional subspaces. Such a low-dimensional representation is extremely useful, because it allows us to visualize the relationships between the various objects of a cluster. However, previous methods of subspace, correlation or projected clustering determine an individual subspace for each cluster. In this paper, we demonstrate that it is even much more valuable to find clusters in one common low-dimensional subspace, because then we can study not only the intra-cluster but also the inter-cluster relationships of objects, and the relationships of the whole clusters to each other. We develop the mathematical foundation ORT (Optimal Rigid Transform) to determine an arbitrarily-oriented subspace, suitable for a given cluster structure. Based on ORT, we propose FOSSCLU (Finding the Optimal Sub Space for Clustering), a new iterative clustering algorithm. Our extensive experiments demonstrate that FOSSCLU outperforms the previous methods even in both aspects: clustering and dimensionality reduction.
Unit Groups of Integral Finite Group Rings with No Noncyclic Abelian Finite p-Subgroups

It is shown that in the units of augmentation one of an integral group ring ℤ G of a finite group G, a noncyclic subgroup of order p 2, for some odd prime p, exists only if such a subgroup exists in G. The corresponding statement for p = 2 holds by the Brauer–Suzuki theorem, as recently observed by Kimmerle.
Ogmios: a scalable NLP platform for annotating large web document collections

While NLP tools are now widely available, their use can be problematic considering the lack of homogeneity of their input/output format, the variation of the granularity of their information, but also the difficulties to process large amounts of heterogeneous documents in a reasonable time, and their tunability to a specific domain. To address these problems, we propose a configurable platform to enrich very large collections of French and English specialised documents. The platform is a modularized framework. Each module carries out an annotation step by using existing NLP tools and can be tuned to a domain by adding specific resources: named entity recognition, sentence and word segmentation, lemmatisation, POS tagging, term tagging and parsing. Linguistic annotations are recorded in a stand-off XML format. We focus on the robustness of the annotation process to help the creation of annotated corpora from the web. We have tested the scalability of the platform on two collections of 55,329 biomedical web documents (107 millions of words) and 47,393 Search Engine News (13 millions of words). The collections have been annotated until the term tagging, respectively in 35 hours and 3 hours.
Protein folding and binding can emerge as evolutionary spandrels through structural coupling

Significance Most proteins must be folded to perform their function, which typically involves binding another molecule. This property enables protein traits of stable folding and strong binding to emerge through adaptation even when the trait itself does not increase the organism’s fitness. Such traits, known as evolutionary “spandrels,” have been investigated across many organisms and scales of biology. Here we show that proteins can spontaneously evolve strong but nonfunctional binding interactions. Moreover, evolution of such interactions can be highly unpredictable, with chance mutation events determining the outcome. In contrast, evolution of functional interactions follows a more predictable pattern of first gaining folding stability and then losing it as the new binding function improves. Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and gene regulation. These interactions often evolve in response to changes in the protein’s chemical or physical environment (such as the addition of an antibiotic). Several recent studies have shown the importance of folding stability in constraining protein evolution. Here we investigate how structural coupling between folding and binding—the fact that most proteins can only bind their targets when folded—gives rise to an evolutionary coupling between the traits of folding stability and binding strength. Using a biophysical and evolutionary model, we show how these protein traits can emerge as evolutionary “spandrels” even if they do not confer an intrinsic fitness advantage. In particular, proteins can evolve strong binding interactions that have no functional role but merely serve to stabilize the protein if its misfolding is deleterious. Furthermore, such proteins may have divergent fates, evolving to bind or not bind their targets depending on random mutational events. These observations may explain the abundance of apparently nonfunctional interactions among proteins observed in high-throughput assays. In contrast, for proteins with both functional binding and deleterious misfolding, evolution may be highly predictable at the level of biophysical traits: adaptive paths are tightly constrained to first gain extra folding stability and then partially lose it as the new binding function is developed. These findings have important consequences for our understanding of how natural and engineered proteins evolve under selective pressure.
How Physical Carrier Sense Affects Protocol Capacity in Multi-hop Wireless Networks: Modeling and Analysis

In recent years, wireless ad hoc networks have become increasingly popular in both military and civilian applications due to its capability of building networks without the need for a pre-existing infrastructure. While a number of studies have been carried out to study the performance of IEEE 802.11 DCF in single-cell wireless LANs, the analysis of IEEE 802.11 DCF in multi-hop wireless networks with consideration of the effects of physical carrier sense, SINR, and collision caused by accumulative interference has been lacking. In this paper, we substantially extend Cal ´ i ’s work and rigorously model, with these effects considered, channel activities governed by IEEE 802.11 DCF in multi-hop wireless networks. We show that as in single-cell WLANs, the choice of the contention window size can greatly impact the system throughput in multi-hop wireless networks. However, the optimal value of the contention window size is quite different. Moreover, the optimal attempt probability p (the optimal window size) derived for multi-hop wireless networks with respect to maximizing the systems throughput is larger (smaller) than that for single-cell WLANs. We also show that, given the minimal SINR threshold β , the optimal carrier sense range is smaller than the conventional value used (provided that the contention window size is tuned accordingly).
Expansion of CD57 and CD62L-CD45RA+ CD8 T lymphocytes correlates with reduced viral plasma RNA after primary HIV infection.

OBJECTIVE CD8 T cells, expressing cell surface molecules distinct from those on resting and naive T cells, are increased in HIV infection. The association of increased CD38 and human leukocyte antigen DR (HLA-DR) CD8 T cells with poor prognosis has suggested that activated CD8 T cells may aggravate HIV infection. We examined whether other immunological parameters might influence the viral setpoint. DESIGN Peripheral T cells from nine untreated patients, obtained after primary HIV infection when plasma HIV had stabilized, were examined for proteins expressed in activated versus resting, memory versus naive, and cytolytic versus non-cytolytic T cells. METHODS The proportion of CD8 T cells that stain for CD38 and HLA-DR, CD28 and CD57 was compared with plasma viraemia and CD4 cell count. These parameters were also compared with the proportion of CD4 and CD8 T cells that express CD62L and CD45RA, present on naive cells and down-modulated in memory cells. Internal staining for the cytotoxic protein granzyme A was also examined. RESULTS An increase in CD38 and CD38 HLA-DR CD8 T cells correlated with increased plasma viral RNA (P < 0.00002, P < 0.03, respectively). An increase in CD8 T cells expressing granzyme A was associated with lower CD4 cell counts (P < 0.04). However, the expansion of CD57 and CD62L CD45RA+ CD8 T cells was associated with a lower viral setpoint (P < 0.01, P < 0.02, respectively). CONCLUSION Phenotypically defined activated CD8 T cells may have different functions in HIV infection. Activated CD8 T cells that are CD57 or CD62L(-)CD45RA+ may be beneficial, because their expansion in untreated patients correlates with a reduced viral setpoint after primary infection.
Minimum Wage

Through the analysis of the consequences of raising the minimum wage in the United States, many different factors have been taken into consideration – disparities in minimum wages in large cities and smaller cities, the effects of policies on small businesses, and the effects of such policies on large corporations. Raising the minimum wage is most detrimental to small businesses, as large corporations are more able to afford such a change while incurring minimal losses. In essence, an increase in the minimum wage would result in various consequences, affecting every business differently depending on their location, size, and structure. ________________________________________________________________________
Circulating MicroRNAs in Relation to EGFR Status and Survival of Lung Adenocarcinoma in Female Non-Smokers

Objectives Lung adenocarcinoma is considered a unique disease for Asian female non-smokers. We investigated whether plasma microRNA (miRNA) expression profiles are different by the EGFR status and are associated with survival outcomes of the patients. Methods Using real-time RT-PCR, we analyzed the expression of 20 miRNAs in the plasma of 105 female patients with lung adenocarcinoma. Kaplan-Meier survival analysis and Cox proportional hazards regression were performed to determine the association between miRNA expression and overall survival. Time dependent receiver operating characteristic (ROC) analysis was also performed. Results In the 20 miRNAs, miR-122 were found differently expressed between wild and mutant EGFR carriers (P=0.018). Advanced disease stage and tumor metastasis were independently associated with poor prognosis of patients with lung adenocarcinoma (P=0.010 and 1.0×10-4). Plasma levels of miR-195 and miR-122 expression were also associated with overall survival in the patients, especially in those with advanced stage (HR=0.23, 95%CI:0.07-0.84; and HR=0.22, 95%CI:0.06-0.77) and EGFR mutation (HR=0.27, 95%CI:0.08-0.96; and HR=0.23, 95%CI=0.06-0.81). Moreover, a model including miR-195, miR-122 may predict survival outcomes of female patients with lung adenocarcinoma (AUC=0.707). Conclusions Circulating miR-195 and miR-122 may have prognostic values in predicting the overall survival as well as predicting EGFR mutation status in non-smoking female patients with lung adenocarcinoma. Measuring plasma levels of miR-195 and miR-122 may especially be useful in EGFR mutant patients with lung adenocarcinoma.
Web Service Adaptation : State of the art and Research Challenges

Service-based applications have been attracting a lot of attention from both academia and industry in recent years. Therefore, as these applications need to operate in a highly dynamic and distributed world, they should adapt their behavior to ensure the expected functionality and quality. Many adaptation techniques have been proposed so far focusing on a single layer of the SBA life-cycle. In this technical report we make a review of the current fragmented stateof-the-art approaches, uncovering the basic research challenges on web service adaptation. Furthermore, we classify these approaches according to adaptation specification and pinpoint the problems stemming from the lack of cross-layer monitoring and adaptation techniques across Service-Based Applications. Finally, we analyze the basic self-* properties of SBAs and propose a tentative research plan for our future work.