bluuebunny/crossref_metadata_2025_split huggingface dataset:
Towards an Ecosystem Approach to Cheese Microbiology
Authors: Wolfe Benjamin E. , Dutton Rachel J. 
Published: April 2014

ABSTRACT
Cheese is an ideal environment to serve as a model for the behavior of microbes in complex communities and at the same time allow detailed genetic analysis. Linking organisms, and their genes, to their role in the environment becomes possible in the case of cheese since cheese microbial communities have been “in culture” for thousands of years, with the knowledge of how to grow these organisms passed down by generations of cheesemakers. Recent reviews have described several emerging approaches to link molecular systems biology to ecosystem-scale processes, known as ecosystems biology. These approaches integrate massive datasets now available through high-throughput sequencing technologies with measurements of ecosystem properties. High-throughput datasets uncover the “parts list” (e.g., the species and all the genes within each species) of an ecosystem as well as the molecular basis of interactions within this parts list. Novel computational frameworks make it possible to link species and their interactions to ecosystem properties. Applying these approaches across multiple temporal and spatial scales makes it possible to understand how changes in the parts lists over space and time lead to changes in ecosystems processes. By manipulating the species present within model systems, we can test hypotheses related to the role of microbes in ecosystem function. Due to the tractability of cheese microbial communities, we have the opportunity to use an ecosystems biology approach from the scale of individual microbial cells within a cheese to replicated cheese microbial communities across continents. Using cheese as a model microbial ecosystem can provide a way to answer important questions concerning the form, function, and evolution of microbial communities.
Cyclic AMP Signaling in Mycobacteria
Authors: Knapp Gwendowlyn S. , McDonough Kathleen A. 
Published: April 2014

ABSTRACT

All cells must adapt to changing conditions, and many use cyclic AMP (cAMP) as a second messenger to sense and respond to fluctuations in their environment. cAMP is made by adenylyl cyclases (ACs), and mycobacteria have an unusually large number of biochemically distinct ACs. cAMP is important for gene regulation in mycobacteria, and the ability to secrete cAMP into host macrophages during infection contributes to
Mycobacterium tuberculosis
pathogenesis. This article discusses the many roles of cAMP in mycobacteria and reviews what is known about the factors that contribute to production, destruction, and utilization of this important signal molecule. Special emphasis is placed on cAMP signaling in
M. tuberculosis
complex bacteria and its importance to
M. tuberculosis
during host infection.
Genetics of Phage Lysis
Authors: Pimentel Madalena 
Published: April 2014

ABSTRACTWe have been witnessing an increased interest in bacteriophage studies focused on their use as antibacterial agents to fight pathogenic bacteria. This interest is a consequence of the phages' ability to lyse a bacterial host. Until recently, little was known about the mechanisms used by mycobacteriophages to induce lysis of their complex hosts. However, studies on Ms6-induced lysis have changed this scenario and provided new insights into the mechanisms of bacteriophage-induced lysis. Specific lysis protein genes have been identified in mycobacteriophage genomes, reflecting the particular mycobacterial cell envelope composition. These include enzymes that target mycolic acid–containing lipids and proteins that participate in the secretion of the phage endolysin, functioning as chaperone-like proteins. This chapter focuses on the current knowledge of mycobacteriophage-induced lysis, starting with an overview of phage lysis and basic features of the lysis players.
Noncoding RNA in Mycobacteria
Authors: Arnvig Kristine B. , Cortes Teresa , Young Douglas B. 
Published: April 2014

ABSTRACT
Efforts to understand the molecular basis of mycobacterial gene regulation are dominated by a protein-centric view. However, there is a growing appreciation that noncoding RNA, i.e., RNA that is not translated, plays a role in a wide variety of molecular mechanisms. Noncoding RNA comprises rRNA, tRNA, 4.5S RNA, RnpB, and transfer-messenger RNA, as well as a vast population of regulatory RNA, often dubbed “the dark matter of gene regulation.” The regulatory RNA species comprise 5′ and 3′ untranslated regions and a rapidly expanding category of transcripts with the ability to base-pair with mRNAs or to interact with proteins. Regulatory RNA plays a central role in the bacterium's response to changes in the environment, and in this article we review emerging information on the presence and abundance of different types of noncoding RNA in mycobacteria.
Gene Transfer in
Mycobacterium tuberculosis
: Shuttle Phasmids to Enlightenment
Authors: Jacobs, Jr. William R. 
Published: April 2014

ABSTRACT

Infectious diseases have plagued humankind throughout history and have posed serious public health problems. Yet vaccines have eradicated smallpox and antibiotics have drastically decreased the mortality rate of many infectious agents. These remarkable successes in the control of infections came from knowing the causative agents of the diseases, followed by serendipitous discoveries of attenuated viruses and antibiotics. The discovery of DNA as genetic material and the understanding of how this information translates into specific phenotypes have changed the paradigm for developing new vaccines, drugs, and diagnostic tests. Knowledge of the mechanisms of immunity and mechanisms of action of drugs has led to new vaccines and new antimicrobial agents. The key to the acquisition of the knowledge of these mechanisms has been identifying the elemental causes (i.e., genes and their products) that mediate immunity and drug resistance. The identification of these genes is made possible by being able to transfer the genes or mutated forms of the genes into causative agents or surrogate hosts. Such an approach was limited in
Mycobacterium tuberculosis
by the difficulty of transferring genes or alleles into
M. tuberculosis
or a suitable surrogate mycobacterial host. The construction of shuttle phasmids—chimeric molecules that replicate in
Escherichia coli
as plasmids and in mycobacteria as mycobacteriophages—was instrumental in developing gene transfer systems for
M. tuberculosis.
This review will discuss
M. tuberculosis
genetic systems and their impact on tuberculosis research.
RNA Viruses: A Case Study of the Biology of Emerging Infectious Diseases
Authors: J. Woolhouse Mark E. , Adair Kyle , Brierley Liam 
Published: April 2014

ABSTRACT
There are 180 currently recognized species of RNA virus that can infect humans, and on average, 2 new species are added every year. RNA viruses are routinely exchanged between humans and other hosts (particularly other mammals and sometimes birds) over both epidemiological and evolutionary time: 89% of human-infective species are considered zoonotic and many of the remainder have zoonotic origins. Some viruses that have crossed the species barrier into humans have persisted and become human-adapted viruses, as exemplified by the emergence of HIV-1. Most, however, have remained as zoonoses, and a substantial number have apparently disappeared again. We still know relatively little about what determines whether a virus is able to infect, transmit from, and cause disease in humans, but there is evidence that factors such as host range, cell receptor usage, tissue tropisms, and transmission route all play a role. Although systematic surveillance for potential new human viruses in nonhuman hosts would be enormously challenging, we can reasonably aspire to much better knowledge of the diversity of mammalian and avian RNA viruses than exists at present.
Factors Impacting the Control of Rabies
Authors: Nel Louis H. 
Published: April 2014

ABSTRACT

Rabies is a classical zoonosis that has been known to man for ages. The disease can be caused by several viral species in the
Lyssavirus
genus, but the type species, rabies virus (RABV), is by far the most important from a zoonosis perspective. The extreme neurotropism of RABV and the evolutionarily conserved elements and structures of the mammalian brain suggest that this virus evolved an ultimate niche for replication, simultaneously exploiting classical social behavior of a wide diversity of hosts among the chiropters and carnivores. There is substantial evidence that RABV originated in bats and later switched hosts to yield globally disseminated canine rabies. Following the revolutionary work of Louis Pasteur, control and elimination of dog rabies was achieved in Europe, but widespread colonial introduction of European strains of dog RABV to other parts of the world occurred. Thus, dog rabies spread rapidly in the 1900s, and today the vast majority of the tens of thousands of annual human rabies cases stem from dog rabies, which has become endemic in the entire developing world. The fact that human rabies is preventable, through control in the dog reservoir on one hand and through effective prophylaxis in cases of exposure on the other hand, is an indictment of public health strategies and practices. This article discusses some of the drivers that have contributed to the recurrent neglect of rabies in the modern world, as well as evolving One Health-based rabies control partnerships and initiatives that have been progressive, productive, and promising of true global benefits.
Combating the Triple Threat: The Need for a One Health Approach
Authors: King Lonnie J. 
Published: April 2014

ABSTRACT
We live in a world that is rapidly changing, complex, and progressively interconnected. The convergence of people, animals, and their products embedded in an ever-changing environment has created a new dynamic. This dynamic is characterized by new threats to the health of humans, animals, and the environment. In addition, the health of each of these three domains is profoundly and inextricably linked and elaborately connected. Our interconnectedness strongly suggests that our future success in improving health will be based on a new integrative, holistic, and collaborative approach termed One Health. One Health demands that we work across professions, disciplines, and old boundaries. The challenges to our health are unique and profound, and old solutions to our new “wicked” problems are no longer as relevant or effective as in the past. The concept of One Health is not new but has reemerged as a concept to both better understand the triple threats to health and to better address these contemporary challenges using new approaches. This article discusses the health threats to each domain and calls for a new model to confront these challenges by shifting strategies and interventions upstream, closer to the origins of the threats. One Health is a new paradigm that can be used to improve the health of people, animals, and our environment as a collective rather than restricting our actions to any single domain.
The spatiotemporal association of non-prescription retail sales with cases during the 2009 influenza pandemic in Great Britain
Authors: Todd Stacy , Diggle Peter J , White Peter J , Fearne Andrew , Read Jonathan M 
Published: April 2014

ObjectiveTo assess whether retail sales of non-prescription products can be used for syndromic surveillance and whether it can detect influenza activity at different spatial scales. A secondary objective was to assess whether changes in purchasing behaviour were related to public health advice or levels of media or public interest.SettingThe UK.ParticipantsNational and regional influenza case estimates and retail sales from a major British supermarket.Outcome measuresWeekly, seasonally adjusted sales of over-the-counter symptom remedies and non-pharmaceutical products; recommended as part of the advice offered by public health agencies; were compared with weekly influenza case estimates. Comparisons were made at national and regional spatial resolutions. We also compared sales to national measures of contemporaneous media output and public interest (Internet search volume) related to the pandemic.ResultsAt a national scale there was no significant correlation between retail sales of symptom remedies and cases for the whole pandemic period in 2009. At the regional scale, a minority of regions showed statistically significant positive correlations between cases and sales of adult ‘cold and flu’ remedies and cough remedies (3.2%, 5/156, 3.8%, 6/156), but a greater number of regions showed a significant positive correlation between cases and symptomatic remedies for children (35.6%, 55/156). Significant positive correlations between cases and sales of thermometers and antiviral hand gels/wash were seen at both spatial scales (Cor 0.477 (95% CI 0.171 to 0.699); 0.711 (95% CI 0.495 to 0.844)). We found no significant association between retail sales and media reporting or Internet search volume.ConclusionsThis study provides evidence that the British public responded appropriately to health messaging about hygiene. Non-prescription retail sales at a national level are not useful for the detection of cases. However, at finer spatial scales, in particular age-groups, retail sales may help augment existing surveillance and merit further study.
Secondary triage in prehospital emergency ambulance services: a systematic review
Authors: Eastwood Kathryn , Morgans Amee , Smith Karen , Stoelwinder Johannes 
Published: May 2014

ObjectiveSecondary telephone triage to divert low-acuity patients to alternative non-ambulance services before ambulance arrival has been trialled in the UK and USA as a management strategy to cope with the increase in ambulance demand. The objective of this systematic review was to examine the literature on the structure, safety and success of secondary triage systems.MethodsFor inclusion in the study, the telephone triage system had to be a secondary process, receiving referred patients who had already been categorised as low priority by a primary triage process. Two independent reviewers conducted the search to identify relevant studies. Six articles and one report were identified.ResultsThe major theme of the papers was the safety and accuracy of secondary telephone triage in identifying low-acuity patients. Two studies also discussed patient satisfaction. There was a low incidence of adverse events, as expected as these patients had already been subjected to primary telephone triage. In the studies identifying ambulance dispatch as a potential final disposition, at least half of the patients were diverted away from ambulance dispatch. In the studies that identified self/home care as a final disposition, a maximum of 31% of patients were categorised to this outcome. Otherwise all patients were recommended for assessment by a healthcare professional other than ambulance clinicians. Patients appeared to be satisfied with secondary telephone triage on follow-up.ConclusionsThese results suggest that, while secondary triage of these patients is safe, further research is required to determine its most appropriate structure and its effect on ambulance demand.
Systemic reactions and anaphylaxis with an acute serum tryptase ≥14 μg/L: retrospective characterisation of aetiology, severity and adherence to National Institute of Health and Care Excellence (NICE) guidelines for serial tryptase measurements and specialist referral
Authors: Srivastava Sapna , Huissoon Aarnoud P , Barrett Victoria , Hackett Scott , Dorrian Susan , Cooke Matthew W , Krishna Mamidipudi T 
Published: April 2014

AimsTo characterise patients with systemic reactions and anaphylaxis with an acute serum tryptase of ≥14 μg/L against recently published World Allergy Organisation (WAO) diagnostic criteria. To also perform a clinical audit to assess adherence to National Institute of Health and Care Excellence (NICE) guideline recommendations regarding serial tryptase measurements and specialist referral.MethodsA systematic retrospective survey (2006–2010) was carried out (n=171; males=86; mean age±SD 48±20 years) and data were extracted from emergency department and specialist allergy clinic records.Results34 patients (20%) had a grade 1 reaction, 61 (36%) grade 2, 46 (27%) grade 3 and 6 patients (4%) grade 4 (24 patients (13%) could not be graded due to lack of adequate clinical details) and 6% developed a biphasic response. Serial tryptase measurements were not available in 117 (69%) of the cohort. 97 (57%) patients were referred for specialist assessment, and 72 (74%) attended. 50% of cases were diagnosed with idiopathic systemic reactions/anaphylaxis and 28%, 14% and 8% triggered by drugs, foods and other allergies including disorders of mast cell overload, respectively. A weak positive correlation was detected between acute serum tryptase and severity.ConclusionsThe correlation between acute serum tryptase and severity of anaphylaxis/systemic reactions is weak. A significant proportion of patients with raised acute serum tryptase had mild reactions which did not meet WAO criteria for anaphylaxis and this may reduce the specificity of the test. The commonest aetiology in this cohort was idiopathic followed by drug and food allergies. NICE guidelines relating to serial tryptase measurements and specialist referral were not followed, and there is an urgent need to raise the awareness among clinicians involved in the management of anaphylaxis.
EVALUATION OF AN AUTOMATED MULTI-PHASE APPROACH FOR PATTERNS DISCOVERY
Authors: BOUASSIDA NADIA , BEN-ABDALLAH HANENE , ISSAOUI IMENE 
Published: April 2014

Design patterns capitalize the knowledge of expert designers and offer reuse that provides for higher design quality and overall faster development. To attain these advantages, a designer must, however, overcome the difficulties in understanding design patterns and determining those appropriate for his/her particular application. On the other hand, one way to benefit from design patterns is to assist inexperienced designers in pattern detection during the design elaboration. Such detection should tolerate variations between the design and the pattern since the exact instantiation of a pattern is infrequent in a design. However, not all variations of a pattern are tolerated. In particular, some structural variations may result in non-optimal instantiations where the requirements are respected but the structure is different; such variations are called spoiled patterns and should also be detected and transformed into acceptable pattern instantiations. This paper first presents an improvement of our design/spoiled pattern detection approach, named MAPeD (Multi-phase Approach for Pattern Discovery). The latter uses an XML information retrieval technique to identify design/spoiled pattern occurrences in a design using, first, static and semantic information and, secondly, dynamic information. This multi-phase detection approach tolerates structural differences between the examined design and the identified design pattern. Furthermore, thanks to the matching information it collects, our identification technique can offer assistance for the improvement of a design. In its second contribution, this paper evaluates MAPeD by comparing its recall and precision rates for five open source systems: JHotDraw, JUnit, JRefactory, MapperXML, QuickUML. The latter were used by other approaches in experimental evaluations. Our evaluation shows that our design pattern identification approach has an average improvement of 9.98% in terms of precision over the best known approach.
Positive solutions for a quasilinear Schrödinger equation involving Hardy potential and critical exponent
Authors: Zeng Xiaoyu , Zhang Yimin , Zhou Huan-Song 
Published: April 2014

We are concerned with positive solutions of a quasilinear Schrödinger equation with Hardy potential and critical exponent. Different from the semilinear equation, the Hardy term in our equation is not only singular, but also nonlinear. It seems unlikely to get solutions for our equation in H1(ℝN) ∩ L∞(ℝN) by using Nehari method as Liu–Liu–Wang [Ground states for quasilinear Schrödinger equations with critical growth, Calc. Var. Partial Differential Equations 46 (2013) 641–669]. In this paper, by transforming the quasilinear equation to a semilinear equation, we established the existence of positive solutions for the quasilinear Schrödinger equation in H1(ℝN) under suitable conditions.
Immunosuppressive Myeloid Cells Induced by Chemotherapy Attenuate Antitumor CD4+ T-Cell Responses through the PD-1–PD-L1 Axis
Authors: Ding Zhi-Chun , Lu Xiaoyun , Yu Miao , Lemos Henrique , Huang Lei , Chandler Phillip , Liu Kebin , Walters Matthew , Krasinski Antoni , Mack Matthias , Blazar Bruce R. , Mellor Andrew L. , Munn David H. , Zhou Gang 
Published: April 2014

AbstractIn recent years, immune-based therapies have become an increasingly attractive treatment option for patients with cancer. Cancer immunotherapy is often used in combination with conventional chemotherapy for synergistic effects. The alkylating agent cyclophosphamide (CTX) has been included in various chemoimmunotherapy regimens because of its well-known immunostimulatory effects. Paradoxically, cyclophosphamide can also induce suppressor cells that inhibit immune responses. However, the identity and biologic relevance of these suppressor cells are poorly defined. Here we report that cyclophosphamide treatment drives the expansion of inflammatory monocytic myeloid cells (CD11b+Ly6ChiCCR2hi) that possess immunosuppressive activities. In mice with advanced lymphoma, adoptive transfer (AT) of tumor-specific CD4+ T cells following cyclophosphamide treatment (CTX+CD4 AT) provoked a robust initial antitumor immune response, but also resulted in enhanced expansion of monocytic myeloid cells. These therapy-induced monocytes inhibited long-term tumor control and allowed subsequent relapse by mediating functional tolerization of antitumor CD4+ effector cells through the PD-1–PD-L1 axis. PD-1/PD-L1 blockade after CTX+CD4 AT therapy led to persistence of CD4+ effector cells and durable antitumor effects. Depleting proliferative monocytes by administering low-dose gemcitabine effectively prevented tumor recurrence after CTX+CD4 AT therapy. Similarly, targeting inflammatory monocytes by disrupting the CCR2 signaling pathway markedly potentiated the efficacy of cyclophosphamide-based therapy. Besides cyclophosphamide, we found that melphalan and doxorubicin can also induce monocytic myeloid suppressor cells. These findings reveal a counter-regulation mechanism elicited by certain chemotherapeutic agents and highlight the importance of overcoming this barrier to prevent late tumor relapse after chemoimmunotherapy. Cancer Res; 74(13); 3441–53. ©2014 AACR.