bluuebunny/crossref_metadata_2025 huggingface dataset:
Group B Streptococcus (Streptococcus agalactiae)
Authors: Le Doare Kirsty , Jones Christine E. , Heath Paul T.
Published: January 2018

Group B Streptococcus (GBS) is a leading cause of early neonatal infection and neonatal mortality, with long-term adverse neurodevelopmental outcomes in up to 50% of survivors of GBS meningitis. GBS has a likely underappreciated role in causing preterm birth and stillbirth. GBS colonizes the vagina and gastrointestinal tract of the pregnant woman, and transmission to the infant occurs during or just before delivery. Although the majority of these infants do not develop invasive disease, maternal colonization is a prerequisite for early onset disease (0–6 days of life, most commonly associated with sepsis and respiratory distress) and a significant risk factor for late onset disease (7–89 days of life, most commonly associated with sepsis and meningitis). The introduction of intrapartum antibiotic prophylaxis has resulted in significant declines in the incidence of early onset disease but provides no protection against late onset disease.
Syphilis (Treponema pallidum)
Authors: Gilroy Mark N. , Salazar Juan C.
Published: January 2018

Syphilis, a chronic, sexually transmitted disease caused by the extracellular spirochete Treponema pallidum, has exhibited a remarkable resurgence in recent years. Despite the existence of inexpensive, easily administered, and highly effective antibiotic treatments, maternal and neonatal syphilis infections continue to be a major global public health problem. In addition to its potential to cause morbidity in the mother, untreated gestational syphilis (GS) can lead to serious adverse outcomes in the offspring, including stillbirth, prematurity, low birth weight, and neonatal death. Congenital syphilis (CS) is regarded as a missed opportunity during the antenatal care of the mother, resulting from socioeconomic, demographic, and behavioral factors that promote mother-to-child transmission (MTCT) of syphilis. This chapter emphasizes emerging concepts about screening aimed at controlling the ongoing epidemic, including serological screening of mother and infant, newer paradigms of “reverse screening,” clinical presentation, therapy, and long-term neurodevelopmental disabilities that must be a component of follow-up care.
Ureaplasma urealyticum and Ureaplasma parvum
Authors: Viscardi Rose M. , Waites Ken B.
Published: January 2018

The Mycoplasma species Ureaplasma parvum and Ureaplasma urealyticum colonize the human adult urogenital tract and are not typically associated with disease. Perinatal transmission, however, has been implicated in the pathogenesis of preterm birth, chorioamnionitis, and other complications of extreme prematurity, including neonatal pneumonitis, bronchopulmonary dysplasia (BPD), meningitis, and necrotizing enterocolitis (NEC). This chapter reviews the biology of these organisms. Epidemiologic and experimental evidence supporting a role for ureaplasmas in the pathogenesis of neonatal disease, clinical manifestations of infection in the infant, current microbiologic diagnostic methods, and the present status of treatment options are reviewed. Macrolide antibiotic therapy is controversial for infected infants, and current concepts regarding candidates for treatment are discussed. Key unanswered questions that need to be addressed in future research studies are also suggested.
Unhealthy and Potentially Harmful Uses of Religion
Authors: Griffith James , Magyar-Russell Gina
Published: January 2018

Religious coping is the most common source of resilience worldwide among people facing harsh adversities, yet it also can do harm. Three major classes of religious acts pose risks for harm to self or others: group religious life that overshadows personal spirituality; religion that expresses symptoms of mental illness; and spiritual struggle that arises from conflicted meanings, motivations, and actions within religious life. Across religious traditions, personal spirituality sets a standard for relational and ethical living against which the moral worth of religious acts can be judged. When group religious life too strongly dominates personal spirituality, inquiry about existential concerns can re-energize personal spirituality in a corrective rebalancing. Discerning mental illness in the guise of religion requires religious professionals to learn about diagnosis, treatment, and risk factors for relapse of mental illnesses. Psychotherapy or spiritual guidance can resolve intrapsychic, interpersonal, and person-God conflicts for religious persons caught in spiritual struggles.
Spiritual and Religious Concerns Presenting in Psychiatric Treatment
Authors: Sperry Len
Published: January 2018

This chapter addresses ethical considerations associated with the various religious and spiritual concerns that patients present in everyday psychiatric practice. It offers a taxonomy of these concerns and describes the necessity of a spiritual assessment and the provision of basic spiritual care expected of all mental health professionals. Ethical considerations discussed include informed consent, competency, and scope of practice, particularly with regard to the appropriate use of spiritual interventions. Finally, key points are illustrated with two case examples.
Ethics Committees and Consultation in Mental Health
Authors: Postema Don C.
Published: January 2018

Understanding the role of ethics committees in providing ethics consultations, ethics education, and ethics-related policies is the context for exploring the relationship of ethics, psychiatry, and religious and spiritual beliefs. After a brief history of biomedical ethics in the United States since the mid-20th century, this chapter presents several case studies that exemplify frequently encountered tensions in these relationships. The central contention is that respecting these beliefs is not equivalent to acquiescing to ethical claims based on them. Rigorous critical reflection and psychiatric insight, coupled with the values embedded in the social practices of healthcare, provide the grounds for evaluating the weight and bearing of religious and spiritual beliefs in ethically complex cases. This is one contribution that ethics committees can make at the intersection of psychiatry and religion.
Practical Implications of Personal Spirituality
Authors: Lomax James W. , Carlin Nathan
Published: January 2018

Mental health providers, as a group, tend to think of themselves as liberal and tolerant because they have a commitment to being nonjudgmental in clinical activities and actions. University professors also often think of themselves as liberal and tolerant, if for different reasons. Rarely do mental health providers and university professors think of themselves as fundamentalists. Indeed, both usually look askance at fundamentalism, especially religious fundamentalism. Yet this chapter suggests, following Adam Phillips, that everyone is a fundamentalist about something, about some key personal value or principle. The chapter provides some historical and cultural context for understanding fundamentalisms broadly. Focusing on transference and countertransference dynamics in clinical and educational settings, it argues that it is good to achieve self-awareness about those fundamentals in advance of provocative challenges in order to avoid unprofessional responses to patients and students and that various fundamentalisms can serve adaptive functions.
Inpatient Psychiatry
Authors: Ali Shad S. , Nussbaum Abraham M.
Published: January 2018

All patients deserve culturally competent, faith-specific, and ethical care regardless of the setting in which they receive it. Inpatient psychiatric services are a unique environment in which to provide such care both because mental illness often affects (and is affected by) a person’s faith and because these facilities are often restrictive environments in which safety is prioritized over other human needs. In this chapter, we present two case examples of how to approach religious and spiritual practices of patients hospitalized in inpatient psychiatric facilities. The first is an HIV positive schizophrenic patient who was a devout Sunni Muslim. The second is an atheist with major depressive and borderline personality disorders admitted after a serious suicide attempt. The clinical presentation and case analysis for each case uses Jonsen’s Four Quadrants Approach, followed by a discussion of salient contextual, cultural, and ethical considerations.
Geriatric and End-of-Life Psychiatry
Authors: Peteet John R.
Published: January 2018

As the number of older individuals grows, ethical challenges in their care become more obvious. When an elder loses critical faculties, do they become less of a person? What does it mean to respect the autonomy of an individual who is becoming increasingly dependent on others? How can a psychiatrist contribute to optimal care at the end of life? What is the most appropriate response to requests for assisted suicide? How should clinicians address the existential challenges and spiritual needs of the elderly, and of their caregivers? Answering these questions requires appreciating deeply both their psychiatric and religious/spiritual dimensions. As an example, we consider a case of depression and loss of faith.
Mental Disorder and Transformation
Authors: Benning Tony
Published: January 2018

Throughout history and in all the world’s major faith traditions, it has been noted that conversion and other important spiritual and religious experiences may share or have features that overlap with signs and symptoms of psychiatric illness. William James, especially in The Varieties of Religious Experience, contributed significantly to the understanding of this overlap. The aim of this chapter is to explore the ethical and clinical dilemmas that arise when clinicians attempt to negotiate the seemingly conflicting imperatives of diagnosing on the one hand and of being open to the transformational significance of mental illness on the other. This is achieved by presenting three clinical cases from the author’s community psychiatric practice and analyzing them through the lens of Jonsen’s Four Quadrants Model for ethical case analysis.
Extramuscular complications occurring in myositis
Authors: Schmidt Jens
Published: January 2018

Extra-muscular complications affecting patients suffering from the idiopathic inflammatory myopathies (IIM) are common, and appear in recognizable patterns affecting the skin, lungs, joints, oesophagus or heart, although these complications rarely all occur simultaneously. During the initial presentation of symptoms, involvement of organs other than muscle can aid the confirmation of the correct IIM subtype. Extra-muscular manifestations can be severe and life-threatening, e.g. with respiratory or cardiac involvement. Escalations of immunosuppression and other treatment modalities will likely be required in such cases since standard immunosuppression usually is not sufficient for an effective treatment of e.g. interstitial lung disease. IIM patients should therefore be regularly checked for extra-muscular manifestations, and management altered as appropriate.
Toxic myopathies
Authors: Lahouti Arash H. , Christopher-Stine Lisa
Published: January 2018

Toxic myopathy symptoms range from myalgia and muscle cramps to severe weakness, bearing similarities to a number of other muscle conditions. Thus, when evaluating patients with muscle symptoms, an iatrogenic muscle problem should always be considered, to be able to distinguish a toxic from any other myopathy early on, preventing further muscle damage and to potentially reverse muscle injury by withdrawal of the toxic agent. Various commonly prescribed medications, as well as illicit drugs, may cause muscle damage. These substances may cause muscle injury through direct myotoxic effects, or indirectly through various mechanisms, such as electrolyte abnormalities and triggering, or disinhibiting the immune system response.
Juvenile myositis
Authors: Boros Christina , Nistala K. , Wedderburn L.R.
Published: January 2018

Idiopathic inflammatory myopathies (IIM) of childhood are rare serious disorders, of which the most common is juvenile dermatomyositis (JDM). It is recognized increasingly that, even within JDM, there is significant heterogeneity. Recently defined biomarkers, such as the myositis-specific autoantibodies (MSA) have been valuable to define juvenile IIM subgroups and may provide novel methods of classification. Although randomized controlled trials in JDM are challenging, an increasing consensus-based body of evidence is being used to drive standardization of treatment and care, with new drugs for severe cases being increasingly tested. Significant differences between adults and children with dermatomyositis (DM) exist, and are reviewed in this chapter. These differences emphasize the importance of specialists in the area of transition of young people who have had JDM to receive their care from a team of health professionals with comprehensive knowledge of JDM, as well as transitional care issues.
Austria
Authors: Likar Rudolf
Published: January 2018

Austria is a member of the European Pain Federation (EFIC). The national pain society works to support the needs of patients with pain, including those with acute pain, chronic pain, cancer pain, pain in later life, and at the end of life. In this chapter of European Pain Management we describe first the geography and history of the country as it relates to the recent demographics of the population, the prevalence of pain and needs for pain management, the pain workforce and its organization, the system pain specialists work within, and specific issues that have been tackled to improve the delivery of pain care. An example of recent innovation is also described.
Latvia
Authors: Golubovska Iveta , Arons Mihails , Miscuks Aleksejs , Logina Inara
Published: January 2018

Latvia is a member of the European Pain Federation (EFIC). The national pain society works to support the needs of patients with pain, including those with acute pain, chronic pain, cancer pain, pain in later life, and at the end of life. In this chapter of European Pain Management we describe first the geography and history of the country as it relates to the recent demographics of the population, the prevalence of pain and needs for pain management, the pain workforce and its organization, the system pain specialists work within, and specific issues that have been tackled to improve the delivery of pain care. An example of recent innovation is also described.
Pain in children
Authors: Wager Julia , Zernikow Boris
Published: January 2018

Pain management in children is a specialized service. Pain aetiology, assessment, and treatment vary at every age from pre-term foetuses at 23 weeks gestation to adolescence. In this chapter of European Pain Management advances in our understanding of pain assessment are reviewed, particularly in the use of developmentally relevant technology. Advances in acute pain, cancer pain, and in chronic pain are also reviewed, with a special focus on innovations in multidisciplinary treatments for chronic pain. There is a need to raise awareness and understanding of the needs of paediatric pain patients, and their family members. Education for all professionals who interact with pain patients is essential, as is the need to invest in specialized pain management services, and professionals, across Europe.
Working at the frontiers of pain management in Europe
Authors: Krcˇevski-Škvarcˇ Nevenka
Published: January 2018

We focus on the development of pain management in the Eastern European countries. Economic, political, and other disparities separate Eastern Europe from the rest of continent. Pain Management is often a neglected healthcare need. The main obstacles in the development of pain medicine and management are the lack of money, insufficient education, the lack of specialists and facilities for pain management, and no interest within healthcare institutions or the entire healthcare system to introduce national plans for pain management. National pain associations from Eastern European countries joined to the European Pain Federation (EFIC) have the federation’s support to improve situation in their countries. The support is given in the grants for education, fellowships, and scientific meetings, consulting and sharing experiences, participation in federation’s activities and the use of federation’s publications.
Building Bottom-up Health and Disaster Risk Reduction Programmes
Authors: Chan Emily Ying Yang
Published: January 2018

Although urban living has accounted for being the lifestyle for more than half of the global population since 2010, nearly half are still living in a rural context. As pointed out by the United Nations as a backdrop of the Sustainable Development Goals (SDGs) (2016–2030), at least 1.8 billion people across the world still consumed faecally contaminated drinking water by 2015, 2.4 million lacked access to basic sanitation services such as toilets or latrines, and nearly 1,000 children died every day of preventable water and sanitation-related diarrhoeal diseases. Rural areas fare far worse: children are about 1.7 times more likely to die before their fifth birthday as those in urban areas. About 16% of the rural population do not use improved drinking water sources, compared to 4% of the urban population. About 50% of people living in rural areas lack improved sanitation facilities, compared to only 18% of people in urban regions. Far too many one-off rural on-site public health knowledge transfer projects fail to deliver long-term results. Theoretical understanding may be strengthened among non-governmental organization (NGO) practitioners and volunteers to support project planning, monitoring, and evaluation. Based on public health theories and illustrated by relevant examples, as well as the insights gained from the long-established CCOUC Ethnic Minority Health Project in China, this book introduces how health, emergency, and disaster preparedness education programmes could be organized in remote rural Asia, which could become a useful reference for organizers and volunteers of rural development projects.
From theory to practice
Authors: Chan Emily Ying Yang
Published: January 2018

This chapter introduces some myths of health promotion, the project cycle of health and disaster preparedness education programmes, needs assessment, project planning, programme implementation and monitoring, programme evaluation, and notes for organizers and participants of health and disaster preparedness education programmes. Concrete examples will be provided to put the abstract framework into use. This chapter integrates the themes in previous chapters with relevant insights gained from actual field experience in Asia, focusing on programme implementation field experience and lessons learnt, as well as the practical challenges and problems encountered in the field in rural Asian settings. It will also discuss the field-policy nexus, that is, the fulfilment of policy ambitions in such international policy frameworks like the United Nations’ Sustainable Development Goals (SDGs), the Sendai Framework for Disaster Risk Reduction (2015–2030), and the Paris Agreement for Climate Change by rural field programmes in health, emergency, and disaster risk reduction.
Epilogue
Authors: Chan Emily Ying Yang
Published: January 2018

As of 2010, the global population has transited from rural-based to urban-based settlement patterns. While urbanization poses much pressure to city residents, ‘rural living’ continues to represent more than 40% of the way our global citizens will be living for the coming century. This chapter provides some concluding remarks for Building Bottom-up Health and Disaster Risk Reduction Programmes, highlighting the importance of building bottom-up health and disaster risk reduction programmes in rural Asia that strengthen resilience in rural communities, and how careful planning, coordination, and contribution from international bodies, national governments, local communities, and the volunteer sector are also required.
Ecology of the Brain
Authors: Fuchs Thomas
Published: January 2018

Overcoming the brain centrism of current neuroscience, Ecology of the Brain develops an ecological and embodied concept of the brain as a mediating or resonance organ. Accordingly, the mind is not a product of the brain: it is an activity of the living being as a whole, which integrates the brain in its superordinate life functions. Similarly, consciousness is not an inner domain located somewhere within the organism, but a continuous process of engaging with the world, which extends to all objects that we are in contact with. The traditional mind–brain problem is thus reformulated as a dual aspect of the living being, conceived both as a lived or subjective body and as a living or objective body. Processes of life and of experiencing life are inseparably linked. Hence, it is not the brain, but the living human person as a whole who feels, thinks, and acts. This concept is elaborated on a broad philosophical, neurobiological, and developmental basis. Based on a phenomenology of the lived body and an enactive concept of the living organism as an autopoietic system, the brain is conceived in this book as a resonance organ, mediating the circular interactions within the body as well as the interactions between the body and the environment. Above all, a person’s relations to others continuously restructure the human brain which thus becomes an organ shaped by social interaction, biography, and culture. This concept is also crucial for a non-reductionist theory of mental disorders, psychiatry, and psychotherapy, which is developed in a special chapter.
Delivering Intensive Rehabilitation in Stroke: Factors Influencing Implementation
Authors: Connell Louise A , Klassen Tara K , Janssen Jessie , Thetford Clare , Eng Janice J
Published: January 2018

Background

The evidence base for stroke rehabilitation recommends intensive and repetitive task-specific practice, as well as aerobic exercise. However, translating these -evidence-based interventions from research into clinical practice remains a major -challenge.

Objective

The objective of this study was to investigate factors influencing implementation of higher-intensity activity in stroke rehabilitation settings.

Design

This qualitative study used a cross-sectional design.

Methods

Semi-structured interviews were conducted with rehabilitation therapists from 4 sites across 2 Canadian provinces who had experience in delivering a higher-intensity intervention as part of a clinical trial (Determining Optimal post-Stroke Exercise [DOSE]). An interview guide was developed, and data were analyzed using implementation frameworks.

Results

Fifteen therapists were interviewed before data saturation was reached. Therapists and patients generally had positive experiences regarding high-intensity interventions. However, therapists felt they would adapt the protocol to accommodate their beliefs about ensuring movement quality. The requirement for all patients to have a graded exercise test and the use of sensors (eg, heart rate monitors) gave therapists confidence to push patients harder than they normally would. Paradoxically, a system that enables routine graded exercise testing and the availability of staff and equipment contribute challenges for implementation in everyday practice.

Conclusions

Even therapists involved in delivering a high-intensity intervention as part of a trial wanted to adapt it for clinical practice; therefore, it is imperative that researchers are explicit regarding key intervention components and what can be adapted to help ensure implementation fidelity. Changes in therapists’ beliefs and system-level changes (staffing and resources) are likely necessary to facilitate higher-intensity rehabilitation in practice.
Extended Ponseti method for failed tenotomy in idiopathic clubfeet: a pilot study
Authors: Agarwal Anil , Agrawal Nargesh , Barik Sitanshu , Gupta Neeraj
Published: January 2018

We evaluated the outcome of a new protocol of an extended Ponseti method in the management of idiopathic club foot with residual equinus following failed Achilles tenotomy. We also compared the failed with a successful tenotomy group to analyze the parameters for failure. The Ponseti technique-treated idiopathic club foot patients with failed percutaneous Achilles tenotomy (failure to achieve <15° dorsiflexion) were treated by continued stretching casts, with a weekly change for a further 3 weeks. Final dorsiflexion more than 15° if achieved with the above protocol was recorded as a success. Twenty-six (16%) patients with failed Achilles tenotomy and residual equinus out of a total of 161 patients with primary idiopathic club foot were tested with the protocol. Ten (38.5%) failed patients had bilateral foot involvement and 16 (61.5%) had unilateral foot involvement. A total of seven (26.9%) patients achieved the end point dorsiflexion of more than 15° in one further cast, 10 (38.5%) in two casts, and four (15.4%) in three casts, respectively. Overall success of the extended Ponseti protocol was achieved in 21/26 (80.8%) patients. The patient’s age, precasting initial Pirani score, number of Ponseti casts, pretenotomy Pirani score, and pretenotomy ankle joint dorsiflexion were statistically different in the failed compared with the successful tenotomy group. The tested extended Ponseti protocol showed a success rate of 80.8% in salvaging failed tenotomy cases. The failed tenotomy group was relatively older at presentation, had high precasting and pretenotomy Pirani scores, received extra number of Ponseti casts, and less pretenotomy ankle joint dorsiflexion compared with successful feet.
Midterm functional outcomes in operatively treated adolescent Lisfranc injuries
Authors: Cheow Xunqi , Lam Kai Yet
Published: January 2018

This study evaluates the midterm outcomes of Lisfranc injuries in adolescents operatively treated with Kirschner wire or screw fixation. Eight adolescent patients with Lisfranc injuries operatively treated in a single institution were included in this study. The mean duration of follow-up was 3.8 years. Analysis of radiographs with respect to the degree of initial displacement and final reduction was carried out in terms of the intermetatarsal distances. All cases were scored functionally using the American Orthopaedic Foot and Ankle Society Midfoot Scale. We concluded that most operatively treated cases of adolescent Lisfranc injuries will do well at the midterm follow-up, with a mean American Orthopaedic Foot and Ankle Society Midfoot score of 93.4. Level of Evidence: Level 4 (Case series).
First Safety and Performance Evaluation of T45K, a Self-Assembling Peptide Barrier Hemostatic Device, After Skin Lesion Excision
Authors: Rahmani George , Prats Jayne , Norchi Terrence , Kates Steven , McInerney Veronica , Woods Jack , Kelly Jack
Published: January 2018

BACKGROUND

The self-assembling peptide barrier T45K (SAPB-T45K) is an oligopeptide that rapidly forms a biocompatible hemostatic barrier when applied to wounds.

OBJECTIVE

Evaluate safety and performance of SAPB-T45K in cutaneous surgery.

MATERIALS AND METHODS

In this single-blind study, after sequential shave excision of 2 lesions, wounds were randomized (intrapatient) to SAPB-T45K or control treatment. Safety was assessed at treatment, Day 7, and Day 30. Performance was evaluated using time to hemostasis (TTH) and ASEPSIS wound scores, with a subgroup analysis for patients with or without antiplatelet therapy.

RESULTS

Each of 46 patients (10 [22%] with antiplatelet therapy) received randomized SAPB-T45K or control treatment for 2 wounds. Safety assessments were similar, and ASEPSIS scores reflected normal healing in both wound groups. SAPB-T45K demonstrated significantly faster median TTH (24.5 [range, 7–165] seconds) compared with control (44 [10–387] seconds), for a 41% median TTH reduction (18 [95% confidence interval, 7–35] seconds, p < .001). SAPB-T45K provided an identical median TTH of 24 seconds, regardless of antiplatelet therapy. Control median TTH was 90 and 40 seconds for patients taking or not taking antiplatelet therapy, respectively.

CONCLUSIONS

SAPB-T45K provided significantly faster median TTH versus control, especially with antiplatelet therapy, and safety profiles were similar.
The Juicebox Assembly Tools module facilitatesde novoassembly of mammalian genomes with chromosome-length scaffolds for under $1000
Authors: Dudchenko Olga , Shamim Muhammad S. , Batra Sanjit S. , Durand Neva C. , Musial Nathaniel T. , Mostofa Ragib , Pham Melanie , Glenn St Hilaire Brian , Yao Weijie , Stamenova Elena , Hoeger Marie , Nyquist Sarah K. , Korchina Valeriya , Pletch Kelcie , Flanagan Joseph P. , Tomaszewicz Ania , McAloose Denise , Pérez Estrada Cynthia , Novak Ben J. , Omer Arina D. , Aiden Erez Lieberman
Published: January 2018

Hi-C contact maps are valuable for genome assembly (Lieberman-Aiden, van Berkum et al. 2009; Burton et al. 2013; Dudchenko et al. 2017). Recently, we developed Juicebox, a system for the visual exploration of Hi-C data (Durand, Robinson et al. 2016), and 3D-DNA, an automated pipeline for using Hi-C data to assemble genomes (Dudchenko et al. 2017). Here, we introduce “Assembly Tools,” a new module for Juicebox, which provides a point-and-click interface for using Hi-C heatmaps to identify and correct errors in a genome assembly. Together, 3D-DNA and the Juicebox Assembly Tools greatly reduce the cost of accurately assembling complex eukaryotic genomes. To illustrate, we generatedde novoassemblies with chromosome-length scaffolds for three mammals: the wombat,Vombatus ursinus(3.3Gb), the Virginia opossum,Didelphis virginiana(3.3Gb), and the raccoon,Procyon lotor(2.5Gb). The only inputs for each assembly were Illumina reads from a short insert DNA-Seq library (300 million Illumina reads, maximum length 2x150 bases) and anin situHi-C library (100 million Illumina reads, maximum read length 2x150 bases), which cost <$1000.
MicroPheno: Predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples
Authors: Asgari Ehsaneddin , Garakani Kiavash , McHardy Alice Carolyn , Mofrad Mohammad R.K.
Published: January 2018

Motivation: Microbial communities play important roles in the function and maintenance of various biosystems, ranging from the human body to the environment. A major challenge in microbiome research is the classification of microbial communities of different environments or host phenotypes. The most common and cost-effective approach for such studies to date is 16S rRNA gene sequencing. Recent falls in sequencing costs have increased the demand for simple, efficient, and accurate methods for rapid detection or diagnosis with proved applications in medicine, agriculture, and forensic science. We describe a reference- and alignment-free approach for predicting environments and host phenotypes from 16S rRNA gene sequencing based on k-mer representations that benefits from a bootstrapping framework for investigating the sufficiency of shallow sub-samples. Deep learning methods as well as classical approaches were explored for predicting environments and host phenotypes.

Results: k-mer distribution of shallow sub-samples outperformed the computationally costly Operational Taxonomic Unit (OTU) features in the tasks of body-site identification and Crohn's disease prediction. Aside from being more accurate, using k-mer features in shallow sub-samples allows (i) skipping computationally costly sequence alignments required in OTU-picking, and (ii) provided a proof of concept for the sufficiency of shallow and short-length 16S rRNA sequencing for phenotype prediction. In addition, k-mer features predicted representative 16S rRNA gene sequences of 18 ecological environments, and 5 organismal environments with high macro-F1 scores of 0.88 and 0.87. For large datasets, deep learning outperformed classical methods such as Random Forest and SVM.

Availability: The software and datasets are available at https://llp.berkeley.edu/micropheno.
From 1D sequence to 3D chromatin dynamics and cellular functions: a phase separation perspective
Authors: Liu Sirui , Zhang Ling , Quan Hui , Tian Hao , Meng Luming , Yang Lijiang , Feng Huajie , Gao Yi Qin
Published: January 2018

The high-order chromatin structure plays a non-negligible role in gene regulation. However, the mechanism for the formation of different chromatin structures in different cells and the sequence dependence of this process remain to be elucidated. As the nucleotide distributions in human and mouse genomes are highly uneven, we identified CGI forest and prairie genomic domains based on CGI density, which better segregates genomic elements along the genome than GC content. The genome is then divided into two sequentially, epigenetically, and transcriptionally distinct regions. These two types of megabase-sized domains spatially segregate, but to a different extent in different cell types. Overall, the forests and prairies gradually segregate from each other in development, differentiation, and senescence. The multi-scale forest-prairie spatial intermingling is cell-type specific and increases in differentiation, thus helps define the cell identity. We propose that the phase separation of the 1D mosaic sequence in space, serving as a potential driving force, together with cell type specific epigenetic marks and transcription factors, shapes the chromatin structure in different cell types and renders them distinct genomic properties. The mosaicity of the genome manifested in terms of alternative forests and prairies of a species could be related to its biological processes such as differentiation, aging and body temperature control.
The biogenesis of extracellular vesicles fromStaphylococcus aureusand their application as a novel vaccine platform
Authors: Wang Xiaogang , Weidenmaier Christopher , Lee Jean C.
Published: January 2018

Gram-positive bacteria secrete extracellular vesicles (EVs) that package diverse bacterial antigens and play key roles in bacterial pathogenesis. However, the mechanisms underlying EV production in Gram-positive bacteria are poorly understood. We purified and characterized EVs from a community-associated methicillin-resistantStaphylococcus aureusisolate (USA300) and investigated mechanisms underlying EV production. Native EVs contained 165 proteins, including cytosolic, surface, and secreted proteins, autolysins, and numerous cytolysins. Staphylococcal alpha-type phenol-soluble modulins (surfactant-like peptides) promoted EV biogenesis, presumably by acting at the cytoplasmic membrane, whereas peptidoglycan crosslinking and autolysin activity were found to increase EV production by altering the permeability of the staphylococcal cell wall. To address the immunogenicity of EVs, we created engineered EVs (eng-EVs) by expressing detoxified proteins HlaH35Land LukE in EVs generated from a nontoxicS. aureus ΔagrΔspamutant. Eng-EVs exhibited no cytotoxicity in vitro, and mice immunized with the eng-EVs produced toxin-neutralizing antibodies and showed reduced lethality in a mouse sepsis model. Our study reveals novel mechanisms underlyingS. aureusEV production and highlights the usefulness of EVs as a novelS. aureusvaccine platform.
Parp3 promotes long-range end-joining in murine cells
Authors: Layer Jacob V. , Patrick Cleary J. , Brown Alexander J. , Stevenson Kristen E. , Morrow Sara N. , Van Scoyk Alexandria , Blasco Rafael B. , Karaca Elif , Meng Fei-Long , Frock Richard L. , Tivey Trevor , Kim Sunhee , Fuchs Hailey , Chiarle Roberto , Alt Frederick W. , Roberts Steven A. , Weinstock David M. , Day Tovah A.
Published: January 2018

Chromosomal rearrangements, including translocations, are early and essential events in the formation of many tumors. Previous studies that defined the genetic requirements for rearrangement formation have identified differences between murine and human cells, most notably in the role of classical‐ and alternative-nonhomologous end joining factors (NHEJ). We reported that poly(ADP)ribose polymerase 3 (PARP3) promotes chromosomal rearrangements induced by endonucleases in multiple human cell types. In contrast to c-NHEJ factors, we show here that Parp3 also promotes rearrangements in murine cells, including translocations in murine embryonic stem cells (mESCs), class switch recombination in primary B cells and inversions in tail fibroblasts that generate Eml4-Alk fusions. In mESCs, Parp3-deficient cells had shorter deletion lengths at translocation junctions. This was corroborated using next-generation sequencing of Eml4-Alk junctions in tail fibroblasts and is consistent with a role for Parp3 in promoting the processing of DNA double-strand breaks. We confirmed a previous report that Parp1 also promotes rearrangement formation. In contrast with Parp3, rearrangement junctions in the absence of Parp1 had longer deletion lengths, suggesting Parp1 may suppress DSB processing. Together, these data indicate that Parp3 and Parp1 promote rearrangements with distinct phenotypes.
The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription
Authors: Mikhaylichenko Olga , Bondarenko Vladyslav , Harnett Dermot , Schor Ignacio E. , Males Matilda , Viales Rebecca R. , Furlong Eileen E.M.
Published: January 2018

Gene expression is regulated by promoters, which initiate transcription, and enhancers, which control their temporal and spatial activity. However, the discovery that mammalian enhancers also initiate transcription questions the inherent differences between enhancers and promoters. Here, we investigate the transcriptional properties of enhancers during Drosophila embryogenesis using characterized developmental enhancers. We show that while the timing of enhancer transcription is generally correlated with enhancer activity, the levels and directionality of transcription are highly varied among active enhancers. To assess how this impacts function, we developed a dual transgenic assay to simultaneously measure enhancer and promoter activities from a single element in the same embryo. Extensive transgenic analysis revealed a relationship between the direction of endogenous transcription and the ability to function as an enhancer or promoter in vivo, although enhancer RNA (eRNA) production and activity are not always strictly coupled. Some enhancers (mainly bidirectional) can act as weak promoters, producing overlapping spatio–temporal expression. Conversely, bidirectional promoters often act as strong enhancers, while unidirectional promoters generally cannot. The balance between enhancer and promoter activity is generally reflected in the levels and directionality of eRNA transcription and is likely an inherent sequence property of the elements themselves.
Synthesis and crystal structure of a new polymorph of potassium europium(III) bis(sulfate) monohydrate, KEu(SO4)2·H2O
Authors: Paul Avijit Kumar
Published: January 2018

The mixed-metal sulfate, KEu(SO4)2·H2O, has been obtained as a new polymorph using hydrothermal conditions. The crystal structure is isotypic with NaCe(SO4)2·H2O and shows a three-dimensional connectivity of the tetrahedral sulfate units with EuIII and KI ions. Tricapped trigonal–prismatic EuO9 units and square-antiprismatic KO8 units link the SO4 tetrahedra, building the three-dimensional structure. Topological analysis reveals the existence of two nodes with 6- and 10-connected nets. The compound was previously reported [Kazmierczak & Höppe (2010). J. Solid State Chem.
183, 2087–2094] in the monoclinic space group P21/c with a similar structural connectivity and coordination environments to the present compound.
Crystal structures of eight- and ten-membered cyclic bisanisylphosphonothioyl disulfanes and comparison with their P-ferrocenyl analogues
Authors: Przychodzeń Witold , Chojnacki Jarosław
Published: January 2018

Two new crystal structures of eight- and ten-membered cyclic bisanisylphosphonothioyl disulfanes, namely 2,5-bis(4-methoxyphenyl)-1,6,3,4,2λ5,5λ5-dioxadithiadiphosphocane-2,5-dithione, C16H18O4P2S4, and 2,5-bis(4-methoxyphenyl)-1,6,3,4,2λ5,5λ5-dioxadithiadiphosphecane-2,5-dithione, C18H22O4P2S4, have been determined and compared to structures of the ferrocenyl analogues. The eight-membered rings have similar conformations (TBC) but the ten-membered macrocycles are differently puckered. Structural parameters of the relevant SPSSPS motif have been analysed and are discussed in detail. Compound 1 was refined as an inversion twin and 2 was refined as a two-component rotational twin.
5-(2-Chlorophenyl)-3-(2H-chromen-3-yl)-1,2,4-oxadiazole
Authors: Baral Nilofar , Nayak Sabita , Pal Satyanarayan , Mohapatra Seetaram
Published: January 2018

In the title compound, C17H11ClN2O2, the central oxadiazole ring carries 2H-chromene and 2-chlorophenyl substituents at the 3- and 5-positions, respectively. C—H...O and C—H...Cl hydrogen bonds form two-dimensional sheets parallel to (212), with each individual molecule involved in six of these weak interactions. The sheets are stacked perpendicular to (212) by offset π–π stacking interactions.
A series-parallel inventory-redundancy green allocation system using a max-min approach via the interior point method
Authors: Niknamfar Amir Hossein , Niaki Seyed Armin Akhavan , karimi Marziyeh
Published: January 2018

Purpose

The purpose of this study is to develop a novel and practical series-parallel inventory-redundancy allocation system in a green supply chain including a single manufacturer and multiple retailers operating in several positions without any conflict of interests. The manufacturer first produces multi-product and then dispatches them to the retailers at different wholesale prices based on a common replenishment cycle policy. In contrast, the retailers sell the purchased products to customers at different retail prices. In this way, the manufacturer encounters a redundancy allocation problem (RAP), in which the solution subsequently enhances system production reliability. Furthermore, to emphasize on global warming and human health concerns, this paper pays attention both the tax cost of industrial greenhouse gas (GHG) emissions of all produced products and the limitation for total GHG emissions.

Design/methodology/approach

The manufacturer intends not only to maximize the total net profit but also to minimize the mean time to failure of his production system using a RAP. To achieve these objectives, the max-min approach associated with the solution method known as the interior point method is utilized to maximize the minimum (the worst) value of the objective functions. Finally, numerical experiments are presented to further demonstrate the applicability of the proposed methodology. Sensitivity analysis on the green supply chain approach is also performed to obtain more insight.

Findings

The computational results showed that increasing the number of products and retailers might lead into a substantial increase in the total net profit. This indicated that the manufacturer would feel adding a new retailer to the green supply chain strongly. Moreover, an increase in the number of machines provides significant improvement in the reliability of the production system. Furthermore, the results of the performed sensitivity analysis on the green approach indicated that increasing the number of machines has a substantial impact on both the total net profit and the total tax cost. In addition, not only the proposed green supply chain was more efficient than the supply chain without green but also the proposed green supply chain was very sensitive to the tax cost of GHG emission rather than the number of machines.

Originality/value

In summary, the motivations are as follows: the development of a bi-objective series-parallel inventory-RAP in a green supply chain; proposing a hybrid inventory-RAP; and considering the interior point solution method. The novel method comes from both theoretical and experimental techniques. The paper also has industrial applications. The advantage of using the proposed approach is to generate additional opportunities and cost effectiveness for businesses and companies that operate utilizing the green supply chain under an inventory model.
Applying EEG in consumer neuroscience
Authors: Lin Meng-Hsien (Jenny) , Cross Samantha N.N. , Jones William J. , Childers Terry L.
Published: January 2018

Purpose

This paper aims to review past papers focused on understanding consumer-related topics in marketing and related interdisciplinary fields to demonstrate the applications of electroencephalogram (EEG) in consumer neuroscience.

Design/methodology/approach

In addition to the review of papers using EEG to study consumer cognitive processes, the authors also discuss relevant decisions and considerations in conducting event-related potential (ERP) studies. Further, a framework proposed by Plassmann et al. (2015) was used to discuss the applications of EEG in marketing research from papers reviewed.

Findings

This paper successfully used Plassmann et al.’s (2015) framework to discuss five applications of neuroscience to marketing research. A review of growing EEG studies in the field of marketing and other interdisciplinary fields reveals the advantages and potential of using EEG in combination with other methods. This calls for more research using such methods.

Research limitations/implications

A technical overview of ERP-related terminology provides researchers with a background for understanding and reviewing ERP studies. A discussion of method-related considerations and decisions provides marketing researchers with an introduction to the method and refers readers to relevant literature.

Practical implications

The marketing industry has been quick to adopt cutting edge technology, including EEG, to understand and predict consumer behavior for the purpose of improving marketing practices. This paper connects the academic and practitioner spheres by presenting past and potential EEG research that can be translatable to the marketing industry.

Originality/value

The authors review past literature on the use of EEG to study consumer-related topics in marketing and interdisciplinary fields, to demonstrate its advantages over-traditional methods in studying consumer-relevant behaviors. To foster increasing use of EEG in consumer neuroscience research, the authors further provide technical and marketing-specific considerations for both academic and market researchers. This paper is one of the first to review past EEG papers and provide methodological background insights for marketing researchers.