bluuebunny/crossref_metadata_2025 huggingface dataset:
Undead Wives and Undone Husbands
Authors: Weinauer Ellen
Published: July 2018

Critics have had very little to say about marriage as an institution in Poe’s work, despite a recent historical turn in Poe studies that might lead in that direction. This essay demonstrates that Poe was in fact deeply engaged with the idea of legal marriage—one of the most important social and political issues of his day—and deeply ambivalent about the losses to which marriage subjected both husbands and wives. In the wasted, undead wives featured in such tales as “Berenice” (1835) and “Ligeia” (1838) and the undone, dispossessed husbands in “The Black Cat” (1843) and “The Oblong Box” (1844), Poe considers the profound transformations that legal marriage works upon women and men, and the terrifying unity between husband and wife that marriage demands.
Deciphering Dupin
Authors: Ross Kelly
Published: July 2018

Poe sits at the intersection of the tightly interwoven fields of computing and mass surveillance. Examining Poe’s Dupin tales through a lens of surveillance, rather than Holmesian detection or Lacanian psychoanalysis, provides new insights into Poe’s relationship to information, communications, and metadata. In the three Dupin tales, I argue, Poe explores various aspects of digital surveillance, from data mining and profiling in “The Murders in the Rue Morgue” and “The Mystery of Marie Rogêt” to metadata in “The Purloined Letter.” Rereading these tales with a surveillant eye allows us to perceive more clearly the sociohistorical forces, rather than interiorized psychodynamics, at play in the Dupin tales.
Poe’s Survival Stories as Dying Colonialisms
Authors: Sandler Matt
Published: July 2018

This chapter focuses on the appearance of historical details in short stories about near-death experiences. It examines in particular how “A Descent into the Maelström” and “The Pit and the Pendulum” refer to pre-Anglo-Saxon forms of New World colonization (Viking and Spanish) as a way of agitating readers’ anxieties about the rise of American civilization. These references provide examples through which to rethink the conflict between historicist and allegorical interpretations of Poe’s work. In particular, his oblique representations of Manifest Destiny and white supremacy look differently when read through the metahistorical notion of the “course of empire,” with its inevitable end in moral decay. The chapter concludes by pointing out how Poe’s scheme of extreme individual experience against the backdrop of long-durational historical narrative was taken up by Frantz Fanon, who focused on the psychological predicament of the native in a very different story of empire.
The Marginal Center
Authors: Rachman Stephen
Published: July 2018

This essay discusses Poe’s magazine pieces that are comprised of brief quotations or fragmentary comments upon other works of literature. First, as these piecemeal pieces were artifacts from “the Magazine Prison-House” in which Poe labored, the essay will set out to establish their functions within Poe’s editorial work and his sense of their relation to public and literary erudition. Second, because Poe recycled or returned to many of these marginal comments in the making of his essays, tales, and poems, they are discussed as building blocks or conceptual nodes for his various creative endeavors. Third, the essay will discuss the critical strategies within these pieces that served Poe more generally as statements of opinion on a range of literary topics (e.g., originality/plagiarism, transcendentalism, rationale of verse). The essay concludes by discussing the importance of the marginal as a critical position from which Poe would make his literary inventions and interventions.
Ancestral Piles
Authors: Moreland Sean
Published: July 2018

This essay examines Poe’s conception and use of the Gothic via his engagements with the work of earlier writers from Horace Walpole through Ann Radcliffe, William Godwin, Charles Brockden Brown, Mary Shelley, and E. T. A. Hoffmann. Poe’s uses of the Gothic, and his relationship with the work of these writers, was informed by his philosophical materialism and framed by his dialogue with the writings of Sir Walter Scott. Tracing these associations reveals Poe’s transformation of the idea of “Gothic structure” from an architectural model, the ancestral pile of the eighteenth-century Gothic, to one of energetic transformation, the electric pile featured in many of Poe’s tales.
Dupin’s Descendants in Print and on Screen
Authors: Gruesser John
Published: July 2018

Edgar Allan Poe envisions detection as competition, staging contests between characters, constructing plots so as to outwit readers, and in effect competing with himself in the two sequels to “The Murders in the Rue Morgue.” By striving to outdo what he has already done, Poe weaves authorial competition into the fabric of detection, inspiring a diverse range of writers to bring innovations to the form. He would likely be amazed to find that the descendants of Auguste Dupin have come in an array of shapes, sizes, nationalities, genders, socioeconomic classes, sexual orientations, subject positions, and ethnic and racial backgrounds. Moreover, even his vivid imagination could not have conceived of detection’s impact on various print and nonprint media in the twentieth and twenty-first centuries, including comic books, graphic novels, animation, computer games, television, and film.
Poe and the Avant-Garde
Authors: Elmer Jonathan
Published: July 2018

Poe’s influence on both avant-garde and mass-cultural production has been puzzling for many. This is because “avant-garde” has been restricted to whatever opposes aesthetic commodification and the culture industry. Placing Poe’s work in the context of nineteenth century physiological aesthetics helps explain Poe’s profound influence on “experimental arts,” whether avant-garde or commercial. Focused on anomalies of attention and the separation of sense modalities, Poe’s texts model and incite experimentation in media other than his own. Using hearing and vision as a red thread, this chapter will advance this argument through reference to visual works by Odilon Redon, Harry Clarke, and Carlo Farneti.
“Boulders, Fighting on the Plain”
Authors: Gunderson Frank
Published: July 2018

The song “Shiganga Jilikenya ku Mabala” (Boulders, fighting on the plain) was composed during World War I by Ng’wana Matonange, a Sukuma singer conscripted into the German Army. Matonange saw the war in economic terms from the point of view of a pastoralist, commenting that the Germans and the British were at war because of cattle. The song enjoyed popularity in dance competitions during the 1920s, before being collected by the anthropologist Hans Cory. The song text was transcribed, and archived with the Hans Cory Papers at the University of Dar es Salaam. The text was referenced in interviews with living musicians and other commentators who were from the village where the song was collected. They were able to elucidate further about the composer, the melody, additional verses, performance practice, and the battle documented in the song. Their commentary informed ethnographic and historical interpretation of the song’s transmission trajectory.
Food and Water Management in the Mediterranean Basin
Authors: Petit Michel , Le Grusse Phillipe
Published: July 2018

The food and water challenges to be faced in the Mediterranean Basin, particularly those on the southern and eastern shores, are daunting. They form a complex nexus of problems and require policies pursuing several important potentially conflicting goals at the same time: reducing or limiting food import dependency through increased agricultural production in environmentally sustainable ways while protecting the natural resource base and keeping food affordable for poorer populations. The worrisome trends affecting countries on the southern and eastern shores of the common sea can also have seriously negative consequences in the North which explains why the North-South collaboration has a long tradition in the region. But, as the case of water management institutions shows, ineffective advocacy for trade liberalization has led to conflicts and tensions on various issues and has distracted attention from potentially much more fruitful areas of collaboration.
The Executive Branch in Israel
Authors: Kenig Ofer
Published: July 2018

As in other parliamentary democracies, the Israeli government is dependent on the confidence of parliament. Israel is a country with a diverse society, divided by multidimensional political issues and using a proportional representation electoral system. It is therefore not surprising to find a multiparty system with a highly fragmented parliament. This setting produces the central institutional feature of its executive branch: coalition politics. This chapter outlines the process of cabinet formation and the types of coalitions formed, presents an overview of the position of the prime minister, describes the work and structure of cabinet ministers and ministries, explains why governments seldom complete a full term, and assesses claims about both instability and nongovernability in Israel.
Noxious Mechanosensation
Authors: Delmas Patrick , Korogod Sergiy Mikhailovych , Coste Bertrand
Published: July 2018

This article introduces a number of critical features of mechanical transduction and neuronal sensory coding, with particular reference to mechanical pain. High threshold mechanoreceptors (HTMRs) in skin are the first relay point for the transduction of noxious mechanical force into the nervous system, and their properties determine how and when nociceptive signal is relayed up to the central nervous system. The article describes the structure and physiology of the mechano-nociceptors and explains the peripheral molecular mechanisms of transduction leading to mechanical pain. In addition, this article also describes a set of computer models of HTMRs and relevant ion channels representing structural and biophysical features of the biological prototype. A better understanding of HTMRs’ function may lead to the development of novel therapeutic pathways in the treatment of chronic mechanical pain.
Phenomenology and Ontology in the Later Heidegger
Authors: Keiling Tobias
Published: July 2018

Heidegger’s later philosophy is marked by two conflicting claims about phenomenology. On the one hand, phenomenology and philosophy generally is tasked with “responding to the claim of what is to be thought” in a novel and unprecedented manner. On the other hand, Heidegger recognizes that there have been earlier attempts at thus doing justice to phenomena; in the ontological commitments of earlier thinkers, Heidegger finds accounts of the “things themselves,” each of which has different implications for what phenomenology should concern itself with. Phenomenology, as Heidegger conceives it, should thus both incorporate the history of philosophy and exceed it, yet it is unclear how these ideas can be reconciled. This chapter calls this problem the “dilemma of the historicity of phenomenology” and identifies different versions of it in Heidegger’s works after 1935/6.
The Later Sartre
Authors: Flynn Thomas R.
Published: July 2018

Toward the midpoint of his career, Sartre famously announced the separation from his previous work which he described as a rationalist philosophy of consciousness. Henceforth, he implied, his focus would be on free organic praxis. It would be dialectical and historical not just analytical and psychological. It seemed that he was distancing himself from classical (constitutive) Husserlian phenomenology in favor of something more fluid, more concrete like the hermeneutic phenomenology that he discovered in the Heidegger of Being and Time and was recommending as an ingredient in his Existential psychoanalysis. But classical phenomenology was not so much passed over as it was placed in abeyance to return in Sartre’s study of Gustave Flaubert, his life and times. The author proposes to chart and critique this methodological circle of applied phenomenology.
An Immense Power
Authors: Lawlor Leonard
Published: July 2018

Derrida’s idea of deconstruction stems from three phenomenological insights: (1) the insight into the experience of others; (2) the insight into the role of documentation for knowledge; and (3) the insight into temporalization. But the chapter argues that there is a fourth phenomenological insight, the insight in the endless expansion of reduction. It is this fourth insight that leads to the idea of power, an immense power. The repeatability of experience implies a potency that goes to infinity. The chapter looks at all of Derrida’s major writings on Husserl: The Introduction to The Origin of Geometry; “Violence and Metaphysics”; Voice and Phenomenon; and Touching—Jean-Luc Nancy.
The Inquietude of Time and the Instance of Eternity
Authors: de Warren Nicolas
Published: July 2018

This chapter explores the meaning and importance of the question “What is time?” in the phenomenological philosophies of Husserl, Heidegger, and Levinas. As developed in this chapter, the question of time is for each of these thinkers inseparable from the question of subjectivity. To pose the question “What is time?” is equally to pose the question “Who is the subject in time?” In addition to a discussion of the relation between time and subjectivity, this chapter further examines how for each of these thinkers their respective understanding of time is configured around a twofold sense of temporal difference: the difference between past, present, and future within time; and the difference between time and eternity.
Introduction
Authors: Zahavi Dan
Published: July 2018

Phenomenology has not only highlighted the importance of historicity, it also has its own complex history. Phenomenology was not only formed and developed in reaction to and under inspiration from various preceding and competing philosophical traditions, the principal figures of the tradition also kept developing and refining their own views over the years. The aim of the present handbook is to analyze historical influences, connections, and developments, thereby contributing to our comprehension and assessment of both the unity and diversity of the phenomenological tradition. How did it start? How did it develop? Where is it heading? Does it have a future?
Practical Intentionality
Authors: Salice Alessandro
Published: July 2018

The aim of this chapter is to mine, reconstruct, and evaluate the phenomenological notion of practical intentionality. It is claimed that the phenomenologists of the Munich and Göttingen Circles substantially modify the idea of practical intentionality originally developed by Franz Brentano. This development, it is further contended, anticipates the switch that occurred within contemporary theory of action from a belief-desire (BD) to a belief-desire-intention (BDI) model of deliberation. While Brentano’s position can be interpreted as a variant of the BD model, early phenomenologists propose a general theory of deliberation that, in line with the BDI account, puts the notion of intention at the very core of practical intentionality. On their understanding, the concept of intention points to a primitive kind of mental state that cannot be reduced to a combination of beliefs and desires.
Understanding the Bio in the Biosocial Theory of BPD
Authors: Niedtfeld Inga , Bohus Martin
Published: July 2018

Originally, the biosocial model of borderline personality disorder (BPD) was based on clinical experience and intuition. Within the last 30 years, tremendous progress has been made strengthening the empirical basis for this model. Currently, most researchers postulate three core domains of BPD psychopathology: affective dysregulation, interpersonal disturbances, and problems in identity. Whereas affective dysregulation research has the strongest empirical support, morphological and functional neuroimaging findings point to alterations of the central regions of the emotion regulation circuitry: prefrontal cortex, amygdala, hippocampus, and insula. It is unclear whether these alterations are due to early adverse childhood experience or instead are more genetically driven, resulting in a pattern of emotional hypersensitivity,. However, evidence shows that successful DBT changes dysfunctional emotions and cognitive patterns as well as related neurobiological underpinnings. This chapter discusses the current state of research on the biological underpinnings of BPD.
Phenomenological Psychopathology and Psychiatric Ethics
Authors: Rosfort René
Published: July 2018

Phenomenological psychopathology and psychiatric ethics are intimately related. The argument of this chapter is that phenomenological psychopathology makes it evident that ethical considerations are not merely an external normative perspective on psychiatry, but fundamental to the experience of mental illness, and as such critical to the medical understanding of what a mental illness is. Norms and values orient human existence, and our endeavor to make sense of and cure the mental suffering of a person involves a clarification of what the person cares about. A phenomenological approach can help us understand that a sense of autonomy is constitutive of human self-awareness, and the demand of responsibility central to human identity. In fact, the dialectics of autonomy and responsibility discloses the fragile character of human identity, and examining this fragility will allow us to see that a person’s mental suffering cannot be understood in isolation from her ideas about the good life.
Underdetermination by Reasons
Authors: Gert Joshua
Published: July 2018

The norms of rationality determine whether an act is irrational, rationally required, or rationally optional. It has seemed theoretically difficult to make significant room for the last category, because rational status is typically taken to be a function of reasons, and reasons are typically taken to have univocal strength values. But there is also a strong intuition that normal choice situations present us with many equally rational options. If this intuition is correct, two questions arise. The first is how it could be true, assuming that rational status is indeed a function of reasons. The second is whether and how we can act in a non-arbitrary way when we are faced with a choice between a number of equally rational options. This chapter examines four strategies for addressing these questions: incommensurability of reasons, parity, the ubiquity of ties, and a distinction between the justifying and requiring roles of practical reasons.
Reliable and Unreliable Judgments About Reasons
Authors: Donovan Caitrin , Fine Cordelia , Kennett Jeanette
Published: July 2018

The new skepticism about practical reason is predicated upon empirical findings which challenge the primacy traditionally afforded to reasoning in contexts of normative deliberation. These findings, which are associated with dual-process theories of cognition, are taken to support two skeptical claims: our reasons for action are not what we take them to be, and reasoning is an unreliable means for arriving at reliable judgments. After providing a critical overview of empirically based skepticism and its implications, we argue that skeptics underestimate the role that reasoning processes play in moral deliberation. We then canvass ways in which threats to the reliability of individual-level moral reasoning can be countenanced by social-level practices such as “nudging,” inter-agent reasoning, and testimonial expertise.
Using Motion Picture Films to Teach Nursing Theory in Graduate Nursing Education
Authors: Hanna Debra R.
Published: July 2018

Teaching strategies that use pedagogy of inquiry and contextualization are needed to ensure that nursing students will be well prepared to manage increasingly complex patient information. The rationale for using motion pictures to teach theoretical thinking is explained, and an assignment that uses motion pictures is described. Film scene assignments facilitate learning theoretical thinking skills, reading clinical situations, and understanding how theory can be useful to problem-solve ambiguous clinical situations. Motion pictures present a text-in-motion that can be studied and analyzed in a repeatable, objective, and collaborative way.
Approaching Spine Research in an Outreach Setting
Authors: Slattery Casey , Verma Kushagra , Rios Fernando , Mundis Gregory M. , Boachie-Adjei Oheneba , Rinella Anthony
Published: July 2018

Organizing medical research in an outreach setting can be a challenging task, especially when it involves complex spine procedures in patients whom it is difficult to follow-up for long term. Disease severity at presentation is often advanced in outreach settings due to limited local resources, surgeon expertise, and hospital infrastructure. Case complexity can present a challenge to local and outreach surgeons alike. This article will describe what encompasses an ideal outreach program as it relates to spine, how to manage cost in an outreach setting, collection of outcome data, and maintaining long-term follow-up. As one of the criticisms of medical outreach is the relative paucity of outcome data, this article discusses methods to collect and report outcomes abroad. We also discuss the value of translating outcome questionnaires to different languages and cross-cultural comparisons. In addition, relatively rare pathologies are often seen with greater frequency abroad. These patients are ideally suited for a focused case series than can guide treatment decisions.
Effects of Proton Pump Inhibitor Coadministration on the Plasma Concentration of Erlotinib in Patients With Non–Small Cell Lung Cancer
Authors: Ohgami Masahiro , Kaburagi Takayuki , Kurosawa Atsuhiko , Doki Kosuke , Shiozawa Toshihiro , Hizawa Nobuyuki , Homma Masato
Published: July 2018

Background:

Erlotinib is used for treating non–small cell lung cancer (NSCLC). Intestinal absorption of erlotinib is impaired under gastric pH elevation; therefore, coadministration of gastric acid suppressants may provide lower blood concentration of erlotinib. We investigated the effects of erlotinib coadministration with proton pump inhibitors (PPIs) and histamine H2 receptor blockers (H2RBs) on the plasma concentration of erlotinib and erlotinib-induced adverse reaction in patients with NSCLC.

Methods:

Forty-two patients receiving erlotinib therapy for NSCLC were recruited for this study. Association of adverse reactions (rash and diarrhea) with plasma concentration of erlotinib was examined. Plasma concentration-to-dose (C/D) ratios and oral clearance (CL/F), which was estimated by population pharmacokinetic analysis of plasma concentrations of erlotinib, were compared among 3 patient groups: without coadministration of gastric acid suppressants (control group), with coadministration of PPI (PPI group), and coadministration of H2RB (H2RB group).

Results:

Patients with grade ≥2 rash had higher plasma concentrations of erlotinib compared with those with grade ≤1 [1.02 (0.43–2.60) versus 0.67 (0.10–1.85) mcg/mL, P < 0.01]. The C/D ratios of erlotinib in the PPI and H2RB groups were lower than that in the control group [0.39 (0.08–0.76) and 0.48 (0.33–0.81) versus 0.51 (0.28–1.28) mcg·mL−1·mg−1·kg−1], where statistical significance was observed between PPI and control groups (P < 0.05). The population pharmacokinetic estimated oral CL/F in the PPI and H2RB groups were higher than that in the control group [5.55 (3.36–14.52) and 4.82 (2.08–6.32) versus 3.95 (2.01–10.44) L/h], where statistical significance was observed between PPI and control groups (P < 0.05).

Conclusions:

Plasma concentrations of erlotinib in patients under coadministration of gastric acid suppressants were lower than those without gastric acid suppressants through drug interaction, suppressing the intestinal absorption of erlotinib. The magnitude of this drug interaction was more pronounced in the coadministration of PPI compared with H2RB.
Successful Cochlear Implantation of a Split Electrode Array in a Patient With Far-advanced Otosclerosis Assisted by Electromagnetic Navigation: A Case Report
Authors: Dejaco Daniel , Prejban David , Fischer Natalie , Freysinger Wolfgang , Stephan Kurt , Seebacher Josef , Widmann Gerlig , Riechelmann Herbert , Schmutzhard Joachim
Published: July 2018

Background:

Incomplete electrode insertion is frequent when implanting ossified cochleae with conventional linear electrodes. If split electrode arrays (SEA) are used, this complication occurs less frequently resulting in improved audiological performance (AP). Additional implementation of electromagnetic navigation systems (EMNS) may add additional safety to this procedure and may further improve AP. However, previously performed SEA cochlea implantations rarely implemented EMNS. The few cases reported a laborious approach with customized, three-dimensional-printed microstereotactic headframes, which limited clinical feasibility. Moreover, no postoperative AP was reported. In this case report a more feasible approach, using a commercially available EMNS, is described and postoperative AP is reported.

Patient:

A 70-year-old man with far-advanced otosclerosis was referred because of unsatisfactory speech intelligibility (monosyllabic word score of 0% at 75 dB sound pressure level) after cochlear implantation of a conventional linear electrode. Preoperative computed tomography revealed subtotal cochlear ossification and incomplete electrode insertion.

Intervention:

Four titanium screws were inserted into the petrous bone for computed tomography-based registration using an EMNS. The previous mastoidectomy was expanded, the misplaced conventional linear electrode extracted and a manual, free-handed superior cochleostomy at the level of the tendon of the tensor tympani muscle was performed. The location and course of the drill-out procedure for the SEA was planned and verified with EMNS.

Results:

Full electrode insertion for both electrode arrays of the SEA was achieved without any nerve dysfunction. Monosyllabic word score, determined 207 days after surgery, improved to 50 and 60% at 65 and 75 dB sound pressure level respectively.

Conclusion:

The implementation of EMNS in SEA cochlear implantation added additional safety to the procedure, which resulted in full electrode insertion and superior AP. Yet, outcome in cochlear implantation may vary. Larger case series to confirm this observation are required. The approach proposed for EMNS-guided SEA in this case report, using commercially available EMNS, may lead to a more frequent implementation in clinical routine due to its good clinical feasibility. Thus, larger case series may be generated.
Temporary Explant of a Transcutaneous Bone Conduction Hearing Implant for Imaging of the Pituitary Gland
Authors: Roesch Sebastian , Kugler Anton , Schlattau Alexander , Rasp Gerd
Published: July 2018

Objective:

Clinical report on feasibility and outcome of a surgical procedure.

Patient:

Nine-year-old child, supplied with a transcutaneous bone conduction hearing implant, requiring magnetic resonance imaging of the head to exclude a tumor of the pituitary gland.

Intervention:

Temporal removal and subsequent reimplantation of the implant in a single surgical procedure.

Main Outcome Measure:

Postoperative audiometric results.

Conclusion:

Under specific clinical circumstances, temporary removal of the transcutaneous bone conduction implant described, is technically accomplishable.
Refeeding syndrome in the gastroenterology practice: how concerned should we be?
Authors: Nunes Gonçalo , Brito Mariana , Santos Carla Adriana , Fonseca Jorge
Published: July 2018

Clinical nutrition is emerging as a major area in gastroenterology practice. Most gastrointestinal disorders interfere with digestive physiology and compromise nutritional status. Refeeding syndrome (RS) may increase morbidity and mortality in gastroenterology patients. Literature search using the keywords “Refeeding Syndrome”, “Hypophosphatemia”, “Hypomagnesemia” and “Hypokalemia”. Data regarding definition, pathophysiology, clinical manifestations, risk factors, management and prevention of RS were collected. Most evidence comes from case reports, narrative reviews and scarse observational trials. RS results from the potentially fatal shifts in fluid and electrolytes that may occur in malnourished patients receiving nutritional therapy. No standard definition is established and epidemiologic data is lacking. RS is characterized by hypophosphatemia, hypomagnesemia, hypokalemia, vitamin deficiency and abnormal glucose metabolism. Oral, enteral and parenteral nutrition may precipitate RS. Awareness and risk stratification using NICE criteria is essential to prevent and manage malnourished patients. Nutritional support should be started using low energy replacement and thiamine supplementation. Correction of electrolytes and fluid imbalances must be started before feeding. Malnourished patients with inflammatory bowel disease, liver cirrhosis, chronic intestinal failure and patients referred for endoscopic gastrostomy due to prolonged dysphagia present high risk of RS, in the gastroenterology practice. RS should be considered before starting nutritional support. Preventive measures are crucial, including fluid and electrolyte replacement therapy, vitamin supplementation and use of hypocaloric regimens. Gastroenterology patients must be viewed as high risk patients but the impact of RS in the outcome is not clearly defined in current literature.
Expression of Peripheral Node Addressins by Plasmacytic Plaque of Children, APACHE, TRAPP, and Primary Cutaneous Angioplasmacellular Hyperplasia
Authors: Fernandez-Flores Angel , Suarez Peñaranda José M. , De Toro Gonzalo , Alvarez Cuesta Cesar C. , Fernández-Figueras Maria T. , Kempf Werner , Monteagudo Carlos
Published: July 2018

High-endothelial venules are a common feature of 3 types of cutaneous pseudolymphomas: pretibial lymphoplasmacytic plaque (PLP) of children, acral pseudolymphomatous angiokeratoma of children (APACHE), and T-cell rich angiomatoid polypoid pseudolymphoma (TRAPP). In addition, primary cutaneous angioplasmacellular hyperplasia (PCAH) overlaps with these other 3 conditions. We intend to study the expression of peripheral node addressins in PLP, APACHE, TRAPP, and PCAH. We studied 1 case of PLP, 2 cases of APACHE, 2 cases of TRAPP, and 2 cases of PCAH. Immunostainings for MECA-79 and WT-1 were obtained in all cases. All cases showed a dense lymphohistiocytic dermal inflammatory infiltrate with abundant plasma cells. In addition, HEV were prominent in all cases. Cases of PLP, APACHE, and TRAPP expressed MECA-1. Cases of PCAH did not express MECA-1. Although PLP, APACHE, and TRAPP seem to fall under the same morphologic spectrum with different clinical representations, PCAH seems to be a different entity, with histopathologic peculiarities and a different immunophenotype.
Then-component nonlinear Schrödinger equations: dark–bright mixedN- and high-order solitons and breathers, and dynamics
Authors: Zhang Guoqiang , Yan Zhenya
Published: July 2018

The generaln-component nonlinear Schrödinger equations are systematically investigated with the aid of the Darboux transformation method and its extension. Firstly, we explore the condition of the existence for dark–bright mixed soliton solutions and derive an explicit formula of dark–bright mixed multi-soliton solutions in terms of the determinant. Secondly, we present the formula of dark–bright mixed high-order semi-rational solitons, and predict their generalNth-order wave structures. Thirdly, we investigate the wing-shaped structures of breather. Finally, we perform the numerical simulations for some representative solitons to study their dynamical behaviours.
Determination of macro-scale soil properties from pore scale structures: image-based modelling of poroelastic structures
Authors: Daly K. R. , Keyes S. D. , Roose T.
Published: July 2018

We show how a combination of X-ray computed tomography (X-CT) and image-based modelling can be used to calculate the effect of moisture content and compaction on the macroscopic structural properties of soil. Our method is based on the equations derived in Daly & Roose (2018Proc. R. Soc. A474, 20170141. (doi:10.1098/rspa.2017.0141)), which we have extended so they can be directly applied to the segmented images obtained from X-CT. We assume that the soils are composed of air-filled pore space, solid mineral grains and a mixed phase composed of both clay particles and water. We considered three different initial soil treatments, composed of two different compaction levels and two different moisture contents. We found that the effective properties of the soils were unaffected by compaction over the range tested in this paper. However, changing the moisture content significantly altered the hydraulic and mechanical properties of the soils. A key strength of this method is that it enables the optimization or even design of soils composed from different constituents, with specific mechanical and hydraulic properties.
Urban versus forest ecotypes are not explained by divergent reproductive selection
Authors: Caizergues Aude E. , Grégoire Arnaud , Charmantier Anne
Published: July 2018

Increasing urbanization offers a unique opportunity to study adaptive responses to rapid environmental change. Numerous studies have demonstrated phenotypic divergence between urban and rural organisms. However, comparing the direction and magnitude of natural selection between these environments has rarely been attempted. Using seven years of monitoring of great tits (
Parus major
) breeding in nest-boxes across the city of Montpellier and in a nearby oak forest, we find phenotypic divergence in four morphological and two life-history traits between urban and forest birds. We then measure reproductive selection on these traits, and compare selection between the habitats. Urban birds had significantly smaller morphological features than their rural counterparts, with a shorter tarsus, lower body mass, and smaller wing and tail lengths relative to their overall body size. While urban female tarsus length was under stabilizing selection, and forest males show positive selection for tarsus length and negative selection for body mass, selection gradients were significantly divergent between habitats only for body mass. Urban great tits also had earlier laying dates and smaller clutches. Surprisingly, we found selection for earlier laying date in the forest but not in the city. Conversely, we detected no linear selection on clutch size in the forest, but positive selection on clutch size in the urban habitat. Overall, these results do not support the hypothesis that contemporary reproductive selection explains differences in morphology and life history between urban- and forest-breeding great tits. We discuss how further experimental approaches will help confirm whether the observed divergence is maladaptive while identifying the environmental drivers behind it.
Deep Learning Based Tumor Type Classification Using Gene Expression Data
Authors: Lyu Boyu , Haque Anamul
Published: July 2018

Differential analysis occupies the most significant portion of the standard practices of RNA-Seq analysis. However, the conventional method is matching the tumor samples to the normal samples, which are both from the same tumor type. The output using such method would fail in differentiating tumor types because it lacks the knowledge from other tumor types. Pan-Cancer Atlas provides us with abundant information on 33 prevalent tumor types which could be used as prior knowledge to generate tumor-specific biomarkers. In this paper, we embedded the high dimensional RNA-Seq data into 2-D images and used a convolutional neural network to make classification of the 33 tumor types. The final accuracy we got was 95.59%, higher than another paper applying GA/KNN method on the same dataset. Based on the idea of Guided Grad Cam, as to each class, we generated significance heat-map for all the genes. By doing functional analysis on the genes with high intensities in the heat-maps, we validated that these top genes are related to tumor-specific pathways, and some of them have already been used as biomarkers, which proved the effectiveness of our method. As far as we know, we are the first to apply convolutional neural network on Pan-Cancer Atlas for classification, and we are also the first to match the significance of classification with the importance of genes. Our experiment results show that our method has a good performance and could also apply in other genomics data.
GEESE: Metabolically driven latent space learning for gene expression data
Authors: Barsacchi Marco , Terre Helena Andres , Lió Pietro
Published: July 2018

Gene expression microarrays provide a characterisation of the transcriptional activity of a particular biological sample. Their high dimensionality hampers the process of pattern recognition and extraction. Several approaches have been proposed for gleaning information about the hidden structure of the data. Among these approaches, deep generative models provide a powerful way for approximating the manifold on which the data reside.

Here we develop GEESE, a deep learning based framework that provides novel insight into the manifold learning for gene expression data, employing a metabolic model to constrain the learned representation. We evaluated the proposed framework, showing its ability to capture biologically relevant features, and encoding that features in a much simpler latent space. We showed how using a metabolic model to drive the autoencoder learning process helps in achieving better generalisation to unseen data. GEESE provides a novel perspective on the problem of unsupervised learning for biological data.

Availability

Source code of GEESE is available athttps://bitbucket.org/mbarsacchi/geese/.
Diagnosis of Osteoarthritis Subtypes with Blood Biomarkers
Authors: Zhao Kun , Lin Junxin , Wu Bingbing , Sun Guofei , An Chengrui , Paul Maswikiti Ewetse , Ouyang Hongwei
Published: July 2018

Objective

To identity osteoarthritis(OA) subtypes with gene expression of peripheral blood mononuclear cells.

Methods

Gene expression data (GSE48556) of Genetics osteoARthritis and Progression (GARP) study was downloaded from Gene Expression Omnibus. Principal component analysis and unsupervised clustering were analyzed to identify subtypes of OA and compare major KEGG pathways and cell type enrichment using GSEA and xCell. Classification of subtypes were explored by the utilization of support vector machine.

Results

Unsupervised clustering identified two distinct OA subtypes: Group A comprised of 60 patients (56.6%) and Group B had 46 patients (43.3%). A classifier including nine genes and CD4+T cell and Regulatory T cell flow cytometry could accurately distinguish patients from each group (area under the curve of 0.99 with gene expression). Group A is typical degenerative OA with glycosaminoglycan biosynthesis and apoptosis. Group B is related to Graft versus host disease and antigen processing and presentation, which indicated OA has a new type of “Antigen processing and presentation” similarly as that of RA.

Conclusion

OA can be clearly classified into two distinguished subtypes with blood transcriptome, which have important significance on the development of precise OA therapeutics.
Judgments of other bias in Cochrane systematic reviews of interventions are highly inconsistent and thus hindering use and comparability of evidence
Authors: Babic Andrija , Pijuk Andela , Brázdilová Lucie , Georgieva Yuliyana , Pereira Marco António Raposo , Poklepovic Tina , Puljak Livia
Published: July 2018

Background

Clinical decisions are made based on Cochrane systematic reviews (CSRs), but implementation of results of evidence syntheses such as CSRs is problematic if the evidence is not prepared consistently. All systematic reviews should assess risk of bias (RoB) in included studies, and in CSRs this is done by using Cochrane RoB tool. However, the tool is not necessarily applied according to the instructions. In this study we aimed to analyze types and judgments of ‘other bias’ in the RoB tool in CSRs of interventions.

Methods

We analyzed CSRs that included randomized controlled trials (RCTs) and extracted data regarding ‘other bias’ from the RoB table and accompanying support for the judgment. We categorized different types of other bias.

Results

We analyzed 768 CSRs that included 11369 RCTs. There were 602 (78%) CSRs that had ‘other bias’ domain in the RoB tool, and they included a total of 7811 RCTs. In the RoB table of 337 CSRs for at least one of the included trials it was indicated that no other bias was found and supporting explanations were inconsistently judged as low, unclear or high RoB. In the 524 CSRs that described various sources of other bias there were 5762 individual types of explanations which we categorized into 31 groups. The judgments of the same supporting explanations were highly inconsistent. Furthermore, we found numerous other inconsistencies in reporting of sources of other bias in CSRs.

Conclusion

Cochrane authors mention a wide range of sources of other bias in the RoB tool and they inconsistently judge the same supporting explanations. Inconsistency in appraising risk of other bias hinders reliability and comparability of Cochrane systematic reviews. Furthermore, discrepant and erroneous judgments of bias in evidence synthesis will inevitably hinder implementation of evidence in routine clinical practice and reduce confidence of practitioners in otherwise trustworthy sources of information.
A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants
Authors: Wagner Alex H , Walsh Brian , Mayfield Georgia , Tamborero David , Sonkin Dmitriy , Krysiak Kilannin , Pons Jordi Deu , Duren Ryan P , Gao Jianjiong , McMurry Julie , Patterson Sara , Del Vecchio Fitz Catherine , Sezerman Ozman U , Warner Jeremy L , Rieke Damian T , Aittokallio Tero , Cerami Ethan , Ritter Deborah , Schriml Lynn M , Freimuth Robert R , Haendel Melissa , Raca Gordana , Madhavan Subha , Baudis Michael , Beckmann Jacques S , Dienstmann Rodrigo , Chakravarty Debyani , Li Xuan Shirley , Mockus Susan , Elemento Olivier , Schultz Nikolaus , Lopez-Bigas Nuria , Lawler Mark , Goecks Jeremy , Griffith Malachi , Griffith Obi L , Margolin Adam A ,   Variant Interpretation for Cancer Consortium
Published: July 2018

Precision oncology relies on the accurate discovery and interpretation of genomic variants to enable individualized diagnosis, prognosis, and therapy selection. We found that knowledgebases containing clinical interpretations of somatic cancer variants are highly disparate in interpretation content, structure, and supporting primary literature, impeding consensus when evaluating variants and their relevance in a clinical setting. With the cooperation of experts of the Global Alliance for Genomics and Health (GA4GH) and six prominent cancer variant knowledgebases, we developed a framework for aggregating and harmonizing variant interpretations to produce a meta-knowledgebase of 12,856 aggregate interpretations covering 3,437 unique variants in 415 genes, 357 diseases, and 791 drugs. We demonstrated large gains in overlap between resources across variants, diseases, and drugs as a result of this harmonization. We subsequently demonstrated improved matching between a patient cohort and harmonized interpretations of potential clinical significance, observing an increase from an average of 33% per individual knowledgebase to 56% in aggregate. Our analyses illuminate the need for open, interoperable sharing of variant interpretation data. We also provide an open and freely available web interface (search.cancervariants.org) for exploring the harmonized interpretations from these six knowledgebases.
Detection ofMycobacterium lepraeDNA in soil; Multiple needles in the haystack?
Authors: Tió-Coma Maria , Wijnands Thomas , Pierneef Louise , Schilling Anna Katarina , Alam Korshed , Roy Johan Chandra , Faber William R. , Menke Henk , Pieters Toine , Stevenson Karen , Richardus Jan Hendrik , Geluk Annemieke
Published: July 2018

Background

Leprosy is an infectious disease caused byMycobacterium lepraeandMycobacterium lepromatosisaffecting the skin and nerves. Despite decades of availability of adequate treatment, transmission is unabated and routes of transmission are not completely understood. Notwithstanding the general assumption that untreatedM. lepraeinfected humans represent the major source of transmission, scarce reports indicate that environmental specimens could play a role as a reservoir as well.

Methodology

In order to identify patterns of bacterial transmission, this study investigated whetherM. lepraeDNA is present in soil of regions where leprosy is endemic or areas with possible animal reservoirs (armadillos and red squirrels). Soil samples were collected in Bangladesh, Suriname and the British Isles. The presence ofM. lepraeDNA was determined by RLEP PCR andM. lepraeSNP types were further identified by Sanger sequencing of loci 1-3.

Results

M. lepraeDNA was identified in soil samples from environments inhabited by leprosy patients (Bangladesh), armadillos (Suriname) and the lepromatous Eurasian red squirrels (British Isles). In Bangladesh SNP type 1 was detected, Suriname soil contained SNP type 1 or 2, whilst SNP typing was not feasible for the British samples.

Conclusions

It is conceivable that, besides humans and animals, environmental reservoirs may play a role in transmission. Frequent, intense contact with multibacillary leprosy patients poses the highest risk of transmission, and even though the risk of environmental contamination is low, it may offer a possible explanation for the occurrence of leprosy in individuals in areas without any reported human leprosy.
Adaptive Phenotypic Plasticity for Life History and Less Fitness-Related Traits
Authors: Acasuso-Rivero Cristina , Murren Courtney J. , Schlichting Carl D. , Steiner Ulrich K.
Published: July 2018

Organisms are faced with variable environments and one of the most common solutions to cope with such variability is phenotypic plasticity, a modification of the phenotype to the environment. These modifications influence ecological and evolutionary processes and are assumed to be adaptive. The assumption of adaptive plasticity allows to derive the prediction that the closer to fitness a trait is, the less plastic it would be. To test this hypothesis, we conducted a meta-analysis of 213 studies and measured the plasticity of each reported trait as coefficient of variation (CV). Traits were categorised according to their relationship to fitness into life-history traits (LHt) including reproduction and survival related-traits, and non-life-history traits (N-LHt) including traits related to development, metabolism and physiology, morphology and behaviour. Our results showed, unexpectedly, that although traits differed in their amounts of plasticity, trait plasticity did not correlate with its proximity to fitness. These findings were independent of taxonomic groups or environmental types assessed and raise questions about the ubiquity of adaptive plasticity. We caution about generalising the assumption that all plasticity is adaptive with respect to evolutionary and ecological population processes. More studies are needed that test the adaptive nature of plasticity, and additional theoretical explorations on adaptive and non-adaptive plasticity are encouraged.