bluuebunny/crossref_metadata_2025 huggingface dataset:
Critical Histories of Comparative Law
Authors: Frankenberg Günter
Published: September 2018

This chapter considers the history of comparative law. The birth of comparative law as a discipline can be traced back to the year 1900, when the Congrès International de Droit Comparé in Paris raised it above the level of singular, disparate, albeit remarkable studies and treatises to a collective, concerted venture guided by theories, methods, and projects. Before 1900 there was little interest in systematic legal comparison. Comparative law was marked, in the Western comparative community, by a significant inferiority syndrome. Comparatists felt neither adequately recognized by their academic peers nor sufficiently represented in the law school curriculum. Today, the (changing) reality of curricular marginality and comparative law’s growing popularity appears to nourish the hope for the well-deserved invitation to the field of the legal sciences.
Indigenous Rights
Authors: Duve Thomas
Published: September 2018

Many indigenous peoples now practice their own laws, their own cultural traditions and customs. In doing so, they draw on history, reconstructing their legal pasts, recreating—or even creating—their identities. At the same time, historical research has increasingly pointed out the intense interaction between indigenous peoples and European invaders during colonial period. Thus, it has become clear that many of the so-called ‘indigenous’ or ‘colonial’ legal traditions are more properly seen as hybridizations of indigenous and colonial laws and legal practices. This chapter introduces this historiography and its relevance to law and presents some methodological challenges in writing the history of indigenous rights in Latin America resulting from this fairly recent shift in (legal) historiography.
Governance Histories of International Law
Authors: Lustig Doreen
Published: September 2018

This chapter problematizes the Hartian perspective in international law’s historiography and explores how it may compound a narrow understanding of international law that concentrates on states and their practices as the main actors of relevance to international law (hereinafter: the statist bias). It begins with a brief sketch of the state of the field and its main historiographical debates. It then revisits the statist bias and how this has been confronted through competing visions of the international lawyer and the institutional and social arenas in which he or she operates. Next, it attempts to unravel how these novel conceptions of agency correspond with key theoretical developments of the post-Cold War era: transnational and global historical writing and international legal theories on global governance. Drawing on the literature from these wide-ranging perspectives, the chapter argues for a broader scope for international legal history.
A History of Violence
Authors: Leonard Gerald
Published: September 2018

This chapter discusses the violence of constitutional law, as verified by American constitutional history. It seeks to illuminate the centrality of violence to American constitutional history, and in so doing, illuminate the shape and trajectory, the limits and possibilities, of American constitutional law in the present. Although nothing could be easier than to find epic examples of injustice in American constitutional history, the object is not to call out injustice as such but to illustrate the violence—justified or not—at the root of and in the continuing history of American constitutional law. Using the history of ongoing controversies in the American constitutional law of crime, the chapter makes the case for the ongoing violence of constitutional law.
The Pragmatist Theory of Truth
Authors: Misak Cheryl
Published: September 2018

In this chapter, an overview is given of the various pragmatist theories of truth, with the most compelling version outlined. That is the position that can be traced from the founder of pragmatism, C. S. Peirce, through to Frank Ramsey. It links truth to human inquiry, and is set against the more “plastic” views of William James, John Dewey, and Richard Rorty, as well as the more realist, for want of a better word, correspondence and deflationist theories. The chapter also indicates how this promising version of the pragmatist account of truth is especially suited to deal with beliefs in ethics and mathematics.
Deflationist Truth
Authors: Azzouni Jody
Published: September 2018

A taxonomy of theories of truth is provided. Two versions of deflationist theories of “true” are distinguished, T-schema deflationism and semantic-descent deflationism. These are distinguished from a deflationist theory of truth-ascription, and distinguished in turn from a deflationist theory of truths—a view that the various truths share no significant property. Opposed to these deflationist positions are various substantivalist truth theories. It is suggested that the semantic-descent deflationist theory of “true” and the deflationist theory of truths are correct, although the considerations that support or attack these different deflationist theories are largely independent of one another. A deflationist theory of truth-ascription is denied, however. Sometimes statements do attribute a truth-property to a set of statements. The chapter ends with an evaluation of the cases where supplementing a formal language with a truth predicate is not conservative. It is argued that these cases do not bear on debates about truth deflationism.
Truth in British Idealism and its Analytic Critics
Authors: Baldwin Thomas
Published: September 2018

Arguments about truth were central to the debates between British idealists such as Bradley and their analytic critics such as Russell. Bradley’s thesis of the “unreality” of relations led him to the holistic monism of the Absolute, within which truth is no relation between judgment and fact but the expansion of judgment until it becomes reality. Russell argued that this idealist monism rests on the mistaken assumption that all relations are internal, and should be replaced by a realist pluralism of facts. Initially Russell followed Moore in holding that truth is a simple property of judgments which are facts. But that position cannot deal sensibly with falsehood, so Russell then moved to his multiple-relation theory of judgment. But having been persuaded by Wittgenstein that this was not a tenable position, he adopted the semantic correspondence theory of logical atomism.
Judgments, Facts, and Propositions
Authors: Sullivan Peter , Johnston Colin
Published: September 2018

In “On the Nature of Truth and Falsehood” Russell offers both a multiple-relation theory of judgment and a correspondence theory of truth. It has been a prevailing understanding of the Tractatus that Wittgenstein rejects Russell’s multiple-relation idea but endorses the correspondence theory. Ramsey took the opposite view. In his “Facts and Propositions,” Ramsey endorses Russell’s multiple-relation idea, rejects the correspondence theory, and then asserts that these moves are both due to Wittgenstein. This chapter will argue that Ramsey’s ascriptions are both correct. The extent of the agreement between Ramsey and Wittgenstein moreover counts definitively against standard understandings of Ramsey as a redundancy theorist of truth. Wittgenstein is no correspondence theorist and Ramsey is no redundancy theorist; rather, both philosophers offer identity theories of truth.
The Correspondence Theory of Truth
Authors: David Marian
Published: September 2018

A classical formulation of the correspondence theory of truth tells us that truth is a general relational property, involving a characteristic relation to some portion of reality. The relation is said to be correspondence; the portion of reality is said to be a fact. Even so, the theory has a lengthy history, and many versions relied on objects rather than facts. This chapter reviews the various options for formulating a correspondence theory of truth, along with the relata they presuppose, and the nature of the correspondence relation they rely upon. It concentrates on fact-based theories, and the nature of the truth-bearers and facts they presuppose.
Estimated energy and nutrient composition of different sources of food waste and their potential for use in sustainable swine feeding programs
Authors: Fung Leonard , Urriola Pedro E , Baker Lawrence , Shurson Gerald C
Published: September 2018

About 40% of the total food produced in the United States is wasted throughout the supply chain. The objective of this study was to determine the energy and nutrient content and variability of food waste sources generated at different stages within the food supply chain in the Minneapolis–St. Paul, MN, metropolitan area, and their potential for use in swine diets. A total of four waste sources were selected: supermarket (SM; retail to consumer), university residential dining hall (RH; consumer to postconsumer), a city waste transfer station (TS; postconsumer to municipal waste disposal), and household source-separated organic recycling program (SSO; postconsumer to municipal waste). Samples were collected (SM: n = 22; RH: n = 60; TS: n = 27; SSO: n =12) and analyzed for GE, proximate analyses, minerals, amino acids, and fatty acid concentrations along with lipid peroxidation indicators including peroxide value (PV) and thiobarbituric reactive substances (TBARS). Data were analyzed using a general linear model that included food waste source as the main factor, and least squared means with adjustment were used for multiple comparisons. Samples of SM food waste contained the greatest (P < 0.05) concentration of GE (5,909 kcal/kg) compared with RH, TS, and SSO sources. Calculated NE of SM (3,740 kcal/kg) was also the greatest compared with the three other food waste sources. Food waste from SM, RH, and SSO, but not TS, had greater (P < 0.05) calculated NE than published values for corn and soybean meal. Concentrations of Lys (1.82%), Met (0.53%), Thr (1.07%), and Trp (0.27) content were greater in SM than in RH, TS, and SSO, but these concentrations were less than published values for soybean meal. There were no differences (P > 0.05) in the phosphorus content of samples among food waste sources (0.30% to 0.64%). PV and TBARS were greatest (P < 0.05) in the SSO samples (PV = 82.4 meq/kg oil; TBARS = 2.44 mg malondialdehyde (MDA) eq/g oil) compared with the other three food waste sources. Although the concentrations of nutrients and calculated energy values of the food waste sources were moderately high compared with corn and soybean meal, their composition was more variable (i.e., greater SD of means). Food waste generated upstream (SM) in the food supply chain appears to have greater nutritional value than postconsumer food waste (RH, TS, and SSO), but all sources appear suitable for use in commercial swine diets provided that ME, NE, and nutrient digestibility values are well characterized.
Growth performance of nursery pigs fed diets containing increasing levels of a novel high-protein corn distillers dried grains with solubles1
Authors: Yang Zhaohui , Urriola Pedro E , Hilbrands Adrienne M , Johnston Lee J , Shurson Gerald C
Published: September 2018

The objective of this study was to use the recently determined ME and standardized ileal digestibility (SID) values of AA for a novel high-protein distillers dried grains with solubles (HP-DDGS; PureStream 40, Lincolnway Energy LLC, Nevada, IA) to determine the optimal dietary inclusion rates in diets for nursery pigs. Three hundred and sixty pigs (BW = 6.79 ± 0.02 kg) were blocked by BW, and pens within blocks were assigned randomly to one of four dietary treatments (10 pens/treatment, 9 pigs/pen). Dietary treatments consisted of adding 0%, 10%, 20%, or 30% HP-DDGS to nursery diets during phase 2 (days 7–21) and phase 3 (days 21–42) of a three-phase nursery feeding program. Diets within each phase were formulated to contain equivalent amounts of ME, SID Lys, Met, Thr, and Trp, Ca, standardized total tract digestible P, vitamins, and trace minerals. Calculated SID Leu to Lys ratios for 0%, 10%, 20%, and 30% HP-DDGS diets were 119%, 137%, 156%, and 173% in phase 2 diets and 120%, 131%, 143%, and 160% in phase 3 diets. The SID Ile to Lys ratios ranged from 60% to 69% in phase 2 diets and from 54% to 59% in phase 3 diets. The SID Val to Lys ratios ranged from 63% to 79% in phase 2 diets and 64% to 68% in phase 3 diets. Body weight and feed disappearance were measured weekly. During phase 2, ADG, ADFI, and G:F were reduced linearly (P < 0.01) as the diet inclusion rate of HP-DDGS increased. Similarly in phase 3, increasing dietary levels of HP-DDGS depressed ADG, ADFI, and G:F linearly (P < 0.01). Overall growth performance of phases 2 and 3 of nursery pigs was negatively affected by increasing levels of HP-DDGS in these diets. Pigs acquired a Streptococcus suis and Escherichia coli disease challenge during the experiment. Although no differences in morbidity were observed throughout the experiment, including HP-DDGS in diets tended to decrease (P = 0.08) mortality. In conclusion, a linear decrease in nursery pig growth performance was observed as increasing levels of HP-DDGS were added in diets, which was probably due to overestimation of SID AA content of the HP-DDGS, antagonistic effects of excess Leu, and the effects of relatively high fiber content.
Promoting Successful Aging Through Faith Community Nursing
Authors: Hixson Lina B. , Loeb Susan J.
Published: September 2018

Promotion of successful aging is imperative for the growing population of U.S. adults 65 and older, who will outnumber those 18 and under by 2035. Faith community nurses (FCNs) provide interventions targeting health promotion and disease prevention, with a focus on faith and health. This study examined the most frequently documented interventions and attended services provided to older adults by FCNs. A secondary analysis of data from the web-based Henry Ford Macomb Hospital Faith Community Nursing/Health Ministries Documentation and Reporting System reveals how FCNs are contributing to successful aging.
Helping Bridge the Great Divides
Authors: Lee Sondra B. , Forehand Jeffery W. , St. Onge Judith L. , Acker Kristi A.
Published: September 2018

Many, especially newer, nurses lack the experience for nuanced skillful communication at end of life. This study incorporated the End-of-Life Nursing Education Consortium (ELNEC) Core Curriculum Communication module into a nurse residency program and tested for change in attitudes toward end-of-life (EOL) care. Researchers found significant differences in attitudes toward care of the dying before and after the ELNEC training, and between nurses with greater than and less than 5 years experience. Findings support that ELNEC education can significantly impact nurse attitudes about EOL care.
A Prospective Study of Immediate Breast Reconstruction with Laser-Assisted Indocyanine Green Angiography
Authors: Mirhaidari Shayda J. , Beddell Gregory M. , Orlando Marc V. , Parker Michael G. , Pedersen John C. , Wagner Douglas S.
Published: September 2018

Background:

Complication rates following immediate breast reconstruction range from 4% to 60%. Mastectomy skin flap necrosis (MSFN) is often the sentinel event leading to secondary complications.

Methods:

All patients undergoing immediate reconstruction were enrolled. Upon mastectomy completion, the surgeon visually interpreted the skin flaps, performed laser-assisted indocyanine green angiography (LAIGA), and intervened if needed. Patients were followed for 90 days, documenting skin necrosis, infection, seroma, hematoma, implant loss, and reoperation.

Results:

There were 126 patients who had 206 immediate breast reconstructions. The complication rate was 22.3%. The incidence of MSFN was 14.1%. The reoperation rate was 8.7%. There was 1 necrosis-related implant loss. Postoperative surveys were completed on 193 breasts: 137 had visual and LAIGA interpretation of well or adequately perfused, resulting in 5.8% rate of necrosis, 2 reoperations, and no implant losses. Twenty breasts had visual and LAIGA interpretation of marginal or poor perfusion. Sixteen of these underwent intervention. The necrosis rate in this group was 35% with no implant losses. A third group with 26 breasts had adequate visual interpretation with marginal or poor perfusion on LAIGA. Ten breasts had no intervention, and 16 received intervention. The overall necrosis rate in this group was 42.3%, with 4 reoperations for necrosis and 1 implant loss.

Conclusions:

LAIGA can more accurately predict complications from MSFN than surgeon assessment alone. When surgeon decision making is supplemented with LAIGA, it reduces the incidence of MSFN, infection, implant loss, and overall unexpected reoperation rate. LAIGA is a valuable adjunct for intraoperative decision making.
RANIBIZUMAB IN PIGMENT EPITHELIAL TEARS SECONDARY TO AGE-RELATED MACULAR DEGENERATION
Authors: Larsen Petra P. , Oishi Akio , Bedar Mohammad Seleman , Heymer Philipp K. R. , Clemens Christoph R. , König Susanna , Gutfleisch Matthias , Pauleikhoff Daniel , Eter Nicole , Wolf Armin , Holz Frank G. , Krohne Tim U.
Published: September 2018

Purpose:

To assess efficacy of intravitreal ranibizumab in retinal pigment epithelium tears secondary to neovascular age-related macular degeneration.

Methods:

The Ranibizumab In Pigment epithelial tears secondary to age-related macular degeneration (RIP) study is a prospective, single-arm, multicenter, investigator-initiated trial. Twenty four eyes of 24 patients with a retinal pigment epithelium tear secondary to age-related macular degeneration received monthly intravitreal injection of 0.5mg ranibizumab for 12 months, together with monthly assessments of morphologic and functional efficacy parameters. Primary outcome measure was mean best-corrected visual acuity at final visit compared with baseline.

Results:

Mean best-corrected visual acuity remained stable over the 12-month study period with 50.3 Early Treatment of Diabetic Retinopathy Study letters (±18.7; Snellen equivalent 20/100) at baseline and 52.9 letters (±19.7; Snellen equivalent 20/100) at final visit (P = 0.39). One eye (4%) experienced a vision loss of ≥15 letters, and 2 eyes (8%) gained ≥15 letters. Mean central retinal thickness decreased from 571 µm (±185 µm) to 436 µm (±171 µm; P = 0.0001). Vision-related quality of life was stable with a mean VFQ-25 score of 79.0 (±10.8) at baseline and 74.3 (±13.9) at final visit (P = 0.12).

Conclusion:

In retinal pigment epithelium tears secondary to age-related macular degeneration, monthly intravitreal ranibizumab therapy results in stabilization of visual acuity over 12 months.
Color Doppler Flow Imaging of Retrobulbar Ocular Blood Flow Changes in Retinal Artery Occlusions Caused by Cosmetic Facial Filler Injections
Authors: Huang Peijie , Liu Ailin , Ren Hui , Xue Kang
Published: September 2018

Purpose:

This study aimed to evaluate the effects of retinal artery occlusions caused by cosmetic facial filler injections on the retrobulbar blood flow parameters.

Methods:

This was a retrospective, noncomparative case series. Ten consecutive patients with fundus artery occlusions caused by facial filler injections were evaluated using color Doppler flow imaging (CDFI). The peak systolic velocity and end diastolic velocity of the ophthalmic artery, central retinal artery, and posterior ciliary arteries were determined. The clinical features, including the filler material, injection site, best-corrected visual acuity, fundus fluorescein angiography, and associated ocular and systemic manifestations were also collected.

Results:

Injected materials included autologous fat (7 cases) and hyaluronic acid (3 cases). In 6 of the patients with ophthalmic artery occlusions, the CDFI showed no or drastic declines in the retrobulbar blood flow in the ophthalmic artery, central retinal artery, and posterior ciliary arteries. In 3 of the patients with central retinal artery occlusions, the CDFI showed no or a grossly decreased retrobulbar blood flow in the central retinal artery. In one patient with anterior ischemic optic neuropathy, the CDFI showed decreased end diastolic velocities and increased pulsatility and resistance indices in the central retinal artery, posterior ciliary arteries, and ophthalmic artery. During the follow-up period, the retrobulbar blood flow recovered to some degree. Overall, ophthalmic artery occlusion patients receiving autologous fat may have neurologic complications.

Conclusions:

The results suggest that the retrobulbar ocular blood flows measured with CDFI were distinctly different in the different types of ophthalmic artery occlusion. Color Doppler flow imaging could provide a practicable and convenient method for the diagnosis and follow up of retinal artery occlusions caused by cosmetic facial filler injections.
A Systematic Review of Criteria-Led Patient Discharge
Authors: Lees-Deutsch Liz , Robinson Jane
Published: September 2018

Background:

This article reports on a systematic review conducted to critique safety, quality, length of stay, and implementation factors regarding criteria-led discharge.

Purpose:

Improving patient flow and timely bed capacity is a global issue. Criteria-led discharge enables accelerated patient discharge in accordance with patient selection.

Methods:

A systematic review was conducted to identify literature on criteria-led discharge from 2007 to 2017. The quality of articles was appraised using a tool for disparate studies. Two reviewers extracted relevant data independently.

Results:

Fifteen studies were identified that showed no increase in patient readmission or complication rates with criteria-led discharge, demonstrating patient safety. The quality of the patient discharge was unremarkable. None of the studies showed an increase in length of stay.

Conclusions:

The safety, quality, and length of stay for patients discharged through criteria-led discharge are inextricably linked to the process adopted for its implementation.
Precipitating events in child and adolescent chronic musculoskeletal pain
Authors: Becker Andrew J. , Heathcote Lauren C. , Timmers Inge , Simons Laura E.
Published: September 2018

Introduction:

The epidemiology of chronic pain in youth has been increasingly documented over the past decade. However, the precipitating events associated with the onset of pediatric chronic pain are not well studied.

Objectives:

Understanding the events that precede the onset of pain, and are reported by patients as germane to the early stages of their pain, may add one piece to the puzzle of the causal etiology of pediatric chronic pain disorders.

Methods:

We conducted a retrospective chart review of 320 young people attending a tertiary care chronic pain clinic with musculoskeletal chronic pain.

Results:

Approximately two-thirds of patients reported a precipitating event for their pain; injury was the most commonly reported event, followed by a chronic disease, then an infection or illness. Surgery was the least commonly reported event. About one-third of patients did not report any precipitating event for their pain. Patients with neuropathic pain were even more likely to report a precipitating event compared to those with localized and diffuse musculoskeletal pain. Patients with localized musculoskeletal pain and neuropathic pain were most likely to report an injury, whereas patients with diffuse musculoskeletal pain were most likely to report a chronic disease. We found little to no evidence that the presence or type of precipitating event was associated with patients' psychological or physical functioning.

Conclusion:

This study adds to the epidemiological evidence base for pediatric chronic pain disorders.
Intergenerational examination of pain and posttraumatic stress disorder symptoms among youth with chronic pain and their parents
Authors: Beveridge Jaimie K. , Neville Alexandra , Wilson Anna C. , Noel Melanie
Published: September 2018

Introduction:

Posttraumatic stress disorder (PTSD) symptoms are prevalent among youth with chronic pain, and associated with poorer pain outcomes and health-related quality of life (HRQoL). Conceptual models suggest that parent factors, including parents' own chronic pain, may be linked to higher co-occurring pain and PTSD symptoms and lower HRQoL in children. However, this has not been empirically examined.

Objectives:

The aim of this study was to examine the relationship between parental chronic pain and (1) parent PTSD symptoms, (2) child PTSD symptoms, (3) child pain outcomes, and (4) child HRQoL in a sample of treatment-seeking youth with chronic pain and their parents.

Methods:

Youth (n = 173) aged 8 to 18 years and parents (n = 204) recruited from a tertiary-level pediatric chronic pain program completed psychometrically-sound measures of pain and PTSD symptoms. Youth also completed measures of pain interference and HRQoL.

Results:

Half of the parents in this sample reported chronic pain. A series of analyses of covariances revealed that parents with vs without chronic pain reported significantly higher PTSD symptoms, and children of parents with vs without chronic pain reported significantly higher PTSD symptoms and pain interference and lower HRQoL.

Conclusion:

Findings from this study suggest that having a parent with chronic pain may confer additional risk for children with chronic pain experiencing higher PTSD symptoms, poorer pain outcomes, and lower HRQoL than having a parent without chronic pain. This could be due to genetics or social learning. Future longitudinal research is needed to understand how parental pain influences co-occurring pain and PTSD symptoms, and HRQoL, in children.
Conceptualizing pain-related stigma in adolescent chronic pain: a literature review and preliminary focus group findings
Authors: Wakefield Emily O. , Zempsky William T. , Puhl Rebecca M. , Litt Mark D.
Published: September 2018

Introduction:

Chronic pain in adolescents is a significant medical condition, affecting the physical and psychological well-being of youth and their families. Pain-related stigma is a significant psychosocial factor in adolescents with chronic pain that has been understudied, despite its implications for negative health outcomes, poor quality of life, and increased healthcare utilization.

Objectives:

To examine pain-related stigma in the literature documenting pediatric and adult health-related stigma and present preliminary findings from a focus group of adolescents with chronic pain.

Methods:

In this narrative review, we explored pain-related stigma research and conceptualized the literature to address pain-related stigma among adolescents with chronic pain. Additionally, we conducted a focus group of four adolescent females with chronic pain and using content analyses, coded the data for preliminary themes.

Results:

We propose a pain-related stigma model and framework based on our review and the findings from our focus group. Findings suggest that medical providers, school personnel (ie, teachers and school nurses), peers and even family members enact pain-related stigma toward adolescents with chronic pain.

Conclusions:

Based on this narrative review, there is preliminary evidence of pain-related stigma among adolescents with chronic pain and future research is warranted to better understand the nature and extent of this stigma within this population.
Defence response mobilization in response to provocation or imagery of interoceptive sensations in adolescents with chronic pain: a study protocol
Authors: Gruszka Piotr , Schaan Luca , Adolph Dirk , Pané-Farré Christiane A. , Benke Christoph , Schneider Silvia , Hechler Tanja
Published: September 2018

Introduction:

Fear of pain seems to be a key factor in the development and maintenance of chronic pain and pain-related disability. Interoceptive fear conditioning is assumed to constitute an important mechanism in the origins and maintenance of fear of pain. If conditioned stimuli such as internal bodily sensations are repeatedly paired with pain (unconditioned stimulus), they in turn elicit a conditioned fear response, including defence mobilization such as startle modulation and changes in heart rate and electrodermal activity. Research into emotional imagery suggests that defensive responses can also be elicited through imagery of fear scripts.

Objectives:

We present 2 novel paradigms adapted from research on anxiety disorders, which allow to test, if perceived or imagined sensations locally proximal to the main pain location trigger heightened defence response mobilization in adolescents with chronic headaches and abdominal pain.

Methods:

The provocation paradigm includes the anticipation and provocation of locally proximal and locally distal interoceptive sensations through disorder-specific muscle tensing tasks (tightening the neck or the abdominal muscles). The imagery paradigm includes 3 imagery scripts (standard neutral, standard fear, and disorder-specific). Startle probes are presented in both paradigms. Defence response mobilization is assessed using psychophysiological measures (startle response modulation, skin conductance level, and heart rate), as well as self-reported measures of fear.

Perspective:

The paradigms will give insight into the defence response of adolescents with chronic pain, when confronted with or imagining interoceptive sensations. Results may inform the improvement of clinical interventions aimed to decrease fear of bodily sensations such as interoceptive exposure or interoceptive imagery exposure.
Interpretable and Accurate Prediction Models for Metagenomics Data
Authors: Prifti Edi , Chevaleyre Yann , Hanczar Blaise , Belda Eugeni , Danchin Antoine , Clément Karine , Zucker Jean-Daniel
Published: September 2018

Biomarker discovery using metagenomic data is becoming more prevalent for patient diagnosis, prognosis and risk evaluation. Selected groups of microbial features provide signatures that characterize host disease states such as cancer or cardio-metabolic diseases. Yet, the current predictive models stemming from machine learning still behave as black boxes. Moreover, they seldom generalize well when learned on small datasets. Here, we introduce an original approach that focuses on three models inspired by microbial ecosystem interactions: the addition, subtraction, and ratio of microbial taxon abundances. While being extremely simple, their performance is surprisingly good and compares to or is better than Random Forest, SVM or Elastic Net. Such models besides being interpretable, allow distilling biological information of the predictive core-variables. Collectively, this approach builds up both reliable and trustworthy diagnostic decisions while agreeing with societal and legal pressure that require explainable AI models in the medical domain.
Replicated point processes with application to population dynamics models
Authors: Favretti Marco
Published: September 2018

In this paper we study spatially clustered distribution of individuals using point process theory. In particular we discuss the spatially explicit model of population dynamics of Shimatani (2010) which extend previous works on Malécot theory of isolation by distance. We reformulate Shimatani model of replicated Neyman-Scott process to allow for a general dispersal kernel function and we show that the random immigration hypothesis can be substituted by the long dispersal distance property of the kernel. Moreover, the extended framework presented here is fit to handle spatially explicit statistical estimators of genetic variability like Moran autocorrelation index, Sørensen similarity index, average kinship coefficient. We discuss the pivotal role of the choice of dispersal kernel for the above estimators in a toy model of dynamic population genetics theory.
Resting-state fMRI data of awake dogs (Canis familiaris) via group-level independent component analysis reveal multiple, spatially distributed resting-state networks
Authors: Szabό Dόra , Czeibert Kálmán , Kettinger Ádám , Gácsi Márta , Andics Attila , Miklόsi Ádám , Kubinyi Enikő
Published: September 2018

Resting-state networks are spatially distributed, functionally connected brain regions. Studying these networks gives us information about the large-scale functional organization of the brain and alternations in these networks are considered to play a role in a wide range of neurological conditions and aging. To describe resting-state networks in dogs, we measured 22 awake, unrestrained animals of either sex and carried out group-level spatial independent component analysis to explore whole-brain connectivity patterns. Using resting-state functional magnetic resonance imaging (rs-fMRI), in this exploratory study we found multiple resting-state networks in dogs, which resemble the pattern described in humans. We report the following dog resting-state networks: default mode network (DMN), visual network (VIS), sensorimotor network (SMN), combined auditory (AUD)-saliency (SAL) network and cerebellar network (CER). The DMN, similarly to Primates, but unlike previous studies in dogs, showed antero-posterior connectedness with involvement of hippocampal and lateral temporal regions. The results give us insight into the resting-state networks of awake animals from a taxon beyond rodents through a non-invasive method.
Generalisation behaviour of predators toward warning signals displayed by harmful prey: answers from a videogame played by humans
Authors: Arias Mónica , Griffiths David , Joron Mathieu , Davey John , Martin Simon , Jiggins Chris , Nadeau Nicola , Llaurens Violaine
Published: September 2018

The persistence of several warning signals in sympatry is a puzzling evolutionary question because selection favours convergence of colour patterns among toxic species. Such convergence is shaped by predators’ reaction to similar but not identical stimulus,i.e.generalisation behaviour. However, studying generalisation behaviour in complex natural communities of predators is challenging, and is thus generally limited to simple variations of prey colour patterns. Here, we used humans as surrogate predators to investigate generalisation behaviours on two prey communities with different level of warning signals complexity. Humans’ generalisation capacities were estimated using a computer game simulating a simple (4 morphs) and a complex (10 morphs) community of defended (associated with a penalty) and palatable butterflies. Colour patterns used in the game are actually observed in natural populations of the defended butterfliesH. numata, and generalisation behaviour of natural predator’s communities on these colour patterns have previously been investigated in the wild, allowing direct comparison with human behaviour. We investigated human predation behaviour by recording attack rates on the different defended and palatable colour patterns, as well as player survival time (i.e. score). Phenotypic similarity among the different colour patterns was precisely quantified using a custom algorithm accounting for both colour and pattern variations (CPM method). By analysing attack behaviours of 491 game players, we found that learning was more efficient in the simple prey community. Additionally, profitable prey gained protection from sharing key visual features with unprofitable prey in both communities while learning, in accordance with natural predator behaviours. Moreover, other behaviours observed in natural predators, such as colour neophobia, were detected in humans and shaped morph vulnerability during the game. Similarities between our results in humans and the reaction of natural predator communities to the same colour patterns validate our video-game as a useful proxy to study predator behaviour. This experimental set-up can thus be compared to natural systems, enabling further investigations of generalisation on mimicry evolution.
Preferential sampling for presence/absence data and for fusion of presence/absence data with presence-only data
Authors: Gelfand Alan. E. , Shirota Shinichiro
Published: September 2018

Presence/absence data and presence-only data are the two customary sources for learning about species distributions over a region. We present an ambitious agenda with regard to such data. We illuminate the fundamental modeling differences between the two types of data. Most simply, locations are considered as fixed under presence/absence data; locations are random under presence-only data. The definition of “probability of presence” is incompatible between the two. So, we take issue with modeling strategies in the literature which ignore this incom-patibility, which assume that presence/absence modeling can be induced from presence-only specifications and therefore, that fusion of presence-only and presence/absence data sources is routine.

We argue that presence/absence data should be modeled at point level. That is, we need to specify a surface which provides the probability of presence at any location in the region. A realization from this surface is a binary map yielding the results of Bernoulli trials across all locations; this surface is only partially observed. Presence-only data should be modeled as a (partially observed) point pattern, arising from a random number of individuals at random locations, driven by specification of an intensity function. There is no notion of Bernoulli trials; events are associated with areas.

We further argue that, with just presence/absence data, preferential sampling, using a shared process perspective, can improve our estimated presence/absence surface and prediction of presence. We also argue that preferential sampling can enable a probabilistically coherent fusion of the two data types.

We illustrate with two real datasets, one presence/absence, one presence-only for invasive species presence in New England in the United States. We demonstrate that potential bias in sampling locations can affect inference with regard to presence/absence and show that in-ference can be improved with preferential sampling ideas. We also provide a probabilistically coherent fusion of the two datasets to again improve inference with regard to presence/absence.

The importance of our work is to provide more careful modeling when studying species distributions. Ignoring incompatibility between data types and offering incoherent modeling specifications implies invalid inference; the community should benefit from this recognition.
Influenza A Virus Ribonucleoproteins Form Liquid Organelles at Endoplasmic Reticulum Exit Sites
Authors: Alenquer Marta , Vale-Costa Sílvia , Sousa Ana Laura , Etibor Temitope Akhigbe , Ferreira Filipe , João Amorim Maria
Published: September 2018

Influenza A virus has an eight-partite RNA genome that during viral assembly forms a supramolecular complex containing one copy of each RNA. Genome assembly is a selective process driven by RNA-RNA interactions and is thought to lead to discrete punctate structures scattered through the cytosol. Here, we show that contrary to the accepted view, formation of these structures is not dependent on RNA-RNA interactions among distinct viral ribonucleoproteins (vRNPs), as they assemble in cells expressing only one vRNP type. We demonstrate that these viral inclusions display characteristics of liquid organelles, segregating from the cytosol without a delimitating membrane, dynamically exchanging material, deforming easily and adapting fast to hypotonic shock. We provide evidence that they develop close to the Endoplasmic Reticulum Exit Sites (ERES), being dependent on continuous ER-Golgi vesicular cycling. We show that viral inclusions do not promote escape to interferon response, and propose that they facilitate selected RNA-RNA interactions in a liquid environment of concentrated vRNPs.
Inspecting Morphological Features of Mosquito Wings for Identification with Image Recognition Tools
Authors: Haarlem Clinton , Vos Rutger
Published: September 2018

Mosquitoes are important disease vectors. Different mosquito genera are associated with different diseases at varying levels of specificity. Hence, quick and low-cost methods of identification, even if relatively coarse and to genus level, will be of use in assessing risk and informing mitigation measures. Here we assess the extent to which digital photographs of mosquito wings taken with common cell phone cameras and clip-on lenses can be used to discriminate among mosquito genera when fed into image feature extraction algorithms. Our results show that genera may be distinguished on the basis of features extracted using the SURF algorithm. However, we also found that the naïve features examined here require very standardized photography and that different phone cameras have different signatures that may need to be taken into account.
Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires
Authors: Laks Emma , Zahn Hans , Lai Daniel , McPherson Andrew , Steif Adi , Brimhall Jazmine , Biele Justina , Wang Beixi , Masud Tehmina , Grewal Diljot , Nielsen Cydney , Leung Samantha , Bojilova Viktoria , Smith Maia , Golovko Oleg , Poon Steven , Eirew Peter , Kabeer Farhia , de Algara Teresa Ruiz , Lee So Ra , Taghiyar M. Jafar , Huebner Curtis , Ngo Jessica , Chan Tim , Vatrt-Watts Spencer , Walters Pascale , Abrar Nafis , Chan Sophia , Wiens Matt , Martin Lauren , Scott R. Wilder , Underhill Michael T. , Chavez Elizabeth , Steidl Christian , Costa Daniel Da , Ma Yusanne , Coope Robin J. N. , Corbett Richard , Pleasance Stephen , Moore Richard , Mungall Andy J. ,   IMAXT Consortium, Marra Marco A. , Hansen Carl , Shah Sohrab P. , Aparicio Samuel
Published: September 2018

Essential features of cancer tissue cellular heterogeneity such as negatively selected genome topologies, sub-clonal mutation patterns and genome replication states can only effectively be studied by sequencing single-cell genomes at scale and high fidelity. Using an amplification-free single-cell genome sequencing approach implemented on commodity hardware (DLP+) coupled with a cloud-based computational platform, we define a resource of 40,000 single-cell genomes characterized by their genome states, across a wide range of tissue types and conditions. We show that shallow sequencing across thousands of genomes permits reconstruction of clonal genomes to single nucleotide resolution through aggregation analysis of cells sharing higher order genome structure. From large-scale population analysis over thousands of cells, we identify rare cells exhibiting mitotic mis-segregation of whole chromosomes. We observe that tissue derived scWGS libraries exhibit lower rates of whole chromosome anueploidy than cell lines, and loss of p53 results in a shift in event type, but not overall prevalence in breast epithelium. Finally, we demonstrate that the replication states of genomes can be identified, allowing the number and proportion of replicating cells, as well as the chromosomal pattern of replication to be unambiguously identified in single-cell genome sequencing experiments. The combined annotated resource and approach provide a re-implementable large scale platform for studying lineages and tissue heterogeneity.
Efect of Sec61 interaction with Mpd1 on Endoplasmic Reticulum- Associated Degradation
Authors: Pereira Fábio , Rettel Mandy , Stein Frank , Savitski Mikhail M. , Collinson Ian , Römisch Karin
Published: September 2018

Proteins that misfold in the endoplasmic reticulum (ER) are transported back to the cytosol for ER-associated degradation (ERAD). The Sec61 channel is one of the candidates for the retrograde transport conduit. Channel opening from the ER lumen must be triggered by ERAD factors and substrates. Here we identified new lumenal interaction partners of Sec61 by chemical crosslinking and mass spectrometry. In addition to known Sec61 interactors we detected ERAD factors including Cue1, Ubc6, Ubc7, Asi3, and Mpd1. We show that the CPY* ERAD factor Mpd1 binds to the lumenal Sec61 hinge region. Deletion of the Mpd1 binding site reduced the interaction between both proteins and caused an ERAD defect specific for CPY* without affecting protein import into the ER or ERAD of other substrates. Our data suggest that Mpd1 binding to Sec61 is a prerequisite for CPY* ERAD and confirm a role of Sec61 in ERAD of misfolded secretory proteins.
Neural basis of learning guided by sensory confidence and reward value
Authors: Lak Armin , Okun Michael , Moss Morgane , Gurnani Harsha , Farrell Karolina , Wells Miles J , Reddy Charu Bai , Kepecs Adam , Harris Kenneth D , Carandini Matteo
Published: September 2018

Making efficient decisions requires combining present sensory evidence with previous reward values, and learning from the resulting outcome. To establish the underlying neural processes, we trained mice in a task that probed such decisions. Mouse choices conformed to a reinforcement learning model that estimates predicted value (reward value times sensory confidence) and prediction error (outcome minus predicted value). Predicted value was encoded in the pre-outcome activity of prelimbic frontal neurons and midbrain dopamine neurons. Prediction error was encoded in the post-outcome activity of dopamine neurons, which reflected not only reward value but also sensory confidence. Manipulations of these signals spared ongoing choices but profoundly affected subsequent learning. Learning depended on the pre-outcome activity of prelimbic neurons, but not dopamine neurons. Learning also depended on the post-outcome activity of dopamine neurons, but not prelimbic neurons. These results reveal the distinct roles of frontal and dopamine neurons in learning under uncertainty.
Association of HLA class I type with prevalence and outcome of patients with acute myeloid leukemia and mutated nucleophosmin
Authors: Kuželová Kateřina , Brodská Barbora , Schetelig Johannes , Röllig Christoph , Ráčil Zdeněk , Walz Juliane Stickel , Helbig Grzegorz , Fuchs Ota , Vraná Milena , Pecherková Pavla , Šálek Cyril , Mayer Jiří
Published: September 2018

Acute myeloid leukemia with mutated nucleophosmin (NPMc+ AML) forms a distinct AML subgroup with better prognosis which can potentially be associated with immune response against the mutated nucleophosmin (NPM). As the T-cell-mediated immunity involves antigen presentation on HLA class I molecules, we hypothesized that individuals with suitable HLA type could be less prone to develop NPMc+ AML. We compared HLA class I distribution in NPMc+ AML patient cohort (398 patients from 5 centers) with the HLA allele frequencies of the caucasian population and found HLA-A*02, B*07, B*40 and C*07 underrepresented in the NPMc+ AML group. Presence of B*07 or C*07:01 antigen was associated with better survival in patients without concomitantFLT3internal tandem duplication. Candidate NPM-derived immunopeptides were found for B*40 and B*07 using prediction software tools. Our findings suggest that a T-cell-mediated immune response could actually explain better prognosis of NPMc+ patients and provide a rationale for attempts to explore the importance of immunosuppressive mechanisms in this AML subgroup.