bluuebunny/crossref_metadata_2025_split huggingface dataset:
Learning structural motif representations for efficient protein structure search
Authors: Liu Yang , Ye Qing , Wang Liwei , Peng Jian 
Published: May 2017

AbstractMotivationUnderstanding the relationship between protein structure and function is a fundamental problem in protein science. Given a protein of unknown function, fast identification of similar protein structures from the Protein Data Bank (PDB) is a critical step for inferring its biological function. Such structural neighbors can provide evolutionary insights into protein conformation, interfaces and binding sites that are not detectable from sequence similarity. However, the computational cost of performing pairwise structural alignment against all structures in PDB is prohibitively expensive. Alignment-free approaches have been introduced to enable fast but coarse comparisons by representing each protein as a vector of structure features or fingerprints and only computing similarity between vectors. As a notable example, FragBag represents each protein by a “bag of fragments”, which is a vector of frequencies of contiguous short backbone fragments from a predetermined library.ResultsHere we present a new approach to learning effective structural motif presentations using deep learning. We develop DeepFold, a deep convolutional neural network model to extract structural motif features of a protein structure. Similar to FragBag, DeepFold represents each protein structure or fold using a vector of learned structural motif features. We demonstrate that DeepFold substantially outperforms FragBag on protein structural search on a non-redundant protein structure database and a set of newly released structures. Remarkably, DeepFold not only extracts meaningful backbone segments but also finds important long-range interacting motifs for structural comparison. We expect that DeepFold will provide new insights into the evolution and hierarchical organization of protein structural motifs.Availabilityhttps://github.com/largelymfs/DeepFoldContactjianpeng@illinois.edu
BENEFICIAL EFFECTS OF KETOGENIC DIETS FOR CANCER PATIENTS – A REALIST REVIEW WITH FOCUS ON EVIDENCE AND CONFIRMATION
Authors: Klement Rainer J. 
Published: May 2017

AbstractBackgroundKetogenic diets (KDs) have gained popularity among patients and researchers alike due to their putative anti-tumor mechanisms. However, the question remains which conclusions can be drawn from the available human data thus far concerning the safety and efficacy of KDs for cancer patients.MethodsA realist review utilizing a matrix-analytical approach was conducted according the RAMEsEs publication standards. All available human studies were systematically analyzed and supplemented with results from animal studies. Evidence and confirmation were treated as separate concepts.Results29 animal and 24 human studies were included in the analysis. The majority of animal studies (72%) yielded evidence for an anti-tumor effect of KDs. Evidential support for such effects in humans was weak and limited to individual cases, but a probabilistic argument shows that the available data strengthen the belief in the anti-tumor effect hypothesis at least for some individuals. Evidence for pro-tumor effects was lacking completely.ConclusionsFeasibility of KDs for cancer patients has been shown in various contexts. The probability of achieving an anti-tumor effect seems greater than that of causing serious side effects when offering KDs to cancer patients. Future controlled trials would provide stronger evidence for or against the anti-tumor effect hypothesis.
The financial impact of retail store closure announcements
Authors: Chowdhury Jaideep , Sarkar Sourish 
Published: May 2017

PurposeWhile store closure announcements frequently appear in newspapers, little is known about the financial impact of store closure decisions on the retailer’s market value. The purpose of this paper is to investigate the stock market reaction to the announcements of retail store closure decisions.Design/methodology/approachThe authors collect data from news articles on store closure announcements in the USA during 1995-2016. Using the four-factor model in an event study, the authors compute the abnormal stock returns for the retail firms due to these announcements.FindingsBased on the authors’ analysis for sample and matching control firms, the abnormal stock returns for store closure announcements are found to be positive overall. The authors find evidence that the positive effects of the announcements are stronger, particularly for the firms which have positive sales growth at the time of the announcements. The authors also report that industry competition acts as a negative moderator in the relationship between announcements and financial impacts.Practical implicationsThe authors’ analysis implies the investors’ positive sentiment of store closure announcements as a viable cost-cutting strategy, especially when it is done proactively by better performing retailers. The findings should be useful to the supply chain managers of retail industries in making store closure decisions.Originality/valueThis paper is believed to be the first to address the impact of retail store closure announcements on the stock market. The authors’ approach of categorizing the firms based on their sales growth seems to be the first in the event study literature on corporate restructuring.
Value creation models in the 3PL industry: what 3PL providers do to cope with shipper requirements
Authors: Marchet Gino , Melacini Marco , Perotti Sara , Sassi Chiara , Tappia Elena 
Published: May 2017

PurposeThe resources and mechanisms required to complete a value proposition are generally considered as crucial aspects in designing a company business model. However, research in the third party logistics (3PL) arena concerned with studying how 3PL providers define their value creation architecture to meet different shippers’ requirements has so far been inadequate. The purpose of this paper is to fill the gap, providing a detailed investigation on how the 3PL providers’ capabilities and logistics expertise can add value to their shippers’ processes.Design/methodology/approachA qualitative exploratory research was conducted involving, first, a systematic combining process to understand the main factors and operational strategies whereby 3PL providers can create value and build a comprehensive framework of their value creation architecture. Second, a qualitative survey was conducted on 44 leading 3PL providers operating in Italy to understand how these providers can organise themselves to create value for shippers.FindingsThe 3PL providers’ value creation architecture is presented within a clear and comprehensive framework, together with 30 potential operational strategies that can be used by 3PL providers and the related factors that enable value to be created for shippers. Three main value creation models (volume-oriented 3PL providers, process-oriented 3PL providers and innovation-oriented 3PL providers) are identified. The importance of the different factors enabling value creation is highlighted for each model, identifying the distinctive operational strategies and those adopted most frequently.Practical implicationsFrom a managerial perspective, 3PL providers will find these results useful for developing suitable strategies to compete on the market. From their side, shippers can understand and evaluate how 3PL providers are able to offer value to their logistics processes, allowing them to select the logistics partner who best fits their needs.Originality/valueThe present paper fulfils the identified need of examining the 3PL providers’ business model in detail. A set of distinct value creation models is identified and thoroughly investigated to reveal the different competitive advantages available to shippers.
Precipitation and environmental constraints on three aspects of flowering in three dominant tallgrass species
Authors: Lemoine Nathan P. , Dietrich John D. , Smith Melinda D. 
Published: May 2017

Summary

Flower production can comprise up to 70% of above‐ground primary production in grasslands. Yet we know relatively little about how the environment and timing of rainfall determine flower productivity. Evidence suggests that deficits or additions of rainfall during phenlologically relevant periods (i.e. growth, storage, initiation of flowering and reproduction) can determine flower production in grasslands.

We used long‐term data from the Konza Prairie LTER to test how fire, soil topography and precipitation amounts during four phenologically relevant periods of the growing season constrain three aspects of flowering in three dominant C4 grass species. Specifically, we examined the probability of flowering, flowering stalk density and individual flowering stalk biomass for Andropogon gerardii, Schizachyrium scoparium and Sorghastrum nutans.

We found that each of the three species responded to the amount of precipitation during phenologically relevant periods in unique ways. All aspects of A. gerardii flowering were sensitive to precipitation during the flowering stalk elongation period (20 June – 3 August). The probability of S. nutans flowering was partly determined by precipitation during the rapid growth phase (21 April – 4 June), whereas flowering stalk density of this species depended on rainfall during flowering stalk elongation (20 June – 3 August). In contrast, all aspects of flowering of S. scoparium were relatively independent of rainfall during any period.

Our results demonstrate that three functionally similar, co‐dominant C4 grass species respond differently to phenologically relevant precipitation periods. As a result, drought during any phenological window during the growing season can adversely impact biomass and flowering production of grasslands via species‐specific reductions in flowering stalk density and biomass.

A lay summary is available for this article.
Archaic man meets a marvellous automaton: posthumanism, social robots, archetypes
Authors: Jones Raya 
Published: May 2017

AbstractPosthumanism is associated with critical explorations of how new technologies are rewriting our understanding of what it means to be human and how they might alter human existence itself. Intersections with analytical psychology vary depending on which technologies are held in focus. Social robotics promises to populate everyday settings with entities that have populated the imagination for millennia. A legend of A Marvellous Automaton appears as early as 350 B.C. in a book of Taoist teachings, and is joined by ancient and medieval legends of manmade humanoids coming to life, as well as the familiar robots of modern science fiction. However, while the robotics industry seems to be realizing an archetypal fantasy, the technology creates new social realities that generate distinctive issues of potential relevance for the theory and practice of analytical psychology.
Tele‐analysis: the use of media technology in psychotherapy and its impact on the therapeutic relationship
Authors: Roesler Christian 
Published: May 2017

AbstractA growing number of approaches in psychotherapy make use of internet‐ and other media‐based interactions. This paper discusses the impact on the therapist‐client relationship of using media technology and gives an overview of the current state of the debate. It is suggested that the technical conditions of internet‐based interactions produce new forms of social relationships that differ significantly from face‐to‐face‐interactions and that unconscious, nonverbal cues get lost. Research on the therapeutic interaction making use of ‘discourse linguistic’ methods is presented.The loss of nonverbal cues has implications for psychotherapy in general and especially for the treatment of patients who have difficulties relying on a secure therapeutic relationship. Emotional security in interactional relationships is transmitted to a much greater extent by nonverbal cues than by verbal content; psychoanalytic methods are specialized to refer to this level of interaction. Two alternative scenarios are discussed based on the psychoanalytic theories of Winnicott and Lacan: the risk of an illusionary, idealized image of the other and the possibility that cyberspace can be used for psychological development as a transitional space.
Demographic histories of three predatory lady beetles reveal complex patterns of diversity and population size change in the United States
Authors: Sethuraman Arun , Janzen Fredric J. , Rubio Michael A. , Vasquez Yumary , Obrycki John J. 
Published: May 2017

AbstractPredatory lady beetles (Coccinellidae) contribute to biological control of agricultural pests, however, multiple species frequently compete for similar resources in the same environment. Numerous studies have examined ecological interactions among the native North American convergent lady beetle (Hippodamia convergens) and two introduced species, the seven‐spotted lady beetle (Coccinella septempunctata) and the Asian lady beetle (Harmonia axyridis), in agricultural fields and described multiyear population dynamics. However, the evolutionary dynamics of these interacting species of predatory beetles are uncharacterized. We utilize publicly available multilocus genotype data from geographically disjunct populations of these three species to estimate demography across North American populations. Coalescent analyses reveal (1) a recent (∼4–5 years) decline (>12 fold) in microsatellite effective population size of H. convergens, while expanding (mutation scaled growth rate in 1/u generations = 2910, SD = 362) over evolutionary time scales, (2) a massive (>150 fold), and very recent, effective population size decline in Ha. axyridis, and (3) population size growth (mutation scaled growth rate = 997, SD = 60) over recent and evolutionary time scales in C. septempunctata. Although these estimates are based on genetic data with different mutation rates and patterns of inheritance (mitochondrial versus nuclear), these dynamic and differing population size histories are striking. Further studies of the interactions of these predatory lady beetles in the field are thus warranted to explore the consequences of population size change and biological control activities for evolutionary trajectories in North America.
On which targets should we compromise in conservation prioritization problems?
Authors: Kaim Andrea , Watts Matthew E. , Possingham Hugh P. 
Published: May 2017

AbstractSystematic conservation planning is an essential part of biodiversity preservation. In the context of conservation prioritization problems, the total cost of the entire reserve system is highly dependent on how big we set targets (e.g. 10% or 30%) for conservation features (e.g. species or habitats). Thus, it is of interest to conservation planners how targets could be adjusted in a reasonable way, in order to decrease total cost. The aim of this paper is to rank features based on their influence on total cost.Focusing on the minimum set coverage problem—an integer linear optimization problem (ILP)—we developed a method to rank features according to their influence on total cost. Since the computation time is often too high to solve the ILP, we approximated its optimal solutions by the results of a linear optimization problem (LP). For the feature ranking, we used the shadow prices of the LP, validating it with rankings created by methods which used an ILP solver and the software Marxan, which uses a simulated annealing algorithm.The results show that shadow prices can be used to rank features in terms of their impact on the total cost of the reserve system thereby identifying those feature targets that could yield better compromises.Thus, the shadow price ranking provides a novel tool for conservation planners to help set feature targets in conservation prioritization problems. Furthermore, the results of the study can be used to improve Marxan.
Editorial: evidence is growing for protective effects of 5‐aminosalicylates against colitis‐associated cancer—authors’ reply
Authors: Bonovas S. , Fiorino G. , Lytras T. , Nikolopoulos G. , Peyrin‐Biroulet L. , Danese S. 
Published: May 2017

Linked ContentThis article is linked to Bonovas et al papers. To view these articles visit https://doi.org/10.1111/apt.14023 and https://doi.org/10.1111/apt.14072.
Editorial: is it time for therapeutic drug monitoring of anti‐TNF agents during pregnancy? Maybe, maybe not. Author's reply
Authors: Seow C. H. 
Published: May 2017

Linked ContentThis article is linked to Seow et al and Kane papers. To view these articles visit https://doi.org/10.1111/apt.14040 and https://doi.org/10.1111/apt.14073.
The Adequacy of Pre‐purchase Due Diligence in Independent Small Business and Franchising
Authors: Buchan Jenny , Frazer Lorelle , Weaven Scott , Tran‐Nam Binh , Grace Anthony 
Published: May 2017

AbstractThis research reports an in‐depth study of the due diligence activities that prospective independent small business operators and franchisees in Australia undertake prior to purchasing or starting up their businesses. Although academic literature and industry publications promote undertaking ‘proper due diligence’, there is a lack of empirical research into the nature of due diligence and its effect on business outcomes. Using a qualitative approach, 60 currently and formerly operating independents and franchisees were personally interviewed, exploring the diversity of approaches to undertaking due diligence prior to entering business. The research revealed that differences occur in both the type and amount of due diligence undertaken by independents and franchisees and highlighted further differences between current and former operators. In general, the due diligence undertaken by participants was relatively unsophisticated with few exceptions of rigour and planning. Where prospective independents and franchisees were entering business for the first time, their appreciation of business was naïve. A steep learning curve followed during which they often recognised flaws in their initial research. As a result of this qualitative in‐depth research, we present a set of propositions regarding due diligence and a model for future testing on a large sample.
Assessment of effect of CYP3A inhibition, CYP induction, OATP1B inhibition, and high‐fat meal on pharmacokinetics of the JAK1 inhibitor upadacitinib
Authors: Mohamed Mohamed‐Eslam F. , Jungerwirth Steven , Asatryan Armen , Jiang Ping , Othman Ahmed A. 
Published: May 2017

AimsUpadacitinib (ABT‐494) is a selective Janus kinase 1 inhibitor being developed for treatment of auto‐immune inflammatory disorders. This work evaluated effects of high‐fat meal, cytochrome P450 (CYP) 3A inhibition, CYP induction, and organic anion transporting polypeptide (OATP) 1B inhibition on upadacitinib pharmacokinetics.MethodsTwo Phase 1 evaluations were conducted, each in 12 healthy subjects. In Study 1, using a randomized, two‐sequence crossover design, a 3 mg dose of upadacitinib (immediate‐release capsules) was administered alone under fasting conditions, after high‐fat meal, or on Day 4 of a 6‐day regimen of 400 mg once‐daily ketoconazole. In Study 2, a 12 mg upadacitinib dose was administered alone, with the first, and with the eighth dose of a 9‐day regimen of rifampin 600 mg once daily. Upadacitinib plasma concentrations were characterized.ResultsAdministration of upadacitinib immediate‐release capsules after a high‐fat meal decreased upadacitinib Cmax by 23% and had no impact on upadacitinib AUC relative to the fasting conditions. Ketoconazole (strong CYP3A inhibitor) increased upadacitinib Cmax and AUC by 70% and 75%, respectively. Multiple doses of rifampin (broad CYP inducer) decreased upadacitinib Cmax and AUC by approximately 50% and 60%, respectively. A single dose of rifampin (also an OATP1B inhibitor) had no effect on upadacitinib AUC. Upadacitinib was well tolerated when co‐administered with ketoconazole, rifampin, or after a high‐fat meal.ConclusionsStrong CYP3A inhibition and broad CYP induction result in a weak and moderate effect, respectively, on upadacitinib exposures. OATP1B inhibition and administration of upadacitinib immediate‐release formulation with food does not impact upadacitinib exposure.
A Critical Note on Treatment of a Severe Diltiazem Intoxication: High‐Dose Calcium and Glucagon Infusions
Authors: Van Veggel Mathilde , Van der Veen Gijs , Jansen Tim , Westerman Elsbeth 
Published: May 2017

AbstractThe morbidity and mortality of a severe calcium channel blocker intoxication is high due to serious toxic cardiac effects. Its treatment is supported by low‐quality evidence from the heterogeneous literature. We describe a case of a severe diltiazem intoxication and critically appraise the efficacy and role of high‐dose calcium and glucagon infusions. A 53‐year‐old woman was admitted to the emergency department with a cardiogenic shock with complete AV block, not responding to atropine, isoprenaline and an external pacemaker. Later on, it became clear that she had a severe diltiazem intoxication which was successfully treated with isotone fluids, inotropes, vasopressors and continuous infusion of high‐dose calcium and glucagon. The patient developed, however, an acute, necrotizing pancreatitis, probably related to iatrogenic high calcium levels. This case demonstrates lack of consensus regarding target levels of serum calcium for treatment of a severe diltiazem intoxication. Goal‐directed tapering of calcium should prevent side effects of iatrogenic hypercalcaemia. The contribution of glucagon infusions is doubtful due to the instability of solubilized glucagon. This might explain why the effect of glucagon is variable in the literature.
The Ethics of Clinical Trials Research in Severe Mood Disorders
Authors: Nugent Allison C. , Miller Franklin G. , Henter Ioline D. , Zarate Carlos A. 
Published: May 2017

AbstractMood disorders, including major depressive disorder (MDD) and bipolar disorder (BD), are highly prevalent, frequently disabling, and sometimes deadly. Additional research and more effective medications are desperately needed, but clinical trials research in mood disorders is fraught with ethical issues. Although many authors have discussed these issues, most do so from a theoretical viewpoint. This manuscript uses available empirical data to inform a discussion of the primary ethical issues raised in mood disorders research. These include issues of consent and decision‐making capacity, including patients’ motivations for participating in research. We also address drug withdrawals, placebo controls, and the overall safety of research. Finally, we examine the extant literature for studies discussing potential indirect benefits of clinical trials research to participants. Taken together, the evidence suggests that clinical trials research incorporating drug withdrawals and placebo controls can be conducted safely and ethically, even in patients with severe or treatment‐resistant mood disorders. In fact, given the dearth of effective treatment options for this population, it is our opinion that a moral imperative exists to extend the offer of research participation to severely ill or treatment‐resistant groups.