bluuebunny/crossref_metadata_2025_split huggingface dataset:
What is data ethics?
Authors: Floridi Luciano , Taddeo Mariarosaria 
Published: November 2016

This theme issue has the founding ambition of landscapingdata ethicsas a new branch of ethics that studies and evaluates moral problems related to data (including generation, recording, curation, processing, dissemination, sharing and use), algorithms (including artificial intelligence, artificial agents, machine learning and robots) and corresponding practices (including responsible innovation, programming, hacking and professional codes), in order to formulate and support morally good solutions (e.g. right conducts or right values). Data ethics builds on the foundation provided by computer and information ethics but, at the same time, it refines the approach endorsed so far in this research field, by shifting the level of abstraction of ethical enquiries, from being information-centric to being data-centric. This shift brings into focus the different moral dimensions of all kinds of data, even data that never translate directly into information but can be used to support actions or generate behaviours, for example. It highlights the need for ethical analyses to concentrate on the content and nature of computational operations—the interactions among hardware, software and data—rather than on the variety of digital technologies that enable them. And it emphasizes the complexity of the ethical challenges posed by data science. Because of such complexity, data ethics should be developed from the start as a macroethics, that is, as an overall framework that avoids narrow, ad hoc approaches and addresses the ethical impact and implications of data science and its applications within a consistent, holistic and inclusive framework. Only as a macroethics will data ethics provide solutions that can maximize the value of data science for our societies, for all of us and for our environments.This article is part of the themed issue ‘The ethical impact of data science’.
Microbiome engineers: Grazers, browsers, and the phytobiome stampede
Authors: Garrett K. A. , Frank E. E. , Dendy S. P. , Leslie J. F. , Saleh A. A. 
Published: November 2016

AbstractWe definemicrobiome engineersas species that modify the microbiome associated with other host species via changes in the physical environment, potentially including the creation of dispersal networks for microbiome consortia across multiple hosts. Grazers such as bison are indirect plant microbiome engineers through alteration of the structure of plant communities in grasslands and forests. They also can directly engineer plant microbiomes if they distribute microbial consortia. Direct engineering may include simpler examples such as the role of truffle-eating animals in structuring forest mycorrhizal communities, as well as more complex roles in structuring the evolution of bacterial, fungal, and viral microbiome networks. Grazers and browsers may have important historic and current roles in engineering microbiomes by (a) stabilizing and homogenizing microbiomes in their preferred plant species, and (b) selecting for microbiomes in their preferred plant species that are differentiated from microbiomes in plant species they rarely consume.
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Authors: Himmelstein Daniel S. , Lizee Antoine , Hessler Christine , Brueggeman Leo , Chen Sabrina L. , Hadley Dexter , Green Ari , Khankhanian Pouya , Baranzini Sergio E. 
Published: November 2016

AbstractThe ability to computationally predict whether a compound treats a disease would improve the economy and success rate of drug approval. This study describes Project Rephetio to systematically model drug efficacy based on 755 existing treatments. First, we constructed Hetionet (neo4j.het.io), an integrative network encoding knowledge from millions of biomedical studies. Hetionet v1.0 consists of 47,031 nodes of 11 types and 2,250,197 relationships of 24 types. Data was integrated from 29 public resources to connect compounds, diseases, genes, anatomies, pathways, biological processes, molecular functions, cellular components, pharmacologic classes, side effects, and symptoms. Next, we identified network patterns that distinguish treatments from non-treatments. Then we predicted the probability of treatment for 209,168 compound–disease pairs (het.io/repurpose). Our predictions validated on two external sets of treatment and provided pharmacological insights on epilepsy, suggesting they will help prioritize drug repurposing candidates. This study was entirely open and received realtime feedback from 40 community members.
Detecting copper toxicity in sediments: from the subindividual level to the population level
Authors: Jeppe Katherine J. , Yang Jianghua , Long Sara M. , Carew Melissa E. , Zhang Xiaowei , Pettigrove Vincent , Hoffmann Ary A. 
Published: November 2016

Summary

Sediments accumulate chemicals that can be toxic to biota and often contribute to aquatic ecosystem decline. Measuring mortality in laboratory‐bred organisms is a common way to assess sediment toxicity. However, mortality‐based responses of resilient laboratory organisms may not reflect indigenous macroinvertebrate responses, which can be relatively more sensitive to sediment toxicants. A possible solution is to also measure responses at the subindividual level.

Several organism responses to sediment copper toxicity were assessed in a field‐based microcosm. Responses of laboratory‐bred chironomids and snails deployed in microcosms were compared at subindividual (metabolomic and gene expression), individual (survival and dry weight) and population (reproduction) levels, and contrasted to the abundance of colonizing macroinvertebrates in the microcosms.

Colonizing macroinvertebrate abundance showed a range of sensitivities based on EC50 (effect dose 50% change). Chironomidae made up 94·5% of the microcosm macroinvertebrates, with Paratanytarsus the most sensitive genus (EC50: 89 mg kg−1 copper) and Procladius the least sensitive (EC50: 681 mg kg−1).

Survival of laboratory‐bred organisms was the least sensitive response, comparable to decreased abundance of the least sensitive macroinvertebrate. Juvenile production in the snail, Potamopyrgus antipodarum, was the most sensitive population‐level response (EC50: 121 mg kg−1), in contrast the snail Physella acuta was relatively more tolerant (EC50: 298 mg kg−1).

Changes in subindividual responses (gene expression and metabolite abundance) in laboratory‐bred chironomid, Chironomus tepperi, were evident at 60 mg kg−1. These changes likely reflect the direct effects of copper exposure and represent metal‐specific responses.

Synthesis and applications. We showed that copper toxicity in sediments could be readily detected through changes in gene expression and metabolites in laboratory‐bred chironomids exposed in field‐based microcosms. These responses were more sensitive than mortality, and detected copper levels that caused microcosm chironomid populations to decline. These novel approaches will provide managers with new tools to better assess sediment toxicity.
Comparison of Rehydration Techniques for Fingerprinting the Deceased after Mummification
Authors: Chen Chun‐Chieh , Yang Chao‐Kai , Chen Chun‐Yu , Lee Henry C. , Wang Sheng‐Meng 
Published: November 2016

AbstractPostmortem decay causes fingertip decomposition, desiccation, shriveling, and rigidity, reducing the possibility of obtaining sufficiently clear fingerprints for identification. In this study, five rehydration solutions (ammonium hydroxide, sodium carbonate, potassium hydroxide, urea, and warm water) followed by three fingerprint recording methods (photograph, inking roll, and dusting tape) were investigated to process mummified fingertips from an unidentified cadaver. The results show that sodium carbonate treatment is the most effective for minutiae restoration, followed by ammonium hydroxide treatment. This study also demonstrates that even those fingertips that previously failed in urea solution, 1% potassium hydroxide solution, and warm water treatment could be further improved with sodium carbonate solution to obtain qualified minutiae for fingerprint matching. The optimal procedure is rehydrating the desiccated fingertips with sodium carbonate solution for 24 h followed by dusting the finger and transferring the print to adhesive tape.
CD48 on blood leukocytes and in serum of asthma patients varies with severity
Authors: Gangwar R. S. , Minai‐Fleminger Y. , Seaf M. , Gutgold A. , Shikotra A. , Barber C. , Chauhan A. , Holgate S. , Bradding P. , Howarth P. , Eliashar R. , Berkman N. , Levi‐Schaffer F. 
Published: November 2016

AbstractBackgroundCD48 is a membrane receptor (mCD48) on eosinophils and mast cells and exists in a soluble form (sCD48). CD48 has a pivotal role in murine asthma and in the proinflammatory interactions of mast cells with eosinophils via its ligand CD244. Thus, CD48 might be important in human asthma.MethodsTherefore, two separate cohorts (IL and UK) comprising mild, moderate, and severe asthma and healthy volunteers were evaluated for blood leukocyte mCD48 expression and sCD48 in serum. Asthmatic bronchial biopsies were immunostained for CD48. sCD48 effect on CD244‐dependent eosinophil activation was evaluated.ResultsEosinophil mCD48 expression was significantly elevated in moderate while downregulated in severe asthma. mCD48 expression on B, T, and NK cells and monocytes in severe asthma was significantly increased. sCD48 levels were significantly higher in mild while reduced in severe asthma. sCD48 optimal cutoff values for differentiating asthma from health were identified as >1482 pg/ml (IL) and >1619 pg/ml (UK). In asthmatic bronchial biopsies, mCD48 was expressed predominantly by eosinophils. sCD48 inhibited anti‐CD244‐induced eosinophil activation.ConclusionsmCD48 and sCD48 are differentially expressed in the peripheral blood of asthma patients of varying severity. sCD48 inhibits CD244‐mediated eosinophil activation. These findings suggest that CD48 may play an important role in human asthma.
Double‐blind placebo‐controlled challenge showed that peanut oral immunotherapy was effective for severe allergy without negative effects on airway inflammation
Authors: Kukkonen Anna Kaarina , Uotila Riikka , Malmberg Leo Pekka , Pelkonen Anna Susanna , Mäkelä Mika Juhani 
Published: November 2016

AbstractAimThis study examined the efficacy and the safety of peanut oral immunotherapy (OIT).MethodsWe recruited 60 patients aged six years to 18 years who had a moderate‐to‐severe reaction to a double‐blind placebo‐controlled peanut challenge: 39 received OIT during an eight‐month build‐up phase and maintenance phase and 21 controls avoided peanuts. We measured specific immunoglobulin E and G4 (IgE and IgG4) to peanuts and to Ara h 1, 2, 3, 8 and 9 and monitored adverse events, bronchial hyper‐responsiveness (BHR) to methacholine and fractional concentrations of exhaled nitric oxide (FeNO). The median follow‐up period was 30 months.ResultsMost (85%) of the OIT patients passed the build‐up phase and 67% tolerated 5 g of peanuts during the post‐treatment challenge. No controls were desensitised, with a risk ratio of 29 and 95% confidence interval of 1.9–455. During OIT, IgE to peanut, Ara h 1, 2 and 3 decreased and IgG4 increased. Consuming peanuts had no harmful effects on BHR or FeNO. The annual incidence rate of emergency visits during the follow‐up period was 11% or 3.0 per 10 000 patient‐days.ConclusionPeanut OIT was efficacious in severe allergies without negative effects on airway inflammation, but unpredictable long‐term reactions might occur.
1H‐1,2,3‐triazole‐tethered uracil‐ferrocene and uracil‐ferrocenylchalcone conjugates: Synthesis and antitubercular evaluation
Authors: Singh Amandeep , Biot Christophe , Viljoen Albertus , Dupont Christian , Kremer Laurent , Kumar Kewal , Kumar Vipan 
Published: November 2016

Copper‐catalyzed azide‐alkyne [3 + 2] cycloaddition has been utilized for preparing a series of 1H‐1,2,3‐triazoles with the purpose of probing structure–activity relationships among a uracil‐ferrocene‐triazole conjugate family. The antitubercular evaluation studies revealed an improvement in activity with the introduction of a ferrocene nucleus among N‐alkylazido‐uracil precursors, with a preference for a bromo‐substituent along with moderate chain lengths of n = 2–6. The reported protocol is a successful approach for integrating uracil‐ferrocene‐chalcone functionalities tethered via 1H‐1,2,3‐triazole rings with apparent physicochemical stability.
Characteristics and outcome of surgically treated pituitary tumours in South Africa: a single‐centre experience
Authors: Elmezughi Khaled K. , Pirie Fraser J. , Motala Ayesha A. 
Published: November 2016

SummaryAimsTo describe the clinical, biochemical, radiological and histological features and to determine the outcome of all patients with pituitary tumours treated surgically at Inkosi Albert Luthuli Central Hospital (ILACH) in Durban over a 5‐year period.Research designRetrospective chart review from 2008 to 2012. Clinical, biochemical and radiological data were collected before and 1 year after surgery. Histopathology findings and perioperative complications were recorded.ResultsSeventy patients were included (age 44·8 ± 14·9 years, 55·7% female). Headache (84·1%) and visual disturbances (78·3%) were the predominant presenting symptoms (84·1% and 78·3%). Most tumours were macroadenomas (97·1%). Trans‐sphenoidal surgery was employed in the majority (90%). A single procedure was required in 55·7% patients, two procedures in 30% and up to six in others. Complete resection was achieved in only nine patients (12·8%), residual tumour postsurgery was found in 48 (68·6%), and no change in tumour size was found in 13 (18·6%) patients. Additional medical therapy was used in 22 (31·4%) and radiotherapy in 13 (18·6%). On biopsy, the most common pathology was nonfunctional adenoma in 33 (47·1%); 29 (41·4%) were secretory tumours, and 8 (11·4%) were craniopharyngiomas. Overall mortality was 4·3%. The commonest surgical complication was cerebrospinal fluid (CSF) leak (10%; n = 7). New postsurgical pituitary hypofunction occurred in 50 (71·4%) patients. The outcome at 1 year was similar to that on discharge.ConclusionsPatients presenting to IALCH had large tumours, and complete resection was achieved in a minority. There was a low overall mortality but high rate of postsurgical pituitary hypofunction.
What makes foster carers think about quitting? Recommendations for improved retention of foster carers
Authors: Randle Melanie , Ernst Dominik , Leisch Friedrich , Dolnicar Sara 
Published: November 2016

AbstractIdeation, or the formulation of ideas pertaining to a particular topic, is the precursor to individuals making significant life decisions. Many individuals think about foster caring long before they actually become carers, and it stands to reason that in many cases, carer discontinuation also follows a period of ideation. This being the case, it is possible that by monitoring ideation, interventions could be introduced to prevent placement disruptions occurring, particularly if the sources of dissatisfaction are known. Using a sample of 205 foster carers, a posteriori segmentation analysis identifies groups of carers dissatisfied with the same aspects of their role. One group is particularly dissatisfied with factors that are within the control of foster care agencies and also reports high levels of discontinuation ideation. Recommendations include that the individual support needs of carers be identified such that customized support can be offered, including boosting initial and ongoing training to manage expectations and ensure carers feel prepared for the role. Results also highlight the important role of caseworkers in making carers feel appreciated and taken seriously.
Role of honey after tonsillectomy: a systematic review and meta‐analysis of randomised controlled trials
Authors: Lal A. , Chohan K. , Chohan A. , Chakravarti A. 
Published: November 2016

BackgroundHoney reduced post‐tonsillectomy pain, but its effects on awakening at night, inflammation and healing of the tonsillar fossa were controversial.ObjectivesThis systematic review and meta‐analysis of randomised controlled trials (RCTs) evaluated the effect of oral honey on pain, consumption of painkillers, awakening at night, healing of tonsillar fossa and adverse effects in children after tonsillectomy.MethodsA search of MEDLINE, EMBASE, Scopus, CINAHL and Cochrane Collaboration Library databases was performed without any restriction of publication year. The end date of search was 30 June 2016. The search was supplemented by search from Google, hand search of cross‐references of selected articles and reviews, and contacting the authors of different studies. The inclusion criteria were RCTs comparing the effect of honey with control on different outcomes, in children after tonsillectomy.ResultsOur search generated 64 studies, and eight RCTs met our inclusion criteria. The methodological quality of RCTs was poor. Compared to control, honey significantly decreased postoperative pain from day 1 to day 7 (P = 0.05 to <0.0001); consumption of painkillers from days 1 to 5 (P = 0.03 to 0.003) and on day 10 (P = 0.002); and number of awakening at night due to pain on days 2 and 4 after tonsillectomy (P = 0.0001, 0.004). The healing of tonsillar fossa was significantly greater with honey compared to control on days 3–4 (P = 0.02) and days ≥9 (P = 0.01) after tonsillectomy. The adverse effects were not significantly different between honey and control groups. The Grading of Recommendation, Assessment, Development and Evaluation (GRADE) of the evidence for different outcomes varied from ‘low’ to ‘very low’.ConclusionsHoney improved pain, requirement of painkillers and awakening at night due to pain in children after tonsillectomy. There was little improvement in healing of tonsillar fossa. The GRADE of the evidence varied from ‘low’ to ‘very low’. A good‐quality, placebo‐controlled RCT of different doses and durations of administration of honey is required to evaluate its clear efficacy and safety in children after tonsillectomy.
Long‐term mortality after acute myocardial infarction among individuals with and without diabetes: A systematic review and meta‐analysis of studies in the post‐reperfusion era
Authors: Gholap Nitin N. , Achana Felix A. , Davies Melanie J. , Ray Kausik K. , Gray Laura , Khunti Kamlesh 
Published: November 2016

AimsTo conduct a systematic review and meta‐analysis with the aim of providing robust estimates of the association between diabetes and long‐term (≥1 year) mortality after acute myocardial infarction (AMI).Material and methodsMedline, Embase and Web of Science databases were searched (January 1985 to July 2016) for terms related to long‐term mortality, diabetes and AMI. Two authors independently abstracted the data. Hazard ratios (HRs) comparing mortality in people with and without diabetes were pooled across studies using Bayesian random‐effects meta‐analysis.ResultsA total of 10 randomized controlled trials and 56 cohort studies, including 714 780 patients, reported an estimated total of 202 411 deaths over the median (range) follow‐up of 2.0 (1‐20) years. The risk of death over time was significantly higher among those with diabetes compared with those without (unadjusted HR 1.82, 95% credible interval [CrI] 1.73‐1.91). Mortality remained higher in the analysis restricted to 23/64 cohorts reporting data adjusted for confounders (adjusted HR 1.48, 95% CrI 1.43‐1.53). The excess long‐term mortality in diabetes was evident irrespective of the phenotype and modern treatment of AMI, and persisted in early survivors (unadjusted HR 1.82, 95% CrI 1.70‐1.95).ConclusionsDespite medical advances, individuals with diabetes have a 50% greater long‐term mortality compared with those without. Further research to understand the determinants of this excess risk are important for public health, given the predicted rise in global diabetes prevalence.
High‐density lipoprotein‐associated sphingosine‐1‐phosphate activity in heterozygous familial hypercholesterolaemia
Authors: Frias Miguel A. , Thomas Aurélien , Brulhart‐Meynet Marie‐Claude , Kövamees Oskar , Pernow John , Eriksson Mats , Angelin Bo , James Richard W. , Brinck Jonas W. 
Published: November 2016

AbstractBackgroundPatients with heterozygous familial hypercholesterolaemia (FH) suffer from high plasma cholesterol and an environment of increased oxidative stress. We examined its potential effects on high‐density lipoprotein (HDL)‐associated sphingosine‐1‐phosphate (S1P) content (HDL‐S1P) and HDL‐mediated protection against oxidative stress, both with and without statin treatment.Materials and methodsIn a case–control study, HDL was isolated from 12 FH patients with and without statin treatment and from 12 healthy controls. The HDL‐S1P content and the capacity of HDL to protect cardiomyocytes against oxidative stress in vitro were measured.ResultsHDL‐associated S1P was significantly correlated with cell protection, but not with HDL‐cholesterol or apolipoprotein AI. The latter did not correlate with HDL‐mediated cell protection. Neither the HDL‐S1P content nor HDL protective capacity differed between nontreated FH patients and controls. The relative amounts of apolipoprotein AI and apolipoprotein M were similar between controls and FH patients. Statin treatment had no effect on any of these measures.ConclusionsThe FH environment is not detrimental to HDL‐S1P content or HDL‐S1P‐mediated cell protection. Statin treatment does not modulate HDL function in this regard.
Memory under stress: from single systems to network changes
Authors: Schwabe Lars 
Published: November 2016

AbstractStressful events have profound effects on learning and memory. These effects are mainly mediated by catecholamines and glucocorticoid hormones released from the adrenals during stressful encounters. It has been known for long that both catecholamines and glucocorticoids influence the functioning of the hippocampus, a critical hub for episodic memory. However, areas implicated in other forms of memory, such as the insula or the dorsal striatum, can be affected by stress as well. Beyond changes in single memory systems, acute stress triggers the reconfiguration of large scale neural networks which sets the stage for a shift from thoughtful, ‘cognitive’ control of learning and memory toward more reflexive, ‘habitual’ processes. Stress‐related alterations in amygdala connectivity with the hippocampus, dorsal striatum, and prefrontal cortex seem to play a key role in this shift. The bias toward systems proficient in threat processing and the implementation of well‐established routines may facilitate coping with an acute stressor. Overreliance on these reflexive systems or the inability to shift flexibly between them, however, may represent a risk factor for psychopathology in the long‐run.