bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracing sources ofListeriacontamination in traditional Italian cheese associated with a US outbreak: investigations in Italy
Authors: ACCIARI V. A. , IANNETTI L. , GATTUSO A. , SONNESSA M. , SCAVIA G. , MONTAGNA C. , ADDANTE N. , TORRESI M. , ZOCCHI L. , SCATTOLINI S. , CENTORAME P. , MARFOGLIA C. , PRENCIPE V. A. , GIANFRANCESCHI M. V. 
Published: November 2015

SUMMARYIn 2012 a US multistate outbreak of listeriosis was linked to ricotta salata imported from Italy, made from pasteurized sheep's milk. Sampling activities were conducted in Italy to trace the source ofListeria monocytogenescontamination. The cheese that caused the outbreak was produced in a plant in Apulia that processed semi-finished cheeses supplied by five plants in Sardinia. During an ‘emergency sampling’, 179 (23·6%) out of 758 end-products tested positive forL. monocytogenes, with concentrations from <10 c.f.u./g to 1·1 × 106c.f.u./g. Positive processing environment samples were found in two out of four processing plants. A ‘follow-up sampling’ was conducted 8 months later, when environmental samples from three out of six plants tested positive forL. monocytogenesand forListeriaspp. PFGE subtyping showed 100% similarity between US clinical strains and isolates from ricotta salata, confirming the origin of the outbreak. The persistence of strains in environmental niches of processing plants was demonstrated, and is probably the cause of product contamination. Two PFGE profiles from clinical cases of listeriosis in Italy in 2011, stored in the MSS-TESSy database, were found to have 100% similarity to one PFGE profile from a US clinical case associated with the consumption of ricotta salata, according to the US epidemiological investigation (sample C, pulsotype 17). However, they had 87% similarity to the only PFGE profile found both in the US clinical case and in 14 ricotta cheese samples collected during the emergency sampling (sample B, pulsotype 1). Sharing of molecular data and availability of common characterization protocols were key elements that connected the detection of the US outbreak to the investigation of the food source in Italy. Simultaneous surveillance systems at both food and human levels are a necessity for the efficient rapid discovery of the source of an outbreak ofL. monocytogenes.
GlyRα2, not GlyRα3, modulates the receptive field surround of OFF retinal ganglion cells
Authors: ZHANG CHI , NOBLES REGINA D. , McCALL MAUREEN A. 
Published: November 2015

AbstractReceptive fields (RFs) of most retinal ganglion cells (RGCs) consist of an excitatory center and suppressive surround. The RF center arises from the summation of excitatory bipolar cell glutamatergic inputs, whereas the surround arises from lateral inhibitory inputs. In the retina, both gamma amino butyric acid (GABA) and glycine are inhibitory neurotransmitters. A clear role for GABAergic inhibition modulating the RGC RF surround has been demonstrated across species. Glycinergic inhibition is more commonly associated with RF center modulation, although there is some evidence that it may contribute to the RF surround. The synaptic glycinergic chloride channels are formed by three homomeric β and two homomeric α subunits that can be glycine receptor (GlyR) α1, α2, α3, or α4. GlyRα composition is responsible for currents with distinct decay kinetics. Their expression within the inner plexiform laminae and neuronal subtypes also differ. We studied the role of GlyR subunit selective modulation of RGC RF surrounds, using mice lacking GlyRα2 (Glra2−/−), GlyRα3 (Glra3−/−), or both (Glra2/3−/−). We chose this molecular genetic approach instead of pharmacological manipulation because there are no subunit selective antagonists and strychnine blocks all GlyRs. Comparisons of annulus-evoked responses among wild type (WT) and GlyRα knockouts (Glra2−/−, Glra3−/− and Glra2/3−/−) show that GlyRα2 inhibition enhances RF surround suppression and post-stimulus excitation in only WT OFF RGCs. Similarities in the responses in Glra2−/− and Glra2/3−/− RGCs verify these conclusions. Based on previous and current data, we propose that GlyRα2-mediated input uses a crossover inhibitory circuit. Further, we suggest that GlyRα2 modulates the OFF RGC RF center and surround independently. In summary, our results define a selective GlyR subunit-specific control of RF surround suppression in OFF RGCs.
Abnormal heart rate recovery and deficient chronotropic response after submaximal exercise in young Marfan syndrome patients
Authors: Peres Paulo , Carvalho Antônio C. , Perez Ana Beatriz A. , Medeiros Wladimir M. 
Published: November 2015

AbstractBackgroundMarfan syndrome patients present important cardiac structural changes, ventricular dysfunction, and electrocardiographic changes. An abnormal heart rate response during or after exercise is an independent predictor of mortality and autonomic dysfunction. The aim of the present study was to compare heart rate recovery and chronotropic response obtained by cardiac reserve in patients with Marfan syndrome subjected to submaximal exercise.MethodsA total of 12 patients on β-blocker therapy and 13 off β-blocker therapy were compared with 12 healthy controls. They were subjected to submaximal exercise with lactate measurements. The heart rate recovery was obtained in the first minute of recovery and corrected for cardiac reserve and peak lactate concentration.ResultsPeak heart rate (141±16 versus 155±17 versus 174±8 bpm; p=0.001), heart rate reserve (58.7±9.4 versus 67.6±14.3 versus 82.6±4.8 bpm; p=0.001), heart rate recovery (22±6 versus 22±8 versus 34±9 bpm; p=0.001), and heart rate recovery/lactate (3±1 versus 3±1 versus 5±1 bpm/mmol/L; p=0.003) were different between Marfan groups and controls, respectively. All the patients with Marfan syndrome had heart rate recovery values below the mean observed in the control group. The absolute values of heart rate recovery were strongly correlated with the heart rate reserve (r=0.76; p=0.001).ConclusionMarfan syndrome patients have reduced heart rate recovery and chronotropic deficit after submaximal exercise, and the chronotropic deficit is a strong determinant of heart rate recovery. These changes are suggestive of autonomic dysfunction.
Archaeology, symmetry and the ontology of things. A response to critics
Authors: Olsen Bjørnar , Witmore Christopher 
Published: November 2015

AbstractThis article responds to recent critiques of ‘symmetrical archaeology’. It addresses three common claims: (1) that symmetrical archaeology fails to see a difference between living and non-living entities, (2) that symmetrical archaeology makes no room for humans and other living things, (3) that symmetrical archaeology lacks any sincere ethical concern for things. This article demonstrates how these claims are based on common misunderstandings or misreadings, and offers further clarifications as to its perspective on ontology, ethics and things.
Agency ‘in itself’. A discussion of inanimate, animal and human agency
Authors: Lindstrøm Torill Christine 
Published: November 2015

Abstract‘Agency’, the concept, its connections to ontology and its uses within archaeological theory, are discussed and criticized. In recent archaeological theory, the term ‘agency’ has been attributed to things, plants, animals and humans. In this paper it is argued that the term ‘agency’ is logically meaningless if applied to everything that moves or has effects on its surroundings, and that we need a new, more precise terminology that discriminates between ‘agency’, ‘effect’, ‘actant’ and ‘effectant’. That people, of all cultures, perceive and experience things/objects as having agency is explained as being due to projections of human characteristics, human psycho-neurological functioning, and the fact that all individuals and cultures are deeply involved with and dependent on things/objects. Connected to this, questions regarding different ontologies, animism, ethics and sciences are discussed. The paper presents a critique of symmetrical archaeology and materiality studies. Broader paradigmatic perspectives, more theoretical and methodological inclusiveness, and more inter- and trans-disciplinary endeavours are suggested to increase archaeology's ‘agency’.
Evaluating the Use of Synthetic Replicas for SEM Identification of Bloodstains (with Emphasis on Archaeological and Ethnographic Artifacts)
Authors: Hortolà Policarp 
Published: November 2015

AbstractSome archaeological or ethnographic specimens are unavailable for direct examination using a scanning electron microscope (SEM) due to methodological obstacles or legal issues. In order to assess the feasibility of using SEM synthetic replicas for the identification of bloodstains (BSs) via morphology of red blood cells (RBCs), three fragments of different natural raw material (inorganic, stone; plant, wood; animal, shell) were smeared with peripheral human blood. Afterwards, molds and casts of the bloodstained areas were made using vinyl polysiloxane (VPS) silicone impression and polyurethane (PU) resin casting material, respectively. Then, the original samples and the resulting casts were coated with gold and examined in secondary-electron mode using a high-vacuum SEM. Results suggest that PU resin casts obtained from VPS silicone molds can preserve RBC morphology in BSs, and consequently that synthetic replicas are feasible for SEM identification of BSs on cultural heritage specimens made of natural raw materials. Although the focus of this study was on BSs, the method reported in this paper may be applicable to organic residues other than blood, as well as to the surface of other specimens when, for any reason, the original is unavailable for an SEM.
Astroblastoma: a rare case report
Authors: Palled Siddanna R. , Thimmaya Naveen , Jagadheesan Sugashwaran , Khaleel Ibrahim 
Published: November 2015

AbstractBackgroundAn astroblastoma is a rare primary glial tumour occurring preferentially in young adults. It is characterised by a perivascular arrangement of tumour cells forming perivascular pseudorosettes mimicking ependymomas. The histogenesis of astroblastoma is unclear.Case descriptionWe present the history of a 13-year-old girl with chief complaints of headache associated with vomiting, blurring of vision on the left eye and a history of diplopia on the right eye. She underwent left parietal parasagittal craniotomy and near-total excision of tumour. She was planned for postoperative radiotherapy 5,940 cGy in 28 fractions along with concurrent temozolamide100 mg. She had no neurological deficit or complaints during her last visit.ConclusionAstroblastomas are a distinct clinic pathologic entity, with well-described radiologic, pathologic and cytogenetic features. Its recurrence is high, and efforts must be made to elucidate the role and usefulness of radiotherapy and chemotherapy in these tumours.
Implementation of NHS Health Checks in general practice: variation in delivery between practices and practitioners
Authors: Krska Janet , du Plessis Ruth , Chellaswamy Hannah 
Published: November 2015

AimTo evaluate NHS Health Check implementation in terms of frequency of data recording, advice provided, referrals to community-based lifestyle support services, statin prescribing and new diagnoses, and to assess variation in these aspects between practices and health professionals involved in delivery.BackgroundMost NHS Health Checks are delivered by general practices, but little detail is known about the extent of variation in how they are delivered in different practices and by different health professionals.MethodsThis was an observational study conducted in a purposively selected sample of 13 practices in Sefton, North West England. Practices used previously recorded information from their clinical management systems to identify patients with cardiovascular disease (CVD) risk ⩾20%, a potentially cost-effective approach. The evaluation was conducted during the first year of delivery in Sefton. Data were extracted from medical records of all patients identified, regardless of Health Check attendance.FindingsOf the 2892 patients identified by the 13 practices, 1070 had received an NHS Health Check at the time of the study. Of these, only 936 (87.5%) had a recorded CVD risk score, with risk ⩾20% confirmed in 92.0%. Estimated risk category was correct in 456/677 (67.4%) of patients with estimated and actual risk scores.Significant variation was found between practices and health professionals in parameters recorded, tests requested, advice given and referrals for lifestyle support. Only 45.3% of patients had body mass index, smoking, alcohol, exercise, blood pressure and cholesterol all recorded.Lifestyle advice and referral into lifestyle services were documented in 80.6% and 6.4% of attenders, respectively, again with significant variation between practices and professionals. Statin prescribing rose in attenders from 19.6% to 34.6%. A similar proportion of attenders and non-attenders received new diagnoses.ConclusionEffort is required to reduce variation in how practices deliver and follow-up NHS Health Checks, to ensure the consistency of the programme.
DNA damage-induced metaphase I arrest is mediated by the spindle assembly checkpoint and maternal age
Authors: Marangos Petros , Stevense Michelle , Niaka Konstantina , Lagoudaki Michaela , Nabti Ibtissem , Jessberger Rolf , Carroll John 
Published: November 2015

AbstractIn mammalian oocytes DNA damage can cause chromosomal abnormalities that potentially lead to infertility and developmental disorders. However, there is little known about the response of oocytes to DNA damage. Here we find that oocytes with DNA damage arrest at metaphase of the first meiosis (MI). The MI arrest is induced by the spindle assembly checkpoint (SAC) because inhibiting the SAC overrides the DNA damage-induced MI arrest. Furthermore, this MI checkpoint is compromised in oocytes from aged mice. These data lead us to propose that the SAC is a major gatekeeper preventing the progression of oocytes harbouring DNA damage. The SAC therefore acts to integrate protection against both aneuploidy and DNA damage by preventing production of abnormal mature oocytes and subsequent embryos. Finally, we suggest escaping this DNA damage checkpoint in maternal ageing may be one of the causes of increased chromosome anomalies in oocytes and embryos from older mothers.
Engineering intracellular biomineralization and biosensing by a magnetic protein
Authors: Matsumoto Yuri , Chen Ritchie , Anikeeva Polina , Jasanoff Alan 
Published: November 2015

AbstractRemote measurement and manipulation of biological systems can be achieved using magnetic techniques, but a missing link is the availability of highly magnetic handles on cellular or molecular function. Here we address this need by using high-throughput genetic screening in yeast to select variants of the iron storage ferritin (Ft) that display enhanced iron accumulation under physiological conditions. Expression of Ft mutants selected from a library of 107 variants induces threefold greater cellular iron loading than mammalian heavy chain Ft, over fivefold higher contrast in magnetic resonance imaging, and robust retention on magnetic separation columns. Mechanistic studies of mutant Ft proteins indicate that improved magnetism arises in part from increased iron oxide nucleation efficiency. Molecular-level iron loading in engineered Ft enables detection of individual particles inside cells and facilitates creation of Ft-based intracellular magnetic devices. We demonstrate construction of a magnetic sensor actuated by gene expression in yeast.
The evolutionary landscape of intergenic trans-splicing events in insects
Authors: Kong Yimeng , Zhou Hongxia , Yu Yao , Chen Longxian , Hao Pei , Li Xuan 
Published: November 2015

AbstractTo explore the landscape of intergenic trans-splicing events and characterize their functions and evolutionary dynamics, we conduct a mega-data study of a phylogeny containing eight species across five orders of class Insecta, a model system spanning 400 million years of evolution. A total of 1,627 trans-splicing events involving 2,199 genes are identified, accounting for 1.58% of the total genes. Homology analysis reveals that mod(mdg4)-like trans-splicing is the only conserved event that is consistently observed in multiple species across two orders, which represents a unique case of functional diversification involving trans-splicing. Thus, evolutionarily its potential for generating proteins with novel function is not broadly utilized by insects. Furthermore, 146 non-mod trans-spliced transcripts are found to resemble canonical genes from different species. Trans-splicing preserving the function of ‘breakup’ genes may serve as a general mechanism for relaxing the constraints on gene structure, with profound implications for the evolution of genes and genomes.
Mechanistic basis of Nek7 activation through Nek9 binding and induced dimerization
Authors: Haq Tamanna , Richards Mark W. , Burgess Selena G. , Gallego Pablo , Yeoh Sharon , O’Regan Laura , Reverter David , Roig Joan , Fry Andrew M. , Bayliss Richard 
Published: November 2015

AbstractMitotic spindle assembly requires the regulated activities of protein kinases such as Nek7 and Nek9. Nek7 is autoinhibited by the protrusion of Tyr97 into the active site and activated by the Nek9 non-catalytic C-terminal domain (CTD). CTD binding apparently releases autoinhibition because mutation of Tyr97 to phenylalanine increases Nek7 activity independently of Nek9. Here we find that self-association of the Nek9-CTD is needed for Nek7 activation. We map the minimal Nek7 binding region of Nek9 to residues 810–828. A crystal structure of Nek7Y97F bound to Nek9810–828 reveals a binding site on the C-lobe of the Nek7 kinase domain. Nek7Y97F crystallizes as a back-to-back dimer between kinase domain N-lobes, in which the specific contacts within the interface are coupled to the conformation of residue 97. Hence, we propose that the Nek9-CTD activates Nek7 through promoting back-to-back dimerization that releases the autoinhibitory tyrosine residue, a mechanism conserved in unrelated kinase families.
High-throughput 3D tracking of bacteria on a standard phase contrast microscope
Authors: Taute K.M. , Gude S. , Tans S.J. , Shimizu T.S. 
Published: November 2015

AbstractBacteria employ diverse motility patterns in traversing complex three-dimensional (3D) natural habitats. 2D microscopy misses crucial features of 3D behaviour, but the applicability of existing 3D tracking techniques is constrained by their performance or ease of use. Here we present a simple, broadly applicable, high-throughput 3D bacterial tracking method for use in standard phase contrast microscopy. Bacteria are localized at micron-scale resolution over a range of 350 × 300 × 200 μm by maximizing image cross-correlations between their observed diffraction patterns and a reference library. We demonstrate the applicability of our technique to a range of bacterial species and exploit its high throughput to expose hidden contributions of bacterial individuality to population-level variability in motile behaviour. The simplicity of this powerful new tool for bacterial motility research renders 3D tracking accessible to a wider community and paves the way for investigations of bacterial motility in complex 3D environments.
Omentin-1 plasma levels and cholesterol metabolism in obese patients with diabetes mellitus type 1: impact of weight reduction
Authors: Lesná J , Tichá A , Hyšpler R , Musil F , Bláha V , Sobotka L , Zadák Z , Šmahelová A 
Published: November 2015

Abstract
Background:
Omentin-1 is an anti-inflammatory adipokine produced preferentially by visceral adipose tissue. Plasma levels of omentin-1 are decreased in obesity and other insulin-resistant states. Insulin resistance contributes to the changes of cholesterol synthesis and absorption as well. The aim of this study was to characterise omentin-1 plasma levels in obese patients with diabetes mellitus type 1 during weight reduction, and to elucidate the relationship between cholesterol metabolism and omentin-1.

Methods:
Plasma levels of omentin-1 were measured in obese type 1 diabetics (n=14, body mass index >30 kg m−2, age 29–62 years) by enzyme-linked immunosorbent assay (BioVendor). Gas chromatography with flame ionisation detector (Fisons Plc.,) was used to measure squalene and non-cholesterol sterols—markers of cholesterol synthesis and absorption (phase I). Measurements were repeated after 1 month (phase II; 1 week of fasting in the hospital setting and 3 weeks on a diet containing 150 g saccharides per day) and after 1 year (phase III) on a diet with 225 g saccharides per day.

Results:
Omentin-1 plasma levels were stable during phases I and II, but significantly increased (P<0.001) during phase III. Omentin-1 plasma dynamics were significantly associated with plasma levels of high-density lipoprotein (P=0.005) and triacylglycerols (P=0.01), as well as with lathosterol (P=0.03).

Conclusion:
Omentin-1 plasma levels significantly increased during the weight reduction programme. Omentin-1 plasma dynamics suggest a close relationship with cholesterol metabolism.
NEFI: Network Extraction From Images
Authors: Dirnberger M. , Kehl T. , Neumann A. 
Published: November 2015

AbstractNetworks are amongst the central building blocks of many systems. Given a graph of a network, methods from graph theory enable a precise investigation of its properties. Software for the analysis of graphs is widely available and has been applied to study various types of networks. In some applications, graph acquisition is relatively simple. However, for many networks data collection relies on images where graph extraction requires domain-specific solutions. Here we introduce NEFI, a tool that extracts graphs from images of networks originating in various domains. Regarding previous work on graph extraction, theoretical results are fully accessible only to an expert audience and ready-to-use implementations for non-experts are rarely available or insufficiently documented. NEFI provides a novel platform allowing practitioners to easily extract graphs from images by combining basic tools from image processing, computer vision and graph theory. Thus, NEFI constitutes an alternative to tedious manual graph extraction and special purpose tools. We anticipate NEFI to enable time-efficient collection of large datasets. The analysis of these novel datasets may open up the possibility to gain new insights into the structure and function of various networks. NEFI is open source and available at http://nefi.mpi-inf.mpg.de.
Doxorubicin-induced necrosis is mediated by poly-(ADP-ribose) polymerase 1 (PARP1) but is independent of p53
Authors: Shin Hyeon-Jun , Kwon Hyuk-Kwon , Lee Jae-Hyeok , Gui Xiangai , Achek Asma , Kim Jae-Ho , Choi Sangdun 
Published: November 2015

AbstractNecrosis, unregulated cell death, is characterized by plasma membrane rupture as well as nuclear and cellular swelling. However, it has recently been reported that necrosis is a regulated form of cell death mediated by poly-(ADP-ribose) polymerase 1 (PARP1). PARP1 is thought to mediate necrosis by inducing DNA damage, although this remains unconfirmed. In this study, we examined the mechanisms of PARP1-mediated necrosis following doxorubicin (DOX)-induced DNA damage in human kidney proximal tubular (HK-2) cells. DOX initiated DNA damage response (DDR) and upregulated PARP1 and p53 expression, resulting in morphological changes similar to those observed during necrosis. Additionally, DOX induced mitochondrial hyper-activation, as evidenced by increased mitochondrial respiration and cytosolic ATP (cATP) production. However, DOX affected mitochondrial mass. DOX-induced DNA damage, cytosolic reactive oxygen species (cROS) generation and mitochondrial hyper-activation decreased in cells with inhibited PARP1 expression, while generation of nitric oxide (NO) and mitochondrial ROS (mROS) remained unaffected. Moreover, DOX-induced DNA damage, cell cycle changes and oxidative stress were not affected by p53 inhibition. These findings suggest that DNA damage induced necrosis through a PARP1-dependent and p53-independent pathway.