bluuebunny/crossref_metadata_2025 huggingface dataset:
Detecting Anti-IIa and Anti-Xa Direct Oral Anticoagulant (DOAC) Agents in Urine using a DOAC Dipstick
Authors: Harenberg Job , Schreiner Rupert , Hetjens Svetlana , Weiss Christel
Published: August 2018

The assessment of the anticoagulant effect of direct oral anticoagulants (DOACs) can be important for rapid medical decision-making, especially in patients needing immediate management. An assay that screens for the absence or presence of a DOAC would help accelerate treatment in these situations. Chromogenic and coagulation methods have several limitations, including limited accuracy, long turnaround time, and their need of specialized laboratories. Oral factor Xa and thrombin inhibitors are also eliminated by the kidneys and can be detected in patient urine samples using a single, rapid, sensitive, and patient-specific qualitative assay. In these tests, the presence or absence of a DOAC in urine can be identified by visually observing specific colors after a few minutes. Several studies have demonstrated the robustness and repeatability of these assays. The specific colors of the test strip also detect creatinine in the urine, which shows whether DOAC excretion is reduced, thus suggesting renal impairment. Persons with amblyopia may use a specific reader. Current indications for using the DOAC Dipstick test include emergency medical situations with severe bleeding and thrombotic events or before urgent major surgical interventions to accelerate medical decision-making.
Spontaneous Epidural Hematoma of the Cervical Spine Mimicking a Cerebrovascular Accident: A Case Report
Authors: Jamali Mohammad , Entezam Sepehr , Ghahramani Sulmaz
Published: August 2018

Objective The present study is a case report of a 57-year-old female with controlled hypertension who presented with spontaneous spinal epidural hematoma (SSEH) mimicking a cerebrovascular accident (CVA) and was successfully treated by surgical decompression.

Methods A 57-year-old woman with a medical history of hypertension presented with a sudden onset of weakness in the right upper and lower extremities. Weakness of grade 3/5 was noted in her right upper and lower extremities, but there was no motor weakness of the right facial muscles. A magnetic resonance imaging (MRI) exam of the cervical spine revealed an epidural hematoma extending from level C5 to level C7, causing spinal cord compression.

Results During surgery, a cervical spinal epidural hematoma (SEH) was evacuated. Postoperatively, the power in both limbs improved to grade 5/5 just after surgery.

Conclusions A high degree of suspicion, meticulous history taking, and physical examination have a great importance in these rare conditions because anticoagulant therapy as a routine treatment for ischemic CVA could be life-threatening.
A Two-Month-Old Child with Vascular Ectasia: A Case Report Diagnosed by Molecular Karyotyping
Authors: Yilmaz Hayri , Bozdogan Sevcan , Bisgin Atıl , Celik Tugçe , Surmelioglu Ozgur , Doran Figen , Kendir Ozlem
Published: August 2018

Gastrointestinal angiodysplasia can be encountered in cases with aortic stenosis, inflammatory gastrointestinal conditions, von Willebrand disease or vascular damage, and degenerative changes. Predisposing factors have been described in four adults with vascular ectasia located in the stomach, duodenum, and the distal esophagus. Here, we report a 2-month-old infant with vascular ectasia in the proximal esophagus and diagnosed by molecular karyotyping. This is the first case of vascular ectasia in the proximal esophagus in a pediatric patient.
Gicht und Lifestyle
Authors: Braun J. , Tausche A.-K. , Kiltz U.
Published: August 2018

Die durch Ablagerung von Natriumuratkristallen verursachte Gicht ist die häufigste rezidivierend auftretende Gelenkentzündung in Deutschland. Aufgrund der besonders im höheren Lebensalter ansteigenden Prävalenz der Gicht wird die Erkrankung in Deutschland sehr wahrscheinlich zunehmend an Bedeutung gewinnen. Wichtige Ziele von therapeutischen Interventionen sind zum einen die symptomatische Behandlung der akuten Arthritis und zum anderen die kausale Behand-lung der zugrundeliegenden metabolischen Ursache, der Hyperurikämie. Neben der zweifelsohne wichtigen medikamentösen Therapie (Harnsäuresenkung und Entzündungshemmung) hat die Veränderung von Lebensgewohnheiten bei Patienten mit Gicht einen möglichen positiven Einfluss auf den Erkrankungsverlauf. Eine bewusstere Ernährung, vor allem die Einschränkung des Alkohol-genusses, und eine dosierte Gewichtsabnahme, verbunden mit ausreichender Bewegung im Alltag, sind Faktoren, die nicht nur zu einem insgesamt besseren metabolischen Profil führen, sondern auch den Harnsäurespiegel positiv beeinflussen und die Lebensqualität der Patienten verbessern können. Letztlich ist es aber nur die konsequente dauerhafte Senkung des Serumharnsäurespiegels, die zur Verhinderung weiterer Gichtanfälle und möglicherweise auch zum Erhalt der Lebensqualität und Erwerbsfähigkeit führt. Die vorbeugende Therapie mit Colchizin unterstützt diesen Vorteil durch Verhinderung von Rezidivattacken.
Ernährung bei rheumatischen Erkrankungen
Authors: Keyßer G.
Published: August 2018

Einflüsse der Ernährung auf das Risiko, eine rheumatische Erkrankung zu entwickeln, sind in erster Linie für die rheumatoide Arthritis (RA), in geringerem Maße auch für Spondyloarthritiden (SpA) und entzündliche Bindegewebserkrankungen gesichert. Die Inzidenz der RA ist mit kindlicher Unterernährung und niedrigem Geburtsgewicht assoziiert, die der SpA mit der Dauer des Stillens im Säuglings-alter. Einzelne Nahrungskomponenten wie Seefisch mit hohem Fettgehalt, Zitrusfrüchte oder geringe Alkoholmengen können protektiv auf das RA-Risiko wirken. Raucher haben ein per se deutlich erhöhtes Risiko für eine RA, welches durch vermehrte Kochsalzzufuhr und Übergewicht potenziert wird. Zahlreiche Interventionsstudien haben versucht, den Nutzen einzelner Kostformen bei etablierter RA nachzuweisen. Dazu gehören neben verschiedenen Fastenformen auch Elementardiäten, Eliminationsdiäten und andere hypoaller-gene Kostformen sowie Studien zu veganer und glutenfreier Ernährung. Die Mehrzahl dieser Untersuchungen ist in Qualität und Aussagekraft unbefriedigend geblieben. Allerdings ist eine an den Prinzipien der Mittelmeerkost ausgerichtete Ernährung wahrscheinlich von Nutzen für RA-Patienten, auch wenn die positiven Effekte in erster Linie die Reduktion des kardiovaskulären Risikos betreffen. Nahrungsergänzungsmittel werden häufig für die Anwendung bei etablierter RA beworben, allerdings lassen sich positive Effekte nur für Fischölkapseln in ausreichend hoher Dosierung von Omega-3-Fettsäuren nachweisen. Die Zufuhr von Eisenpräparaten und Vitamin D sollte nicht unkritisch erfolgen, sondern an objektiven Kriterien ausgerichtet werden. Probiotika sind aufgrund neuer Erkenntnisse zu Pathogenese rheumatischer Erkrankungen in kleineren Studien bei RA und SpA zum Einsatz gekommen, haben jedoch bisher keinen überzeugenden Wirksamkeitsnachweis gezeigt.
Ergometrie – Schritt für Schritt
Authors: Kenn Carola , May Andreas
Published: August 2018

Exercise testing belongs to the most important cardiologic diagnostic prozedures. Even if sensitivity and specifity of ergometry are low, it is used widely for the following: screening for coronary artery disease, as a component of imaging and cardiopulmonary exercise testing, for assessment of arrhythmias, hypertension and congenital heart diseases.
A new control approach to improve the dynamic performance and ride through capability of PMSG wind energy system
Authors: Sagiraju Dileep Kumar Varma , Yeddulapeda Obulesh , Choppavarapu Sai Babu
Published: August 2018

The increasing penetration of wind power into the modern power system forces many countries to adopt and revise grid codes for wind farms. The latest grid codes demand the wind energy systems to remain online during grid disturbances to meet the Low Voltage Ride-Through Capability (LVRT). The disconnection of the grid connected wind farm under abnormal grid disturbances significantly impacts the stability of the grid system. This paper proposes the robust active disturbance rejection control for permanent magnet synchronous generator (PMSG) based wind energy systems to enhance the dynamic performance and ride through capability under abnormal grid disturbances. The proposed approach is applied to the machine and grid side converter of PMSG to improve its ride through capability in compliance with the grid codes. Besides external grid disturbances, the proposed approach also considers the internal disturbances such as random parameter variations, parameter uncertainties, and cross-coupling terms to improve the dynamic performance of the wind energy system. The proposed approach is particularly effective in real-time estimation and compensation of the internal and external disturbances. The simulation results are performed in Matlab/Simulink to support the theoretical considerations, demonstrating the potential contributions of the proposed control strategy. The superiority of the proposed control strategy to improve the LVRT potentiality for the grid-connected PMSG wind energy system is verified by comparing with the traditional vector PI control scheme.
Correspondence between light-absorption spectrum and nonequilibrium work distribution as a mean to access free energy differences between electronic states
Authors: Giovannelli Edoardo , Gellini Cristina , Pietraperzia Giangaetano , Cardini Gianni , Procacci Piero , Pagliai Marco , Volkov Victor , Chelli Riccardo
Published: August 2018

The problem of recovering the free energy difference between two electronic states has been investigated by Frezzato [Chem. Phys. Lett. 533, 106 (2012)], exploring the equivalence between light-absorption spectra and work distribution, hence opening to the application of a spectroscopic version of the Jarzynski equality (JE) [Phys. Rev. Lett. 78, 2690 (1997)]. Here, assuming the validity of the time-dependent perturbation theory, we demonstrate that such equivalence does not lead to the known form of the JE. This is ascribed to the fact that light-absorption processes cannot be described as stochastic processes. To emphasize such an aspect, we devise a stochastic model for the UV-vis (ultraviolet and visible) absorption, suitable for determining the free energy difference between two generic quantum manifolds in a JE-like fashion. However, the model would require explicit knowledge of the transition dipole moments, which are in general not available. Nonetheless, we derive a spectroscopic version of the JE that allows us to recover the free energy difference between the ground and an excited electronic state when the latter state is the only one observed in the spectrum.
High-resolution collision energy control through ion position modulation in atom-ion hybrid systems
Authors: Puri Prateek , Mills Michael , West Elizabeth P. , Schneider Christian , Hudson Eric R.
Published: August 2018

We demonstrate an ion shuttling technique for high-resolution control of atom-ion collision energy by translating an ion held within a radio-frequency trap through a magneto-optical atom trap. The technique is demonstrated both experimentally and through numerical simulations, with the experimental results indicating control of ion kinetic energies from 0.05 to 1 K with a fractional resolution of ∼10 and the simulations demonstrating that kinetic energy control up to 120 K with a maximum predicted resolution of ∼100 is possible, offering order-of-magnitude improvements over most alternative techniques. Finally, we perform a proof-of-principle chemistry experiment using this technique and outline how the method may be refined in the future and applied to the study of molecular ion chemistry.
Optical addressing of nanomechanical metamaterials with subwavelength resolution
Authors: Ou Jun-Yu , Plum Eric , Zheludev Nikolay I.
Published: August 2018

Metamaterials that offer “on-demand” control of individual metamolecules are termed “randomly accessible metamaterials.” They can be useful for manipulation of the wavefront of electromagnetic radiation, for tailoring of the nearfield, and ultimately for multichannel data processing. Here, we demonstrate how light can be used to actuate individual metamaterial elements on demand. Selectivity is achieved by constructing the metamaterial from nanomechanical elements that are designed to have slightly different mechanical resonance frequencies. Actuation is controlled by modulation of the optical control signal at the mechanical resonance frequencies of targeted elements, providing an all-optical route to randomly accessible metamaterials with spatial resolution beyond the diffraction limit.
Analysis of ohmic losses in Tesla transformers utilizing the open magnetic-core
Authors: He Shi , Li Jun-na , Guo Fan , Chen Zhi-qiang , Chen Wei-qing , Qiu Ai-ci
Published: August 2018

For typical Tesla transformers with open magnetic-core, a novel coaxial design of the primary side using a mechanically controlled spark gap is introduced to obtain a more compact configuration. The primary winding has several alternative ports to vary the current distribution by changing the position of the capacitor component, and the entire primary circuit is built inside the outer cylinder. For this new primary configuration, we estimate the series parameters and ohmic losses: Polypropylene film capacitors and combined metallized film capacitors are used in the verification tests, and the former capacitor exhibits a lower parasitic resistance below 10 mΩ. The ohmic losses caused by the windings and spark gap are also considered. The results of the experiments show that the voltage gain has an 8.2% drop when the parasitic resistance of C1 increased from 10 mΩ to 24 mΩ, and we deduce that the contact resistance of this primary structure can be limited to below 10 mΩ according to the circuit analysis results and the verification test.
Exceptional points in two dissimilar coupled diode lasers
Authors: Kominis Yannis , Choquette Kent D. , Bountis Anastassios , Kovanis Vassilios
Published: August 2018

We show the abundance of exceptional points in the generic asymmetric configuration of two coupled diode lasers, under nonzero optical detuning and differential pumping. We pinpoint the location of these points with respect to the stability domains and the Hopf bifurcation points of phase-locked modes, in the solution space as well as in the space of experimentally controlled parameters.
Mechanical deformation effects on ion conduction in stretchable polymer electrolytes
Authors: Berg S. , Kelly T. , Porat I. , Moradi-Ghadi B. , Ardebili H.
Published: August 2018

Flexible and stretchable energy storage devices, including batteries, supercapacitors, and ionic piezoelectrics, have garnered substantial research interest in recent years to address a wide range of applications such as smart textiles and medical implants. These devices are intended to undergo mechanical deformation, and the impact of deformation on electrochemical performance is not well understood. One important area of focus is studying how mechanical deformation influences ion conduction in polymer electrolytes. In this work, a dual theoretical and experimental approach is taken to further evaluate this phenomenon. A stretchable solid polymer electrolyte film subjected to tensile deformation (approximately 48% strain), through which ion diffusion occurs, is analyzed using a continuum approach treating ion diffusion and mechanical deformation as coupled. Thermodynamic laws are applied to obtain governing multiphysics equations accounting for large deformation mechanics and material nonlinearity. The theoretical solution obtained demonstrates how through-plane ionic conductivity changes when the polymer is subjected to stretching. Evolutionary materials deformation of the polymer electrolyte is considered to elucidate the underlying driving physical mechanisms of ion conduction. An experiment was also conducted to measure change in through-plane ionic conductivity with applied uniaxial strain in a sample of polyethylene oxide (PEO), a material commonly used as the electrolyte in solid polymer electrolyte lithium ion batteries. The experimental results show a greater than 1600% ionic conductivity enhancement for approximately 48% strain. The theoretical and experimental results are in good agreement and show that ion conduction is enhanced with increasing strain following an exponential function for a PEO electrolyte.
Alteration in contact line dynamics of fluid-fluid interfaces in narrow confinements through competition between thermocapillary and electrothermal effects
Authors: Kunti Golak , Bhattacharya Anandaroop , Chakraborty Suman
Published: August 2018

The paper reports the results of our numerical investigation on contact line dynamics of a thermal field assisted flow configuration of two immiscible fluids in a narrow thermofluidic pathway. The surfaces of the channel are wetted with predesigned wettabilities and interdigitated electrodes are mounted on the substrates to generate a non-uniform electric field. In this study, the interplay of thermocapillary and electrothermal forces on interfacial dynamics are considered. The former is caused by temperature-induced surface tension gradients while the latter is originated from the temperature-induced gradients in permittivity and electrical conductivity. Our investigations reveal that the relative strength of interfacial forces and electrothermal forces and their interactions can be effectively used to control the capillary filling time as well as flow dynamics. For the same strength of thermocapillary and electrothermal forces (characterized by individual dimensionless numbers), electrothermal effects dominate over thermocapillary effects. However, interfacial forces dominate over electrothermal forces at certain wettabilities (characterized by the imposed contact angle on the surfaces), and depending on the direction of the interfacial forces, the contact line travels toward the entry or exit of the channel.
Evaluating root cause: The distinct roles of hydrogen and firing in activating light- and elevated temperature-induced degradation
Authors: Jensen M. A. , Zuschlag A. , Wieghold S. , Skorka D. , Morishige A. E. , Hahn G. , Buonassisi T.
Published: August 2018

The root cause of light- and elevated temperature-induced degradation (LeTID) in multicrystalline silicon p-type passivated emitter and rear cell (PERC) devices is still unknown. Microwave-induced remote hydrogen plasma (MIRHP) is employed to vary the concentration of bulk hydrogen and to separate the effects of hydrogen and firing temperature in LeTID-affected wafers. We find that hydrogen is required for degradation to occur, and that samples fired prior to the introduction of hydrogen do not degrade. Importantly, samples with hydrogen that have not been fired do degrade, implying that the firing time-temperature profile does not cause LeTID. Together, these results suggest that the LeTID defect reaction consists of at least two reactants: hydrogen and one or more defects that can be separately modified by high-temperature firing. We assess the leading hypotheses for LeTID in the context of our new understanding of the necessary reactants.
Three-dimensional stability of leapfrogging quantum vortex rings
Authors: Ruban Victor P.
Published: August 2018

It is shown by numerical simulations within a regularized Biot-Savart law that dynamical systems of two or three leapfrogging coaxial quantum vortex rings having a core width ξ and initially placed near a torus of radii R0 and r0 can be three-dimensionally (quasi-)stable in some regions of parameters Λ = ln(R0/ξ) and W = r0/R0. At fixed Λ, stable bands on W are intervals between non-overlapping main parametric resonances for different (integer) azimuthal wave numbers m. The stable intervals are most wide (ΔW ∼ 0.01–0.05) between m-pairs (1, 2) and (2, 3) at Λ ≈ 4–12, thus corresponding to micro/mesoscopic sizes of vortex rings in the case of superfluid 4He. With four and more rings, at least for W > 0.1, resonances overlap for all Λ and no stable domains exist.
Intrauterine growth-restricted piglets defined by their head shape have impaired survival and growth during the suckling period
Authors: Hansen C. F. , Hales J. , Amdi C. , Moustsen V. A.
Published: August 2018

Increased litter sizes in modern pig breeds have led to a significant number of pigs being born undersised and/or exposed to different degrees of intrauterine growth restriction (IUGR). The aim of this study was to examine the effect of piglet head shape as an identification method on performance indices. Data included all piglets from 203 litters, in total 3402 crossbred piglets. Piglets were classified at birth based on their head morphology (normal, mild IUGR and IUGR) and weighed at birth, Day 14 and at weaning (mean ± s.d.: 25.5 ± 1.23 days). The relative weight of the brain (to bodyweight) was greater in the mild IUGR (4.2%) and in the IUGR piglets (5.5%) compared with the normal piglets (2.8%) (P < 0.001). Weaning weight of the mild IUGR and IUGR piglets was reduced by 1.3 kg and 1.8 kg, respectively, compared with the normal piglets (P < 0.001). The average daily gain of the normal piglets (228 g/day) was higher than the mild IUGR (195 g/day) and IUGR piglets (181 g/day) (P < 0.001). The fractional growth rate (weight gained per day per starting weight) was, however, highest in the IUGR piglets followed by the mild IUGR and the normal piglets (P < 0.001) indicating the potential for catch up growth. Mild IUGR that were liveborn had twice as high a risk of dying before weaning than normal piglets; whereas liveborn IUGR piglets had a 4.7 times greater risk of dying pre-weaning. The present study showed that piglets born with a ‘dolphin-like’ head shape have an impaired growth and increased risk of dying in the suckling period.
Effects of water level fluctuations and substratum drying on the survival and behaviour of the invasive freshwater snail Physa acuta Draparnaud, 1805
Authors: Gulanicz Tomasz , Kobak Jarosław , Poznańska-Kakareko Małgorzata
Published: August 2018

Pulmonate snails live in nearshore zones of waterbodies, experiencing water level fluctuations. In the present study we investigated the resistance of Physa acuta to desiccation and its behavioural responses (horizontal migrations and burrowing) to drying. Determining the adaptations of P. acuta to extreme ranges of environmental factors may be crucial for understanding its invasiveness. Survival in gradually drying sand was determined as LT50 and LT90 (i.e. the time until death of 50 and 90% of individuals respectively). Horizontal migration was studied at shorter and longer distances (24 and 48cm), with gradual or sudden (longer distance only) dewatering. Burrowing was studied during a gradual decrease in water level. Snails were highly resistant to drying as the LT50 and LT90 values on the exposed substratum were 8 and 11 days respectively. In addition, snails exhibited horizontal migrations at shorter distances during gradual dewatering. Migration was less pronounced at the longer distance. After a sudden dewatering, snail movement was limited, suggesting that the snails stayed passive rather than risked a migration over the exposed substratum. Snails never burrowed in sediments in response to dewatering. Resistance to drying and ability to migrate enables P. acuta to survive in harsh environments and can contribute to its invasiveness.
Morphological intelligence counters foot slipping in the desert locust and dynamic robots
Authors: Woodward Matthew A. , Sitti Metin
Published: August 2018

Significance

Animals in natural environments necessarily come into contact with surfaces having differing orientations and materials. However, not much is known about how their feet contribute to friction, particularly in the case of dual-attachment mechanisms and passive mechanics (morphological intelligence). We study the desert locust’s (
Schistocerca gregaria
) morphology, spines and adhesive pads, and jumping behavior to extract traits that contribute to enhancing friction. Our results demonstrate the potential contribution of morphological intelligence to solving complex dynamic locomotion problems. We anticipate that this study will inspire further research of the strategies used by animals to interact dynamically with diverse surfaces. Furthermore, the concepts presented can be easily adapted to, for the enhancement of, existing simple miniature and state-of-the-art large-legged terrestrial robots.
Evaluation of microstructure and properties of AZ31/Al2O3 composites prepared by solid-phase synthesis
Authors: Wei Shuaihu , Hu Maoliang , Ji Zesheng , Xu Hongyu , Wang Ye
Published: August 2018

Solid-phase synthesis was used to prepare AZ31/Al2O3 composites and the effect of Al2O3 particles on its microstructure and mechanical properties was investigated. The composites were characterised by optical microscopy, scanning electron microscopy, transmission electron microscopy, vickers hardness tester and electron universal strength tester. The results show that the grains of the composites are significantly refined and the mechanical properties increase obviously. While the content of Al2O3 particles is 2 wt-%, the hardness, ultimate tensile strength and elongation to failure reach the maximum of 85HV, 308 MPa, 6.83%, respectively. The addition of Al2O3 particles promotes the dynamic recrystallisation.
Prediction of abandonment in Spanish fitness centres
Authors: Clavel San Emeterio Iván , García‐Unanue Jorge , Iglesias‐Soler Eliseo , Luis Felipe Jose , Gallardo Leonor
Published: August 2018

Research question: The increase of physical exercise in fitness centres has turned these facilities in important active lifestyle promoters. However, only between 30% and 60% of subscribers still linked to the sports centre after a year. The aim of this study is to design a model to predict the drop out in fitness centres. Research methods: Monthly data corresponding to the actual behaviour of 14,522 members of three sport centres in Spain were recorded over the course of one year. In order to calculate the likelihood of drop out, logistic regressions were used to create predictive models for each centre. Results and findings: It was possible to predict abandonment of users of sport centres from their historical behaviour, although the predictive models obtained for each centre were not completely coincident. The effectiveness of the models was around 70%. Implications: The analysis of users’ behaviour in a fitness centre can allow to avoid the drop out and therefore the abandonment of physical activity. Segmenting the customers based on the likelihood of drop out may be useful for improving the effectiveness of the strategies of loyalty and for optimizing the organization of human and material resources.
The effect of athletic expertise and trait emotional intelligence on decision‐making
Authors: Vaughan Robert , Laborde Sylvain , McConville Christopher
Published: August 2018

The quality of decision and assessment of risk are key determinants of successful sport performance. Athletes differ fundamentally in their decision‐making ability according to their athletic expertise level. Moreover, given the influence of emotions on decision‐making, it is likely that a trait reflecting emotional functioning, trait emotional intelligence, may also influence decision‐making. Therefore, the aim of this research was to investigate the respective contribution of athletic expertise and trait emotional intelligence to non‐athletic decision‐making. In total, 269 participants aged between 18 and 26 years with a range of athletic experience i.e. none (n = 71), novice (n = 54), amateur (n = 55), elite (n = 45) and super‐elite (n = 44), completed the Emotional Intelligence Scale and the Cambridge Gambling Task. Regression modelling indicated a significant positive relationship of athletic expertise and trait emotional intelligence with the quality of decision‐making, and a negative relationship with deliberation time and risk‐taking. Cognitive skills transfer may explain the higher decision‐making scores associated with higher athletic expertise, while individuals with higher trait emotional intelligence may anticipate better the emotional consequences linked with a gambling task, which may help individuals make better decisions and take less risks.
The tetraspanin CD82 regulates bone marrow homing and engraftment of hematopoietic stem and progenitor cells
Authors: Saito-Reis Chelsea A. , Marjon Kristopher D. , Pascetti Erica M. , Floren Muskan , Gillette Jennifer M.
Published: August 2018

Hematopoietic stem and progenitor cell (HSPC) transplantation represents a treatment option for patients with malignant and nonmalignant hematological diseases. Initial steps in transplantation involve the bone marrow homing and engraftment of peripheral blood–injected HSPCs. In recent work, we identified the tetraspanin CD82 as a potential regulator of HSPC homing to the bone marrow, although its mechanism remains unclear. In the present study, using a CD82 knockout (CD82KO) mouse model, we determined that CD82 modulates HSPC bone marrow maintenance, homing, and engraftment. Bone marrow characterization identified a significant decrease in the number of long-term hematopoietic stem cells in the CD82KO mice, which we linked to cell cycle activation and reduced stem cell quiescence. Additionally, we demonstrate that CD82 deficiency disrupts bone marrow homing and engraftment, with in vitro analysis identifying further defects in migration and cell spreading. Moreover, we find that the CD82KO HSPC homing defect is due at least in part to the hyperactivation of Rac1, as Rac1 inhibition rescues homing capacity. Together, these data provide evidence that CD82 is an important regulator of HSPC bone marrow maintenance, homing, and engraftment and suggest exploiting the CD82 scaffold as a therapeutic target for improved efficacy of stem cell transplants.
Wage and Employment Growth in America's Drug Epidemic: Is All Growth Created Equal?
Authors: Betz Michael R. , Jones Lauren E.
Published: August 2018

The rise in drug overdose deaths in the United States since the turn of the millennium has been extraordinary. A popular narrative paints a picture whereby opioid overdoses among white, male, less‐educated, rural workers have been caused by reduced economic opportunities borne by such people. In this article, we causally test the validity of this theory by using Bartik‐type variables to explore the relationship between local economic conditions and county opioid overdose death rates. We add to the literature by exploring how both employment and wage growth in different types of industries are related to opioid overdose deaths for the population as a whole, as well as for rural (vs. urban), male (vs. female) and white (vs. black) populations. We find mixed evidence. Our results confirm that wage and employment growth in industries more likely to employ low‐skill workers are important protective factors for rural, white males. However, we also find evidence that economic improvements in low‐skill industries are just as important in protecting blacks and women against opioid overdoses, and for workers in metro counties. We also find evidence that employment growth in high‐paying industries has led to increases in opioid overdoes rates.
Establishing a Long-Term Model for Analysis and Improvement of Underfilled Blood Culture Volumes
Authors: Zaleski Michael , Erdman Patrick , Adams Joshua , Michael Amanda , Rudy Abigail , Boesch Robert , Allison Lauren , Mailander Patricia , Hess Wendell , Myers Debra , Craft David
Published: August 2018

Objectives

Underfilling of blood culture bottles decreases the sensitivity of the culture. We attempt to increase average blood culture fill volumes (ABCFVs) through an educational program.

Methods

Partnerships were established with four hospital units (surgical intensive care unit [SICU], medical intensive care unit [MICU], medical intermediate care unit [MIMCU], and hematology and oncology unit [HEME/ONC]). ABCFVs were continuously tracked and communicated to each unit monthly. Educational sessions were provided to each unit.

Results

ABCFVs for the SICU, MICU, MIMCU, and HEME/ONC were 4.8, 5.0, 5.0, and 6.3 mL/bottle, respectively. After the final education session, the SICU, MICU, MIMCU, and HEME/ONC were able to maintain an ABCFV of 6.8, 8.1, 7.9, and 8.2 mL/bottle, respectively.

Conclusions

Partnering with a specific unit and providing monthly volume reports with educational sessions has a direct positive correlation on increasing ABCFVs. Increasing ABCFVs has the potential to decrease false-negative blood cultures, time to detection of positive blood cultures, and time to appropriate and specific antimicrobial therapy, as well as improve patient outcomes in high-acuity patient care units.
DASHR 2.0: integrated database of human small non-coding RNA genes and mature products
Authors: Kuksa Pavel P , Amlie-Wolf Alexandre , Katanić Živadin , Valladares Otto , Wang Li-San , Leung Yuk Yee
Published: August 2018

Motivation

Small non-coding RNAs (sncRNAs, <100 nts) are highly abundant RNAs that regulate diverse and often tissue-specific cellular processes by associating with transcription factor complexes or binding to mRNAs. While thousands of sncRNA genes exist in the human genome, no single resource provides searchable, unified annotation, expression and processing information for full sncRNA transcripts and mature RNA products derived from these larger RNAs.

Results

Our goal is to establish a complete catalog of annotation, expression, processing, conservation, tissue-specificity and other biological features for all human sncRNA genes and mature products derived from all major RNA classes. DASHR (Database of small human non-coding RNAs) v2.0 database is the first that integrates human sncRNA gene and mature products profiles obtained from multiple RNA-seq protocols. Altogether, 185 tissues/cell types and sncRNA annotations and >800 curated experiments from ENCODE and GEO/SRA across multiple RNA-seq protocols for both GRCh38/hg38 and GRCh37/hg19 assemblies are integrated in DASHR. Moreover, DASHR is the first to contain both known and novel, previously un-annotated sncRNA loci identified by unsupervised segmentation (13 times more loci with 1 678 800 total). Additionally, DASHR v2.0 adds >3 200 000 annotations for non-small RNA genes and other genomic features (long-noncoding RNAs, mRNAs, promoters, repeats). Furthermore, DASHR v2.0 introduces an enhanced user interface, interactive experiment-by-locus table view, sncRNA locus sorting and filtering by biological features. All annotation and expression information directly downloadable and accessible as UCSC genome browser tracks.

Availability and implementation

DASHR v2.0 is freely available at https://lisanwanglab.org/DASHRv2.

Supplementary information

Supplementary data are available at Bioinformatics online.
WIlsON: Web-based Interactive Omics VisualizatioN
Authors: Schultheis Hendrik , Kuenne Carsten , Preussner Jens , Wiegandt Rene , Fust Annika , Bentsen Mette , Looso Mario
Published: August 2018

Motivation

High throughput (HT) screens in the omics field are typically analyzed by automated pipelines that generate static visualizations and comprehensive spreadsheet data for scientists. However, exploratory and hypothesis driven data analysis are key aspects of the understanding of biological systems, both generating extensive need for customized and dynamic visualization.

Results

Here we describe WIlsON, an interactive workbench for analysis and visualization of multi-omics data. It is primarily intended to empower screening platforms to offer access to pre-calculated HT screen results to the non-computational scientist. Facilitated by an open file format, WIlsON supports all types of omics screens, serves results via a web-based dashboard, and enables end users to perform analyses and generate publication-ready plots.

Availability and implementation

We implemented WIlsON in R with a focus on extensibility using the modular Shiny and Plotly frameworks. A demo of the interactive workbench without limitations may be accessed at http://loosolab.mpi-bn.mpg.de. A standalone Docker container as well as the source code of WIlsON are freely available from our Docker hub https://hub.docker. com/r/loosolab/wilson, CRAN https://cran.r-project.org/web/packages/wilson/, and GitHub repository https://github.molgen.mpg.de/loosolab/wilson-apps, respectively.
Bigmelon: tools for analysing large DNA methylation datasets
Authors: Gorrie-Stone Tyler J , Smart Melissa C , Saffari Ayden , Malki Karim , Hannon Eilis , Burrage Joe , Mill Jonathan , Kumari Meena , Schalkwyk Leonard C
Published: August 2018

Motivation

The datasets generated by DNA methylation analyses are getting bigger. With the release of the HumanMethylationEPIC micro-array and datasets containing thousands of samples, analyses of these large datasets using R are becoming impractical due to large memory requirements. As a result there is an increasing need for computationally efficient methodologies to perform meaningful analysis on high dimensional data.

Results

Here we introduce the bigmelon R package, which provides a memory efficient workflow that enables users to perform the complex, large scale analyses required in epigenome wide association studies (EWAS) without the need for large RAM. Building on top of the CoreArray Genomic Data Structure file format and libraries packaged in the gdsfmt package, we provide a practical workflow that facilitates the reading-in, preprocessing, quality control and statistical analysis of DNA methylation data.

We demonstrate the capabilities of the bigmelon package using a large dataset consisting of 1193 human blood samples from the Understanding Society: UK Household Longitudinal Study, assayed on the EPIC micro-array platform.

Availability and implementation

The bigmelon package is available on Bioconductor (http://bioconductor.org/packages/bigmelon/). The Understanding Society dataset is available at https://www.understandingsociety.ac.uk/about/health/data upon request.

Supplementary information

Supplementary data are available at Bioinformatics online.
ST viewer: a tool for analysis and visualization of spatial transcriptomics datasets
Authors: Fernández Navarro José , Lundeberg Joakim , Ståhl Patrik L
Published: August 2018

Motivation

Spatial Transcriptomics (ST) is a technique that combines high-resolution imaging with spatially resolved transcriptome-wide sequencing. This novel type of data opens up many possibilities for analysis and visualization, most of which are either not available with standard tools or too complex for normal users.

Results

Here, we present a tool, ST Viewer, which allows real-time interaction, analysis and visualization of Spatial Transcriptomics datasets through a seamless and smooth user interface.

Availability and implementation

The ST Viewer is open source under a MIT license and it is available at https://github.com/SpatialTranscriptomicsResearch/st_viewer.

Supplementary information

Supplementary data are available at Bioinformatics online.
PANDA: A comprehensive and flexible tool for quantitative proteomics data analysis
Authors: Chang Cheng , Li Mansheng , Guo Chaoping , Ding Yuqing , Xu Kaikun , Han Mingfei , He Fuchu , Zhu Yunping
Published: August 2018

As the experiment techniques and strategies in quantitative proteomics are improving rapidly, the corresponding algorithms and tools for protein quantification with high accuracy and precision are continuously required to be proposed. Here, we present a comprehensive and flexible tool named PANDA for proteomics data quantification. PANDA, which supports both label-free and labeled quantifications, is compatible with existing peptide identification tools and pipelines with considerable flexibility. Compared with MaxQuant on several complex datasets, PANDA was proved to be more accurate and precise with less computation time. Additionally, PANDA is an easy-to-use desktop application tool with user-friendly interfaces.

Availability and implementation

PANDA is freely available for download at https://sourceforge.net/projects/panda-tools/.

Supplementary information

Supplementary data are available at Bioinformatics online
Benchmarking optimization methods for parameter estimation in large kinetic models
Authors: Villaverde Alejandro F , Fröhlich Fabian , Weindl Daniel , Hasenauer Jan , Banga Julio R
Published: August 2018

Motivation

Kinetic models contain unknown parameters that are estimated by optimizing the fit to experimental data. This task can be computationally challenging due to the presence of local optima and ill-conditioning. While a variety of optimization methods have been suggested to surmount these issues, it is difficult to choose the best one for a given problem a priori. A systematic comparison of parameter estimation methods for problems with tens to hundreds of optimization variables is currently missing, and smaller studies provided contradictory findings.

Results

We use a collection of benchmarks to evaluate the performance of two families of optimization methods: (i) multi-starts of deterministic local searches and (ii) stochastic global optimization metaheuristics; the latter may be combined with deterministic local searches, leading to hybrid methods. A fair comparison is ensured through a collaborative evaluation and a consideration of multiple performance metrics. We discuss possible evaluation criteria to assess the trade-off between computational efficiency and robustness. Our results show that, thanks to recent advances in the calculation of parametric sensitivities, a multi-start of gradient-based local methods is often a successful strategy, but a better performance can be obtained with a hybrid metaheuristic. The best performer combines a global scatter search metaheuristic with an interior point local method, provided with gradients estimated with adjoint-based sensitivities. We provide an implementation of this method to render it available to the scientific community.

Availability and implementation

The code to reproduce the results is provided as Supplementary Material and is available at Zenodo https://doi.org/10.5281/zenodo.1304034.

Supplementary information

Supplementary data are available at Bioinformatics online.
Computational Feature Analysis of Body Movements Reveals Hierarchical Brain Organization
Authors: Vaessen Maarten J , Abassi Etienne , Mancini Maurizio , Camurri Antonio , de Gelder Beatrice
Published: August 2018

Social species spend considerable time observing the body movements of others to understand their actions, predict their emotions, watch their games, or enjoy their dance movements. Given the important information obtained from body movements, we still know surprisingly little about the details of brain mechanisms underlying movement perception. In this fMRI study, we investigated the relations between movement features obtained from automated computational analyses of video clips and the corresponding brain activity. Our results show that low-level computational features map to specific brain areas related to early visual- and motion-sensitive regions, while mid-level computational features are related to dynamic aspects of posture encoded in occipital–temporal cortex, posterior superior temporal sulcus and superior parietal lobe. Furthermore, behavioral features obtained from subjective ratings correlated with activity in higher action observation regions. Our computational feature-based analysis suggests that the neural mechanism of movement encoding is organized in the brain not so much by semantic categories than by feature statistics of the body movements.
Comparison of mechanical disturbance in soft sediments due to tickler-chain SumWing trawl vs. electro-fitted PulseWing trawl
Authors: Depestele Jochen , Degrendele Koen , Esmaeili Moosa , Ivanović Ana , Kröger Silke , O’Neill Finbarr G , Parker Ruth , Polet Hans , Roche Marc , Teal Lorna R , Vanelslander Bart , Rijnsdorp Adriaan D
Published: August 2018

Tickler-chain SumWing and electrode-fitted PulseWing trawls were compared to assess seabed impacts. Multi-beam echo sounder (MBES) bathymetry confirmed that the SumWing trawl tracks were consistently and uniformly deepened to 1.5 cm depth in contrast to 0.7 cm following PulseWing trawling. MBES backscatter strength analysis showed that SumWing trawls (3.11 dB) flattened seabed roughness significantly more than PulseWing trawls (2.37 dB). Sediment Profile Imagery (SPI) showed that SumWing trawls (mean, SD) homogenised the sediment deeper (3.4 cm, 0.9 cm) and removed more of the oxidised layer than PulseWing trawls (1 cm, 0.8 cm). The reduced PulseWing trawling impacts allowed a faster re-establishment of the oxidised layer and micro-topography. Particle size analysis suggested that SumWing trawls injected finer particles into the deeper sediment layers (∼4 cm depth), while PulseWing trawling only caused coarsening of the top layers (winnowing effect). Total penetration depth (mean, SD) of the SumWing trawls (4.1 cm, 0.9 cm) and PulseWing trawls (1.8 cm, 0.8 cm) was estimated by the depth of the disturbance layer and the layer of mobilized sediment (SumWing = 0.7 cm; PulseWing trawl = 0.8 cm). PulseWing trawls reduced most of the mechanical seabed impacts compared to SumWing trawls for this substrate and area characteristics.
Efferocytosis and autoimmune disease
Authors: Kawano Mahiru , Nagata Shigekazu
Published: August 2018

An enormous number of cells in the body die by apoptosis during development and under homeostasis. Apoptotic cells are swiftly engulfed by macrophages and digested into units. This removal of apoptotic cells is called ‘efferocytosis’. For efferocytosis, macrophages recognize phosphatidylserine (PtdSer) exposed on the cell surface as an ‘eat me’ signal. In healthy cells, PtdSer is exclusively localized to the inner leaflet of the plasma membrane by the action of flippases. When cells undergo apoptosis, caspase cleaves flippases to inactivate them, while it cleaves pro-scramblases to active scramblases, which quickly translocate PtdSer to the cell surface. The PtdSer is then recognized by PtdSer-binding proteins or by PtdSer receptors on macrophages, which subsequently engulf the apoptotic cells. When efferocytosis fails, apoptotic cells can rupture, releasing cellular materials that can evoke an autoimmune response. Thus, a defect in the PtdSer-exposing or PtdSer-recognizing processes triggers autoimmunity, leading to a systemic lupus erythematosus-type autoimmune disease.
Risks of Colorectal Cancer and Cancer-Related Mortality in Familial Colorectal Cancer Type X and Lynch Syndrome Families
Authors: Choi Yun-Hee , Lakhal-Chaieb Lajmi , Kröl Agnieszka , Yu Bing , Buchanan Daniel , Ahnen Dennis , Le Marchand Loic , Newcomb Polly A , Win Aung Ko , Jenkins Mark , Lindor Noralane M , Briollais Laurent
Published: August 2018

Background

The risk of cancers is well characterized in Lynch syndrome (LS) families but has been less studied in familial colorectal cancer type X (FCCTX) families.

Methods

In this article, we compare the risk estimates of first and second colorectal cancers (CRCs) in 168 FCTTX and 780 LS families recruited through the Colon Cancer Family Registry as well as the risk of cancer-related deaths and disease-free survival (DFS) after a first CRC. Our methodology is based on a survival analysis approach, developed specifically to model the occurrence of successive cancers (ie, first and second CRCs) in the presence of competing risk events (ie, death from any causes).

Results

We found an excess risk of first and second CRC in individuals with LS compared to FCCTX family members. However, for an average age at first CRC of 60 years in FCCTX families and 50 years in LS families, the DFS rates were comparable in men but lower in women from FCCTX vs LS families, eg , 75.1% (95% confidence interval [CI] = 69.0% to 80.9%) vs 78.9% (95% CI = 76.3% to 81.3%) for the 10-year DFS. The 10-year risk of cancer-related death was higher in FCCTX families vs LS families, eg, 15.4% in men (95% CI = 10.9% to 19.8%) and 19.3% in women (95% CI = 13.6% to 24.7%) vs 8.9% (95% CI = 7.5% to 11.4%) and 8.7% (95% CI = 7.1% to 10.8%), respectively.

Conclusions

Individuals with CRCs arising in the context of FCCTX do not experience the same improved DFS and overall survival of those with LS, and that difference may be relevant in management decisions.