bluuebunny/crossref_metadata_2025 huggingface dataset:
Low‐cost microfluidics: materials and methods
Authors: Fan Yiqiang
Published: July 2018

Microfluidics has been widely used in the biological, chemical and recently in the energy field. In the past decade, microfluidics has experienced tremendous growth in academia; researchers in various fields have been using microfluidics as a powerful tool for the enchantments of their research. However, the fabrication technologies of microfluidics are sourced from microelectromechanical systems and integrated circuit industry, which the fabrication process is costly and time‐consuming, with the need of highly sophisticated instruments and experienced technical personnel to conduct fabrication process in the cleanroom environment. To lower the technical barriers for microfluidics, more and more researchers in different fields have invented various low‐cost fabrication methods for microfluidics using polymers or paper materials. Comparing to the conventional microfabrication process conducted in the cleanroom, the low‐cost fabrication methods are more flexible, with significant reduction in material cost, fabrication cost and processing time. This review is trying to introduce the most recent developments in low‐cost microfluidics, from the aspects of materials, microfabrication and bonding technologies. The comparison and scope of application for different low‐cost fabrication technologies for microfluidics were also provided in this review.
Period spacings in red giants
Authors: Mosser B. , Gehan C. , Belkacem K. , Samadi R. , Michel E. , Goupil M.-J.
Published: July 2018

Context. Oscillation modes with a mixed character, as observed in evolved low-mass stars, are highly sensitive to the physical properties of the innermost regions. Measuring their properties is therefore extremely important to probe the core, but requires some care, due to the complexity of the mixed-mode pattern.

Aims. The aim of this work is to provide a consistent description of the mixed-mode pattern of low-mass stars, based on the asymptotic expansion. We also study the variation of the gravity offset εg with stellar evolution.

Methods. We revisit previous works about mixed modes in red giants and empirically test how period spacings, rotational splittings, mixed-mode widths, and heights can be estimated in a consistent view, based on the properties of the mode inertia ratios.

Results. From the asymptotic fit of the mixed-mode pattern of a large set of red giants at various evolutionary stages, we derive unbiased and precise asymptotic parameters. As the asymptotic expansion of gravity modes is verified with a precision close to the frequency resolution for stars on the red giant branch (10−4 in relative values), we can derive accurate values of the asymptotic parameters. We decipher the complex pattern in a rapidly rotating star, and explain how asymmetrical splittings can be inferred. We also revisit the stellar inclinations in two open clusters, NGC 6819 and NGC 6791: our results show that the stellar inclinations in these clusters do not have privileged orientation in the sky. The variation of the asymptotic gravity offset with stellar evolution is investigated in detail. We also derive generic properties that explain under which conditions mixed modes can be observed.
The escape speed curve of the Galaxy obtained from Gaia DR2 implies a heavy Milky Way
Authors: Monari G. , Famaey B. , Carrillo I. , Piffl T. , Steinmetz M. , Wyse R. F. G. , Anders F. , Chiappini C. , Janßen K.
Published: July 2018

We measure the escape speed curve of the Milky Way based on the analysis of the velocity distribution of ~2850 counter-rotating halo stars from the Gaia Data Release 2. The distances were estimated through the StarHorse code, and only stars with distance errors smaller than 10% were used in the study. The escape speed curve is measured at Galactocentric radii ranging from ~5 kpc to ~10.5 kpc. The local Galactic escape at the Sun’s position is estimated to be ve(r⊙) = 580 ± 63 km s−1, and it rises towards the Galactic centre. Defined as the minimum speed required to reach three virial radii, our estimate of the escape speed as a function of radius implies for a Navarro–Frenk–White profile and local circular velocity of 240 km s−1 a dark matter mass M200 = 1.28−0.50+0.68 × 1012 M⊙ and a high concentration c200 = 11.09−1.79+2.94. Assuming the mass-concentration relation of ΛCDM, we obtain M200 = 1.55−0.51+0.64 × 1012 M⊙ and c200 = 7.93−0.27+0.33 for a local circular velocity of 228 km s−1.
Experimental study of the strengthening effect of reinforced concrete columns jacketed under service load level
Authors: Krainskyi Pavlo , Blikharskyy Yaroslav , Khmil Roman , Blikharskyy Zinoviy
Published: July 2018

The need of structural retrofitting and strengthening of different buildings, engineering structures or their elements is always present. Among the main reasons are demages and material deterioration due to aging, improper maintenance or physical damages; planed repairs; reconstruction or extension of the building; technical modification or complete change of operations inside the building or the structure, etc. In some cases operation of the building during retrofitting or strengthening of its structures has to be partially or fully stopped. In other cases the strengthening process takes place while the building is still operational which means that structures are strengthened under service loads. The main goal of this research is to determine the strengthening effect of reinforced concrete jacketing applied to columns under service load level. For that the experimental study of six reinforced concrete columns were carried out: four reference columns, both strengthened by jacketing and unstrengthened and two strengthened under service load. The main results of the research are presented.
Significance of the quality of short - link chains for work environment
Authors: Midor Katarzyna
Published: July 2018

In the article basic elements influencing the quality and safety of the chain are discussed. The conducted analysis clearly indicates that price ought not to be the only determinant to take into account when choosing a supplier - instead, the users of these products should first of all consider certificates and approvals provided with the product by its manufacturer.
Instruments of identification of hydraulic components potential failures
Authors: Fabiś-Domagała Joanna , Filo Grzegorz , Momeni Hassan , Domagała Mariusz
Published: July 2018

This paper presents an analysis of potential failures of hydraulic components on the example of a hydraulic gear pump with the use of instruments of quality management. The “five why” method was implemented to evaluate failures as well as the bases for the causes which have an influence on pumps failures. The causes are connected with operation condition of gear pumps and the quality of working fluid. In the next step, by using a systematic diagram, appropriate improvement actions for the identified causes were determined.
Continuous and discrete models in the mechanics of deformable solid bodies
Authors: Lámer Géza
Published: July 2018

The study provides an overview of modelling possibilities for the mechanical behaviour of media. The discrete, continuous or differential geometric as well as the discrete nature and continuous description grid continuum model in particular are highlighted. We point out that the differential geometric model is based on the concept of continuity and interprets a continuous medium model. We reveal that the grid continuum model is based on the application of numerical method and interprets a discrete medium model.
Contributions on experimental research of fuel consumption and management system in K9K892 Diesel engine from Dacia-Renault
Authors: Baldean Doru , Borzan Adela-Ioana
Published: July 2018

The present paper develops an experimental study that highlights some aspects of fuel consumption in engine's cylinders in order to outline the influence of engine's management system and operating conditions upon economy and fuel consumption, with corresponding effect on sustainability and adequate socio-economic development. The present work makes a theoretical and applied enquiry in the system features from Euro 5 diesel engine management in relation with fuel consumption and different driving scenarios. There were closely monitored engine temperatures, driving stiles and the values displayed ON-BOARD-DIAGNOSIS screens. The importance and opportunity for experimental inquiry of the fuel consumption and economy problems in compression ignited engine resides in the state of the art equipment and managing systems available today for monitoring all the engine's activities and for making possible to outline the economical operating regime, in order to reduce undesired losses. The experimental data are analyzed in detail.
The requirement elicitation process of designing a collaborative environment – The CRE@TIVE.BIZ case
Authors: Alexa Lidia , Avasilcai Silvia
Published: July 2018

The software development industry is one that is under a constant pressure to deliver products that are innovative, fast to market and better suited to the costumers’ needs and expectations. In this context, the traditional approaches to product development can become obsolete, as the market and the end-users are dynamic and rather unpredictable and the latter’s active participation can sometimes make the difference between success and failure. The Agile approach, on the other hand considers extensive collaboration with all stakeholders paramount in all the stages of the software development process and for this, a variety of requirements elicitations techniques are used in order to obtain extensive input that leads to designing and developing enhanced products and applications. This paper presents the requirement elicitation process and techniques used in the development process of an open collaboration and innovation platform – CRE@TIVE.BIZ which is an experimental model dedicated to create a community where all relevant stakeholders from three specific creative industries, namely design, fashion design and crafts, can meet, interact, gain access and share information, knowledge and resources.
Understanding the organizational critical activities of manufacturers in case studies
Authors: Hung Wei-Hsi , Lu Tsung-Yueh , Wu Mei-Fang , Lin Yun-Chen
Published: July 2018

Manufacturers tend to carry out certain important and continuous activities with respect to internal operations which could contribute to their success. These activities are termed organization critical activities (OCAs). The main objective of this study is to elicit the OCAs in the manufacturing industry to understand what can cause them to be successful. Through the case study approach including the interviews with the senior managers from three manufacturing companies in Taiwan and a series of prioritizing activities, 12 OCAs have been identified. This study found that Taiwanese manufacturers placed more importance on the activities of quality and cost control while placed relatively less importance on the marketing related activities. More findings and future research suggestions are also provided.
A study of microstructure and tensile property with casting S45C welding
Authors: Kuo Chin-Guo , Hwang Lih-Ren , Kang Yen-Tien
Published: July 2018

For energy saving and longer life time of a large casting iron may use of weld repairs or make up to more save manufacture time and energy than re-casting. Such as breakage, crack and wear in large casting iron castings used weld to repair casting for eco-energy.

The purpose of this study is to investigate the dissimilar joint property of S45C carbon steel with the multi-layer method and the multi-pass welding method. Four weld rods, experimentally examined the influence on microstructures, which were marked as A, B, C and D, respectively. The microstructures of joint bead were observed by the optical microscope. The specimens of tensile test were made according to ASTM E8M. The experimental results were shown as following:

1. The pearlite structures and the bainite structures were formed in welded zone by the weld rod of middle carbon steels. The yield strength and ultimate strength of the specimens were 360MPa and 460MPa.

2. The feature of welded specimen was close to stainless steel due to the stainless steel rod included some Cr and Ni. In addition, a ferritic-austenitic two-phase stainless steel was observed in optical microscope.
Material analysis and characterization of working electrodes of dye-sensitized solar cells
Authors: Lai Yeong-Lin , Hsu Hung-Ru , Lai Yeong-Kang , Chou Yung-Hua , Hsu Nai-Kun , Zheng Chun-Yi
Published: July 2018

The aim of this paper is to demonstrate the influence of the TiO2 with different sintered time regarding the performance of photovoltaic characteristics of DSSCs. A layer of TiO2 with a thickness of ~8-10 μm and an area of 0.25 cm2 was prepared by depositing TiO2 nanoparticles paste onto a fluorine-doped tin oxide (FTO) sbustrate by doctor blade technique, followed by sinterring at 450°C with 4 differennt sintering times: 10 min, 20 min, 30 min, and 40 min. The Pt solution was dripped on FTO substrate works as counter electrode. SEM, XRD and I-V curve were conducted for the material analysis. The photovoltaic characteristics were measured under AM 1.5 sunlight simulator. The results reveal that the different sintered time of TiO2 working electrode did affect the photovoltaic conversion efficiency. In conclusion, TiO2 sintered for 30 min yields the highest power conversion efficiency of 6.273%.
Automatic waste water treatment, aeration, and retrieval for a hybrid aquarium/plant system
Authors: Cheng An-Bang , Chiu Min-Chie , Chiu Che-Min
Published: July 2018

Because of the greenhouse effect, global climate changes will adversely influence the water supply in the future. As can be seen in traditional reservoirs, the crisis will be exacerbated due to the reservoir‘s sedimentation. From a global view, 70 % of freshwater resources are used for agricultural purposes. Thus, water management and infrastructure changes are needed to improve the situation if current climate conditions continue into the future. In order to save water resources, an attempt to reuse a pond‘s wastewater for agricultural irrigation is proposed. Utilizing waste water treatment via nitrification (with nitrifying bacteria) and aeration processes, the plant will receive enough fertilizer extracted from fish dung. Additionally, to assure a safe environment, the temperature, dissolved oxygen, and pH (potential of hydrogen) value of the aquarium will be monitored online and shown on the interface of the server device. Various automatic functions such as an aquarium filtering system, a waste water treatment system, a plant irrigation system, a waste water aeration system, and a water retrieval system are also designed in the hybrid aquarium/plant system. Consequently, a prototype of a PC-based automatic plant/aquarium hybrid system is established.
Control and synchronization of hyperchaotic states in mathematical models of Bènard-Marangoni convective experiments
Authors: Mancini Héctor , Becheikh Rabei , Vidal Gerard
Published: July 2018

Mathematical models are of great interest for experimentalists since they provide a way for controlling and synchronizing different chaotic states. In previous works, we have used a Takens-Bogdanov (T-B) system under hyperchaotic dynamic conditions (two or more positive Lyapunov exponents) because they adequately reflect the dynamics of the patterns in small aspect ratio pre-turbulent Bènard-Marangoni convection near a codimension-2 point (with resonance between 2:1 modes), in square symmetry (D4). In this paper, we discuss the coupling of two different four dimensional hyperchaotic models derived from the Lorenz equations by using the same method introduced in previous works. As in the former system of used equations, we found that two identical hyperchaotic systems based on either Chen or Lü equation systems evolve into different states in the pattern space, where the synchronization state or the complexity could be controlled by a small external signal, as was shown in T-B equations.
Elastic properties of crystalline Li–Ge phases with increasing Li concentration: A first-principles study
Authors: Zhang Panpan , Jia Meili , Ma Zengsheng
Published: July 2018

To obtain a better understanding of the failure mechanism of Ge anode during the charging and discharging process, in this paper, we systematically studied the mechanical properties of Li–Ge alloys based on density functional theory. The results show that the bulk, shear, and Young’s moduli of Li–Ge alloys decrease almost linearly with increasing Li concentration. In addition, based on the analysis of shear to bulk modulus and Poisson’s ratios, Li−Ge alloys demonstrate enhanced brittleness during the lithiation process which would make electrode materials fragile to cracks and failure. The weakened elastic moduli and enhanced brittleness would lead to the poor cycle performance and crushing failure of Ge anode materials during charging and discharging process.
Population density of the eastern pygmy-possum in a heath–woodland habitat
Authors: Goldingay Ross L. , Keohan Jo
Published: July 2018

The eastern pygmy-possum (Cercartetus nanus) has posed a challenge in attempts to describe its population density due to low rates of capture, preference for patchy habitats and periodic influxes of subadult individuals. We conducted a mark–recapture study of this species using a grid of nest boxes in a 9-ha patch of banksia heath–woodland. We captured 54 adults across the two years of our study. We estimated the density of adult pygmy-possums to be 1.5–4.2 ha–1 from different population models. This is substantially lower than previous estimates in equivalent habitat because we focussed on adults and recognised that they were not confined to the area bounded by our grid. We captured 36 subadults over the two years but they could not be reliably modelled due to extremely low recapture rates, which reflect high rates of dispersal and also mortality. For this reason, only the number of adults should be used to characterise populations of this species. Further study is required to investigate population dynamics over time and to describe the density of eastern pygmy-possums in other habitats.
Comparative genomic investigation of high-elevation adaptation in ectothermic snakes
Authors: Li Jia-Tang , Gao Yue-Dong , Xie Liang , Deng Cao , Shi Peng , Guan Meng-Long , Huang Song , Ren Jin-Long , Wu Dong-Dong , Ding Li , Huang Zi-Yan , Nie Hu , Humphreys Devon P. , Hillis David M. , Wang Wen-Zhi , Zhang Ya-Ping
Published: July 2018

Significance

Snakes of the genus
Thermophis
are endemic to the Tibetan plateau and occur at elevations over 3,500 m and present an opportunity to study the genetics mechanisms of adaptation to high-elevation conditions in ectotherms. Here, we provide a de novo genome of the Tibetan hot-spring snake,
Thermophis baileyi
, and conduct a series of comparisons with other reptiles. We identify genes under positive selection and test properties of allelic variants of proteins that are involved in DNA damage repair and responses to hypoxia. Functional assays reveal convergent genetic mechanisms that underlie high-elevation adaptation in both endotherms and ectotherms.
Influence of force‐vector and force application plyometric training in young elite basketball players
Authors: Gonzalo‐Skok Oliver , Sánchez‐Sabaté Jorge , Izquierdo‐Lupón Luis , Sáez de Villarreal Eduardo
Published: July 2018

Plyometric training composed by unilateral exercises with horizontal jumping direction seems to be an effective way to improve physical performance in athletes. The present study aimed to compare the influence of a combined jumping direction and force application (horizontal‐unilateral vs. vertical‐bilateral) plyometric training on linear sprinting, jumping, change of direction (COD) and dynamic balance in young elite basketball players. Twenty young (U‐13 to U‐14) male basketball players (age: 13.2 ± 0.7 years, body mass: 59.5 ± 12.7 kg, height: 172.9 ± 7.9 cm) were randomly assigned either to a unilateral‐horizontal (UH, n = 10) or bilateral‐vertical (BV, n = 10) plyometric group, twice a week for 6‐wk. Both groups performed between 60 and 100 jumps/session. UH executed all jumps unilaterally with horizontal direction, while jumps in the BV were bilaterally with vertical direction. Performance was assessed by a linear sprinting test, vertical and horizontal jumping tests, COD tests (V‐cut and 5+5 m with a 180°COD test), an ankle dorsiflexion test and dynamic balance tests (anterior and postero‐lateral directions). Within‐group differences showed substantial improvements (Effect size (ES):0.31–1.01) in unilateral vertical and horizontal jumping, V‐cut test and postero‐lateral direction with right leg after both training interventions. Furthermore, UH group also substantially improved (ES:0.33–0.78) all sprinting times and postero‐lateral direction with left leg, while BV enhanced anterior direction with left leg (ES:0.25). Between‐group analyses showed substantially greater improvements (ES:0.33) in 10‐m and V‐cut test in UH than in BV. The likely beneficial effect (small ES) achieved in sprinting abilities suggests the combination of unilateral‐horizontal jumps to improve such abilities.
Dizziness handicap inventory and vestibular activities of living scale in patients with temporomandibular dysfunction
Authors: Zeigelboim Bianca S. , Lacerda Adriana B. , Fonseca Vinicius R. , Liberalesso Paulo B. , Marques Jair M. , Malisky Jéssica S. , Stechman Neto José
Published: July 2018

Objective:

To verify the sensitivity of the Dizziness Handicap Inventory (DHI) and the Vestibular Disorders Activities of Daily Living Scale (VADL) questionnaires in order to apprehend the impact of vestibulocochlear symptoms on patients with unilateral and bilateral temporomandibular joint dysfunction (TMD).

Materials and Methods:

A descriptive, retrospective, transverse cohort study was conducted that evaluated 20 female patients, 26-72 years of age (mean age, 52.3 ± 12.2 years) from February 2015 to July 2016. The procedures were as follows: anamnesis, otorhinolaryngological and vestibular assessments, as well as the application of the DHI and VADL questionnaires.

Results:

(a) Prevalence of peripheral vestibular deficit disorder was observed, disregarding the affected side; (b) Dizziness symptom was more evident in the emotional aspect and tinnitus in the functional aspect in the DHI; (c) The VADL revealed greater difficulty in the functional, locomotion and instrumental aspects for activities (F5, L15 and I22); (d) In the correlation between the results of the vestibular testing and the VADL, dizziness had a significant effect (p < .05); (e) In the correlation between VADL and DHI, there was statistical significance for the functional and physical aspects (p < .05).

Conclusion:

The DHI and VADL questionnaires were sensitive to capture the impact of symptoms on daily activities in TMD patients.
Age-Related Expression of Human AT1R Variants and Associated Renal Dysfunction in Transgenic Mice
Authors: Jain Sudhir , Rana Anita , Jain Kavita , Perla Sravan K , Puri Nitin , Kumar Ashok
Published: July 2018

BACKGROUND

The contribution of single nucleotide polymorphisms in transcriptional regulation of the human angiotensin receptor type I (hAT1R) gene in age-related chronic pathologies such as hypertension and associated renal disorders is not well known. The hAT1R gene has single nucleotide polymorphisms in its promoter that forms 2 haplotypes (Hap), Hap-I and Hap-II. Hap-I of AT1R gene is associated with hypertension in Caucasians. We have hypothesized here that age will alter the transcriptional environment of the cell and will regulate the expression of hAT1R gene in a haplotype-dependent manner. This could likely make subjects with Hap-I increasingly susceptible to age-associated, AT1R-mediated complications.

METHOD

We generated transgenic (TG) mice with Hap-I and Hap-II. Adults (10–12 weeks) and aged (20–24 months) TG male mice containing either Hap-I or Hap-II were divided into 4 groups to study (i) the age-associated and haplotype-specific transcriptional regulation of hAT1R gene and (ii) their physiological relevance.

RESULTS

In aged animals, TG mice with Hap-I show increased expression of hAT1R and higher blood pressure (BP); suppression of antioxidant defenses (hemoxygenase, superoxide dismutase) and antiaging molecules (ATRAP, Klotho, Sirt3); increased expression of pro-inflammatory markers (IL-6, TNFα, CRP, NOX1); and increased insulin resistance. In vivo ChIP assay shows stronger binding of transcription factor USF2 to the chromatin of Hap-I mice.

CONCLUSION

Our results suggest that in aged animals, as compared with Hap-II, the TG mice with Hap-I overexpress hAT1R gene due to the stronger transcriptional activity, thus resulting in an increase in their BP and associated renal disorders.
Amodal completion and knowledge
Authors: Helton Grace , Nanay Bence
Published: July 2018

Amodal completion is the representation of occluded parts of perceived objects. We argue for the following three claims: First, at least some amodal completion-involved experiences can ground knowledge about the occluded portions of perceived objects. Second, at least some instances of amodal completion-grounded knowledge are not sensitive, that is, it is not the case that in the nearest worlds in which the relevant claim is false, that claim is not believed true. Third, at least some instances of amodal completion-grounded knowledge are not safe, that is, it is not the case that in all or nearly all near worlds where the relevant claim is believed true, that claim is in fact true. Thus, certain instances of amodal completion-grounded knowledge refute both the view that knowledge is necessarily sensitive and the view that knowledge is necessarily safe.
Glyphosate-based herbicides and cancer risk: a post-IARC decision review of potential mechanisms, policy and avenues of research
Authors: Davoren Michael J , Schiestl Robert H
Published: July 2018

Since its initial sales in the 1970s, the herbicide glyphosate attained widespread use in modern agriculture, becoming the most commercially successful and widely used herbicide of all time as of 2016. Despite a primary mechanism that targets a pathway absent from animal cells and regulatory studies showing safety margins orders of magnitude better than many other, more directly toxic herbicides, the safety status of glyphosate has recently been brought into question by a slow accumulation of studies suggesting more subtle health risks, especially when considered in combination with the surfactants it is usually applied with. Current, official views of respected international regulatory and health bodies remain divided on glyphosate’s status as a human carcinogen, but the 2015 International Agency for Research on Cancer decision to reclassify the compound as Category 2A (probably carcinogenic to humans) marked a sea change in the scientific community’s consensus view. The goal of this review is to consider the state of science regarding glyphosate’s potential as a human carcinogen and genotoxin, with particular focus on studies suggesting mechanisms that would go largely undetected in traditional toxicology studies, such as microbiome disruption and endocrine mimicry at very low concentrations.
Decomposing Parietal Memory Reactivation to Predict Consequences of Remembering
Authors: Lee Hongmi , Samide Rosalie , Richter Franziska R , Kuhl Brice A
Published: July 2018

Memory retrieval can strengthen, but also distort memories. Parietal cortex is a candidate region involved in retrieval-induced memory changes as it reflects retrieval success and represents retrieved content. Here, we conducted an fMRI experiment to test whether different forms of parietal reactivation predict distinct consequences of retrieval. Subjects studied associations between words and pictures of faces, scenes, or objects, and then repeatedly retrieved half of the pictures, reporting the vividness of the retrieved pictures (“retrieval practice”). On the following day, subjects completed a recognition memory test for individual pictures. Critically, the test included lures highly similar to studied pictures. Behaviorally, retrieval practice increased both hit and false alarm (FA) rates to similar lures, confirming a causal influence of retrieval on subsequent memory. Using pattern similarity analyses, we measured two different levels of reactivation during retrieval practice: generic “category-level” reactivation and idiosyncratic “item-level” reactivation. Vivid remembering during retrieval practice was associated with stronger category- and item-level reactivation in parietal cortex. However, these measures differentially predicted subsequent recognition memory performance: whereas higher category-level reactivation tended to predict FAs to lures, item-level reactivation predicted correct rejections. These findings indicate that parietal reactivation can be decomposed to tease apart distinct consequences of memory retrieval.
Effects of different antibiotic feeding programs on morbidity and mortality and growth performance of nursery pigs housed in a wean-to-finish facility
Authors: Puls Christopher L , Allee Gary L , Hammer James M , Carr Scott N
Published: July 2018

The objective of this study was to evaluate the effects of two antibiotic feeding programs in comparison to nonmedicated controls on the incidence of morbidity and mortality and growth performance of nursery pigs in a commercial setting. The study used 2,250 crossbred pigs in a randomized complete block design (blocking factor = start date). There were two dietary phases with three treatments in each phase: 1) nonmedicated controls vs. 2) 39 mg/kg (35 g/ton) tiamulin + 441 mg/kg (400 g/ton) chlortetracycline fed for 14 d (TIACTC) followed by 39 mg/kg (35 g/ton) tiamulin fed for 21 d (TIA) vs. 3) 28 mg/kg (25 g/ton) carbadox + 441 mg/kg (400 g/ton) oxytetracycline fed for 14 d (CAROTC) followed by 55 mg/kg (50 g/ton) carbadox fed for 21 d (CAR). Necropsy results from mortalities during the study confirmed the presence of pathogens including Pasteurella multocida and Escherichia coli, as well as Mycoplasma hyopneumoniae, Haemophilus parasuis, and Streptococcus suis. The study was carried out for a fixed time of 35 d from 6.7 ± 0.57 to 25.5 ± 2.23 kg BW. Pigs were housed in single-sex pens of 25 in a commercial wean-to-finish facility and there were 30 replicates of each treatment. All pigs were weighed as a group (i.e., pen) on days 0 (start), 14, and 35 (end) of study. Pigs had ad libitum access to feed and water throughout the study period; all feed additions to the feeder were recorded. There was no effect (P > 0.05) of antibiotic feeding program on the incidence of morbidity and mortality at any point during the study. During phase 1, TIACTC- and CAROTC-fed pigs were heavier (P < 0.05) at day 14 and had greater (P < 0.05) ADG (8.3% and 5.6% for TIACTC and CAROTC, respectively) and ADFI (4.3% and 6.5%, respectively) than controls. Pigs fed TIACTC in the first 14 d had greater (P < 0.05) G:F than the other treatments, which were similar for this measurement. In phase 2, feeding CAR resulted in greater (P < 0.05) ADG than controls, with pigs fed TIA being intermediate and different (P < 0.05) than the other treatments. Feeding antibiotics, regardless of treatment, resulted in greater (P < 0.05) ADFI than controls, but there were no differences in G:F. For the overall 35-d study period, feeding antibiotics resulted in greater (P < 0.05) ADG than controls (3.8% and 5.8%, respectively), but no difference (P > 0.05) between treatments for overall G:F. The results of this study confirm the advantage of feeding antibiotics on nursery pig growth.
On the feasibility of accessing acute pain–related facial expressions in the human fetus and its potential implications: a case report
Authors: Bernardes Lisandra Stein , Ottolia Juliana Fontan , Cecchini Marina , Filho Antônio Gomes de Amorim , Teixeira Manoel Jacobsen , Francisco Rossana Pulcineli Vieira , de Andrade Daniel Ciampi ,   Grupo de Estudo da Dor Fetal (Fetal Pain Study Group)
Published: July 2018

Introduction:

Although pain facial assessment is routinely performed in term and preterm newborns by the use of facial expression–based tools such as the Neonatal Facial Coding System, the assessment of pain during the intrauterine life has not been extensively explored.

Objective:

Describe for the first time, an experimental model to assess and quantify responses due to acute pain in fetuses undergoing anaesthesia for intrauterine surgery recorded by high-resolution 4D ultrasound machines.

Methods/results-case report:

A 33-year-old pregnant woman had congenital left diaphragmatic hernia of poor prognosis diagnosed, and her fetus was treated by fetoscopic endotracheal occlusion. Later, during the removal of the fetal endotracheal balloon by ultrasound-guided puncture, we have recorded facial expressions of the foetus before and after the anaesthetic puncture by the use of 4D ultrasound recordings, which were presented to 3 blinded coders instructed to use the Neonatal Facial Coding System for acute pain facial coding. The procedure was safe and feasible.

Conclusion:

This is the first description of a recordable acute pain model in the human fetus by the use of a facial expression–based tool. The possibility to assess pain-related intrauterine behaviours would allow not only for the monitoring of the efficacy of anaesthetic procedures in the fetus but would also open the way to explore the evolution of pain-related facial responses during the fetal neurodevelopment. This method may pave the way for objective assessments of pain in fetuses, should it endure the steps of formal validation studies.
Identification of a primitive intestinal transcription factor network shared between oesophageal adenocarcinoma and its pre-cancerous precursor state
Authors: Rogerson Connor , Britton Edward , Withey Sarah , Hanley Neil , Ang Yeng S. , Sharrocks Andrew D.
Published: July 2018

Oesophageal adenocarcinoma (OAC) is one of the most frequent causes of cancer deaths and yet compared to other common cancers, we know relatively little about the molecular composition of this tumour type. To further our understanding of this cancer we have used open chromatin profiling to decipher the transcriptional regulatory networks that are operational in OAC. We have uncovered a transcription factor network that is usually found in primitive intestinal cells during embryonic development, centred on HNF4A and GATA6. These transcription factors work together to control the OAC transcriptome. Importantly, we show that this network is activated in Barrett’s oesophagus, the putative precursor state to OAC thereby providing novel molecular evidence in support of stepwise malignant transition. Furthermore, we show that HNF4A alone, is sufficient to drive chromatin opening and activation of a Barrett’s-like chromatin signature when expressed in normal human epithelial cells. Collectively, these data provide a new way to categorise OAC at a genome scale and implicate HNF4A activation as a potential pivotal event in regulating its malignant transition from healthy cells.
Commonly-used FRET fluorophores promote collapse of an otherwise disordered protein
Authors: Riback Joshua A , Bowman Micayla A , Zmyslowski Adam M , Plaxco Kevin W , Clark Patricia L , Sosnick Tobin R
Published: July 2018

The dimensions that unfolded proteins, including intrinsically disordered proteins (IDPs), adopt at low or no denaturant remains controversial. We recently developed an innovative analysis procedure for small-angle X-ray scattering (SAXS) profiles and found that even relatively hydrophobic IDPs remain nearly as expanded as the chemically denatured ensemble, rendering them significantly more expanded than generally inferred using fluorescence resonance energy transfer (FRET) measurements. We show here that fluorophores typical of those employed in FRET can contribute to this discrepancy. Specifically, we find that addition of Alexa488 to a normally expanded IDP causes contraction of its ensemble. In parallel, we also tested the recent suggestion that FRET and SAXS results can be reconciled if, in contrast to homopolymers, the radius of gyration (Rg) of an unfolded protein chain can vary independently from its end-to-end distance (Ree). To do so, we developed an analysis procedure that can accurately extract both Rg and Ree from SAXS profiles even if they are decoupled. Using this procedure, we find that Rg and Ree remain tightly coupled even for heteropolymeric IDPs. We thus conclude that, when combined with improved analysis procedures for both SAXS and FRET, fluorophore-driven interactions are sufficient to explain the preponderance of existing data regarding the nature of polypeptide chains unfolded in the absence of denaturant.
Extracting human data from published figures: implications for data science and bioethics
Authors: Cox Brian J.
Published: July 2018

The advent of text mining and natural text reading artificial intelligence has opened new research opportunities on the large collections of research publications available through journal and other resources. These systems have begun to identify novel connections or hypotheses due to an ability to read and extract information from more literature than a single individual could in their lifetime. Most research publications contain figures where data is represented in a graph. Modern publication guidelines are strongly encouraging publication of graphs where all data is displayed as apposed to summary figures such as bar charts. Figures are often encoded in a graphing language that is interpreted and displayed as a graphics. Conversion figures in publications to the underlying code should enable text-based mining to extract the underlying raw data of the graph. Here I show that data from publications greater than 15 years old that contain time series data on human patients is extractable from the original publication and can be reassessed using modern tools. This could benefit cases where data sets are not available due to file loss or corruption. This may also create and issue for the publication of human data as sharing of human data often requires research ethics approval.

Author summary

Figures embedded in published research manuscripts are a minable resource similar to text mining. Figures are text based code that draws the image, as such the underlying text of the code can be used to reassemble the original data set.
Transdiagnostic characterization of neuropsychiatric disorders by hyperexcitation-induced immaturity
Authors: Murano Tomoyuki , Hagihara Hideo , Tajinda Katsunori , Matsumoto Mitsuyuki , Miyakawa Tsuyoshi
Published: July 2018

Biomarkers are needed to improve the diagnosis of neuropsychiatric disorders. Promising candidates are imbalance of excitation and inhibition in the brain, and maturation abnormalities. Here, we characterized different disease conditions by mapping changes in the expression patterns of maturation-related genes whose expression was altered by experimental neural hyperexcitation in published studies. This revealed two gene expression patterns: decreases in maturity markers and increases in immaturity markers. These two groups of genes were characterized by the overrepresentation of genes related to synaptic function and chromosomal modification, respectively. We used these two groups in a transdiagnostic analysis of 80 disease datasets for eight neuropsychiatric disorders and 12 datasets from corresponding animal models, and found that transcriptomic pseudoimmaturity inducible by neural hyperexcitation is shared by multiple neuropsychiatric disorders, such as schizophrenia, Alzheimer disorders, and ALS. Our results indicate that this endophenotype serve as a basis for transdiagnostic characterization of these disorders.
A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs
Authors: Soneson Charlotte , Love Michael I , Patro Rob , Hussain Shobbir , Malhotra Dheeraj , Robinson Mark D.
Published: July 2018

Most methods for statistical analysis of RNA-seq data take a matrix of abundance estimates for some type of genomic features as their input, and consequently the quality of any obtained results are directly dependent on the quality of these abundances. Here, we present the junction coverage compatibility (JCC) score, which provides a way to evaluate the reliability of transcript-level abundance estimates as well as the accuracy of transcript annotation catalogs. It works by comparing the observed number of reads spanning each annotated splice junction in a genomic region to the predicted number of junction-spanning reads, inferred from the estimated transcript abundances and the genomic coordinates of the corresponding annotated transcripts. We show that while most genes show good agreement between the observed and predicted junction coverages, there is a small set of genes that do not. Genes with poor agreement are found regardless of the method used to estimate transcript abundances, and the corresponding transcript abundances should be treated with care in any downstream analyses.
Breaking the ladder: Evolution of the ventral nerve cord in Annelida
Authors: Helm Conrad , Beckers Patrick , Bartolomaeus Thomas , Drukewitz Stephan H. , Kourtesis Ioannis , Weigert Anne , Purschke Günter , Worsaae Katrine , Struck Torsten H. , Bleidorn Christoph
Published: July 2018

A median, segmented, annelid nerve cord has repeatedly been compared to the arthropod and vertebrate nerve cords and became the most used textbook representation of the annelid nervous system. Recent phylogenomic analyses, however, challenge the hypothesis that a subepidermal rope-ladder-like ventral nerve cord (VNC) composed of a paired serial chain of ganglia and somata-free connectives represents neither a plesiomorphic nor a typical condition in annelids.

Using a comparative approach by combining phylogenomic analyses with morphological methods (immunohistochemistry and CLSM, histology and TEM), we compiled a comprehensive dataset to reconstruct the evolution of the annelid VNC. Our phylogenomic analyses generally support previous topologies. However, the so far hard-to-place Apistobranchidae and Psammodrilidae are now incorporated among the basally branching annelids with high support. Based on this topology we reconstruct an intraepidermal VNC as ancestral state in Annelida. Thus, a subepidermal ladder-like nerve cord clearly represents a derived condition.

Based on the presented data, a ladder-like appearance of the ventral nerve cord evolved repeatedly, and independently of the transition from an intraepidermal to a subepidermal cord during annelid evolution. Our investigations thereby question a common origin of the bilaterian median ganglionated VNC and propose an alternative set of neuroanatomical characteristics of the last common ancestor of Annelida or perhaps even Spiralia.
Sleep/wake synchronization across latitude
Authors: Martín-Olalla José María
Published: July 2018

Analysis of time use surveys in seventeen European countries and two American countries suggest that the winter sunrise —the latest sunrise year round— is a synchronizer for the sleep/wake cycle in standard population below 54° latitude, in competition with the noon synchronizer.

When comparing industrialized data to data from hunter/gatherer, pre-industrial, Tropical societies only the late event survives as a synchronizer below 54° latitude. People rise immediately before sunrise —winter sunrise in industrialized mid-latitude societies— and abhor morning darkness. Synchronization propagates through the sleep/wake cycle so that people go to bed with increasing distance to sunset in winter as latitude increases in a scenario dominated by artificial light. This suggests a leading role of the homeostatic sleep pressure in understanding sleep/wake cycle at social level.

WARNING

This pre-print has been largely upgraded and restyled in “Sleep timing in industrial and pre-industrial societies sync to the light/dark cycle” (https://doi.org/10.1101/392035). In this new pre-print data coming from the Harmonsized European Time Use Surveys (HETUS) and referred to the “sleep/wake and other personal care” cycle were not analyzed. Instead two new pre-industrial data are included.

Therefore this old pre-print you are about to read remains as a source for these data (see Figure 3 and Table III, Table VII to IX) and a source of information in the range of latitude above 54°.
Consistent pre-stimulus influences on auditory perception across the lifespan
Authors: McNair Steven W. , Kayser Stephanie J. , Kayser Christoph
Published: July 2018

As we get older, perception in cluttered environments becomes increasingly difficult as a result of changes in peripheral and central neural processes. Given the aging society it is important to understand the neural mechanisms constraining perception in the elderly. In young participants, the state of rhythmic brain activity prior to a stimulus has been shown to modulate the neural encoding and perceptual impact of this stimulus – yet it remains unclear whether, and if so, how, the perceptual relevance of pre-stimulus activity changes with age. Using the auditory system as a model, we recorded EEG activity during a frequency discrimination task from younger and older human listeners. By combining single-trial EEG decoding with linear modelling we demonstrate consistent statistical relations between pre-stimulus power and the encoding of sensory evidence in short-latency EEG components, and more variable relations between prestimulus phase and subjects’ decisions in fronto-parietal EEG components. At the same time, we observed a significant slowing of auditory evoked responses and a flattening of the overall EEG frequency spectrum in the older listeners. Our results point to mechanistically consistent relations between rhythmic brain activity and sensory encoding that emerge in large despite changes in neural response latencies and the relative amplitude of rhythmic brain activity with age.
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies
Authors: Alghamdi Sarah M. , Sundberg Beth A. , Sundberg John P. , Schofield Paul N. , Hoehndorf Robert
Published: July 2018

Data are increasingly annotated with multiple ontologies to capture rich information about the features of the subject under investigation. Analysis may be performed over each ontology separately, but, recently, there has been a move to combine multiple ontologies to provide more powerful analytical possibilities. However, it is often not clear how to combine ontologies or how to assess or evaluate the potential design patterns available. Here we use a large and well-characterized dataset of anatomic pathology descriptions from a major study of aging mice. We show how different design patterns based on the MPATH and MA ontologies provide orthogonal axes of analysis, and perform differently in over-representation and semantic similarity applications. We discuss how such a data-driven approach might be used generally to generate and evaluate ontology design patterns.