bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessing the effect of extra nitrogen on Kandelia obovata growth under cadmium stress using high-resolution thermal infrared remote sensing and the three-temperature model
Authors: Shen Xiaoxue , Li Ruili , Chai Minwei , Yu Ke , Zan Qijie , Qiu Guo Yu
Published: July 2018

Mangrove forests provide many ecological services and are among the most productive intertidal ecosystems on earth. Currently, these forests frequently face significant heavy metal pollution as well as eutrophication. The present study assessed the response of Kandelia obovata Sheue, H.Y. Liu & J. Yong to combined NH4+–N addition and Cd stress based on a three-temperature (3T) model using high-resolution thermal infrared remote sensing. The results show that leaf surface temperature (Tc) and the plant transpiration transfer coefficient (hat) became larger with increasing NH4+–N concentrations in the same Cd treatment, especially under high NH4+–N (50 and 100 mg·L−1) and Cd stress. The thermal bioindicators, growth responses and photosynthetic parameters changed in a consistent fashion, indicating that combined high NH4+–N addition and Cd stress led to stomatal closure, reduced the cooling effect of transpiration, and increased Tc and hat values. Furthermore, appropriate NH4+–N supply reduced stomatal conductance (gs) and the transpiration rate (Tr), which were increased by Cd stress, and then maintained Tc and hat at normal levels. The normalised hat helped to reduce the influence of environmental variation during the diagnosis of mangrove plant health. This indicated that the 3T model with high-resolution thermal infrared remote sensing provides an effective technique for determining the health status of mangrove plants under stress.
cAMP response element-binding protein 1 controls porcine ovarian cell proliferation, apoptosis, and FSH and insulin-like growth factor 1 response
Authors: Sirotkin A. V. , Benčo A. , Tandlmajerová A. , Lauková M. , Vašíček D. , Laurinčik J. , Kornhauser J. , Alwasel S. , Harrath A. H.
Published: July 2018

The aim of the present study was to examine the role of cAMP response element-binding protein (CREB) and its phosphorylation in the regulation of ovarian cell proliferation and apoptosis, and of the response of proliferation and apoptosis to the upstream hormonal stimulators FSH and insulin-like growth factor (IGF) 1. In the first series of experiments, porcine ovarian granulosa cells, transfected or not with a gene construct encoding wild-type CREB1 (CREB1WT), were cultured with and without FSH (0, 1, 10 or 100 ng mL−1). In the second series of experiments, these cells were transfected or not with CREB1WT or non-phosphorylatable mutant CREB1 (CREB1M1) and cultured with and without FSH (0, 1, 10 or 100 ng mL−1) or IGF1 (0, 1, 10 and 100 ng mL−1). Levels of total and phosphorylated (p-) CREB1, proliferating cell nuclear antigen (PCNA), a marker of proliferation, and BAX, a marker of apoptosis, were evaluated by western immunoblotting and immunocytochemical analysis. Transfection of cells with CREB1WT promoted accumulation of total CREB1 within cells, but p-CREB1 was not detected in any cell group. Both CREB1WT and CREB1M1 reduced cell proliferation and apoptosis. Addition of 10 and 100 ng mL−1 FSH to non-transfected cells promoted CREB1 accumulation and apoptosis, whereas cell proliferation was promoted by all concentrations of FSH tested. FSH activity was not modified in cells transfected with either CREB1WT or CREB1M1. IGF1 at 100 ng mL−1 promoted cell proliferation, whereas all concentrations of IGF1 tested reduced apoptosis. Transfection with either CREB1WT or CREB1M1 did not modify the effects of either FSH or IGF1, although CREB1M1 reversed the effect of IGF1 on apoptosis from inhibitory to stimulatory. These observations suggest that CREB1 is involved in the downregulation of porcine ovarian cell proliferation and apoptosis. The absence of visible CREB1 phosphorylation and the similarity between the effects of CREB1WT and CREB1M1 transfection indicate that phosphorylation is not necessary for CREB1 action on these processes. Furthermore, the observations suggest that FSH promotes both ovarian cell proliferation and apoptosis, whereas IGF1 has proliferation-promoting and antiapoptotic properties. The effect of FSH on CREB1 accumulation and the ability of CREB1M1 to reverse the effects of IGF1 on apoptosis indicate that CREB1 is a mediator of hormonal activity, but the inability of either CREB1WT or CREBM1transfection to modify the primary effects of FSH and IGF1 suggest that CREB1 and its phosphorylation do not mediate the action of these hormones on ovarian cell proliferation and apoptosis.
Direction of flagellum beat propagation is controlled by proximal/distal outer dynein arm asymmetry
Authors: Edwards Beatrice Freya Lucy , Wheeler Richard John , Barker Amy Rachel , Moreira-Leite Flávia Fernandes , Gull Keith , Sunter Jack Daniel
Published: July 2018

Significance

The motile flagellum/cilium is found across eukaryotic life, and it performs critical functions in many organisms including humans. A fundamental requirement for a motile flagellum is that it must undergo the appropriate waveform for its specific function. Much is known about the generation of asymmetry in flagellum movement; however, it is unknown how a motile flagellum specifies where waves should start and whether waves should go from base to tip, or from tip to base. We show here in two flagellum model organisms (the human parasitesTrypanosoma bruceiandLeishmania mexicana) that differences in the outer dynein arms between the distal and proximal regions of the flagellum determine wave propagation direction and are generated and maintained by the flagellum growth machinery.
Quantum optics approach to radiation from atoms falling into a black hole
Authors: Scully Marlan O. , Fulling Stephen , Lee David M. , Page Don N. , Schleich Wolfgang P. , Svidzinsky Anatoly A.
Published: July 2018

Significance

Using a combination of quantum optics and general relativity, we show that the radiation emitted by atoms falling into a black hole looks like, but is different from, Hawking radiation. This analysis also provides insight into the Einstein principle of equivalence between acceleration and gravity.
A cross-dialectal analysis of Nuosu adjectival comparative constructions
Authors: Ding Hongdi
Published: July 2018

Current analyses (Hu 2005;Gerner 2013;Liu et al. 2013) of Nuosu adjectival comparative constructions are not observationally adequate because they are only based on the semantic distinction between dimensional adjectives and other adjectives. A better analysis should make a further morphological consideration by dividing the Nuosu adjectives into root-sharing prefixed adjectives, non-root-sharing prefixed adjectives and simplex adjectives.

Moreover, the existing analyses are not consistent. Some unacceptable comparative sentences inHu (2005)are acceptable inGerner (2013)andLiu et al. (2013). I have found out that the inconsistency results from different rigorousness to adjectival morphosyntactic restrictions among different varieties or dialects of Nuosu.

After a cross-dialectal investigation with three major dialects of Nuosu, i.e. Shynra, Yynuo and Suondi, it is concluded that Nuosu comparative constructions have a restricted form and a general form for superiority, inferiority and equality respectively. Different dialects or varieties have varying rigorousness to Nuosu adjectival morphosyntax, thus resulting in different choices of the forms for comparison. Accordingly, the available Nuosu varieties are classified into three types: varieties with more morphosyntactic rigorousness, transitional varieties and varieties with less morphosyntactic rigorousness. It is found that Shynra Nuosu is morphosyntactically less rigorous than Yynuo and Suondi Nuosu. I will also address the relationship between the two structural forms of comparative constructions. To conclude, a prediction is made on the development of Nuosu adjectival comparatives.
Finite causative complements in Middle English
Authors: Lowrey Brian
Published: July 2018

This paper examines the use of causative verbs with two kinds of finite complements in Middle English (ME): a simple finite clause (V+that) and one involving both a finite clause and a separate NP (V+NP+that). I attempt to determine in which contexts these structures appear, and to what extent they are related. I suggest that V+that is probably a survivor from Old English and V+NP+that a later innovation. I also examine the factors likely to have contributed to the persistence of V+that in ME, and to the emergence of V+NP+that, such as language contact and the influence of other existing Middle English constructions which may have played a role in the spread of V+NP+that.
From Microscopes to Optogenetics: Ian Hacking Vindicated
Authors: Bickle John
Published: July 2018

I introduce two new tools in experimental neurobiology, optogenetics and DREADDs (designer receptors exclusively activated by designer drugs). These tools permit unprecedented control over activity in specific neurons in behaving animals. In addition to their inherent scientific interest, these tools make an important contribution to philosophy of science. They illustrate the very premises of Ian Hacking’s “microscope” argument for the relative independence of experiment from theory. This new example is important for generalizing Hacking’s argument because the background sciences (optics for microscopes, molecular biology for optogenetics, and DREADDs) and the fields of engineering producing these tools differ significantly.
MinIONQC: fast and simple quality control for MinION sequencing data
Authors: Lanfear R , Schalamun M , Kainer D , Wang W , Schwessinger B
Published: July 2018

MinIONQC provides rapid diagnostic plots and quality control data from one or more flowcells of sequencing data from Oxford Nanopore Technologies’ MinION instrument. It can be used to assist with the optimisation of extraction, library preparation, and sequencing protocols, to quickly and directly compare the data from many flowcells, and to provide publication-ready figures summarising sequencing data.

Availability and implementation

MinIONQC is implemented in R and released under an MIT license. It is available for all platforms from https://github.com/roblanf/minion_qc.
Musicians at the Cocktail Party: Neural Substrates of Musical Training During Selective Listening in Multispeaker Situations
Authors: Puschmann Sebastian , Baillet Sylvain , Zatorre Robert J
Published: July 2018

Musical training has been demonstrated to benefit speech-in-noise perception. It is however unknown whether this effect translates to selective listening in cocktail party situations, and if so what its neural basis might be. We investigated this question using magnetoencephalography-based speech envelope reconstruction and a sustained selective listening task, in which participants with varying amounts of musical training attended to 1 of 2 speech streams while detecting rare target words. Cortical frequency-following responses (FFR) and auditory working memory were additionally measured to dissociate musical training-related effects on low-level auditory processing versus higher cognitive function. Results show that the duration of musical training is associated with a reduced distracting effect of competing speech on target detection accuracy. Remarkably, more musical training was related to a robust neural tracking of both the to-be-attended and the to-be-ignored speech stream, up until late cortical processing stages. Musical training-related increases in FFR power were associated with a robust speech tracking in auditory sensory areas, whereas training-related differences in auditory working memory were linked to an increased representation of the to-be-ignored stream beyond auditory cortex. Our findings suggest that musically trained persons can use additional information about the distracting stream to limit interference by competing speech.
Characteristics of the healthcare information technology workforce in the HITECH era: underestimated in size, still growing, and adapting to advanced uses
Authors: Hersh William R , Boone Keith W , Totten Annette M
Published: July 2018

Objective

There is little readily available data about the size and characteristics of the healthcare information technology workforce. We sought to update a previous description of the size, growth, and characteristics of this workforce based on the Healthcare Information Management Systems Society (HIMSS) Analytics® Database, a resource that includes hospital size, number of beds, amount of staffing, and an eight-stage model of electronic health record adoption (Electronic Medical Record Adoption Model, EMRAM℠).

Materials and Methods

We updated an analysis done using a 2007 snapshot of the HIMSS Analytics Database with a comparable snapshot from 2014 in order to estimate the size of the current workforce and project future needs. For the 2014 data, we applied the same weighted average analysis used in 2007 to obtain a ratio of information technology (IT) hospital full-time equivalent (FTE) to staffed beds, extrapolate the results to all US hospitals, and project the workforce needs as hospitals achieve higher EMRAM stages.

Results

Our estimated size of the healthcare information technology workforce in the US in 2014 was 161 160, which was 8.0% larger than the estimate based on the 2007 data. Based on the new data, we project a potential need for an additional 19 852 and 153 114 FTE, if all hospitals were to achieve EMRAM Stages 6 and 7, respectively. The distribution of FTE across job function category varies by EMRAM stage.

Discussion and Conclusions

Although these data are limited, especially for EMRAM Stage 7, there is likely need for substantial workforce growth as hospitals increase their adoption of advanced healthcare information technology. Further research with data better focused on workforce characteristics will provide a better picture of staffing requirements.
Pitfalls in anaphylaxis
Authors: De Feo Giulia , Parente Roberta , Triggiani Massimo
Published: July 2018

Purpose of review

Anaphylaxis is an acute medical emergency characterized by sudden presentation of life-threatening respiratory and cardiovascular symptoms. Rapid diagnosis of anaphylaxis is crucial to implement an appropriate treatment and management plan. However, mistakes in the diagnosis of anaphylaxis may occur because of the limited time during which the diagnosis must be made, the stressful environment of the emergency room, the often aspecific or incomplete clinical features of early anaphylaxis and the lack of useful laboratory markers.

Recent findings

Several disorders may mimick anaphylaxis and cause wrong or delayed diagnosis increasing chances of fatal outcomes. In addition, certain clinical situations, like general anesthesia, may complicate detection of early signs of anaphylaxis. Drugs like beta-blockers, angiotensin converting enzyme-inhibitors, antihistamines or steroids may hide or blunt initial clinical manifestations of anaphylaxis.

A careful evaluation of clinical signs in all organs is mandatory to quickly establish and confirm a diagnosis of anaphylaxis. Alternative diagnosis should be considered, particularly in the case of unresponsive patients. Avoiding pitfalls in anaphylaxis diagnosis will help to establish rapidly effective treatments and would further reduce the rate of fatal events.
Increased Proportion of Fusion Surgery for Degenerative Lumbar Spondylolisthesis and Changes in Reoperation Rate
Authors: Kim Chi Heon , Chung Chun Kee , Choi Yunhee , Kim Min-Jung , Kim Myo Jeong , Shin Sukyoun , Yang Seung Heon , Hwang Sung Hwan , Kim Dong Hwan , Park Sung Bae , Lee Jun Ho
Published: July 2018

Study Design.

A retrospective cohort study.

Objective.

The objectives of the present study were to examine the changes in the number of surgeries, surgical methods selected, and reoperation rates between the years 2003 and 2008.

Summary of Background Data.

The selection of the appropriate surgical method between decompression-only (D) and decompression plus fusion (DF) represents a challenging clinical dilemma in patients with degenerative lumbar spinal spondylolisthesis. DF is selected in greater than 90% of patients, mostly due to the associated low reoperation rate. However, the outcomes of D have been improved with minimally invasive decompression surgery techniques.

Methods.

The Health Insurance Review and Assessment Service database was used to create cohorts of all Korean patients who underwent surgery for degenerative lumbar spinal spondylolisthesis in 2003 (2003 cohort, n = 5624) and 2008 (2008 cohort, n = 11,706). All patients were followed up for at least 5 years. Reoperation was defined as the occurrence of any type of second lumbar surgery during the follow-up period. The probabilities of reoperation were calculated using the Kaplan-Meier method.

Results.

The number of surgeries increased 2.08-fold in 2008. Patients older than 60 years comprised 38.6% of the 2003 cohort and 52.4% of the 2008 cohort. The proportion of DF surgery was 31.13% in the 2003 cohort but 91.54% in the 2008 cohort. However, the high proportion of fusion surgery failed to reduce the reoperation probability in the 2008 cohort (8.1%) compared with that in the 2003 cohort (6.2%). The cost of DF was US$5264 and that of D was $2719 in 2008. DF decreased the reoperation probability by 1% at the cost of $421/patient in the 2008 cohort.

Conclusion.

The increased proportion of fusion surgery without improvement in reoperation probability in an aging society may be cautiously addressed in deciding future health policies.

Level of Evidence: 4
Anterior Segment Changes After Femtosecond Laser-Assisted Implantation of a 355-Degree Intrastromal Corneal Ring Segment in Advanced Keratoconus
Authors: Abd Elaziz Mohamed Samy , El Saebay Sarhan Abdel Rahman , Ibrahim Asmaa Mohammed , Elshafy Haggag Haidy Abd
Published: July 2018

Purpose:

To study anterior segment changes after implantation of a Keraring with a 355-degree arc length in central advanced keratoconus.

Methods:

Thirty eyes of 22 patients with advanced central keratoconus (grade 3) and absent corneal scarring underwent femtosecond laser-assisted (VisuMax) implantation of a Keraring 355-degree arc length intrastromal corneal ring segment (ICRS) with a segment thickness of 300 μm. Comprehensive ocular evaluations were performed preoperatively and postoperatively to assess uncorrected distance visual acuity, corrected distance visual acuity, K1, K2, Kmax, corneal volume, anterior chamber depth, corneal elevations, and actual segment position 6 months after the procedure.

Results:

Corrected distance visual acuity in decimal notation improved significantly from 0.22 ± 0.17 to 0.49 ± 0.22 (P < 0.01). Statistically significant changes were found in the measured parameters with marked reconstruction of the cornea and anterior chamber. However, the actual depth percent of the ring segment was 61.7% ± 5.9%, which was shallower than the intended depth of 80% of corneal thickness.

Conclusions:

These findings may help explain the marked improvement in visual parameters obtained from the Keraring 355 degrees in advanced central keratoconus. In addition, these types of rings may be a safe, effective, and minimally invasive way to avoid corneal grafting in advanced keratoconus with a clear cornea.
High proportions of liver fibrosis and cirrhosis in an ageing population of people who use drugs in Amsterdam, The Netherlands
Authors: van Santen Daniëla K. , Schim van der Loeff Maarten F. , Cartier van Dissel Judith , Martens Jonie P.D. , van der Valk Marc , Prins Maria
Published: July 2018

Background

The incidence and prevalence of hepatitis C virus (HCV) infection among people who use drugs (PWUD) peaked in the 1980s in Amsterdam. As liver cirrhosis develops several decades after HCV infection and PWUD have other risk factors for liver fibrosis, we hypothesized that significant liver fibrosis or cirrhosis is now common among PWUD in Amsterdam.

Methods

PWUD were recruited from the Amsterdam Cohort Studies, methadone programmes and addiction clinics during 2009–2016. Transient elastography was performed to assess liver stiffness. We estimated METAVIR fibrosis levels on the basis of the following liver stiffness measurements (LSMs) cut-offs: F0–F2 (no/mild) less than 7.65 kPa; F2–F3 (moderate/severe) at least 7.65 to less than 13 kPa; and F4 (cirrhosis) at least 13 kPa. Using linear regression models, we assessed the association between LSM and sociodemographic, clinical and behavioural determinants in (a) all PWUD and (b) chronic hepatitis C virus (cHCV)-infected PWUD.

Results

For 140 PWUD, the median LSM was 7.6 kPa (interquartile range=4.9–12.0); 26.4% had moderate/severe fibrosis and 22.9% had cirrhosis. Of 104 chronically infected PWUD, 57.7% had evidence of significant fibrosis (≥F2). In multivariable analysis including all PWUD, increased LSM was associated significantly with cHCV monoinfection and HIV/HCV coinfection. In cHCV-infected PWUD, older age was associated significantly with increased LSM. In all groups, longer duration of heavy alcohol drinking was associated with increased LSM.

Conclusion

A high proportion of PWUD had significant fibrosis or cirrhosis that were associated with cHCV infection, HIV/HCV coinfection and duration of heavy alcohol drinking. Increased uptake of HCV treatment and interventions to reduce alcohol use are needed to decrease the liver disease burden in this population.
A Rare Cause of Pancytopenia in an Exclusively Breastfed Infant
Authors: Bobb-Semple Aisha A. , Lau Ching-See , Teruya-Feldstein Julie , Wistinghausen Birte
Published: July 2018

Vitamin B12 (B12) deficiency in infancy can present with nonspecific symptoms. We report a 5-month old exclusively breastfed full-term infant with emesis, lethargy, progressive pancytopenia, hemolysis, hypofibrinogenemia, elevated lactate dehydrogenase and a hypercellular bone marrow with dyserythropoiesis. The B12 level in the serum was undetectable. The infant’s lethargy resolved within 48 hours of intramuscular B12 injection, followed by rapid improvement of pancytopenia. The asymptomatic mother had a normal hemoglobin and mean corpuscular volume, but undetectable B12 level and positive antibodies to intrinsic factor, consistent with pernicious anemia masked by folate supplementation in the mother but causing symptoms in her infant.
Spatiotemporal Pattern of Gadodiamide-Related T1 Hyperintensity Increase Within the Deep Brain Nuclei
Authors: Marie Guillaume P.O. , Pozeg Polona , Meuli Reto A. , Maeder Philippe , Forget Joachim
Published: July 2018

Objectives

The purpose of the study was to systematically evaluate the precise spatial and temporal pattern of gadolinium-related changes in T1-weighted signal intensity on unenhanced magnetic resonance (MR) images, occurring in the deep brain nuclei of adult patients exposed to at least 10 consecutive doses of gadodiamide.

Materials and Methods

In this monocentric retrospective longitudinal study, we analyzed the brain MR images of 30 patients (12 women, 18 men; mean age, 43 ± 11.6 years) acquired between December 1998 and March 2008. We drew the regions of interest in the dentate nucleus, globus pallidus, putamen, pulvinar, ventral posterior nucleus of the thalamus, superior colliculus, substantia nigra, and white matter on unenhanced T1-weighted images. Each region of interest’s mean signal intensity was normalized by the mean intensity of the pons. The normalized signal intensities were measured at the baseline before first gadodiamide administration and at each of 10 successive MR imaging examinations. We used linear mixed effects models to analyze the data.

Results

We observed a significant linear increase of signal intensity ratios across 10 successive gadodiamide administrations (all basal nuclei were significant at P < 0.001, except the ventral posterior thalamus, where P < 0.05), with the fastest signal intensity increase in the dentate nucleus (B = 0.010), followed by the globus pallidus (B = 0.0068), putamen (B = 0.0063), pulvinar (B = 0.0062), superior colliculus (B = 0.0057), substantia nigra (B = 0.0034), and ventral posterior nucleus of the thalamus (B = 0.0031). No significant signal increase was observed in the white matter (P > 0.05).

Conclusions

Multiple consecutive administration of gadodiamide is associated with an increase in T1-weighted hypersignal on the unenhanced scans, displaying a gradual and nonuniform pattern across different deep brain nuclei, including the ventral posterior thalamus, which was used as a reference tissue in previous studies.
Interictal Epileptiform Discharge Detection in EEG in Different Practice Settings
Authors: Halford Jonathan J. , Westover M. Brandon , LaRoche Suzette M. , Macken Micheal P. , Kutluay Ekrem , Edwards Jonathan C. , Bonilha Leonardo , Kalamangalam Giridhar P. , Ding Kan , Hopp Jennifer L. , Arain Amir , Dawson Rachael A. , Martz Gabriel U. , Wolf Bethany J. , Waters Chad G. , Dean Brian C.
Published: July 2018

Objective:

The goal of the study was to measure the performance of academic and private practice (PP) neurologists in detecting interictal epileptiform discharges in routine scalp EEG recordings.

Methods:

Thirty-five EEG scorers (EEGers) participated (19 academic and 16 PP) and marked the location of ETs in 200 30-second EEG segments using a web-based EEG annotation system. All participants provided board certification status, years of Epilepsy Fellowship Training (EFT), and years in practice. The Persyst P13 automated IED detection algorithm was also run on the EEG segments for comparison.

Results:

Academic EEGers had an average of 1.66 years of EFT versus 0.50 years of EFT for PP EEGers (P < 0.0001) and had higher rates of board certification. Inter-rater agreement for the 35 EEGers was fair. There was higher performance for EEGers in academics, with at least 1.5 years of EFT, and with American Board of Clinical Neurophysiology and American Board of Psychiatry and Neurology-E specialty board certification. The Persyst P13 algorithm at its default setting (perception value = 0.4) did not perform as well at the EEGers, but at substantially higher perception value settings, the algorithm performed almost as well human experts.

Conclusions:

Inter-rater agreement among EEGers in both academic and PP settings varies considerably. Practice location, years of EFT, and board certification are associated with significantly higher performance for IED detection in routine scalp EEG. Continued medical education of PP neurologists and neurologists without EFT is needed to improve routine scalp EEG interpretation skills. The performance of automated detection algorithms is approaching that of human experts.
Retrotransposon-induced mosaicism in the neural genome
Authors: Bodea Gabriela O. , McKelvey Eleanor G. Z. , Faulkner Geoffrey J.
Published: July 2018

Over the past decade, major discoveries in retrotransposon biology have depicted the neural genome as a dynamic structure during life. In particular, the retrotransposon LINE-1 (L1) has been shown to be transcribed and mobilized in the brain. Retrotransposition in the developing brain, as well as during adult neurogenesis, provides a milieu in which neural diversity can arise. Dysregulation of retrotransposon activity may also contribute to neurological disease. Here, we review recent reports of retrotransposon activity in the brain, and discuss the temporal nature of retrotransposition and its regulation in neural cells in response to stimuli. We also put forward hypotheses regarding the significance of retrotransposons for brain development and neurological function, and consider the potential implications of this phenomenon for neuropsychiatric and neurodegenerative conditions.
Thermal effect on the compression coefficient of heavy oil reservoir rocks
Authors: Chao Zhang , Chuanliang Yan , Yuwen Liu , Yang Li , Yuanfang Cheng , Ji Tian
Published: July 2018

The ever-decreasing oil resources receive more and more attention for the exploration and development of heavy oil reservoirs. Owing to the high viscosity and poor fluidity of heavy oil, it is necessary to use the method of injecting high-temperature fluid in the development process. But, this will cause a significant increase in the temperature in oil reservoir, and thus the compression coefficient of reservoir rock has a greater impact. The compression coefficient of heavy oil reservoirs at different temperatures was tested. The results show that the compression coefficient of rock is closely related to the nature of rock itself and its stress and temperature environment: the compression coefficient increases with the increase in rock porosity; the compression coefficient decreases with the increase in the effective confining pressure and increases with the increase in temperature. When the temperature is low, the increase in the compression coefficient is larger. As the temperature increases, the increase in the compression coefficient tends to decrease gradually. Because the temperature of the reservoir is higher than that of the ground, the influence of the temperature on the reservoir compression coefficient should be taken into account when carrying out the production forecast.
Parental and offspring larval diets interact to influence life-history traits and infection with dengue virus inAedes aegypti
Authors: Zirbel Kylie , Eastmond Bradley , Alto Barry W.
Published: July 2018

The environmental conditions experienced by parents can influence offspring phenotype along with the conditions experienced by offspring. These parental effects are clear in organisms that display parental care and are less clear in other organisms. Here, we consider effects of parental and offspring larval nutrition on offspring development time, survivorship and infection with dengue virus inAedes aegypti, the mosquito vector of dengue, chikungunya, yellow fever and Zika. Parents were raised on either high or low larval detritus inputs with subsequent offspring being divided into two groups, one receiving high nutrients and the other low. Low nutrient females from low nutrient parents (LL) developed significantly slower than those from high nutrient parents (HL). Females from all parent by offspring nutrient treatment groups were equally likely to become infected with dengue virus at 24 h, 3 days and 14 days. After 14 days, high nutrient females from low nutrient parents (LH) had 11 times higher viral titres and more disseminated infections than high nutrient females from high nutrient parents (HH). These results suggest that carry-over environmental stress from the parental generation can influence life histories and arbovirus infection inAe. aegyptifemales. We found males to be robust to the life-history parameters measured, suggesting sex-specific differences which may relate to their lower nutrient requirements for metamorphosis.
Decomposing the effects of ocean environments on predator–prey body-size relationships in food webs
Authors: Dobashi Tomoya , Iida Midori , Takemoto Kazuhiro
Published: July 2018

Body-size relationships between predators and their prey are important in ecological studies because they reflect the structure and function of food webs. Inspired by studies on the impact of global warming on food webs, the effects of temperature on body-size relationships have been widely investigated; however, the impact of environmental factors on body-size relationships has not been fully evaluated because climate warming affects various ocean environments. Thus, here, we comprehensively investigated the effects of ocean environments and predator–prey body-size relationships by integrating a large-scale dataset of predator–prey body-size relationships in marine food webs with global oceanographic data. We showed that various oceanographic parameters influence prey size selection. In particular, oxygen concentration, primary production and salinity, in addition to temperature, significantly alter body-size relationships. Furthermore, we demonstrated that variability (seasonality) of ocean environments significantly affects body-size relationships. The effects of ocean environments on body-size relationships were generally remarkable for small body sizes, but were also significant for large body sizes and were relatively weak for intermediate body sizes, in the cases of temperature seasonality, oxygen concentration and salinity variability. These findings break down the complex effects of ocean environments on body-size relationships, advancing our understanding of how ocean environments influence the structure and functioning of food webs.
A Virus-Packageable CRISPR Screen Identifies Host Factors Mediating Interferon Inhibition of HIV
Authors: Ohainle Molly , Pendergast Louisa , Vermiere Jolien , Roesch Ferdinand , Humes Daryl , Basom Ryan , Delrow Jeffrey J. , Overbaugh Julie , Emerman Michael
Published: July 2018

Interferon (IFN) inhibits HIV replication by inducing an array of antiviral effectors. Here we describe a novel CRISPR knockout screening approach to identify the ensemble of these HIV restriction factors. We assembled a CRISPR sgRNA library specific for Interferon Stimulated Genes (ISGs) into a modified lentiviral vector that allows for packaging of sgRNA-encoding genomesin transinto budding HIV-1 particles. We observed that knockout of Zinc Antiviral Protein (ZAP) improved the performance of the screen due to ZAP-mediated inhibition of the vector. We identify a small panel of IFN-induced HIV restriction factors, including MxB, IFITM1, Tetherin/BST2 and TRIM5 which together explain the inhibitory effects of IFN on the HIV-1 LAI strain in THP-1 cells. Further, we identify novel HIV dependency factors, including SEC62 and TLR2. The ability of IFN-induced restriction factors to inhibit an HIV strain to replicate in human cells suggests that these human restriction factors are incompletely antagonized.
In vivo fate of free and encapsulated iron oxide nanoparticles after injection of labelled stem cells
Authors: Ashraf Sumaira , Taylor Arthur , Sharkey Jack , Barrow Michael , Murray Patricia , Wilm Bettina , Poptani Harish , Rosseinsky Matthew J. , Adams Dave , Lévy Raphaël
Published: July 2018

Nanoparticle contrast agents are useful tools to label stem cells and monitor the in vivo bio-distribution of labeled cells in pre-clinical models of disease. In this context, understanding the in vivo fate of the particles after injection of labelled cells is important for their eventual clinical use as well as for the interpretation of imaging results. We examined how the formulation of superparamagnetic iron oxide nanoparticles (SPIONs) impacts the labelling efficiency, magnetic characteristics and fate of the particles by comparing individual SPIONs with polyelectrolyte multilayer capsules containing SPIONs. At low labelling concentration, encapsulated SPIONs served as an efficient labelling agent for stem cells. The bio-distribution after intra-cardiac injection of labelled cells was monitored longitudinally by MRI and as an endpoint by inductively coupled plasma-optical emission spectrometry. The results suggest that, after being released from labelled cells after cell death, both formulations of particles are initially stored in liver and spleen and are not completely cleared from these organs 2 weeks post-injection.
γ-proteobacteria eject their polar flagella under nutrient depletion, retaining flagellar motor relic structures
Authors: Ferreira Josie L. , Gao Forson Z. , Rossmann Florian M. , Nans Andrea , Brenzinger Susanne , Hosseini Rohola , Briegel Ariane , Thormann Kai M. , Rosenthal Peter B. , Beeby Morgan
Published: July 2018

Bacteria switch only intermittently to motile planktonic lifestyles under favourable conditions. Under chronic nutrient deprivation, however, bacteria orchestrate a switch to stationary phase, conserving energy by altering metabolism and stopping motility. About two-thirds of bacteria use flagella to swim, but how bacteria deactivate this large-molecular machine remains poorly studied. Here we describe the previously unreported ejection of polar sodium-driven motors by γ-proteobacteria. We show that these bacteria eject their flagella at the base of the flagellar hook when nutrients are depleted, leaving a relic of a former flagellar motor in the outer membrane. Subtomogram averages of the full motor and relic reveal that this is an active process, as a plug protein appears in the relic, likely to prevent leakage across their outer membrane. We show that this is a widespread phenomenon demonstrated by the appearance of relic structures in varied γ-proteobacteria including Plesiomonas shigelloides, Vibrio cholerae, Vibrio fischeri, Shewanella putrefaciens and Pseudomonas aeruginosa.
Preservation of cellular nano-architecture by the process of chemical fixation for nanopathology
Authors: Zhou Xiang , Almassalha Luay , Li Yue , Eshein Adam , Cherkezyan Lusik , Viswanathan Parvathi , Subramanian Hariharan , Szleifer Igal , Backman Vadim
Published: July 2018

Transformation in chromatin organization is one of the most universal markers of carcinogenesis. Microscale chromatin alterations have been a staple of histopathological diagnosis of neoplasia, and nanoscale alterations have emerged as a promising marker for cancer prognostication and the detection of predysplastic changes. While numerous methods have been developed to detect these alterations, most methods for sample preparation remain largely validated via conventional microscopy, and have not been examined with nanoscale sensitive imaging techniques. For these nanoscale sensitive techniques to become standard of care screening tools, new histological protocols must be developed that preserve nanoscale information. Partial Wave Spectroscopic (PWS) microscopy has recently emerged as a novel imaging technique sensitive to length scales ranging between 20 and 200 nanometers. As a label-free, high-throughput, and non-invasive imaging technique, PWS microscopy offers many advantages for risk stratification of early cancer, and is an ideal tool to quantify structural information during sample preparation. Therefore, in this work we applied PWS microscopy to systematically evaluate the effects of cytological preparation on the nanoscales changes of chromatin using two cell line models: Hela cells differentially treated with daunorubicin and TP53 differentially mutated ovarian carcinoma cells. Notably, we show that existing cytological preparation can be modified in order to maintain clinically relevant nanoscopic differences, paving the way for the emerging field of nanopathology.
MHCSeqNet: A deep neural network model for universal MHC binding prediction
Authors: Phloyphisut Poomarin , Pornputtanapong Natapol , Sriswasdi Sira , Chuangsuwanich Ekapol
Published: July 2018

Immunotherapy is an emerging approach in cancer treatment that activates the host immune system to destroy cancer cells that express unique peptide signatures (neoepitopes). Administrations of cancer-specific neoepitopes in the form of synthetic peptide vaccine have been proven effective in both mouse models and human patients. Because only a tiny fraction of cancer-specific neoepitopes actually elicit immune response, selection of potent, immunogenic neoepitopes remains a challenging step in cancer vaccine development. A basic approach for immunogenicity prediction is based on the premise that effective neoepitope should bind with the Major Histocompatibility Complex (MHC) with high affinity. In this study, we developed MHCSeqNet, an open-source deep learning model, which not only competes favorably with state-of-the-art predictors but also exhibits promising generalization to new MHC class I and class II alleles. MHCSeqNet employed neural network architectures developed for natural language processing to model amino acid sequence representations of MHC allele and epitope peptide as sentences with amino acids as individual words. This consideration allows MHCSeqNet to accept new MHC alleles as well as peptides of any length. The flexibility offered by MHCSeqNet should make it a valuable tool for screening effective neoepitopes in cancer vaccine development.

Availability and implementation

https://github.com/cmbcu/MHCSeqNet
Using SMOG 2 to simulate complex biomolecular assemblies
Authors: Levi Mariana , Bandarkar Prasad , Yang Huan , Wang Ailun , Mohanty Udayan , Noel Jeffrey K. , Whitford Paul C.
Published: July 2018

Over the last 20 years, the application of structure-based (Gō-like) models has ranged from protein folding with coarse-grained models to all-atom representations of large-scale molecular assemblies. While there are many variants that may be employed, the common feature of these models is that some (or all) of the stabilizing energetic interactions are defined based on knowledge of a particular experimentally-obtained conformation. With the generality of this approach, there was a need for a versatile computational platform for designing and implementing this class of models. To this end, the SMOG 2 software package provides an easy-to-use interface, where the user has full control of the model parameters. This software allows the user to edit XML-formatted files in order to provide definitions of new structure-based models. SMOG 2 reads these “template” files and maps the interactions onto specific structures, which are provided in PDB format. The force field files produced by SMOG 2 may then be used to perform simulations with a variety of popular molecular dynamics suites. In this chapter, we describe some of the key features of the SMOG 2 package, while providing examples and strategies for applying these techniques to complex (often large-scale) molecular assemblies, such as the ribosome.
How fluorescent tags modify oligomer size distributions of the Alzheimer-peptide Aβ(1-40)
Authors: Wägele J. , De Sio S. , Voigt B. , Balbach J. , Ott M.
Published: July 2018

Within the complex aggregation process of Aβ-peptides into fibrils, oligomeric species, play a central role and reveal fundamental properties of the underlying mechanism of aggregation. In particular, low molecular weight aggregates have attracted increasing interest because of their role in cytotoxicity and neuronal apoptosis, typical of aggregation related diseases. One of the main techniques used to characterize such early stages of aggregation is fluorescence spectroscopy. To this end, Aβ-peptide chains are functionalized with fluorescent tags, often covalently bound to the disordered N-terminus region of the peptide, with the assumption that functionalization and presence of the fluorophore will not modify the process of self-assembly nor the final fibrillar structure. Up to date, experimental findings reveal size distributions of thermodynamically stable oligomers ranging from very narrow distributions of dimers to octamers, to very broad distributions up to 50-mers. In the present investigation we systematically study the effects of five of the most commonly used fluorophores on the aggregation of Aβ(1-40)-peptides. Time-resolved and single-molecule fluorescence spectroscopy have been chosen to monitor the oligomer populations at different fibrillation times, TEM, AFM and X-ray diffraction to investigate the structure of mature fibrils. While the structures of the mature fibrils were only slightly affected by the fluorescent tags, the sizes of the detected oligomeric species varied significantly depending on the chosen fluorophore. In particular, we relate the presence of high molecular weight oligomers (as found for the fluorophores HiLyte 647, Atto 647N and Atto 655) to net-attractive, hydrophobic fluorophore-peptide interactions, which are weak in the case of HiLyte 488, and Atto 488. The latter form low molecular weight oligomers only. Our findings reveal the potentially high impact of the properties of fluorophores on transient aggregates which needs to be included in the interpretation of experimental data of oligomers of fluorescently labeled peptides.
Corrective muscle activity reveals subject-specific sensorimotor recalibration
Authors: Iturralde Pablo A. , Torres-Oviedo Gelsy
Published: July 2018

Recent studies suggest that planned and corrective actions are recalibrated during some forms of motor adaptation. However, corrective (a.k.a., reactive) movements in human locomotion are thought to simply reflect sudden environmental changes independently from sensorimotor recalibration. Thus, we asked if corrective responses can indicate the motor system’s adapted state following prolonged exposure to a novel walking situation inducing sensorimotor adaptation. We recorded electromyographic signals bilaterally on 15 leg muscles before, during, and after split-belts walking (i.e., novel walking situation), in which the legs move at different speeds. We exploited the rapid temporal dynamics of corrective responses upon introduction or removal of an unexpected speed transition to isolate them from the overall motor output. We found that corrective muscle activity was structurally different following short vs. long exposures to split-belts walking. Only after a long exposure, removal of the novel environment elicited corrective muscle patterns that matched those expected in response to a perturbation opposite to the one originally experienced. This indicated that individuals who recalibrated their motor system adopted split-belts environment as their new “normal” and transitioning back to the original walking environment causes subjects to react as if it was novel to them. Interestingly, this learning declined with age, but steady state modulation of muscle activity during split-belts walking did not, suggesting potentially different neural mechanisms underlying these motor patterns. Taken together, our results show that corrective motor commands reflect the adapted state of the motor system, which is less flexible as we age.

Significance statement

We showed that corrective muscle activity elicited by sudden environmental transitions is revealing of the underlying recalibration process during sensorimotor adaptation. This allowed us to identify age-related decline in motor learning that was not discernible from kinematic measures conventionally used in motor adaptation studies. These findings suggest that older populations may have limited potential to correct their movements through error-based protocols simply given their age. Moreover, we describe the distinct motor patterns recruited during and after the split condition, informing our understanding of the therapeutic effect of this task. Therefore, our detailed EMG characterization provides valuable normative data of muscle activity that could be reinforced with repeated exposure of split-belts walking.
Cortical suppressive waves shape the representation of long-range apparent motion
Authors: Chemla S , Reynaud A , di Volo M , Zerlaut Y , Perrinet L , Destexhe A , Chavane F
Published: July 2018

How does the brain link visual stimuli across space and time? Visual illusions provide an experimental paradigm to study these processes. When two stationary dots are flashed in close spatial and temporal succession, human observers experience a percept of motion. Large spatio-temporal separation challenges the visual system to keep track of object identity along the apparent motion path. Here, we utilize voltage-sensitive dye imaging in primary visual cortex (V1) of the awake monkey to investigate whether intra-cortical connections within V1 can shape cortical dynamics to represent the illusory motion. We find that the arrival of the second stimulus in V1 creates a suppressive wave traveling toward the retinotopic representation of the first. Computational approaches show that this suppressive wave can be explained by recurrent gain control fed by the intra-cortical network and contributes to precisely encode the expected motion velocity. We suggest that non-linear intra-cortical dynamics preformat population responses in V1 for optimal read-out by downstream areas.