bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantum mechanical static dipole polarizabilities in the QM7b and AlphaML showcase databases
Authors: Yang Yang , Lao Ka Un , Wilkins David M. , Grisafi Andrea , Ceriotti Michele , DiStasio Robert A.
Published: August 2019

While density functional theory (DFT) is often an accurate and efficient methodology for evaluating molecular properties such as energies and multipole moments, this approach often yields larger errors for response properties such as the dipole polarizability (α), which describes the tendency of a molecule to form an induced dipole moment in the presence of an electric field. In this work, we provide static α tensors (and other molecular properties such as total energy components, dipole and quadrupole moments, etc.) computed using quantum chemical (QC) and DFT methodologies for all 7,211 molecules in the QM7b database. We also provide the same quantities for the 52 molecules in the AlphaML showcase database, which includes the DNA/RNA nucleobases, uncharged amino acids, several open-chain and cyclic carbohydrates, five popular pharmaceutical molecules, and 23 isomers of C8Hn. All QC calculations were performed using linear-response coupled-cluster theory including single and double excitations (LR-CCSD), a sophisticated approach for electron correlation, and the d-aug-cc-pVDZ basis set to mitigate basis set incompleteness error. DFT calculations employed the B3LYP and SCAN0 hybrid functionals, in conjunction with d-aug-cc-pVDZ (B3LYP and SCAN0) and d-aug-cc-pVTZ (B3LYP).
Analysis of the length polymorphisms in sequence-tagged-site sY1291 on Y chromosome in Vietnamese men of infertile couples
Authors: Cao Nguyen Thi Tai , Nguyen Kien Trung , Vu Nhuan Thi , Nguyen Vieng Chung , Trinh Thiet Minh , Nguyen Ngoc Thi Bich , Trinh Lien Thi Bich , Lam Tien Thi Thuy , Cao Binh Luong , Dang Tra Ngoc
Published: August 2019

This study aims to analyze the length polymorphisms in sequence-tagged-site (STS) sY1291 of the Y chromosome in Vietnamese men of infertile couples. All 322 DNA samples were amplified with the sY1291 primer by the quantitative fluorescent polymerase chain reaction (QF-PCR) assay. DNA sequencing technique was employed to evaluate the accuracy of QF-PCR results. The study showed 273 out of 322 DNA samples had the presence of STS sY1291, accounted for 84.78%. The QF-PCR results showed that there were various lengths in STS sY1291: 507 bp, 512 bp, 523 bp and 527 bp. The most prevalent length in STS sY1291 was 507 bp (87.5%), the others were 512 bp (4.8%), 523 bp (4.8%) and 527 bp (2.9%). We found that the observed length polymorphisms derived from differences in the number of mononucleotide Thymine (T) repeats in its structure. It stretched from 22 T to 39 T. DNA sequencing results identified that the number of mononucleotide T repeats causes these polymorphisms. However, the pair-wise alignment between the obtained and reference sequence was 77%. It can be seen that the length polymorphisms in STS sY1291 observed in QF-PCR results was accurate but it is still difficult to sequence fragments with mononucleotide repeats.
Effects of remote ischemic conditioning on kidney injury in at-risk patients undergoing elective coronary angiography (PREPARE study): a multicenter, randomized clinical trial
Authors: Roubille François , Macia Jean-Christophe , Ivanes Fabrice , Angoulvant Denis , Mateus Victor , Belle Loïc , Elbaz Meyer , Morel Olivier , Furber Alain , Bière Loïc , Prunier Fabrice
Published: August 2019

The ability of remote ischemic preconditioning (RIPC) to prevent contrast-induced nephropathy (CIN) following percutaneous coronary angiography in at-risk patients is controversial. No evidence exists regarding potential RIPC positive effects on renal function and clinical outcomes in the long-term. The PREPARE study was a randomized, prospective, multicenter, and double-blinded trial. A total of 222 patients scheduled for coronary angiography and/or percutaneous transluminal coronary angioplasty with an estimated glomerular filtration rate (eGFR) < 40 mL/min/1.73 m2, or eGFR between 40 and 60 mL/min/1.73 m2 and two further risk factors were allocated to RIPC or control groups. Preventive measures were applied to all patients, including continuous intravenous saline infusion, withdrawal of nephrotoxic drugs, and limited volume of contrast medium. The primary endpoint, namely incidence of CIN, was 3.8% in the control group and 5.1% in the RIPC group (p = 0.74). The secondary endpoints, i.e., changes in serum creatinine and eGFR levels from baseline to 48 hours and from baseline to 12 months following contrast medium exposure, did not differ between both groups. The incidences of all major clinical events at 12 months were similar in both groups. In this population at risk of CIN, preventive strategies were associated with low CIN incidence. RIPC impacted neither the CIN incidence nor both the renal function and clinical outcomes at 1-year follow-up.
Age-dependent carry-over effects in a long-distance migratory bird
Authors: López Calderón Cosme , Balbontín Arenas Javier , Hobson Keith A. , Møller Anders Pape
Published: August 2019

Migratory birds usually respond to climate change by modifying breeding and/or wintering areas, as well as by reproducing earlier. In addition, changes in winter habitat use or breeding phenology could have important carry-over effects on subsequent breeding success. Here, we studied age- and sex-dependent carry-over effects from wintering to the breeding stage of a small aerial insectivorous long-distance migratory bird, the barn swallows (Hirundo rustica) breeding in Denmark during 1984–2013. First, we used stable isotope analyses combined with ringing recoveries to identify wintering areas. Second, we found that environmental conditions as inferred by Normalized Difference Vegetation Index (NDVI) have improved at the wintering grounds. Third, we used confirmatory path analysis to quantify the indirect effect of winter conditions on subsequent breeding success. Males delayed onset of breeding and raised fewer fledglings in the first brood when ecological conditions during the previous winter improved. This response was age dependent, since yearlings did not respond to this environmental cue but the response was increasingly stronger as males aged. Females showed a similar response to winter conditions, although not statistically significant. These results highlight the importance of studying carry-over effects within the context of climate change, especially in relation to age of individuals.
A panoramic continuous compressive beamformer with cuboid microphone arrays
Authors: Yang Yang , Chu Zhigang , Yang Yong-Xin , Xu Zhongming , Zhang Yongxiang
Published: August 2019

Compressive beamforming is a powerful approach for the direction-of-arrival (DOA) estimation and strength quantification of acoustic sources. The conventional grid-based discrete compressive beamformer suffers from the basis mismatch conundrum. Its result degrades under the situation that sources fall off the grid. The existing continuous compressive beamformer with linear or planar microphone arrays can circumvent the conundrum, but work well only for sources in a local region. Here we develop a panoramic continuous compressive beamformer with cuboid microphone arrays based on an atomic norm minimization (ANM) and a matrix pencil and paring method. To solve the positive semidefinite programming equivalent to the ANM efficiently, we formulate a solving algorithm based on the alternating direction method of multipliers. We also present an iterative reweighted ANM to enhance sparsity and resolution. The beamformer is capable of estimating the DOAs and quantifying the strengths of acoustic sources panoramically and accurately, whether a standard uniform or a sparse cuboid microphone array is utilized.
The Influence Of Intrauterine Pressure On Embryo Retention In A Catheter After Embryo Transfer
Authors: Kozikowska Małgorzata , Grusza Miroslaw , Mrugacz Grzegorz , Gagan Jerzy , Zbucka-Krętowska Monika , Grygoruk Cezary
Published: August 2019

The retention of the embryo in the transfer catheter after embryo transfer (ET) during in vitro fertilization is a very common phenomenon, encountered by even the most experienced operators, and embryos retained in the transfer catheter or its sleeve require a repeat transfer. The exact mechanism of embryo retention has not been explained. Therefore, the present study aimed to investigate the mechanism of embryo retention in the catheter during embryo transfer by using a transparent uterus model equipped with pressure sensors and a video recorder. The results indicate that pressure changes in the uterine cavity during ET can influence the distribution of the transferred fluid containing the embryo. Under certain conditions, the transferred fluid can flow backward in the catheter, which may lead to retention of the embryo in the catheter.
Colletotrichum Species Associated with Japanese Plum (Prunus salicina) Anthracnose in South Korea
Authors: Hassan Oliul , Lee Yong Se , Chang Taehyun
Published: August 2019

A total of 24 Colletotrichum isolates were isolated from diseased Japanese plum (Prunus salicina) fruits showing chlorotic regions with whitish-brown sunken necrotic lesions and phylogenetic relationships among the collected Colletotrichum isolates were determined. A subset of 11 isolates was chosen for further taxonomic study based on morphology and molecular characteristics identified using the internal transcribed spacer (ITS) and beta-tubulin (TUB2) genes. Isolates in the C. acutatum complex were analyzed using partial sequencing of five gene regions (ITS, GAPDH, ACT, TUB2, and CHS), and C. gloeosporioides sensu lato (s.l.) isolates were analyzed using seven gene regions (ITS, TUB2, GAPDH, ACT, CAL, CHS-1, and ApMat). Morphological assessments in combination with phylogenetic analysis delineated four species of Colletotrichum including C. gloeosporioides sensu stricto (s.s.), C. nymphaeae, C. foriniae, and C. siamense; these data identify Colletotrichum fioriniae and C. siamense two new species associated with plum anthracnose in South Korea. Finally, the pathogenicity of these four species in the development of plum anthracnose in South Korea was confirmed by inoculations of plum fruit.
A flow through device for simultaneous dielectrophoretic cell trapping and AC electroporation
Authors: Punjiya Meera , Nejad Hojatollah Rezaei , Mathews Juanita , Levin Michael , Sonkusale Sameer
Published: August 2019

Isolation of cells and their transfection in a controlled manner is an integral step in cell biotechnology. Electric field approaches such as dielectrophoresis (DEP) offers a more viable method for targeted immobilization of cells without any labels. For transfection of cells to incorporate exogenous materials, electrical methods such as electroporation, are preferred over chemical and viral delivery methods since they minimally affect cell viability and can target many types. However prior approaches to both methods required multiple excitation sources, an AC source for DEP-based trapping and another DC source for electroporation. In this paper, we present a first of its kind flow through lab-on-chip platform using a single AC excitation source for combined trapping using negative dielectrophoresis (nDEP) and AC electroporation. Use of AC fields for electroporation eliminates the unwanted side effects of electrolysis or joule heating at electrodes compared to DC electroporation. Adjusting the flow rate and the electrical parameters of the incident AC field precisely controls the operation (trap, trap with electroporation and release). The platform has been validated through trapping and simultaneous transfection of HEK-293 embryonic kidney cells with a plasmid vector containing a fluorescent protein tag. Numerical scaling analysis is provided that indicates promise for individual cell trapping and electroporation using low voltage AC fields.
Contactless actuation of perfluorinated ionomer membranes in salt solution: an experimental investigation
Authors: Boldini Alain , Rosen Maxwell , Cha Youngsu , Porfiri Maurizio
Published: August 2019

A variety of modeling frameworks have been proposed for ionic polymer metal composites (IPMCs), but the physical underpinnings of their actuation remain elusive. A critical step toward the validation of existing theories and transition to engineering practice entails the design of new experimental paradigms that could support hypothesis-driven research. While several factors exacerbate the complexity of experimenting with IPMCs, the presence of the electrodes plays a major role by hindering the repeatability of the results and bringing a number of difficult-to-measure parameters into the picture. Here, we seek to address these experimental confounds by investigating contactless actuation of perfluorinated ionomer membranes in salt solution. In contrast to IPMCs that bend toward the anode in response to an applied voltage, ionomer membranes display a consistent deflection toward the cathode. Through hypothesis-driven experiments where the membrane width, solution concentration, and voltage applied across the electrodes are systematically varied, we elucidate electrochemistry and mechanics of contactless actuation. The applied voltage and solution concentration have a dominant role on the electrochemistry, while mechanics is mainly affected by the applied voltage and membrane width. Our results depict a complex scenario, which is expected to inform future theoretical inquiries about IPMC actuation.
Land Use Change Increases Wildlife Parasite Diversity in Anamalai Hills, Western Ghats, India
Authors: Chakraborty Debapriyo , Reddy Mahender , Tiwari Sunil , Umapathy Govindhaswamy
Published: August 2019

Anthropogenic landscape changes such as land use change and habitat fragmentation are known to alter wildlife diversity. Since host and parasite diversities are strongly connected, landscape changes are also likely to change wildlife parasite diversity with implication for wildlife health. However, research linking anthropogenic landscape change and wildlife parasite diversity is limited, especially comparing effects of land use change and habitat fragmentation, which often cooccur but may affect parasite diversity substantially differently. Here, we assessed how anthropogenic land use change (presence of plantation, livestock foraging and human settlement) and habitat fragmentation may change the gastrointestinal parasite diversity of wild mammalian host species (n = 23) in Anamalai hills, India. We found that presence of plantations, and potentially livestock, significantly increased parasite diversity due possibly to spillover of parasites from livestock to wildlife. However, effect of habitat fragmentation on parasite diversity was not significant. Together, our results showed how human activities may increase wildlife parasite diversity within human-dominated landscape and highlighted the complex pattern of parasite diversity distribution as a result of cooccurrence of multiple anthropogenic landscape changes.
The effect of preventive use of corticosteroids on postoperative complications after esophagectomy: A retrospective cohort study
Authors: Jeong Heejoon , Choi Ji Won , Ahn Hyun Joo , Choi Yong Soo , Kim Jie Ae , Yang Mikyung , Kim Jin Kyoung , Kim Duk Kyung , Shin Byung Seop , Lee Sang Hyun , Kim Young Ri , Park Mihye , Chung Yoon Joo
Published: August 2019

Corticosteroids have been empirically administered to reduce the rate of acute respiratory distress syndrome (ARDS) after esophagectomy. However, their efficacy remains controversial, and corticosteroids may increase the risk of graft dehiscence and infection, which are major concerns after esophagectomy. Therefore, we compared the incidence of composite complications (ARDS, graft dehiscence and infection) after esophagectomy between patients who received a preventive administration of corticosteroids and those who did not. All patients who underwent esophagectomy from 2010 to 2015 at a tertiary care university hospital were reviewed retrospectively (n = 980). Patients were divided into Steroid (n = 120) and Control (n = 860) groups based on the preventive administration of 100 mg hydrocortisone during surgery. The primary endpoint was the incidence of composite complications. The incidence of composite complications was not different between the Control and Steroid groups (17.4% vs. 21.7% respectively; P = 0.26). The incidence rates of complications in each category were not different between the Control and Steroid groups: ARDS (3.8% vs. 5.0%; P = 0.46), graft dehiscence (4.8% vs. 6.7%; P = 0.37), and infection (12.8% vs. 15.8%; P = 0.36). Propensity score matching revealed that composite complications (20.0% vs. 21.7%; P = 0.75), ARDS (4.3% vs. 5.2%; P = 0.76) and infection (16.5% vs. 15.7%; P = 0.86) were not different between the Control and Steroid group, but the incidence of graft dehiscence was higher in the Steroid group than in the Control group (0.9% vs. 7.0%; P = 0.0175). In conclusions, the preventive use of corticosteroids did not reduce the incidence of ARDS, but may be related to an increased incidence of graft dehiscence. Therefore, routine administration of corticosteroids to prevent ARDS is not recommended in esophagectomy.
Biomarkers for oralization during long-term proton pump inhibitor therapy predict survival in cirrhosis
Authors: Horvath Angela , Rainer Florian , Bashir Mina , Leber Bettina , Schmerboeck Bianca , Klymiuk Ingeborg , Groselj-Strele Andrea , Durdevic Marija , Freedberg Daniel E. , Abrams Julian A. , Fickert Peter , Stiegler Philipp , Stadlbauer Vanessa
Published: August 2019

Proton pump inhibitors (PPI) are an invaluable therapy option for acid related diseases; however, PPI therapy is also linked to a series of side effects in cirrhosis, such as microbiome alterations, spontaneous bacterial peritonitis and hepatic encephalopathy. Decision tools to balance benefits and risks of PPI therapy are largely missing. In this study, we tested gut-derived biomarkers to identify PPI-associated dysbiosis, its association with gut barrier function and liver-related mortality. In this observational study, faecal microbiome composition data obtained from 16S rDNA sequencing of 90 cirrhotic patients with and without long-term PPI use and additional potential biomarkers identified from the literature were evaluated for their predictive value regarding PPI-associated dysbiosis and liver-related three-year mortality. In addition, faecal calprotectin, faecal zonulin and serum lipopolysaccharides were assessed as markers for intestinal inflammation, gut permeability and bacterial translocation. Streptococcus salivarius, Veillonella parvula and the genus Streptococcus were significantly increased in patients with long-term PPI therapy and performed well as biomarkers for PPI-associated dysbiosis (accuracy: 74%, 72% and 74%, respectively). The abundance of Streptococcus salivarius was linked to intestinal inflammation and gut barrier dysfunction, whereas the abundance of Veillonella parvula showed associations with liver disease severity; both were independent predictors for liver-related three-year mortality. Gut-derived biomarkers of PPI-associated dysbiosis are linked to worse outcome and a potential option to evaluate the risks of adverse events during long-term PPI therapy.
A Tat/Rev Induced Limiting Dilution Assay to Measure Viral Reservoirs in Non-Human Primate Models of HIV Infection
Authors: Frank Ines , Acharya Arpan , Routhu Nanda K. , Aravantinou Meropi , Harper Justin L. , Maldonado Stephanie , Sole Cigoli Maria , Semova Stanka , Mazel Svetlana , Paiardini Mirko , Derby Nina , Byrareddy Siddappa N. , Martinelli Elena
Published: August 2019

The establishment of latent infection and poorly characterized viral reservoirs in tissues represent major obstacles to a definitive cure for HIV. Non-human primate (NHP) models of HIV infection are critical to elucidate pathogenic processes and an essential tool to test novel therapeutic strategies. Thus, the availability of novel assays to measure residual viral replication and reservoirs in NHP models may increase their utility in the search for an HIV cure. We developed a tat/rev induced limiting dilution assay to measure the frequency of CD4+ T cells that express multiply-spliced(ms)_SIV RNA in presence and absence of stimulation. We validated the assay using cell lines and cells from blood and lymph nodes of SIV infected macaques. In vitro, SIV/SHIV TILDA detects only cells expressing viral proteins. In SIV/SHIV-infected macaques, CD4+ T cells that express msSIV/SHIV RNA (TILDA data) were detected also in the setting of very low/undetectable viremia. TILDA data were significantly higher after stimulation and correlated with plasma viral load (pVL). Interestingly, TILDA data from early cART initiation correlated with peak and AUC pVL post-cART interruption. In summary, we developed an assay that may be useful in characterizing viral reservoirs and determining the effect of HIV interventions in NHP models.
Risk for pneumonia requiring hospitalization or emergency room visit according to delivery device for inhaled corticosteroid/long-acting beta-agonist in patients with chronic airway diseases as real-world evidence
Authors: Park Ju-Hee , Kim Yunjung , Choi Seongmi , Jang Eun Jin , Kim Jimin , Lee Chang-Hoon , Yim Jae-Joon , Yoon Ho-il , Kim Deog Kyeom
Published: August 2019

A fixed-dose combination of inhaled corticosteroid and long-acting beta agonist (ICS/LABA) may increase the risk of pneumonia in patients with chronic airway diseases including chronic obstructive pulmonary disease and asthma. Although lung deposition of ICS/LABA is dependent on the inhaler device and inhalation technique, there have been few studies comparing the risk for pneumonia according to the type of device used to deliver ICS/LABA in real-world practice. A retrospective cohort study was performed using the National Health Insurance Database of the Korean Health Insurance Review & Assessment Service. New users who began ICS/LABA were selected and followed-up 180 days after ICS/LABA initiation. The risk for pneumonia requiring emergency room (ER) visit or admission was compared according to inhaler device used—pressurized metered-dose inhaler (pMDI) or dry powder inhaler (DPI)—after individual exact matching (1:5). Among the eligible cohort of 245,477 new ICS/LABA users, 7,942 patients who used pMDI only were matched with 39,690 patients who used DPI only. The incidence of pneumonia was higher in the pMDI group (1.6%) than the DPI group (1.1%); the adjusted hazard ratio (HR) for pneumonia was 1.6 (95% CI 1.3–2.0; p < 0.0001). In subgroup analyses, a significantly higher risk for pneumonia was found in the pMDI group compared with the DPI group regardless of the presence of history of pneumonia (HR 1.7 [95% CI 1.2–2.3]; p = 0.002), COPD (HR 1.6 [95% CI 1.2–2.0]; p = 0.0007), or asthma (HR 1.6 [95% CI 1.2–2.2]; p = 0.0008). In analyses of real-world data, pMDI users incurred a higher risk for pneumonia requiring hospitalization or ER visit compared with DPI users.
Engineering a Polyspecific Pyrrolysyl-tRNA Synthetase by a High Throughput FACS Screen
Authors: Hohl Adrian , Karan Ram , Akal Anastassja , Renn Dominik , Liu Xuechao , Ghorpade Seema , Groll Michael , Rueping Magnus , Eppinger Jörg
Published: August 2019

The Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNAPyl are extensively used to add non-canonical amino acids (ncAAs) to the genetic code of bacterial and eukaryotic cells. However, new ncAAs often require a cumbersome de novo engineering process to generate an appropriate PylRS/tRNAPyl pair. We here report a strategy to predict a PylRS variant with novel properties. The designed polyspecific PylRS variant HpRS catalyzes the aminoacylation of 31 structurally diverse ncAAs bearing clickable, fluorinated, fluorescent, and for the first time biotinylated entities. Moreover, we demonstrated a site-specific and copper-free conjugation strategy of a nanobody by the incorporation of biotin. The design of polyspecific PylRS variants offers an attractive alternative to existing screening approaches and provides insights into the complex PylRS-substrate interactions.
The genetic relationship between female reproductive traits and six psychiatric disorders
Authors: Ni Guiyan , Amare Azmeraw T. , Zhou Xuan , Mills Natalie , Gratten Jacob , Lee S. Hong
Published: August 2019

Female reproductive behaviours have important implications for evolutionary fitness and health of offspring. Here we used the second release of UK Biobank data (N = 220,685) to evaluate the association between five female reproductive traits and polygenic risk scores (PRS) projected from genome-wide association study summary statistics of six psychiatric disorders (N = 429,178). We found that the PRS of attention-deficit/hyperactivity disorder (ADHD) were strongly associated with age at first birth (AFB) (genetic correlation of −0.68 ± 0.03), age at first sexual intercourse (AFS) (−0.56 ± 0.03), number of live births (NLB) (0.36 ± 0.04) and age at menopause (−0.27 ± 0.04). There were also robustly significant associations between the PRS of eating disorder (ED) and AFB (0.35 ± 0.06), ED and AFS (0.19 ± 0.06), major depressive disorder (MDD) and AFB (−0.27 ± 0.07), MDD and AFS (−0.27 ± 0.03) and schizophrenia and AFS (−0.10 ± 0.03). These associations were mostly explained by pleiotropic effects and there was little evidence of causal relationships. Our findings can potentially help improve reproductive health in women, hence better child outcomes. Our findings also lend partial support to the evolutionary hypothesis that causal mutations underlying psychiatric disorders have positive effects on reproductive success.
Intercomparing varied erosion, deposition and transport process representations for simulating sediment yield
Authors: Zi Tan , Kumar Mukesh , Albertson John
Published: August 2019

Over the past several decades there has been an enormous proliferation of sediment models, ranging from empirical to physically-based. Most of these models aim to capture the impacts of three primary sediment processes viz. erosion, deposition, and transport. As a range of process representations exist for simulating these three processes, it is natural to wonder about their influence on estimates of suspended sediment yield from a watershed. While several studies have focused on intercomparison of sediment models, their scopes have generally been restricted to comparing the individual model performances, rather than understanding the role of process representations on sediment model output. Here, six model configurations, which span the different permutations of erosion, deposition and transport process representations being used in extant models, are considered to evaluate the role of process representations on sediment yield estimates. The numerical experiments are designed to evaluate the extent to which the sediment dynamics as modeled by a physically-based model with coupled surface-subsurface hydrologic interactions are captured by simpler models. The presented work delineates the applicability and limitations of widely used representations of sediment processes, and could help users identify the pros and cons of using a sediment model at a given temporal scale.
Ocean acidification effects on in situ coral reef metabolism
Authors: Doo Steve S. , Edmunds Peter J. , Carpenter Robert C.
Published: August 2019

The Anthropocene climate has largely been defined by a rapid increase in atmospheric CO2,causing global climate change (warming) and ocean acidification (OA, a reduction in oceanic pH). OA is of particular concern for coral reefs, as the associated reduction in carbonate ion availability impairs biogenic calcification and promotes dissolution of carbonate substrata. While these trends ultimately affect ecosystem calcification, scaling experimental analyses of the response of organisms to OA to consider the response of ecosystems to OA has proved difficult. The benchmark of ecosystem-level experiments to study the effects of OA is provided through Free Ocean CO2Enrichment (FOCE), which we use in the present analyses for a 21-d experiment on the back reef of Mo’orea, French Polynesia. Two natural coral reef communities were incubatedin situ, with one exposed to ambient pCO2(393 µatm), and one to high pCO2(949 µatm). Our results show a decrease in 24-h net community calcification (NCC) under high pCO2, and a reduction in nighttime NCC that attenuated and eventually reversed over 21-d. This effect was not observed in daytime NCC, and it occurred without any effect of high pCO2on net community production (NCP). These results contribute to previous studies on ecosystem-level responses of coral reefs to the OA conditions projected for the end of the century, and they highlight potential attenuation of high pCO2effects on nighttime net community calcification.
Lyso-Gb3 modulates the gut microbiota and decreases butyrate production
Authors: Aguilera-Correa John-Jairo , Madrazo-Clemente Patricia , Martínez-Cuesta María del Carmen , Peláez Carmen , Ortiz Alberto , Sánchez-Niño María Dolores , Esteban Jaime , Requena Teresa
Published: August 2019

Fabry disease is a rare X-linked lysosomal storage disorder resulting from deficient activity of α-galactosidase A, leading to the accumulation of glycosphingolipids such as globotriaosylsphingosine (lyso-Gb3). The gastrointestinal symptoms of this disease may be disabling, and the life expectancy of affected patients is shortened by kidney and heart disease. Our hypothesis was that lyso-Gb3 may modify the gut microbiota. The impact of a clinically relevant concentration of lyso-Gb3 on mono- or multispecies bacterial biofilms were evaluated. A complex bacterial community from the simulated transverse colon microbiota was studied using quantitative PCR to estimate different bacterial group concentrations and a HPLC was used to estimate short-chain fatty acids concentrations. We found that lyso-Gb3 increased the biofilm-forming capacity of several individual bacteria, including Bacteroides fragilis and significantly increased the growth of B. fragilis in a multispecies biofilm. Lyso-Gb3 also modified the bacterial composition of the human colon microbiota suspension, increasing bacterial counts of B. fragilis, among others. Finally, lyso-Gb3 modified the formation of short-chain fatty acids, leading to a striking decrease in butyrate concentration. Lyso-Gb3 modifies the biology of gut bacteria, favoring the production of biofilms and altering the composition and short-chain fatty-acid profile of the gut microbiota.
Rodent mothers increase vigilance behaviour when facing infanticide risk
Authors: Breedveld Merel C. , Folkertsma Remco , Eccard Jana A.
Published: August 2019

Infanticide, the killing of unrelated young, is widespread and frequently driven by sexual conflict. Especially in mammals with exclusive maternal care, infanticide by males is common and females suffer fitness costs. Recognizing infanticide risk and adjusting offspring protection accordingly should therefore be adaptive in female mammals. Using a small mammal (Myodes glareolus) in outdoor enclosures, we investigated whether lactating mothers adjust offspring protection, and potential mate search behaviour, in response to different infanticide risk levels. We presented the scent of the litter’s sire or of a stranger male near the female’s nest, and observed female nest presence and movement by radiotracking. While both scents simulated a mating opportunity, they represented lower (sire) and higher (stranger) infanticide risk. Compared to the sire treatment, females in the stranger treatment left their nest more often, showed increased activity and stayed closer to the nest, suggesting offspring protection from outside the nest through elevated alertness and vigilance. Females with larger litters spent more time investigating scents and used more space in the sire but not in the stranger treatment. Thus, current investment size affected odour inspection and resource acquisition under higher risk. Adjusting nest protection and resource acquisition to infanticide risk could allow mothers to elicit appropriate (fitness-saving) counterstrategies, and thus, may be widespread.
Quantitative modeling of transcription and translation of an all-E. coli cell-free system
Authors: Marshall Ryan , Noireaux Vincent
Published: August 2019

Cell-free transcription-translation (TXTL) is expanding as a polyvalent experimental platform to engineer biological systems outside living organisms. As the number of TXTL applications and users is rapidly growing, some aspects of this technology could be better characterized to provide a broader description of its basic working mechanisms. In particular, developing simple quantitative biophysical models that grasp the different regimes of in vitro gene expression, using relevant kinetic constants and concentrations of molecular components, remains insufficiently examined. In this work, we present an ODE (Ordinary Differential Equation)-based model of the expression of a reporter gene in an all E. coli TXTL that we apply to a set of regulatory elements spanning several orders of magnitude in strengths, far beyond the T7 standard system used in most of the TXTL platforms. Several key biochemical constants are experimentally determined through fluorescence assays. The robustness of the model is tested against the experimental parameters, and limitations of TXTL resources are described. We establish quantitative references between the performance of E. coli and synthetic promoters and ribosome binding sites. The model and the data should be useful for the TXTL community interested either in gene network engineering or in biomanufacturing beyond the conventional platforms relying on phage transcription.
Regular exercise improves asthma control in adults: A randomized controlled trial
Authors: Jaakkola Jouni J. K. , Aalto Sirpa A. M. , Hernberg Samu , Kiihamäki Simo-Pekka , Jaakkola Maritta S.
Published: August 2019

We conducted a randomized controlled trial to test the hypothesis that a 24-week exercise intervention improves asthma control in adults. Adults with mild or moderate asthma were randomly assigned to either the exercise intervention group (IG) or the reference group (RG). Participants in IG received an individualized exercising program, including aerobic exercise at least three times a week for ≥30 minutes, muscle training, and stretching. The primary outcome was asthma control, measured by Asthma Control Test (ACT), asthma-related symptoms, and peak expiratory flow (PEF) variability. We estimated the risk (i.e. probability) of improvement in asthma control and the risk difference (RD) between IG and RG. Of 131 subjects (67 IG/64 RG) entered, 105 subjects (51/54) completed the trial (80%), and 89 (44/45) were analysed (68%). The ACT became better among 26 (62%) participants in IG and among 17 (39%) participants in RG. The effect of intervention on improving asthma control was 23% (RD = 0.23, 95% CI 0.027–0.438; P = 0.0320). The intervention also reduced shortness of breath by 30.1% (RD = 0.301, 95% CI 0.109–0.492; P = 0.003). The change in PEF variability was similar in both groups. Regular exercise improves asthma control measured by the ACT, while has little effect on PEF variability.
Efficacy of TIMOLOL nasal spray as a treatment for epistaxis in hereditary hemorrhagic telangiectasia. A double-blind, randomized, placebo-controlled trial
Authors: Dupuis-Girod Sophie , Pitiot Vincent , Bergerot Cyrille , Fargeton Anne-Emmanuelle , Beaudoin Marjolaine , Decullier Evelyne , Bréant Valentine , Colombet Bettina , Philouze Pierre , Faure Frédéric , Letievant Jean-Charles
Published: August 2019

Hereditary hemorrhagic telangiectasia is a rare vascular genetic disease. Epistaxis is the most frequent and disabling manifestation, and timolol appears to be a new therapeutic option as non-selective beta-blockers have in vitro and in vivo anti-angiogenic properties. Our main objective was to evaluate the efficacy of TIMOLOL nasal spray as a treatment for epistaxis in hereditary hemorrhagic telangiectasia. This study is a single-center, randomized, phase 2, double-blind placebo-controlled study with an allocation ratio of 1:1. It was proposed to patients with hereditary hemorrhagic telangiectasia monitored at the French Reference Center, and we included patients aged over 18 years, diagnosed with hereditary hemorrhagic telangiectasia and epistaxis. The treatment was self-administered by the patient with a posology of one spray (50 µL) of timolol 0.5% or placebo in each nostril twice a day for 28 consecutive days. The primary efficacy endpoint was mean monthly epistaxis duration, assessed by monitoring epistaxis grids. A total of 58 patients were randomized and treated. The baseline characteristics were similar in the 2 groups. Mean monthly epistaxis duration measured at 3 months was not significantly different in the 26 patients receiving the drug in comparison with the placebo group (p = 0.54). Toxicity was low and no severe adverse events were reported. One limitation is that we included all HHT patients with nosebleeds and did not take into account history of nasal surgery or nasal crusts. Timolol, administered by nasal spray at a dose of 0.25 mg in each nostril twice a day for 28 consecutive days, did not improve epistaxis in patients with hereditary hemorrhagic telangiectasia at 4 months after the beginning of the treatment.
Role of S2− ions on the microstructure change and the pitting behaviour of aluminum in saline solution
Authors: EL-Deeb Mohamed M.
Published: August 2019

The electrochemical behaviour and the passive film microstructure of aluminum during its exposure to 3.5 wt% NaCl solution in the absence and presence of S2−ions are investigated using potentiodynamic polarization curves, electrochemical impedance spectroscopy measurements, XRD, XRF, SEM and AFM. Electrochemical measurements show that the presence of S2−ions enhances the uniform corrosion of aluminum in NaCl solution, but delay its susceptibility to the pitting corrosion. In addition, EIS analysis illustrate that the formation of more compact and protective passive layer in the presence of S2−ions compared to its rough surface in the absence of S2−ions as evidenced by the lower value of constant phase element (CPE) and higher value of phase shift (N). Cracks, non- homogenous and open large pits with high degree of roughness are clearly observed on the aluminum surface in the absence of S2−ions, compared to oriented grooves, elongated ridges with the accumulation of the corrosion products inside the pits in the presence of S2−ions. The inhibitory effect of S2−ions for the pitting corrosion of aluminum is interpreted on the basis of the change in its microstructure of the passive film in the absence and presence of S2−ions.
Evaluation of the effects of humic acids on maize root architecture by label-free proteomics analysis
Authors: Nunes Rosane Oliveira , Domiciano Giselli Abrahão , Alves Wilber Sousa , Melo Ana Claudia Amaral , Nogueira Fábio Cesar Sousa , Canellas Luciano Pasqualoto , Olivares Fábio Lopes , Zingali Russolina Benedeta , Soares Márcia Regina
Published: August 2019

Humic substances have been widely used as plant growth promoters to improve the yield of agricultural crops. However, the mechanisms underlying this effect remain unclear. Root soluble protein profiles in plants 11 days after planting and cultivated with and without humic acids (HA, 50 mg CL−1), were analyzed using the label-free quantitative proteomic approach. Cultivation of maize with HA resulted in higher fresh weight of roots than in untreated plants (control). Plants treated with HA showed increased number, diameter and length of roots. In the proteomics analysis, differences were detected in the following categories: energy metabolism, cytoskeleton, cellular transport, conformation and degradation of proteins, and DNA replication. Thirty-four proteins were significantly more abundant in the seedlings treated with HA, whereas only nine proteins were abundant in the control. The effects on root architecture, such as the induction of lateral roots and biomass increase were accompanied by changes in the energy metabolism-associated proteins. The results show that the main effect of HA is protective, mainly associated with increased expression of the 2-cys peroxidase, putative VHS/GAT, and glutathione proteins. Indeed, these proteins had the highest fold-difference. Overall, these results improve our understanding of the molecular mechanisms of HA-promoted plant growth.
Physiological responses of Goji berry (Lycium barbarum L.) to saline-alkaline soil from Qinghai region, China
Authors: Zhang Zhenzhong , He Kangning , Zhang Tan , Tang Da , Li Runjie , Jia Shaofeng
Published: August 2019

Recently, Goji berry (Lycium barbarum L.) has been extensively cultivated to improve the fragile ecological environment and increase the income of residents in Qinghai Province, northwestern China. However, few studies have focused on the physiological responses of Goji berry under salt stress and alkali stress. Gas exchange, photosynthetic pigments, and chlorophyll fluorescence were evaluated in response to neutral (NaCl) and alkali (NaHCO3) salt stresses. Nine irrigation treatments were applied over 30 days and included 0(Control group), 50, 100, 200, and 300 mM NaCl and NaHCO3. The results showed that salt and alkali stress reduced all the indicators and that alkali stress was more harmful to Goji berry than salt stress under the same solution concentrations. The salt tolerance and alkali resistance thresholds were identified when the index value exceeded the 50% standard of the control group, and threshold values of 246.3 ± 2.9 mM and 108.4.7 ± 2.1 mM, respectively, were determined by regression analysis. These results were used to identify the optimal water content for Goji berry. The minimum soil water content to cultivate Goji berry should be 16.22% and 23.37% under mild and moderate salt stress soils, respectively, and 29.10% and 42.68% under mild and moderate alkali stress soil, respectively.
Ephrin-A5 potentiates netrin-1 axon guidance by enhancing Neogenin availability
Authors: Croteau L.-P. , Kao T.-J. , Kania A.
Published: August 2019

Axonal growth cones are guided by molecular cues in the extracellular environment. The mechanisms of combinatorial integration of guidance signals at the growth cone cell membrane are still being unravelled. Limb-innervating axons of vertebrate spinal lateral motor column (LMC) neurons are attracted to netrin-1 via its receptor, Neogenin, and are repelled from ephrin-A5 through its receptor EphA4. The presence of both cues elicits synergistic guidance of LMC axons, but the mechanism of this effect remains unknown. Using fluorescence immunohistochemistry, we show that ephrin-A5 increases LMC growth cone Neogenin protein levels and netrin-1 binding. This effect is enhanced by overexpressing EphA4 and is inhibited by blocking ephrin-A5-EphA4 binding. These effects have a functional consequence on LMC growth cone responses since bath addition of ephrin-A5 increases the responsiveness of LMC axons to netrin-1. Surprisingly, the overexpression of EphA4 lacking its cytoplasmic tail, also enhances Neogenin levels at the growth cone and potentiates LMC axon preference for growth on netrin-1. Since netrins and ephrins participate in a wide variety of biological processes, the enhancement of netrin-1 signalling by ephrins may have broad implications.
Comparison of the effects of an ERAS program and a single-port laparoscopic surgery on postoperative outcomes of colon cancer patients
Authors: Kim Min Ki , Kim Jun-Gi , Lee Gyeora , Won Daeyoun David , Lee Yoon Suk , Kye Bong-Hyeon , Kim Jihoon , Lee In Kyu
Published: August 2019

Advancement of the surgical modality and perioperative care are the two main dimensions for the modern improvement of surgical outcome. The purpose of this study was to compare the effectiveness of the two by using the data from the single-port laparoscopic surgery and the early recovery after surgery (ERAS) program. Patients who underwent elective surgery for primary adenocarcinoma of the colon were divided into three groups and compared: ERAS (multi-port laparoscopic surgery with ERAS perioperative care), Conventional-SILS (single-port surgery with conventional perioperative care), or Conventional-Multi (multi-port laparoscopic surgery with conventional perioperative care). Ninety-one, 83, and 96 patients were registered, respectively. There were no differences among the three groups in baseline characteristics except pathological stage and operation site in colon. Although the ERAS group started a soft diet earlier and had earlier discharge, there were no differences in intra- and post-operative morbidity rate, readmission rate, or reoperation rate. The ERAS perioperative care was a significant factor for reducing length of hospital stay in the multivariate analysis, while single-port surgery was not. In modern laparoscopic colon cancer treatment, a systemic approach such as the ERAS program appears to be more effective than a technical approach for significantly improving short-term surgical outcomes.
Evaluation of antigenic differences between wild and Sabin vaccine strains of poliovirus using the pseudovirus neutralization test
Authors: Arita Minetaro , Iwai-Itamochi Masae
Published: August 2019

In the endgame of global polio eradication, serosurveillance is essential to monitor each country’s vulnerability to poliomyelitis outbreaks. Previously, we developed pseudovirus poliovirus (PV) neutralization test (pPNT) with type 1, 2, and 3 PV pseudovirus (PVpv), which possess a luciferase-encoding PV replicon in the capsids of wild-type strains (PVpv[WT]), showing that pPNT with type 2 and 3 PVpv(WT) but not type 1 shows high correlation with the conventional PV neutralization test (cPNT) performed with vaccine strains. Here, we analyse the antigenicity of PVpv(WT) and PVpv with capsid proteins of Sabin vaccine strains (PVpv[Sabin]) in human serum. Type 2 and 3 PVpv(WT) and PVpv(Sabin) show similar antigenicity in the analysed set of human sera in contrast to type 1 PVpv. The levels of PVpv(Sabin) infection (%), including about 70% of PVpv infection (%) measured in the presence of human serum diluted to the cPNT titre, serve as the optimal threshold values for pPNT (5% for type 1 and 2, 10% for type 3) to show high correlation with cPNT results. Our results suggest that pPNT with PVpv(Sabin) could serve as an alternative to cPNT and provide a rationale for pPNT threshold values.
Serum Vitamin D Level Does not Affect The Sensitivity of Parathyroid Adenoma Localization Tests
Authors: Sencar Muhammed Erkam , Sakiz Davut , Unsal Ilknur Ozturk , Hepsen Sema , Calapkulu Murat , Gumus Pelin , Ucan Bekir , Ozbek Mustafa , Cakal Erman
Published: August 2019

The aim of the present study was to evaluate the predictive value of 25-hydroxyvitamin D, calcium and parathormone level, co-existence of thyroid nodule, thyroidectomy history and adenoma volume on the success of neck ultrasound (US) and technetium-99m sestamibi (MIBI) scan in primary hyperparathyroidism (PHP) patients. This study included 256 patients with PHP who underwent parathyroidectomy. 169 (%66) patients had vitamin D deficiency and 56 (%22) of patients had insufficiency. The sensitivity of US and MIBI studies showed no difference between vitamin D deficiency, insufficiency and replete groups (%80.5, %82 and %71 (p > 0.05) and %81, %84 and %71 respectively (p > 0.05)). Vitamin D level was not found to be an independent predictor of localization on either US or MIBI scan after adjusting for different variables (p > 0.05). Calcium level was found to be an independent predictor for US sensitivity (r2:0,033, p:0,032) and parathormone level for MIBI sensitivity (r2:0,05, p:0,025). The co-existence of nodular thyroid disease and history of thyroidectomy significantly decreased the sensitivity of US (%76 and %43). MIBI sensitivity was not impaired by nodular disease but the history of thyroidectomy also impaired the sensitivity of MIBI (%43). As a result vitamin D level does not affect the sensitivity of preoperative localization tests.