bluuebunny/crossref_metadata_2025 huggingface dataset:
Esophageal collateral veins in predicting esophageal variceal recurrence and rebleeding after endoscopic treatment: a systematic review and meta-analysis
Authors: Li Qian-Qian , Li Hong-Yu , Bai Zhao-Hui , Philips Cyriac Abby , Guo Xiao-Zhong , Qi Xing-Shun
Published: January 2020

Background

Endoscopic treatment is recommended for the management of esophageal varices. However, variceal recurrence or rebleeding is common after endoscopic variceal eradication. Our study aimed to systematically evaluate the prevalence of esophageal collateral veins (ECVs) and the association of ECVs with recurrence of esophageal varices or rebleeding from esophageal varices after endoscopic treatment.

Methods

We searched the relevant literature through the PubMed, EMBASE, and Cochrane Library databases. Prevalence of paraesophageal veins (para-EVs), periesophageal veins (peri-EVs), and perforating veins (PVs) were pooled. Risk ratio (RR) and odds ratio (OR) with 95% confidence intervals (CIs) were calculated for cohort studies and case–control studies, respectively. A random-effects model was employed. Heterogeneity among studies was calculated.

Results

Among the 532 retrieved papers, 28 were included. The pooled prevalence of para-EVs, peri-EVs, and PVs in patients with esophageal varices was 73%, 88%, and 54%, respectively. The pooled prevalence of para-EVs and PVs in patients with recurrence of esophageal varices was 87% and 62%, respectively. The risk for recurrence of esophageal varices was significantly increased in patients with PVs (OR = 9.79, 95% CI: 1.95–49.22, P = 0.006 for eight case–control studies), but not in those with para-EVs (OR = 4.26, 95% CI: 0.38–38.35, P = 0.24 for four case–control studies; RR = 1.81, 95% CI: 0.83–3.97, P = 0.14 for three cohort studies). Patients with para-EVs had a significantly higher incidence of rebleeding from esophageal varices (RR = 13.00, 95% CI: 2.43–69.56, P = 0.003 for two cohort studies). Statistically significant heterogeneity was notable across the meta-analyses.

Conclusions

ECVs are common in patients with esophageal varices. Identification of ECVs could be helpful for predicting the recurrence of esophageal varices or rebleeding from esophageal varices after endoscopic treatment.
Health promotion program for office workers with SEM based on the WHO’s healthy workplace framework
Authors: Ryu Hosihn , Jung Jiyeon , Moon Jihyun
Published: January 2020

This study attempts to develop and verify the effectiveness of a health promotion program for office workers based on the social ecological model and the World Health Organization’s Healthy Workplace Framework. This study involved 272 office workers of a small and medium-sized enterprise in Korea. Data were analyzed through descriptive statistics, repeated measures analysis of variance (ANOVA) and Bonferroni correction using SPSS/WIN 23.0. Workplace environmental support was provided to all workers, while a 6-month intensive core program based on social support was implemented for the intensive management group. Based on the participation rate, individuals were divided into the core and dropout groups. In all office workers, there were negative changes in high-density lipoprotein cholesterol and job stress during the period. Meanwhile, the intensive group showed significant changes in body mass index and diastolic blood pressure. The study suggests that the organization’s support for a healthy environment and an individual’s continued participation based on social support are essential for the effectiveness of a health promotion program for office workers.
Using NS1 Flavivirus Protein Microarray to Infer Past Infecting Dengue Virus Serotype and Number of Past Dengue Virus Infections in Vietnamese Individuals
Authors: Thao Tran Thi Nhu , de Bruin Erwin , Phuong Huynh Thi , Thao Vy Nguyen Ha , van den Ham Henk-Jan , Wills Bridget A , Tien Nguyen Thi Hanh , Le Duyen Huynh Thi , Trung Dinh The , Whitehead Stephen S , Boni Maciej F , Koopmans Marion , Clapham Hannah E
Published: January 2020

Background

In recent years, researchers have had an increased focus on multiplex microarray assays, in which antibodies are measured against multiple related antigens, for use in seroepidemiological studies to infer past transmission.

Methods

We assess the performance of a flavivirus microarray assay for determining past dengue virus (DENV) infection history in a dengue-endemic setting, Vietnam. We tested the microarray on samples from 1 and 6 months postinfection from DENV-infected patients (infecting serotype was determined using reverse-transcription polymerase chain reaction during acute, past primary, and secondary infection assessed using plaque reduction neutralization tests 6 months postinfection).

Results

Binomial models developed to discriminate past primary from secondary infection using the protein microarray (PMA) titers had high area under the curve (0.90–0.97) and accuracy (0.84–0.86). Multinomial models developed to identify most recent past infecting serotype using PMA titers performed well in those with past primary infection (average test set: κ = 0.85, accuracy of 0.92) but not those with past secondary infection (κ = 0.24, accuracy of 0.45).

Conclusions

Our results suggest that the microarray will be useful in seroepidemiological studies aimed at classifying the past infection history of individuals (past primary vs secondary and serotype of past primary infections) and thus inferring past transmission intensity of DENV in dengue-endemic settings. Future work to validate these models should be undertaken in different transmission settings and with samples later after infection.
Evaluation of Genotypic Antiviral Resistance Testing as an Alternative to Phenotypic Testing in a Patient with DOCK8 Deficiency and Severe HSV-1 Disease
Authors: Casto Amanda M , Stout Sean C , Selvarangan Rangaraj , Freeman Alexandra F , Newell Brandon D , Stahl Erin D , Ahmed Atif A , Greninger Alexander L , Yin Dwight E
Published: January 2020

Antiviral resistance frequently complicates the treatment of herpes simplex virus (HSV) infections in immunocompromised patients. Here we present the case of an adolescent boy with dedicator of cytokinesis 8 (DOCK8) deficiency, who experienced recurrent infections with resistant HSV-1. We used both phenotypic and genotypic methodologies to characterize the resistance profile of HSV-1 in the patient and conclude that genotypic testing outperformed phenotypic testing. We also present the first analysis of intrahost HSV-1 evolution in an immunocompromised patient. While HSV-1 can remain static in an immunocompetent individual for decades, the virus from this patient rapidly acquired genetic changes throughout its genome. Finally, we document a likely case of transmitted resistance in HSV-1 between the patient and his brother, who also has DOCK8 deficiency. This event demonstrates that resistant HSV-1 is transmissible among immunocompromised persons.
Characterization of drug resistance and the defective HIV reservoir in virally suppressed vertically infected children in Mali
Authors: Brice Josephine , Sylla Mariam , Desire Nathalie , Sayon Sophie , Telly Fatoumata , Bocar-Fofana Djeneba , Murphy Robert , Peytavin Gilles , Diallo Souleymane , Nastouli Eleni , Calvez Vincent , Marcelin Anne-Geneviève , Maiga Almoustapha Issiaka , Lambert-Niclot Sidonie
Published: January 2020

Background

In the perspective of ART-free HIV remission, vertically infected children treated with suppressive ART from early infancy represent an optimal population model to better understand the genetic complexity of the reservoir.

Objectives

To evaluate the proportion of defective viral population and the genotypic resistance patterns in cell-associated HIV DNA.

Methods

In a cohort including 93 ART-treated vertically HIV-infected (VHIV) children in Mali with plasma HIV-1 RNA ≤50 copies/mL for at least 6 months, we studied total HIV DNA, percentage of defective genomes and resistance by reverse transcriptase and protease bulk sequencing from whole blood in dried blood spots.

Results

Children had a median age of 9.9 years at the time of inclusion (IQR = 7.6–13.4) and 3.3 years (IQR = 2–7) at ART initiation; median ART duration was 5.5 years (IQR = 3.7–7.3). The median level of total HIV DNA was 470 copies/106 cells with one patient presenting undetectable HIV DNA (<66 copies/106 cells). We observed the presence of at least one stop codon in viruses from 34 patients (37%). The presence of stop codons was not correlated with the level of HIV DNA or duration of ART. We showed a high prevalence of HIV-1 resistance in DNA with 26% of children harbouring virus resistant to at least one NRTI and 40% to at least one NNRTI.

Conclusions

While these VHIV children were successfully treated for a long time, they showed high prevalence of resistance in HIV DNA and a moderate defective HIV reservoir.
Leaf hydraulic conductance is linked to leaf symmetry in bifacial, amphistomatic leaves of sunflower
Authors: Richardson Freya , Jordan Gregory J , Brodribb Timothy J
Published: January 2020

The hydraulic implications of stomatal positioning across leaf surfaces and the impact on internal water flow through amphistomatic leaves are not currently well understood. Amphistomaty potentially provides hydraulic efficiencies if the majority of hydraulic resistance in the leaf exists outside the xylem in the mesophyll. Such a scenario would mean that the same xylem network could equally supply a hypostomatic or amphistomatic leaf. Here we examine leaves of Helianthus annuus to determine whether amphistomaty in this species is associated with higher hydraulic efficiency compared with hypostomatic leaves. We identified asymmetry in the positioning of minor veins which were significantly closer to the abaxial than the adaxial leaf surface, combined with lower Kleaf when transpiration was driven through the adaxial rather than the abaxial surface. We also identified a degree of coordination in stomatal behaviour driven by leaf hydraulics, where the hydraulic conditions experienced by an individual leaf surface affected the stomatal behaviour on the opposite surface. We found no advantage to amphistomaty based on efficiencies in construction costs of the venous system, represented by vein density:stomatal density, only limited hydraulic independence between leaf surfaces. These results suggest that amphistomaty does not substantially increase whole-leaf hydraulic efficiency.
‘I felt like the mountains were coming for me.’—The role of place attachment and local lifestyle opportunities for labour migrants’ staying aspirations in two Norwegian rural municipalities
Authors: Lynnebakke Brit
Published: January 2020

This article discusses two relatively underexplored topics in international migration research: place attachment processes and staying intentions in the new place of residence. The analysis is based on findings from semi-structured interviews with internal and international labour migrants in two rural Norwegian municipalities. In a study that primarily focused on migrants’ local social inclusion and belonging processes, several migrants on their own initiative brought up and elaborated on the importance of local material aspects (nature, climate, and localisation) and lifestyle options for their local contentment and staying aspirations. The interviewee accounts suggest that numerous factors can influence staying intentions, including social ties, work/career opportunities, local materiality, and lifestyle opportunities. By focusing on processes of place attachment, the findings bring to light some of the mechanisms that may lay behind the common proposition within international migration research that length of residence makes return less likely. The findings on these processes highlight how local contentment—and by extension staying aspirations—can change over time, thereby connecting the usually separated fields of migration and post-migration processes. Moreover, the findings show how local place attachment may also influence international migrants’ aspirations/decisions of internal migration within the new country of residence. Finally, the centrality of lifestyle for staying aspirations and place attachment in these labour migrants’ accounts underline a call by lifestyle migration researchers for increased attention to the role of lifestyle in all kinds of migration. The article’s conclusion notes the findings’ relevance also for urban settings.
Failures of Halofit model for computation of Fisher matrices: a response function analysis
Authors: Reimberg P , Bernardeau F , Nishimichi T , Rizzato M
Published: January 2020

The response function of a linear system undergoing a non-linear transformation measures the sensitivity of the non-linear output with respect to the initial linear state. This concept can also be applied to the non-linear growth of structures in the Universe. In this paper, we study the response function for the Halofit model, we present its analytic structure and we compare its theoretical prediction with the one as measured from simulations. We find a major departure between the two. We argue that a consequence of unmatched response functions is an intrinsic theoretical limitation on Halofit to predict the derivatives of the non-linear power spectrum with respect to cosmological parameters, and hence a possible systematic effect on Fisher matrices based forecasts using Halofit. In particular, we use a simple cosmological model with two parameters (As, ns) to illustrate the impact of using Halofit for this kind of forecasts for a 1 h−3 Gpc3 volume survey. We report a maximum impact on the figure of merit of $20{{\ \rm per\ cent}}$.
The stellar photosphere–hydrogen ionization front interaction in classical pulsators: a theoretical explanation for observed period–colour relations
Authors: Das Susmita , Kanbur Shashi M , Bellinger Earl P , Bhardwaj Anupam , Singh Harinder P , Meerdink Brett , Proietti Nicholas , Chalmers Anthony , Jordan Ryan
Published: January 2020

Period–colour and amplitude–colour (PCAC) relations can be used to probe both the hydrodynamics of outer envelope structure and evolutionary status of Cepheids and RR Lyraes. In this work, we incorporate the PCAC relations for RR Lyraes, BL Her, W Vir, and classical Cepheids in a single unifying theory that involves the interaction of the hydrogen ionization front (HIF) and stellar photosphere and the theory of stellar evolution. PC relations for RR Lyraes and classical Cepheids using the Optical Gravitational Lensing Experiment (OGLE-IV) data are found to be consistent with this theory: RR Lyraes have shallow/sloped relations at minimum/maximum light, whilst long-period (P > 10 d) Cepheids exhibit sloped/flat PC relations at minimum/maximum light. The differences in the PC relations for Cepheids and RR Lyraes can be explained based on the relative location of the HIF and stellar photosphere which changes depending on their position on the Hertzsprung–Russell diagram. We also extend our analysis of PCAC relations for type II Cepheids in the Galactic bulge, Large and Small Magellanic Clouds using OGLE-IV data. We find that BL Her stars have sloped PC relations at maximum and minimum light similar to short-period (P < 10 d) classical Cepheids. W Vir stars exhibit sloped/flat PC relation at minimum/maximum light similar to long-period classical Cepheids. We also compute state-of-the-art 1D radiation hydrodynamic models of RR Lyraes, BL Her and classical Cepheids using the radial stellar pulsation code in mesa to further test these ideas theoretically and find that the models are generally consistent with this picture. We are thus able to explain PC relations at maximum and minimum light across a broad spectrum of variable star types.
Significance levels of common frequencies extracted from multiple data sets
Authors: Koen Chris
Published: January 2020

Large monitoring campaigns, particularly those using multiple filters, have produced replicated time series of observations for literally millions of stars. The search for periodicities in such replicated data can be facilitated by comparing the periodograms of the various time series. In particular, frequency spectra can be searched for common peaks. The sensitivity of this procedure to various parameters (e.g. the time base of the data, length of the frequency interval searched, number of replicate series, etc.) is explored. Two additional statistics that could sharpen results are also discussed: the closeness (in frequency) of peaks identified as common to all data sets, and the sum of the ranks of the peaks. Analytical expressions for the distributions of these two statistics are presented. The method is illustrated by showing that a ‘dubious’ periodicity in an 'Asteroid Terrestrial-impact Last Alert System' data set is highly significant.
The spectral evolution of disc dominated tidal disruption events
Authors: Mummery Andrew , Balbus Steven A
Published: January 2020

We perform a detailed numerical and analytical study of the properties of observed light curves from relativistic thin discs, focussing on observational bands most appropriate for comparison with tidal disruption events (TDEs). We make use of asymptotic expansion techniques applied to the spectral emission integral, using time-dependent disc temperature profiles appropriate for solutions of the relativistic thin disc equation. Rather than a power law associated with bolometric disc emission L ∼ t−n, the observed X-ray flux from disc-dominated TDEs will typically have the form of a power law multiplied by an exponential (see equation 91). While precise details are somewhat dependent on the nature of the ISCO stress and disc-observer orientational angle, the general form of the time-dependent flux is robust and insensitive to the exact disc temperature profile. We present numerical fits to the UV and X-ray light curves of ASASSN-14li, a particularly well observed TDE. This modelling incorporates strong gravity optics. The full 900 d of ASASSN-14li X-ray observations are very well fit by a simple relativistic disc model, significantly improving upon previous work. The same underlying model also fits the final 1000 d of ASASSN-14li observations in three different UV bandpasses. Finally, we demonstrate that the analytic formulae reproduce the properties of full numerical modelling at both UV and X-ray wavelengths with great fidelity.
NGC 6712: the variable star population of a tidally disrupted globular cluster
Authors: Deras D , Arellano Ferro A , Lázaro C , Bustos Fierro I H , Calderón J H , Muneer S , Giridhar Sunetra
Published: January 2020

We present an analysis of ${VI}$ CCD time-series photometry of globular cluster NGC 6712. Our main goal is to study the variable star population as indicators of the cluster mean physical parameters. We employed the Fourier decomposition of RR Lyrae light curves to confirm that ${}[\rm Fe/H]_{UVES} = -1.0 \pm 0.05$ is a solid estimate. We estimated the reddening to the cluster as E(B − V) = 0.35 ± 0.04 from the RRab stars colour curves. The distance to the cluster was estimated using three independent methods which yielded a weighted mean distance  = 8.1 ± 0.2 kpc. The distribution of RRab and RRc stars on the horizontal branch shows a clear segregation around the first overtone red edge of the instability strip, which seems to be a common feature in OoI-type cluster with a very red horizontal branch. We carried out a membership analysis of 60 447 stars in our field of view (FoV) using the data from Gaia-DR2 and found 1529 likely members; we possess the light curves of 1100 among the member stars. This allowed us to produce a clean colour–magnitude diagram, consistent with an age of 12 Gyr, and enabled us to discover close unresolved contaminants for several variable stars. From the proper motion analysis, we found evidence of non-member stars in the FoV of the cluster being tidally affected by the gravitational pull of the bulge of the Galaxy. We found that the RRab variable V6, shows a previously undetected Blazhko effect. Finally, we report 16 new variables of the EW-type (9) and SR-type (7).
Stellar properties of the host galaxy of an ultraluminous X-ray source in NGC 5252
Authors: Kim Minjin , López Kristhell M , Jonker Peter G , Ho Luis C , Im Myungshin
Published: January 2020

An ultraluminous X-ray source (ULX) in NGC 5252 has been known as a strong candidate for an off-nuclear intermediate-mass black hole (IMBH). We present near-infrared imaging data of the ULX obtained with the William Herschel Telescope. Using this data we estimate a stellar mass associated with the ULX of ≈107.9 ± 0.1$\, \mathrm{M}_\odot$, suggesting that it could be (the remnant of) a dwarf galaxy that is in the process of merging with NGC 5252. Based on a correlation between the mass of the central black hole (BH) and host galaxy, the ULX is powered by a 105 $\, \mathrm{M}_\odot$ BH. Alternatively, if the BH mass is ≈106$\, \mathrm{M}_\odot$ or larger, the host galaxy of the ULX must have been heavily stripped during the merger. The ULX Ks-band luminosity is two orders of magnitude smaller than that expected from an ordinary active galactic nucleus with the observed [O iii] luminosity, which also suggests the ULX lacks a dusty torus. We discuss how these findings provide suggestive evidence that the ULX is hosting an IMBH.
Placement of C1 Lateral Mass Screw—Alternative Technique: 2-Dimensional Operative Video
Authors: Jha R Tushar , Dietz Nicholas , Dowlati Ehsan , Sandhu Faheem
Published: January 2020

This operative video demonstrates a C1 lateral mass instrumentation technique that is an alternative to the traditional Goel and Harms techniques.
1,2
The advantages of the alternative technique include minimized blood loss from the rich venous plexus surrounding the C2 dorsal root ganglia (DRG), avoidance and preservation of the C2 DRG, and placement of a robust fully threaded screw without risking neuralgia. These are discussed in detail and presented through a case of atlantoaxial instability. Patient's consent was obtained for creating this surgical video. The patient is a 50-yr-old woman with a 17-yr history of rheumatoid arthritis. She presented with 1 yr of neck pain that failed conservative measures. Flexion-extension radiographs demonstrated an atlantodental index (ADI) that reduced from 7 mm on flexion to 0 mm on extension. The patient underwent a C1-C2 posterior instrumented fusion using the alternative technique of C1 lateral mass instrumentation.
2
The steps of this technique are explained in great detail through a microsurgical video. The patient's postoperative course was uneventful. Postoperative radiographs and computed tomography (CT) scan demonstrated reduction of ADI and well-placed instrumentation and fusion construct. Her neck pain was completely resolved by 3 mo following surgical stabilization. In the senior author's experience with placing over 120 C1 lateral mass screws with this alternative technique, there have been no instances of vascular injury, sacrifice of C2 DRG, or instrumentation failure. The alternative technique for placement of C1 lateral mass screw is safe, efficient, and holds certain advantages in comparison to the traditionally described method.

 Images within the video have been reproduced from AOSpine section of the AO Surgery Reference, www.aosurgery.org, with permission from AO Surgery. Copyright by AOSpine International, Switzerland; and reprinted from World Neurosurgery, 78(1-2), Kang MM et al, C2 Nerve Root Sectioning in Posterior C1-2 Instrumented Fusions, 170-177, Copyright 2012, with permission from Elsevier.
Left Occipital Craniotomy for Resection of Arteriovenous Malformation: 2-Dimensional Operative Video
Authors: Hendricks Benjamin K , Spetzler Robert F
Published: January 2020

Medial parieto-occipital arteriovenous malformations (AVMs) are fed by distal cortical posterior cerebral artery branches and are generally considered eloquent given the proximity to the calcarine fissure and paracentral lobule. This patient was a neurologically intact 12-yr-old girl with an incidentally discovered left occipital AVM. The patient underwent preoperative angiographic evaluation with embolization of a dominant posterior cerebral artery feeding vessel. The AVM was removed in the standard manner using circumdissection. Indocyanine green angiography was utilized to demonstrate disconnection of the AVM before sacrificing the draining veins. The AVM was removed entirely, as evidenced on postoperative angiography. The patient had a partial right hemianopsia after the operation but was otherwise neurologically intact. The patient gave informed consent for surgery and video recording. Institutional review board approval was deemed unnecessary. Used with permission from Barrow Neurological Institute, Phoenix, Arizona.
Endoscopic Paramedian Sitting Craniotomy for Resection of a Dorsal Midbrain Cavernous Malformation: 2-Dimensional Operative Video
Authors: Choudhri Omar A , Glauser Gregory , Abdullah Kalil G , Lee John Y K
Published: January 2020

This case video demonstrates the surgical technique for resection of a cavernous malformation in the right dorsal midbrain. This video was deemed exempt by the University of Pennsylvania Institutional Review Board (IRB), as it is considered a case report, which does not require IRB approval or patient consent. The patient was a 57-yr-old male with cerebral cavernous malformation syndrome with multiple intracranial cavernomas. He was noticed to have progressively slowed speech with worsening confusion and drowsiness. On exam, the patient exhibited worsening in swallowing and upward gaze paresis, secondary to Parinaud phenomena. The patient was treated with microsurgical resection, utilizing stereotactic navigation and intraoperative neurophysiologic monitoring. Intraoperative view provided in the video was captured using a Karl Storz Endoscope (Karl Storz SE & Co KG, Tuttlingen, Germany). Postoperatively, the patient had worsening double vision, which improved on follow-up, in addition to improvement in sensorium and swallowing.
LEVELS OF EXPOSURE TO IONIZING RADIATION AMONG THE PERSONNEL ENGAGED IN CYCLOTRON OPERATION AND THE PERSONNEL ENGAGED IN THE PRODUCTION OF RADIOPHARMACEUTICALS, BASED ON RADIATION MONITORING SYSTEM
Authors: Biegała Michał , Jakubowska Teresa
Published: January 2020

This paper aims to determine the levels of exposure to neutron and photon radiation among the personnel engaged in cyclotron operation and the personnel engaged in the production of radiopharmaceuticals, with the use of the environmental radiation monitoring system (RMS) installed in the positron emission tomography laboratory. The annual exposures of employees operating the cyclotron measured with the use of the RMS system are: 1.39 ± 0.16 mSv in case of photon radiation and 2.61 ± 0.14 mSv in case of neutron radiation. In the case of employees in the radiopharmaceuticals’ production zone, the annual exposures measured by means of the RMS system are 0.15 ± 0.03 mSv in case of photon radiation and 0.11 ± 0.01 mSv in case of neutron radiation. The exposure levels among the personnel engaged in cyclotron operation and the personnel engaged in the production of radiopharmaceuticals are below the permissible radiation dose limits.
Puteibacter caeruleilacunae gen. nov., sp. nov., a facultatively anaerobic bacterium isolated from Yongle Blue Hole in the South China Sea
Authors: Sun Wen , Fu Tianyu , Jia Chao , Fu Liang , Zhou Shun , Yao Peng , Gao Xueyu , Liu Lijun , Yang Zuosheng , Shi Xiaochong , Zhang Xiao-Hua
Published: January 2020

Blue holes are unique geomorphological units characterized by steep redox and biogeochemical gradients. Yongle Blue Hole is located on the largest atoll (Yongle Atoll) of the western Xisha Islands in the South China Sea. A Gram-stain-negative, facultatively anaerobic, non-motile, non-flagellated marine bacterium with creamy white colonies, designated JC036T, was isolated from Yongle Blue Hole. Cells were short-rod-shaped and catalase-negative. 16S rRNA gene sequence analysis showed that sequence similarities were lower than 91.6 % against all validly named species in the familyProlixibacteraceae; a reconstructed phylogenetic tree indicated that strain JC036Tformed a lineage with strains in the familyProlixibacteraceae. Growth occurred at 4–37 °C (optimum, 28 °C), at pH 5.0–9.0 (optimum, 7.0) and in the presence of 2–6 % (w/v) NaCl (optimum, 3 %). The prevalent isoprenoid quinone of strain JC036Twas menaquinone-7 (MK-7). Iso-C15 : 0and iso-C17 : 03-OH were the predominant fatty acids. The major polar lipids included a phospholipid, phosphatidylethanolamine, an aminophospholipid and four unidentified lipids. The genomic DNA G+C content of strain JC036Twas 37.8 mol%. Based on physiological and biochemical characteristics and whole genome comparisons, we propose a new genus and species,Puteibacter caeruleilacunaegen. nov., sp. nov., within the familyProlixibacteraceae. The type strain ofPuteibacter caeruleilacunaeis JC036T(=JCM 33128T=MCCC 1K03579T). From this study, a deeper understanding of the community of the microorganism and their roles in biogeochemical cycles, especially anaerobic bacteria, is provided.
The language network reemerges during recovery from severe traumatic brain injury
Authors: Coffey Brian J. , Threlkeld Zachary D. , Bodien Yelena G. , Edlow Brian L.
Published: January 2020

Regaining the ability to express and understand language is a key milestone for patients recovering from severe traumatic brain injury (TBI). However, the neurobiological correlates of language recovery after TBI have not been identified. We explored whether recovery of language in patients with acute severe TBI is associated with functional MRI (fMRI) changes within and outside the canonical language network (i.e. bilateral superior temporal gyri [STG] and inferior frontal gyri [IFG]). We consecutively enrolled 16 adult patients with acute severe TBI and performed fMRI assessment using a spoken language stimulus in the intensive care unit. Eight patients, all of whom recovered language function, returned for follow-up fMRI at median [interquartile range] 220.5 [189-473.5] days post-injury. Sixteen age- and sex-matched healthy subjects also completed the fMRI paradigm. Language function was behaviorally assessed immediately before fMRI using the Coma Recovery Scale-Revised and components of the Confusion Assessment Protocol. At follow-up, patients also completed the California Verbal Learning Test-II. We compared acute and follow-up fMRI responses by calculating mean Z-scores of suprathreshold voxels in bilateral STG and IFG regions-of-interest (ROI). We also performed a whole-brain analysis. Significant longitudinal increases to language stimuli were found in the left STG but not the right STG, left IFG, or right IFG. Whole-brain analysis revealed longitudinal changes in the right supramarginal and middle temporal gyri, regions known to be involved in language processing. Both acute and follow-up fMRI responses in patients were indistinguishable from those of healthy subjects at a stringent statistical threshold of Z ≥ 3.1. At lower statistical thresholds (e.g. Z ≥ 2.1) patients assessed acutely demonstrated decreased fMRI responses in right STG and IFG compared to healthy subjects. Collectively, these results provide initial evidence that responses in bihemispheric language-processing regions of cerebral cortex reemerge with recovery of language function in patients with severe TBI.
Therapeutic use of blood products for the treatment of autoimmune hemolytic anemia: A network meta-analysis protocol
Authors: Deng Jiawen
Published: January 2020

Autoimmune hemolytic anemia is a rare blood disorder that can result in anemic hypoxia. Currently, red blood cell (RBC) transfusion is the only effective method of treating this condition. We propose a network meta-analysis that investigates whether the use of different types of blood products (e.g. suspended RBC, leukoreduced RBC, washed RBC, etc.) can decrease adverse events, increase the rate of remission and improve lab results, including hemoglobin, RBC, reticulocyte counts, hematocrit and total bilirubin.
Uses of pathogen detection data to estimate vaccine direct effects in case-control studies
Authors: Lewnard Joseph A.
Published: January 2020

The diagnosis of infectious disease syndromes such as fever, diarrhea, and pneumonia is complicated by the potential for shedding or carriage of putatively etiologic pathogens among individuals experiencing symptoms due to other causes. Symptomatic individuals among whom a pathogen is detected, but whose symptoms are caused by other factors, may be misclassified by diagnostic criteria based on pathogen detection. Case-control studies are commonly undertaken to estimate vaccine effectiveness, and present an opportunity to compare pathogen detection among individuals with and without clinically-relevant symptoms. Considering this study context, we derive simple estimators for the direct effects of vaccination on various aspects of host susceptibility. These include protection against acquisition of the pathogen of interest, and protection against progression of this pathogen to disease following acquisition. We assess the impact of test sensitivity on these estimators, and extend our framework to identify a “vaccine probe” estimator for pathogen-specific etiologic fractions. We also derive biases affecting vaccine effectiveness estimates under the test-negative design, an alternative approach using similar data. Our results provide strategies for estimation of pathogen-specific vaccine effectiveness in the absence a diagnostic gold standard. These approaches can inform the design and analysis of studies addressing numerous pathogens and vaccines.
Effect of nitrogen on fungal growth efficiency
Authors: Di Lonardo D.P. , van der Wal A. , Harkes P. , de Boer W.
Published: January 2020

The contribution of fungi to carbon (C) and nitrogen (N) cycling is related to their growth efficiency (amount of biomass produced per unit of substrate utilized). The concentration and availability of N influences the activity and growth efficiency of saprotrophic fungi. When N is scarce in soils, fungi have to invest more energy to obtain soil N, which could result in lower growth efficiencies. Yet, the effect of N on growth efficiencies of individual species of fungi in soil has not been studied extensively. In this study we investigated the influence of different concentrations of mineral N on the growth efficiency of two common soil fungi, Trichoderma harzanium and Mucor hiemalis in a soil-like environment. We hypothesized that a higher N availability will coincide with higher biomass production and growth efficiency. To test this, we measured fungal biomass production as well as the respiration fluxes in sand microcosms amended with cellobiose and mineral N at different C:N ratios. We found that for both fungal species lower C:N ratios resulted in the highest biomass production as well as the highest growth efficiency. This may imply that when N is applied concurrently with a degradable C source, a higher amount of N will be temporarily immobilized into fungal biomass.
Tyrosine phosphorylation is critical for ACLY activity in lipid metabolism and cancer
Authors: Basappa Johnvesly , ElAzzouny Mahmoud A. , Rolland Delphine C.M. , Sahasrabuddhe Anagh A. , Ma Kaiyu , Bazilevsky Gleb A. , Hwang Steven R. , Basrur Venkatesha , Conlon Kevin P. , Bailey Nathanael G. , Frederiksen John K. , Schnell Santiago , Zhou Yeqiao , Cookmeyer David , Pawlicki Jan M. , Amin Amit Dipak , Riley James L. , Faryabi Robert B. , Schatz Jonathan H , Wellen Kathryn E. , Marmorstein Ronen , Burant Charles F. , Elenitoba-Johnson Kojo S.J. , Lim Megan S.
Published: January 2020

A fundamental requirement for growth of rapidly proliferating cells is metabolic adaptation to promote synthesis of biomass1. ATP citrate lyase (ACLY) is a critical enzyme responsible for synthesis of cytosolic acetyl-CoA, the key building component forde novofatty acid synthesis and links vital pathways such as carbohydrate and lipid metabolism2. The mechanisms of ACLY regulation are not completely understood and the regulation of ACLY function by tyrosine phosphorylation is unknown. Here we show using mass-spectrometry-driven phosphoproteomics and metabolomics that ACLY is phosphorylated and functionally regulated at an evolutionary conserved residue, Y682. Physiologic signals promoting rapid cell growth such as epidermal growth factor stimulation in epithelial cells and T-cell receptor activation in primary human T-cells result in rapid phosphorylation of ACLY at Y682.In vitrokinase assays demonstrate that Y682 is directly phosphorylated by multiple tyrosine kinases, including ALK, ROS1, SRC, JAK2 and LTK. Oncogenically activating structural alterations such as gene-fusions, amplification or point mutations of ALK tyrosine kinase result in constitutive phosphorylation of ACLY in diverse forms of primary human cancer such as lung cancer, anaplastic large cell lymphoma (ALCL) and neuroblastoma. Expression of a phosphorylation-defective ACLY-Y682F mutant in NPM-ALK+ ALCL decreases ACLY activity and attenuates lipid synthesis. Metabolomic analyses reveal that ACLY-Y682F expression results in increased β-oxidation of13C-oleic acid-labeled fatty acid with increased labeling of +2-citrate (p<0.01) and +18-oleyol carnitine (p<0.001). Similarly, oxygen consumption rate (OCR) is significantly increased in cells expressing ACLY-Y682F (p<0.001). Moreover, expression of ACLY-Y682F dramatically decreases cell proliferation, impairs clonogenicity and abrogates tumor growthin vivo. Our results reveal a novel mechanism for direct ACLY regulation that is subverted by multiple oncogenically-activated tyrosine kinases in diverse human cancers. These findings have significant implications for novel therapies targeting ACLY in cancer and metabolism.
Neural oscillations track the maintenance and proceduralization of novel instructions
Authors: Formica Silvia , González-García Carlos , Senoussi Mehdi , Brass Marcel
Published: January 2020

Humans are capable of flexibly converting symbolic instructions into novel behaviors. Previous evidence and theoretical models suggest that the implementation of a novel instruction requires the reformatting of its declarative content into an action-oriented code optimized for the execution of the instructed behavior. While neuroimaging research focused on identifying the brain areas involved in such a process, the temporal and electrophysiological mechanisms remain poorly understood. These mechanisms, however, can provide information about the specific cognitive processes that characterize the proceduralization of information. In the present study, we recorded EEG activity while we asked participants to either simply maintain declaratively the content of novel S-R mappings or to proactively prepare for their implementation. By means of time-frequency analyses, we isolated the oscillatory features specific to the proceduralization of instructions. Implementation of the instructed mappings elicited stronger theta activity over frontal electrodes and suppression in mu and beta activity over central electrodes. On the contrary, activity in the alpha band, which has been shown to track the attentional deployment to task-relevant items, showed no differences between tasks. Together, these results support the idea that proceduralization of information is characterized by specific component processes such as orchestrating complex task settings and configuring the motor system that are not observed when instructions are held in a declarative format.

Highlights

Frontal theta power is increased during instructions implementation

Attentional orienting in WM is analogous across maintenance and implementation

Instructions implementation involves motor recruitment
Urban colonization is driven by a mixture of evolutionarily conserved and labile traits
Authors: Duchene David A. , Pardo-Diaz Carolina , Iglesias-Carrasco Maider
Published: January 2020

Urbanization is a fast and dramatic transformation of habitat that generally forces native fauna into novel ecological challenges. The biological prerequisites necessary to establish in urban areas have been widely studied, but the macroevolutionary characteristics of traits that allow urban colonization remain poorly understood. Urban colonization might be facilitated by traits that are evolutionarily conserved and which lead to a diversity of closely related species. Alternatively, urban colonization might be associated with labile traits that frequently arise and are lost. In a large data set from passerine birds, we find that urban colonization has a signal of highly labile traits, despite many traits associated with colonization being highly conserved. Urban colonization is associated with traits that allow faster speciation than non-urban-colonizing counterparts, and more frequently transition to non-urban trait states than in the opposite direction. Overall, the traits that facilitate urban colonization are a mix of highly conserved and labile traits and appear to provide an evolutionarily successful strategy.
Underground deserts below fertility islands? – Woody species desiccate lower soil layers in sandy drylands
Authors: Tolgyesi Csaba , Torok Peter , Habenczyus Alida Anna , Batory Zoltan , Orsolya Valko , Deak Balazs , Tothmeresz Bela , Erdos Laszlo , Kelemen Andras
Published: January 2020

Woody plants in water-limited ecosystems affect their environment on multiple scales: locally, natural stands can create islands of fertility for herb layer communities compared to open habitats, but afforestation has been shown to negatively affect regional water balance and productivity. Despite these contrasting observations, no coherent multiscale framework has been developed for the environmental effects of woody plants in water-limited ecosystems. To link local and regional effects of woody species in a spatially explicit model, we simultaneously measured site conditions (microclimate, nutrient availability and topsoil moisture) and conditions of regional relevance (deeper soil moisture), in forests with different canopy types (long, intermediate and short annual lifetime) and adjacent grasslands in sandy drylands. All types of forests ameliorated site conditions compared to adjacent grasslands, although natural stands did so more effectively than managed ones. At the same time, all forests desiccated deeper soil layers during the vegetation period, and the longer the canopy lifetime, the more severe the desiccation in summer and more delayed the recharge after the active period of the canopy. We conclude that the site-scale environmental amelioration brought about by woody species is bound to co-occur with the desiccation of deeper soil layers, leading to deficient ground water recharge. This means that the cost of creating islands of fertility for sensitive herb layer organisms is an inevitable negative impact on regional water balance. The canopy type or management intensity of the forests affects the magnitude but not the direction of these effects. The outlined framework of the effects of woody species should be considered for the conservation, restoration, or profit-oriented use of forests as well as in forest-based carbon sequestration and soil erosion control projects in water-limited ecosystems.
Inferring a simple mechanism for alpha-blocking by fitting a neural population model to EEG spectra
Authors: Hartoyo Agus , Cadusch Peter J. , Liley David T. J. , Hicks Damien G.
Published: January 2020

Alpha blocking, a phenomenon where the alpha rhythm is reduced by attention to a visual, auditory, tactile or cognitive stimulus, is one of the most prominent features of human electroencephalography (EEG) signals. Here we identify a simple physiological mechanism by which opening of the eyes causes attenuation of the alpha rhythm. We fit a neural population model to EEG spectra from 82 subjects, each showing different degrees of alpha blocking upon opening of their eyes. Although it is notoriously difficult to estimate parameters from fitting such models, we show that, by regularizing the differences in parameter estimates between eyes-closed and eyes-open states, we can reduce the uncertainties in these differences without significantly compromising fit quality. From this emerges a parsimonious explanation for the spectral changes between states: Just a single parameter,pei, corresponding to the strength of a tonic, excitatory input to the inhibitory population, is sufficient to explain the reduction in alpha rhythm upon opening of the eyes. When comparing parameter estimates across different subjects we find that the inferred differential change inpeifor each subject increases monotonically with the degree of alpha blocking observed. In contrast, other parameters show weak or negligible differential changes that do not scale with the degree of alpha attenuation in each subject. Thus most of the variation in alpha blocking across subjects can be attributed to the strength of a tonic afferent signal to the inhibitory cortical population.

Author summary

One of the most striking features of the human electroencephalogram (EEG) is the presence of neural oscillations in the range of 8-13 Hz. It is well known that attenuation of these alpha oscillations, a process known as alpha blocking, arises from opening of the eyes, though the cause has remained obscure. In this study we infer the mechanism underlying alpha blocking by fitting a neural population model to EEG spectra from 82 different individuals. Although such models have long held the promise of being able to relate macroscopic recordings of brain activity to microscopic neural parameters, their utility has been limited by the difficulty of inferring these parameters from fits to data. Our approach is to fit both eyes-open and eyes-closed EEG spectra together, minimizing the number of parameter changes required to transition from one spectrum to the other. Surprisingly, we find that there is just one parameter, the external input to the inhibitory neurons in cortex, that is responsible for attenuating the alpha oscillations. We demonstrate how the strength of this inhibitory input scales monotonically with the degree of alpha blocking observed over all 82 subjects.
EnhancerP-2L: A Gene regulatory site identification tool for DNA enhancer region using CREs motifs
Authors: Butt Ahmad Hassan , Alkhalaf Salem , Iqbal Shaukat , Khan Yaser Daanial
Published: January 2020

Enhancers are DNA fragments that do not encode RNA molecules and proteins, but they act critically in the production of RNAs and proteins by controlling gene expression. Prediction of enhancers and their strength plays significant role in regulating gene expression. Prediction of enhancer regions, in sequences of DNA, is considered a difficult task due to the fact that they are not close to the target gene, have less common motifs and are mostly tissue/cell specific. In recent past, several bioinformatics tools were developed to discriminate enhancers from other regulatory elements and to identify their strengths as well. However the need for improvement in the quality of its prediction method requires enhancements in its application value practically. In this study, we proposed a new method that builds on nucleotide composition and statistical moment based features to distinguish between enhancers and non-enhancers and additionally determine their strength. Our proposed method achieved accuracy better than current state-of-the-art methods using 5-fold and 10-fold cross-validation. The outcomes from our proposed method suggest that the use of statistical moments based features could bear more efficient and effective results. For the accessibility of the scientific community, we have developed a user-friendly web server for EnhancerP-2L which will increase the impact of bioinformatics on medicinal chemistry and drive medical science into an unprecedented resolution. Web server is freely accessible athttp://www.biopred.org/enpred.