bluuebunny/crossref_metadata_2025 huggingface dataset:
Prognosis of Traumatic Ulnar Nerve Injuries
Authors: Lan Ching-Yu , Tien Huey-Yuan , Lin Yu-Te , Hsu Chun-Cheng , Lin Cheng-Hung , Chen Shih-Heng
Published: December 2018

Ulnar nerve injury (UNI) is not uncommon and often results in incomplete motor recovery after the initial nerve repair and requires secondary functional reconstruction. To clarify the prognosis and predicting factor of UNI, and if it is reasonable to wait after the initial repair, a systematic literature review from PubMed computerized literature database and Google scholar was performed. The PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) checklist and guidelines were followed to develop the search protocol for this literature review. Two reviewers independently assessed titles, abstracts, and full-text articles, and a third reviewer resolved any disagreements. Seventeen articles with 260 cases were found with sufficient data and enough follow-up. After multiple logistic regression, age, injury level, gap of lesion, and delayed time to surgery were significant prognostic factors in UNI. If considering only high-level injuries (injury at or above proximal forearm), age became the only predicting factor. In cases with likely poor prognosis, their motor recovery tends to be unsatisfactory, and observation for months after the initial repair might not be reasonable. Other surgical interventions such as early nerve transfer may be an option to improve the outcome.
Using Simulation to Teach Echocardiography
Authors: Rambarat Cecil A. , Merritt Justin M. , Norton Hannah F. , Black Erik , Winchester David E.
Published: December 2018

Summary Statement

We identified 24 studies of high-fidelity simulation being used to teach echocardiography. A variety of study designs were used with outcomes ranging from reports of learner self-confidence up to improvement in organizational practice. Most studies were carried out in graduate medical populations, specifically in anesthesia trainees. The substantial majority of studies (91.6%) concluded that simulation has positive outcomes for teaching echocardiography. Future investigations would benefit from application of educational theory and should focus on demonstrating whether simulation can improve care delivery and patient outcomes.
Why Does Postoperative Pancreatic Fistula Occur After Hand-sewn Parenchymal Closure and Staple Closure in Distal Pancreatectomy?
Authors: Nagakawa Yuichi , Hijikata Yosuke , Osakabe Hiroaki , Matsudo Takaaki , Soya Ryoko , Sahara Yatsuka , Takishita Chie , Shirota Tomoki , Kobayashi Nao , Nakajima Tetsushi , Hosokawa Yuichi , Ishizaki Tetsuo , Katsumata Kenji , Tsuchida Akihiko
Published: December 2018

Hand-sewing (HS) and stapling are common parenchymal closure techniques after distal pancreatectomy. However, these methods cannot completely prevent postoperative pancreatic fistula (POPF). The mechanisms of POPF formation after closure are unknown. We performed distal pancreatectomy in mongrel dogs to identify the mechanisms of POPF formation after HS and staple closure. We measured the closed pancreatic duct burst pressures and examined the histology of the remnant pancreas. The after staple-closure burst pressures depended on stapler height; lower pressures were associated with greater stapler heights. Post-HS closure burst pressures were significantly higher than those at each stapler height (P<0.01). Post-HS closure pathologic findings showed extensive necrosis (day 3), and some regenerated pancreatic duct stumps (day 5). Necrosis was not observed around the stapled tissues. Although HS completely closes the pancreatic ducts, stump necrosis and blood flow disturbances may cause POPF. With stapler closure, pancreatic fluid leakage may occur even with appropriate stapler heights.
Is it Necessary to Send the Sleeve Gastrectomy Specimens to Pathology?
Authors: Demirbas Baha Tolga , Erdim Aylin , Celikel Cigdem , Akbas Gamze , Cingi Asim
Published: December 2018

Background:

Laparoscopic sleeve gastrectomy (LSG) has become more popular among other bariatric procedures. The histopathologic changes in the sleeve gastrectomy specimens have not been widely investigated among the Turkish population.

Objective:

The purpose of this study was to delineate these histopathologic findings of the LSG specimens of morbidly obese patients from a single center.

Materials and Methods:

A prospective database of all patients who have undergone LSG at a single center was reviewed. Demographic parameters, that is, sex, age, and body mass index were examined. The incidence of Helicobacter pylori, and other pathologic findings in the specimens were studied.

Results:

In total, 253 patients who had undergone LSG between the period spanning from April 2012 to January 2017 were included in the study. The 183 patients were female individuals and 70 patients were male individuals. The mean age at the time of operation was 38.5 years (range, 18 to 65 y). The mean body mass index was 47.7 kg/m2. The pathologic findings were H. pylori positivity in 69 patients (27%), chronic active gastritis in 52 patients (20.5%), chronic gastritis in 135 patients (53.4%), and intestinal metaplasia in 5 patients (2%), whereas normal histopathologic findings were observed in 65 patients (25.7%). As regards surgical complications, the mortality rate was 0%, the staple-line leak was observed in 2 patients (0.8%), and intra-abdominal hemorrhage occurred in 2 patients (0.8%).

Conclusions:

The majority of patients who underwent LSG had pathologic findings in the resected specimens. With regard to the high incidence of pathologic findings in this study, we conclude that it is essential to send the gastrectomy materials for pathologic investigation after sleeve gastrectomy.
Symptomatic, Radiological, and Quality of Life Outcome of Paraesophageal Hernia Repair With Urinary Bladder Extracellular Surgical Matrix: Comparison With Primary Repair
Authors: Wang Chloe Q. , Tran Thanh , Montera Beth , Karlnoski Rachel , Feldman John , Albrink Michael H. , Velanovich Vic
Published: December 2018

Introduction:

Paraesophageal hernia repairs are prone to recurrence and mesh reinforcement is common. Both biologic and prosthetic meshes have been used. We report a comparison of a new type of biologically derived graft, Gentrix Surgical Urinary Bladder Matrix (UBM).

Methods:

The medical records of 65 patients who underwent paraesophageal hernia repair (PEHR) were reviewed. Primary data points included demographics, first-time or recurrent hernia, operative approach, graft or primary repair, operative time, and postoperative complications. Patients then underwent upper gastrointestinal series, completed the GERD-HRQL symptom severity questionnaire, and the SF-36 generic quality of life instrument.

Results:

A total of 32 patients underwent graft-reinforced repair, 33 underwent primary repair. More patients in the UBM group were being treated for recurrent PEH. Demographic data and postoperative complications were similar. There was no difference in recurrence rates, size of recurrence, postoperative symptomatic or quality of life improvement. Patients who suffered recurrence in the primary repair group had more severe symptoms and a higher rate of dissatisfaction. Of the 3 patients with recurrences after Gentrix placement, reoperation demonstrated anterior failure where no reinforcement had occurred because of the posteriorly placed U-shaped graft.

Conclusions:

The use of UBM was not associated with an increased complications despite use in more difficult patients. Although there appeared to be no difference in recurrence rate or size, it was associated with less severe symptomatic recurrences. The U-shape configuration is prone to recurrence at the site of the repair not covered by the graft, suggesting that a keyhole configuration may be superior.
Autophagy in crop plants: what's new beyond
Arabidopsis
?
Authors: Tang Jie , Bassham Diane C.
Published: December 2018

Autophagy is a major degradation and recycling pathway in plants. It functions to maintain cellular homeostasis and is induced by environmental cues and developmental stimuli. Over the past decade, the study of autophagy has expanded from model plants to crop species. Many features of the core machinery and physiological functions of autophagy are conserved among diverse organisms. However, several novel functions and regulators of autophagy have been characterized in individual plant species. In light of its critical role in development and stress responses, a better understanding of autophagy in crop plants may eventually lead to beneficial agricultural applications. Here, we review recent progress on understanding autophagy in crops and discuss potential future research directions.
Determining consistent prognostic biomarkers of overall survival and vascular invasion in hepatocellular carcinoma
Authors: Menyhárt Otília , Nagy Ádám , Győrffy Balázs
Published: December 2018

Background:
Potential prognostic biomarker candidates for hepatocellular carcinoma (HCC) are abundant, but their generalizability is unexplored. We cross-validated markers of overall survival (OS) and vascular invasion in independent datasets.
Methods:
The literature search yielded 318 genes related to survival and 52 related to vascular invasion. Validation was performed in three datasets (RNA-seq,
n
= 371; Affymetrix arrays,
n
= 91; Illumina gene chips,
n
= 135) by uni- and multivariate Cox regression and Mann–Whitney
U
-test, separately for Asian and Caucasian patients.
Results:
One hundred and eighty biomarkers remained significant in Asian and 128 in Caucasian subjects at
p
< 0.05. After multiple testing correction
BIRC5
(
p
= 1.9 × 10
−10
),
CDC20
(
p
= 2.5 × 10
−9
) and
PLK1
(
p
= 3 × 10
−9
) endured as best performing genes in Asian patients; however, none remained significant in the Caucasian cohort. In a multivariate analysis, significance was reached by stage (
p
= 0.0018) and expression of
CENPH
(
p
= 0.0038) and
CDK4
(
p
= 0.038).
KIF18A
was the only gene predicting vascular invasion in the Affymetrix and Illumina cohorts (
p
= 0.003 and
p
= 0.025, respectively).
Conclusion:
Overall, about half of biomarker candidates failed to retain prognostic value and none were better than stage predicting OS. Impact: Our results help to eliminate biomarkers with limited capability to predict OS and/or vascular invasion.
Pitch profile across the cuticle of the scarab beetle
Cotinis
mutabilis
determined by analysis of Mueller matrix measurements
Authors: Mendoza-Galván Arturo , Muñoz-Pineda Eloy , Järrendahl Kenneth , Arwin Hans
Published: December 2018

Helicoidal structures of lamellae of nanofibrils constitute the cuticle of some scarab beetles with iridescent metallic-like shine reflecting left-handed polarized light. The spectral and polarization properties of the reflected light depend on the pitch of the helicoidal structures, dispersion of effective refractive indices and thicknesses of layers in the cuticle. By modelling the outer exocuticle of the scarab beetle
Cotinis mutabilis
as a stack of continuously twisted biaxial slices of transparent materials, we extract optical and structural parameters by nonlinear regression analysis of variable-angle Mueller-matrix spectroscopic data. Inhomogeneities in the beetle cuticle produce depolarization with non-uniformity in cuticle thickness as the dominant effect. The pitch across the cuticle of
C
.
mutabilis
decreased with depth in a two-level profile from 380 to 335 nm and from 390 to 361 nm in greenish and reddish specimens, respectively, whereas in a yellowish specimen, the pitch decreased with depth in a three-level profile from 388 to 326 nm.
Behavioural thermoregulation via microhabitat selection of winter sleeping areas in an endangered primate: implications for habitat conservation
Authors: Campbell Liz A. D. , Tkaczynski Patrick J. , Mouna Mohamed , Derrou Abderrahim , Oukannou Lahcen , Majolo Bonaventura , van Lavieren Els
Published: December 2018

Strategic microhabitat selection allows animals in seasonally cold environments to reduce homeostatic energy costs, particularly overnight when thermoregulatory demands are greatest. Suitable sleeping areas may therefore represent important resources for winter survival. Knowledge of microhabitat use and potential impacts of anthropogenic habitat modification can aid species conservation through development of targeted habitat management plans. Wild, endangered Barbary macaques (Macaca sylvanus) in logged cedar-oak forest were studied to investigate (1) the hypothesis that macaques select winter sleeping areas with microhabitat characteristics that may reduce thermoregulatory costs, and, if so, (2) how to minimize damage to sleeping areas from logging. Macaques slept only in Atlas cedars (Cedrus atlantica). Consistent with predictions, macaques preferred sleeping in sheltered topography and dense vegetation, which may reduce exposure to wind, precipitation and cold, and preferred large trees that facilitate social huddling. This suggests that Barbary macaques employ strategic nocturnal microhabitat selection to reduce thermoregulatory costs and thus suitable sleeping areas may influence winter survival. To minimize negative impacts of logging on macaque sleeping areas, results suggest avoiding logging in topographical depressions and maintaining cedar densities greater than 250 ha−1with average breast height greater than 60 cm. This study demonstrates how animal behaviour can be used to guide species-specific habitat management plans.
Voltammetric determination of phenylephrine hydrochloride using a multi-walled carbon nanotube-modified carbon paste electrode
Authors: Zhou Q. , Zhai H. Y. , Pan Y. F.
Published: December 2018

A chemically modified carbon paste electrode (CPE) was designed by mixing graphite and multi-walled carbon nanotubes (MWCNT). The electrochemical behaviour was studied, and the determination method of phenylephrine hydrochloride (PHE) on this sensor was established. According to the results, the optimal ratio of MWCNTs was approximately 12.5% (w/w). MWCNT-modified carbon paste electrodes (MWCNT-CPEs) showed high electrochemical activity for PHE, producing a sharp oxidation peak current (
I
p
) at approximately +0.816 V versus a saturated calomel electrode (SCE) reference electrode in phosphate buffer solution (PBS, pH 6.45), and the
I
p
increased by approximately two times compared to that of the bare CPE. The anodic
I
p
was linearly related with 5.0 × 10
−6
–7.5 × 10
−4
mol l
−1
PHE, with a detection limit of 3.7 × 10
−7
mol l
−1
. Furthermore, MWCNT-CPEs were successfully applied to the determination of PHE in injection, eye drop and nasal spray liquid samples as a simple, rapid and low-cost method.
Reporting of thermography parameters in biology: a systematic review of thermal imaging literature
Authors: Harrap Michael J. M. , Hempel de Ibarra Natalie , Whitney Heather M. , Rands Sean A.
Published: December 2018

Infrared (IR) thermography, where temperature measurements are made with IR cameras, has proven to be a very useful and widely used tool in biological science. Several thermography parameters are critical to the proper operation of thermal cameras and the accuracy of measurements, and these must usually be provided to the camera. Failure to account for these parameters may lead to less accurate measurements. Furthermore, the failure to provide information of parameter choices in reports may compromise appraisal of accuracy and replicate studies. In this review, we investigate how well biologists report thermography parameters. This is done through a systematic review of biological thermography literature that included articles published between years 2007 and 2017. We found that in primary biological thermography papers, which make some kind of quantitative temperature measurement, 48% fail to report values used for emissivity (an object's capacity to emit thermal radiation relative to a black body radiator), which is the minimum level of reporting that should take place. This finding highlights the need for life scientists to take into account and report key parameter information when carrying out thermography, in the future.
Three-dimensional localization of point acoustic sources using a planar microphone array combined with beamforming
Authors: Ding Hao , Bao Yumei , Huang Qi , Li Chunxiao , Chai Guozhong
Published: December 2018

This paper presents a beamforming-based acoustic imaging (BBAI) method employing a two-dimensional (2D) microphone array that not only can locate an acoustic source in the
XY
plane parallel to the array, but can also identify the distance between the source and array in the
Z
direction, denoted as the source depth, and thus provides three-dimensional (3D) localization ability. In this method, the acoustic field is reconstructed on virtual
XY
planes at different distances along the
Z
direction. The source depth is then determined according to the virtual plane providing the maximum response of the acoustic field. The location of the source in the
X
and
Y
directions of the identified virtual plane can then be easily determined based on the standard beamforming principles of a planar array. The proposed BBAI method is evaluated based on simulations involving single- and multiple-point sources, and corresponding experimental evaluations are similarly conducted in an anechoic chamber. Both simulation and experimental results demonstrate that the proposed method is capable of locating acoustic sources in 3D space.
Adsorptive removal of adsorbable organic halogens by activated carbon
Authors: Qin Chengrong , Liu Baojie , Huang Lingzhi , Liang Chen , Gao Cong , Yao Shuangquan
Published: December 2018

Current research mainly focuses on the reduction of adsorbable organic halogen (AOX) sources, while studies on AOX monitoring and management in the environment are scarce. Organic pollutants in water are mainly fixed by sediments. Thus, in this paper, activated carbon was used to simulate the adsorption of AOX by sediments. AOX volatilization and degradation were also studied to exclude their effect on adsorption. Micromolecule chlorides were more easily volatilized and degraded than chlorobenzene and chlorophenol. The adsorption of activated carbon to AOX in bleaching wastewater was also studied and the optimum conditions for AOX removal were elucidated (particle size, 62 µm; time, 120 min; pH, 2.5; temperature, 40°C; and activated carbon dosage, 1.75 g l−1). AOX adsorption by activated carbon is a chemical process. Hence, the chemical compositions of the bleaching effluent with and without adsorption were analysed by GC-MS. The results revealed that activated carbon exhibits a good AOX removal effect, thereby providing a theoretical basis for monitoring the AOX distribution in the environment.
Computational tools to detect signatures of mutational processes in DNA from tumours: a review and empirical comparison of performance
Authors: Hanane Omichessan , Gianluca Severi , Vittorio Perduca
Published: December 2018

Mutational signatures refer to patterns in the occurrence of somatic mutations that reflect underlying mutational processes. To date, after the analysis of tens of thousands of genomes and exomes from about 40 different cancers types, 30 mutational signatures characterized by a unique probability profile across the 96 mutation types have been identified, validated and listed on the COSMIC (Catalogue of Somatic Mutations in Cancer) website. Simultaneously with this development, the last few years saw the publication of several concurrent methods (mathematical algorithms implemented in publicly available software packages) for either the quantification of the contribution of prespecified signatures (e.g. COSMIC signatures) in a given cancer genome or the identification of new signatures from a sample of cancer genomes. A review about existing computational tools has been recently published to guide researchers and practitioners in conducting their mutational signatures analysis, however, other tools have been introduced since its publication and, to date, there has not been a systematic evaluation and comparison of the performance of such tools. In order to fill this gap, we carry on an empirical evaluation study of all available packages to date, using both real and simulated data.
Theory of mechano-chemical patterning in biphasic biological tissues
Authors: Recho Pierre , Hallou Adrien , Hannezo Edouard
Published: December 2018

The formation of self-organized patterns is key to the morphogenesis of multicellular organisms, although a comprehensive theory of biological pattern formation is still lacking. Here, we propose a biologically realistic and unifying approach to emergent pattern formation. Our biphasic model of multicellular tissues incorporates turnover and transport of morphogens controlling cell differentiation and tissue mechanics in a single framework, where one tissue phase consists of a poroelastic network made of cells and the other is the extracellular fluid permeating between cells. While this model encompasses previous theories approximating tissues to inert monophasic media, such as Turing’s reaction-diffusion model, it overcomes some of their key limitations permitting pattern formation via any two-species biochemical kinetics thanks to mechanically induced cross-diffusion flows. Moreover, we unravel a qualitatively different advection-driven instability which allows for the formation of patterns with a single morphogen and which single mode pattern scales with tissue size. We discuss the potential relevance of these findings for tissue morphogenesis.
Diversity Converges During Community Assembly In Methanogenic Granules, Suggesting A Biofilm Life-Cycle
Authors: Trego Anna Christine , Morabito Cristina , Bourven Isabelle , Guibaud Gilles , Mills Simon , Connelly Stephanie , Quince Christopher , Ijaz Umer Zeeshan , Collins Gavin
Published: December 2018

Anaerobic biological decomposition of organic matter is ubiquitous in Nature wherever anaerobic environments prevail, and is catalysed by hydrolytic, fermentative, acetogenic, methanogenic, and various other groups, including syntrophic bacteria. It is also harnessed in innovative ways in engineered systems that may rely on small (0.1-4.0 mm), spherical, anaerobic granules, which we have found to be highly-replicated, whole-ecosystems harbouring the entire community necessary to mineralise complex organics. We hypothesised distinct granule sizes correspond to stages in a biofilm life-cycle, in which small granules are young and larger ones are old. Here, granules were separated into 10 size fractions used for physico-chemical and ecological characterisation. Gradients of volatile solids, density, settleability, biofilm morphology, methanogenic activity, and EPS profiles were observed across size fractions. Sequencing of 16S rRNA genes indicated linear convergence of diversity during community assembly as granules increased in size. A total of 155 discriminant OTUs were identified, and correlated strongly with physico-chemical parameters. Community assembly across sizes was influenced by a niche effect, whereby Euryarchaeota dominated a core microbiome presumably as granules became more anaerobic. The findings indicate opportunities for precision management of environmental biotechnologies, and the potential of aggregates as playgrounds to study assembly and succession in whole microbiomes.
Concerted 2-5A-Mediated mRNA Decay and Transcription Reprogram Protein Synthesis in dsRNA Response
Authors: Rath Sneha , Prangley Eliza , Donovan Jesse , Demarest Kaitlin , Meir Yigal , Wingreen Ned , Korennykh Alexei
Published: December 2018

RNA degradation by RNase L during 2-5A-mediated decay (2-5AMD) is a conserved mammalian stress response to viral and endogenous double-stranded RNA (dsRNA). 2-5AMD onsets rapidly and facilitates a switch of protein synthesis from homeostasis to production of interferons (IFNs). To understand the mechanism of this protein synthesis reprogramming, we examined 2-5AMD in human cells. 2-5AMD triggers polysome collapse characteristic of a translation initiation defect, but translation initiation complexes and ribosomes purified from the translation-arrested cells remain functional. Using spike-in RNA-seq we found that basal messenger RNAs (mRNAs) rapidly decay, while mRNAs encoding IFNs and IFN-stimulated genes evade 2-5AMD and accumulate. The IFN evasion results from the combined effect of better mRNA stability and positive feedback amplification in the IFN response. Therefore, 2-5AMD and transcription act in concert to revamp the cellular mRNA composition. The resulting preferential accumulation of innate immune mRNAs establishes 'prioritized' synthesis of defense proteins.
Reconciling biodiversity conservation, food production and farmers’ demand
Authors: Montoya Daniel , Gaba Sabrina , de Mazancourt Claire , Bretagnolle Vincent , Loreau Michel
Published: December 2018

Agricultural management should consider multiple services and stakeholders. Yet, it remains unclear how to guarantee the provision of ecosystem services that reaches stakeholders’ demands, especially considering the observed biodiversity decline and the current global change predictions that may affect food security. Here, we use a model to examine how landscape composition – fraction of semi-natural habitat (SNH) – affects biodiversity and crop production services in intensively-managed agricultural systems. We analyse three groups of stakeholders assumed to value different ecosystem services most – individual farmers (crop yield per area), agricultural unions (landscape production) and conservationists (biodiversity). We find that trade-offs among stakeholders’ demands strongly depend on the degree of pollination dependence of crops, the strength of environmental and demographic stochasticity, and the relative amount of an ecosystem service demanded by each stakeholder, i.e. function thresholds. Intermediate amounts of SNH can allow for the delivery of relatively high levels of the three ecosystem services. Our analysis further suggests that the current levels of SNH protection lie below these intermediate amounts of SNH in intensively-managed agricultural landscapes. Given the worldwide trends in agriculture and global change, these results suggest ways of managing landscapes to reconcile the demands of several actors and ensure for biodiversity conservation and food production.
De novoassembly of thePasteuria penetransgenome reveals high plasticity, host dependency, and BclA-like collagens
Authors: Orr Jamie N , Mauchline Tim H , Cock Peter J , Blok Vivian C , Davies Keith G
Published: December 2018

1.

Pasteuria penetransis a gram-positive endospore forming bacterial parasite ofMeloidogynespp. the most economically damaging genus of plant parasitic nematodes globally. The obligate antagonistic nature ofP. penetransmakes it an attractive candidate biological control agent. However, deployment ofP. penetransfor this purpose is inhibited by a lack of understanding of its metabolism and the molecular mechanics underpinning parasitism of the host, in particular the initial attachment of the endospore to the nematode cuticle. Several attempts to assemble the genomes of species within this genus have been unsuccessful. Primarily this is due to the obligate parasitic nature of the bacterium which makes obtaining genomic DNA of sufficient quantity and quality which is free from contamination challenging. Taking advantage of recent developments in whole genome amplification, long read sequencing platforms, and assembly algorithms, we have developed a protocol to generate large quantities of high molecular weight genomic DNA from a small number of purified endospores. We demonstrate this method via genomic assembly ofP. penetrans. This assembly reveals a reduced genome of 2.64Mbp estimated to represent 86% of the complete sequence; its reduced metabolism reflects widespread reliance on the host and possibly associated organisms. Additionally, apparent expansion of transposases and prediction of partial competence pathways suggest a high degree of genomic plasticity. Phylogenetic analysis places our sequence within the Bacilli, and most closely related toThermoactinomycesspecies. Seventeen predicted BclA-like proteins are identified which may be involved in the determination of attachment specificity. This resource may be used to developin vitroculture methods and to investigate the genetic and molecular basis of attachment specificity.
Anatomical basis and physiological role of cerebrospinal fluid transport through the murine cribriform plate
Authors: Norwood Jordan N. , Zhang Qingguang , Card David , Craine Amanda , Ryan Timothy M. , Drew Patrick J.
Published: December 2018

Cerebrospinal fluid (CSF) flows through the brain, transporting chemical signals and removing waste. CSF production in the brain is balanced by a constant outflow of CSF, the anatomical basis of which is poorly understood. Here we characterized the anatomy and physiological function of the CSF outflow pathway along the olfactory sensory nerves through the cribriform plate, and into the nasal epithelia. Chemical ablation of olfactory sensory nerves greatly reduced outflow of CSF through the cribriform plate. The reduction in CSF outflow did not cause an increase in intracranial pressure (ICP), consistent with an alteration in the pattern of CSF drainage or production. Our results suggest that damage to olfactory sensory neurons (such as from air pollution) could contribute to altered CSF turnover and flow, providing a potential mechanism for neurological diseases.
Glendonite occurrences in the Tremadocian of Baltica: first Early Palaeozoic evidence of massive ikaite precipitation at temperate latitude
Authors: Popov Leonid E. , Álvaro J. Javier , Holmer Lars E. , Bauert Heikki , Pour Mansoureh Ghobadi , Dronov Andrei V. , Lehnert Oliver , Hints Olle , Männik Peep , Zhang Zhifei , Zhang Zhiliang
Published: December 2018

The Tremadocian (Early Ordovician) is currently considered a time span of greenhouse conditions with tropical water surface temperature estimates, interpolated from oxygen isotopes, approaching 40°C. In the high-latitude Baltoscandian Basin, these data are in contrast with the discovery of glendonite, a pseudomorph of ikaite (CaCO3·6H2O) and valuable indicator of near-freezing bottom-water conditions. The massive precipitation of this climatically sensitive mineral is associated with transgressive conditions and high organic productivity. Surprisingly, the precipitation of glendonite is contemporaneous with the record of conodonts displaying low δ18O values, which would suggest high temperatures (>40°C) in the water column. Therefore, the early Tremadocian sediments of Baltoscandia contain both “greenhouse” pelagic signals and near-freezing substrate indicators. This apparent paradox suggests both the influence of isotopically depleted freshwater yielded by fluvial systems, and the onset of sharp thermal stratification patterns in a semi-closed basin, which should have played an important role in moderating subpolar climates and reducing latitudinal gradients.
Anthropogenic risk factors as the major cause of cancer driver events
Authors: Belikov Aleksey V.
Published: December 2018

Background

I have recently shown that the number of rate-limiting driver events per tumor can be estimated from the age distribution of cancer incidence using the gamma/Erlang probability distribution. It is important to understand how these predictions relate to established risk factors.

Methods

The number of rate-limiting driver events per tumor was estimated using the gamma/Erlang distribution and correlated to the percentage of cancer cases attributable to modifiable risk factors.

Results

The predicted number of rate-limiting driver events per tumor strongly correlates with the proportion of cancer cases attributable to modifiable risk factors for all cancers except those induced by infection or ultraviolet radiation. The correlation was confirmed for three countries, three corresponding incidence databases and risk estimation studies, as well as for both sexes: USA, males [r=0.80, P=0.002], females [r=0.81, P=0.0003]; England, males [r=0.90, P<0.0001], females [r=0.67, P=0.002]; Australia, males [r=0.90, P=0.0004], females [r=0.68, P=0.01].

Conclusions

It is thus confirmed that predictions based on interpreting the age distribution of cancer incidence as the gamma/Erlang probability distribution have biological meaning, validating the underlying Poisson process as the law governing the development of the majority of cancer types, especially those driven by chemical mutagens. Importantly, this study suggests that the majority of driver events (60-80% in males, 50-70% in females) are induced by anthropogenic carcinogens, and not by cell replication errors or other internal processes.
An archaeal symbiont-host association from the deep terrestrial subsurface
Authors: Schwank Katrin , Bornemann Till L. V. , Dombrowski Nina , Spang Anja , Banfield Jillian F. , Probst Alexander J.
Published: December 2018

DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal host-symbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense has a similar metabolism as Nanoarchaeum equitans and potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.
Persister Cells Resuscitate Using Membrane Sensors that Activate Chemotaxis, Lower cAMP Levels, and Revive Ribosomes
Authors: Yamasaki Ryota , Song Sooyeon , Benedik Michael J. , Wood Thomas K.
Published: December 2018

Persistence, the stress-tolerant state, is arguably the most vital phenotype since nearly all cells experience nutrient stress, which causes a sub-population to become dormant. However, how persister cells wake to reconstitute infections is not understood well. Here, using single-cell observations, we determined thatEscherichia colipersister cells resuscitate primarily when presented with specific carbon sources, rather than spontaneously. In addition, we found that the mechanism of persister cell waking is through sensing nutrients by chemotaxis and phosphotransferase membrane proteins. Furthermore, nutrient transport reduces the level of secondary messenger cAMP through enzyme IIA; this reduction in cAMP levels leads to ribosome resuscitation and rescue. Resuscitating cells also immediately commence chemotaxis toward nutrients, although flagellar motion is not required for waking. Hence, persister cells wake by perceiving nutrients via membrane receptors which relay the signal to ribosomes via the secondary messenger cAMP, and persisters wake and utilize chemotaxis to acquire nutrients.
Schizotypy-related magnetization of cortex in healthy adolescence is co-located with expression of schizophrenia-related genes
Authors: Romero-Garcia Rafael , Seidlitz Jakob , Whitaker Kirstie J , Morgan Sarah E , Fonagy Peter , Dolan Raymond J , Jones Peter B , Goodyer Ian M , Suckling John ,   the NSPN Consortium, Vértes Petra E , Bullmore Edward T
Published: December 2018

Background

Genetic risk is thought to drive clinical variation on a spectrum of schizophrenia-like traits but the underlying changes in brain structure that mechanistically link genomic variation to schizotypal experience and behaviour are unclear.

Methods

We assessed schizotypy using a self-reported questionnaire, and measured magnetization transfer (MT), as a putative micro-structural MRI marker of intra-cortical myelination, in 68 brain regions, in 248 healthy young people (aged 14-25 years). We used normative adult brain gene expression data, and partial least squares (PLS) analysis, to find the weighted gene expression pattern that was most co-located with the cortical map of schizotypy-related magnetization (SRM).

Results

Magnetization was significantly correlated with schizotypy in bilateral posterior cingulate cortex and precuneus (and for disorganized schizotypy also in medial prefrontal cortex; all FDR-corrected P < 0.05), which are regions of the default mode network specialized for social and memory functions. The genes most positively weighted on the whole genome expression map co-located with SRM were enriched for genes that were significantly down-regulated in two prior case-control histological studies of brain gene expression in schizophrenia. Conversely, the most negatively weighted genes were enriched for genes that were transcriptionally up-regulated in schizophrenia. Positively weighted (down-regulated) genes were enriched for neuronal, specifically inter-neuronal, affiliations and coded a network of proteins comprising a few highly interactive “hubs” such as parvalbumin and calmodulin.

Conclusions

Microstructural MRI maps of intracortical magnetization can be linked to both the behavioural traits of schizotypy and to prior histological data on dysregulated gene expression in schizophrenia.
A novel mutation alters the stability of PapA2 resulting in the complete abrogation of sulfolipids in clinical mycobacterial strains
Authors: Panchal Vipul N , Jatana Nidhi , Malik Anchal , Taneja Bhupesh , Pal Ravikant , Bhatt Apoorva , Besra Gurdyal S , Thukral Lipi , Chaudhary Sarika , Rao Vivek
Published: December 2018

The analysis of whole genome has revealed specific geographical distribution of Mycobacterium tuberculosis (Mtb) strains across the globe suggestive of unique host dependent adaptive mechanisms in Mtb evolved out of selective pressures. We provide an important correlation of a genome-based mutation to a molecular phenotype across two predominant clinical Mtb lineages of the Indian subcontinent. We have identified a distinct lineage specific mutation-G247C, translating into an alanine to proline conversion in the papA2 gene of Indo oceanic lineage 1 [L1] Mtb strains; restoration of cell wall sulfolipids by simple genetic complementation of papA2 from lineage 3 [L3] or from H37Rv (Lineage 4- L4) attributed the loss of this glycolipid to this specific mutation in Indo oceanic L1 Mtb. Investigation into the structure of Mtb PapA2 revealed a distinct non-ribosomal peptide synthetase (NRPS) C domain conformation with an unconventional presence of Zinc binding motif. Surprisingly, the A83P mutation did not map to either the catalytic centre in the N-terminal subdomain or any of the substrate binding region of the protein. On the contrary, the inherent ability of mutant PapA2 to form insoluble aggregates and molecular simulations with the Wt/ mut PapA2 purports an important role for the surface associated 83rd residue in protein conformation. The present study demonstrates the importance of a critical structural residue in the papA2 protein of Mtb and helps establish a link between observed genomic alteration and its molecular consequence in the successful human pathogen Mtb.
Genomic diversity and novel genome-wide association with fruit morphology in Capsicum, from 746k polymorphic sites
Authors: Colonna Vincenza , D’Agostino Nunzio , Garrison Erik , Meisner Jonas , Albrechtsen Anders , Facchiano Angelo , Cardi Teodoro , Tripodi Pasquale
Published: December 2018

Background

Capsicum is one of the major vegetable crops grown world-wide. Current subdivision in clades and species is based on morphological traits and coarse sets of genetic markers. Fruits broad variability has been driven by breeding programs and has been mainly studied by linkage analysis.

Results

We discovered 746k variable sites by sequencing 1.8% of the genome in a collection of 373 accessions belonging to 11 Capsicum species from 51 countries. We describe genomic variation at population-level, confirm major subdivision in clades and species, and show that the known subdivision of C. annuum in two groups separates large and bulky fruits form small ones. In C. annuum, we identify four novel loci associated with phenotypes determining the fruit shape, including a non-synonymous mutation in the gene Longifolia 1-like (CA03g16080).

Conclusions

Our collection covers all the economically important species of Capsicum widely used in breeding programs, and represent the widest and largest study so far in terms of the number of species and genetic variants analyzed. We identified a large set of markers that can be used for population genetic studies and genetic association analyses. Our results foster fine genetic association studies and foresee genomic variability at population-level.
Horizontal gene transfer as an indispensable driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage
Authors: Murphy Chelsea L. , Youssef Noha H. , Hanafy Radwa A. , Couger MB , Stajich Jason E. , Wang Y. , Baker Kristina , Dagar Sumit S. , Griffith Gareth W. , Farag Ibrahim F. , Callaghan TM , Elshahed Mostafa S.
Published: December 2018

Survival and growth of the anaerobic gut fungi (AGF, Neocallimastigomycota) in the herbivorous gut necessitate the possession of multiple abilities absent in other fungal lineages. We hypothesized that horizontal gene transfer (HGT) was instrumental in forging the evolution of AGF into a phylogenetically distinct gut-dwelling fungal lineage. Patterns of HGT were evaluated in the transcriptomes of 27 AGF strains, 22 of which were isolated and sequenced in this study, and 4 AGF genomes broadly covering the breadth of AGF diversity. We identified 283 distinct incidents of HGT in AGF transcriptomes, with subsequent gene duplication resulting in an HGT frequency of 2.1-3.6% in AGF genomes. The majority of HGT events were AGF specific (91.5%) and wide (70.7%), indicating their occurrence at early stages of AGF evolution. The acquired genes allowed AGF to expand their substrate utilization range, provided new venues for electron disposal, augmented their biosynthetic capabilities, and facilitated their adaptation to anaerobiosis. The majority of donors were anaerobic fermentative bacteria prevalent in the herbivorous gut. This work strongly indicates that HGT indispensably forged the evolution of AGF as a distinct fungal phylum and provides a unique example of the role of HGT in shaping the evolution of a high rank taxonomic eukaryotic lineage.

Importance

The anaerobic gut fungi (AGF) represent a distinct basal phylum lineage (Neocallimastigomycota) commonly encountered in the rumen and alimentary tracts of herbivores. Survival and growth of anaerobic gut fungi in these anaerobic, eutrophic, and prokaryotes dominated habitats necessitates the acquisition of several traits absent in other fungal lineages. This manuscript assesses the role of horizontal gene transfer as a relatively fast mechanism for trait acquisition by the Neocallimastigomycota post sequestration in the herbivorous gut. Analysis of twenty-seven transcriptomes that represent the broad Neocallimastigomycota diversity identified 283 distinct HGT events, with subsequent gene duplication resulting in an HGT frequency of 2.1-3.6% in AGF genomes. These HGT events have allowed AGF to survive in the herbivorous gut by expanding their substrate utilization range, augmenting their biosynthetic pathway, providing new routes for electron disposal by expanding fermentative capacities, and facilitating their adaptation to anaerobiosis. HGT in the AGF is also shown to be mainly a cross-kingdom affair, with the majority of donors belonging to the bacteria. This work represents a unique example of the role of HGT in shaping the evolution of a high rank taxonomic eukaryotic lineage.
The lupus susceptibility locus Sgp3 encodes the suppressor of endogenous retrovirus expression SNERV
Authors: Treger Rebecca S , Pope Scott D , Kong Yong , Tokuyama Maria , Taura Manabu , Iwasaki Akiko
Published: December 2018

Elevated endogenous retrovirus (ERV) transcription and anti-ERV antibody reactivity are implicated in lupus pathogenesis. Overproduction of non-ecotropic ERV (NEERV) envelope glycoprotein, gp70, and resultant nephritis occur in lupus-prone mice. However, a NEERV repressor has not been identified to test if this association is causal. Here we identified suppressor of NEERV (Snerv) 1 & 2, Kruppel-associated box zinc finger proteins (KRAB-ZFP) that repressed NEERV by binding the NEERV long terminal repeat to recruit the transcriptional regulator KAP1. Germline Snerv1/2 deletion increased activating chromatin modifications, transcription, and gp70 expression from NEERV loci. F1 crosses of lupus-prone NZB and 129 mice to Snerv1/2-/- mice failed to restore NEERV repression, demonstrating that loss of SNERV underlies the lupus autoantigen gp70 overproduction that promotes nephritis in susceptible mice. Increased ERV expression in lupus patients was inversely correlated with expression of three putative ERV-suppressing KRAB-ZFP, suggesting that KRAB-ZFP-mediated ERV misexpression may contribute to human lupus pathogenesis.
Endocrine aryl hydrocarbon receptor signaling is induced by moderate cutaneous exposure to ultraviolet light
Authors: Memari Babak , Nguyen-Yamamoto Loan , Salehi-Tabar Reyhaneh , Zago Michela , Fritz Jorg , Baglole Carolyn J. , Goltzman David , White John H.
Published: December 2018

Links between solar UV exposure and immunity date back to the ancient Greeks with the development of heliotherapy. Skin contains several UV-sensitive chromophores and exposure to sunlight can produce molecules, such as vitamin D3, that act in an endocrine manner. We investigated whether the aryl hydrocarbon receptor (AHR), an environmental sensor and ligand-regulated transcription factor activated by numerous planar compounds of dietary or environmental origin, could be the target of endocrine photoproducts produced by cutaneous UV exposure. 15-to 30-minute exposure of cells to a minimal erythemal dose of UVB irradiationin vitroinduced translocation of the AHR to the nucleus, rapidly inducing site-specific DNA binding and target gene regulation. Importantly,ex vivostudies withAhrwild-type or null fibroblasts showed that serum from mice whose skin was exposed to a 15 min UVB dose, but not control serum, contained agonist activity within 30 min of UV irradiation, inducing AHR-dependent gene expression. Moreover, a 15-min cutaneous UVB exposure induced AHR site-specific DNA binding and target gene regulationin vivowithin 3-6 hr post-irradiation in blood and in peripheral tissues, including intestine. These results show that cutaneous exposure of mice to a single minimal erythemic dose of UVB induces rapid AHR signaling in multiple peripheral organs, providing compelling evidence that moderate sun exposure can exert endocrine control of immunity through the AHR.