bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogeography and evolution of a fungal–insect association on theTibetanPlateau
Authors: Zhang Yongjie , Zhang Shu , Li Yuling , Ma Shaoli , Wang Chengshu , Xiang Meichun , Liu Xin , An Zhiqiang , Xu Jianping , Liu Xingzhong 
Published: September 2014

AbstractParasitoidism refers to a major form of interspecies interactions where parasitoids sterilize and/or kill their hosts typically before hosts reach reproductive age. However, relatively little is known about the evolutionary dynamics of parasitoidism. Here, we investigate the spatial patterns of genetic variation of Chinese cordyceps, including both the parasitoidal fungusOphiocordyceps sinensisand its host insects. We sampled broadly from alpine regions on the Tibetan Plateau and obtained sequences on seven fungal and three insectDNAfragments from each of the 125 samples. Seven and five divergent lineages/cryptic species were identified within the fungus and host insects, respectively. Our analyses suggested thatO. sinensisand host insects originated at similar geographic regions in southern Tibet/Yunnan, followed by range expansion to their current distributions. Cophylogenetic analyses revealed a complex evolutionary relationship betweenO. sinensisand its host insects. Significant congruence was found between host and parasite phylogenies and the time estimates of divergence were similar, raising the possibility of the occurrence of cospeciation events, but the incongruences suggested that host shifts were also prevalent. Interestingly, one fungal genotype was broadly distributed, consistent with recent gene flow. In contrast, the high‐frequency insect genotypes showed limited geographic distributions. The dominant genotypes from both the fungus and the insect hosts may represent ideal materials from which to develop artificial cultivation of this important Chinese traditional medicine. Our results demonstrate that both historical and contemporary events have played important roles in the phylogeography and evolution of theO. sinensis–ghost moth parasitoidism on the Tibetan Plateau.
Bead study: a novel method to measure gastrointestinal transit in mice
Authors: Reed D. E. , Pigrau M. , Lu J. , Moayyedi P. , Collins S. M. , Bercik P. 
Published: September 2014

AbstractBackgroundIntestinal transit assessment in mice using existing methods requires long recording periods or euthanization of animals to localize a tracer. We have developed a novel in vivo method to assess gastrointestinal (GI) transit in mice based on a clinically used ‘shapes study’.MethodsMice (n = 70) were gavaged with 5 steel beads and barium 3 h before, with another dose of barium gavaged 10 min before imaging. Mice were fluoroscoped for 20–60 s, and then most of them were euthanized and the GI tract removed to confirm the localization of the beads fluoroscopically. The in vivo and postmortem recordings were analyzed and each bead was scored depending on its location; a total score was calculated by adding individual bead scores. Total scores obtained from the two methods were compared. A group of mice (n = 10) were examined on three occasions, before and after treatment with loperamide or prucalopride.Key ResultsThe stomach and cecum were consistently outlined by barium, serving as reference landmarks. There was an excellent overall correlation between in vivo and postmortem transit scores (r = 0.93). Analysis of scores for individual gut segments revealed high agreement for stomach, cecum, and expelled beads, and moderate agreement for the small bowel and colon. Gastrointestinal transit scores were decreased by loperamide and increased by prucalopride compared with baseline.Conclusions & InferencesMetallic beads are reliably localized by videofluoroscopy in vivo within the GI tract. This novel imaging method enables repetitive measurements of GI transit in vivo and detects changes induced by motility‐modifying agents.
The sensitivity of acoustic cough recording relative to intraesophageal pressure recording and patient report during reflux testing
Authors: Rosen R. , Amirault J. , Heinz N. , Litman H. , Khatwa U. 
Published: September 2014

AbstractBackgroundOne of the primary indications for reflux testing with multichannel intraluminal impedance with pH (pH‐MII) is to correlate reflux events with symptoms such as cough. Adult and pediatric studies have shown, using cough as a model, that patient report of symptoms is inaccurate. Unfortunately, intraesophageal pressure recording (IEPR) to record coughs is more invasive which limits its utility in children. The primary aim of this study was to validate the use of acoustic cough recording (ACR) during pH‐MII testing.MethodsWe recruited children undergoing pH‐MII testing for the evaluation of cough. We simultaneously placed IEPR and pH‐MII catheters and an ACR device in each patient. Each 24 h ACR, pH‐MII, and IEPR tracing was scored by blinded investigators. Sensitivities for each method of symptom recording were calculated.Key ResultsA total of 2698 coughs were detected; 1140 were patient reported PR, 2425 were IEPR detected, and 2400 were ACR detected. The sensitivity of PR relative to ACR was 45.9% and the sensitivity of IEPR relative to ACR was 93.6%. There was strong inter‐rater reliability (κ = 0.78) for the identification of cough by ACR.Conclusions & InferencesAcoustic recording is a non‐invasive, sensitive method of recording cough during pH‐MII testing that is well suited for the pediatric population.
Sex Differences in Patients with Chronic Pain Following Whiplash Injury: The Role of Depression, Fear, Somatization, Social Support, and Personality Traits
Authors: Malfliet Anneleen , De Kooning Margot , Inghelbrecht Els , Hachimi‐Idrissi Said , Willems Bert , Bernheim Jan , Nijs Jo 
Published: September 2014

AbstractBackgroundChronic whiplash‐associated disorders (chronic WAD) cover a large variety of clinical manifestations that can occur after a whiplash injury. Women have an increased risk of developing chronic WAD, and it is suggested that psychosocial factors are related to long‐term pain and functioning following whiplash injury and persistence of chronic pain. This leads to the question whether there are sex differences in psychosocial factors in chronic WAD.MethodsThis study included 117 subjects who had experienced a whiplash injury at least 3 months before the start of the study (mean duration of pain: 67.29 ± 63.86 months, range: 297 months). They were selected as chronically symptomatic, by excluding those who had recovered from their whiplash injury. Psychosocial aspects (including depression, fear, somatization, social support, and personality traits) were assessed by validated questionnaires, and sex differences were tested using a univariate analysis of variance (ANCOVA), with age and time from whiplash injury as covariates.ResultsNo differences in depression, fear, somatization, discrepancy in social support personality trait, Neck Disability Index scores, physical functioning, bodily pain, or general health were present between women and men with chronic WAD. Women with chronic WAD reported higher levels of emotional support in problem situations and social companionship.ConclusionExcept for emotional support in problem situations and social companionship, psychosocial factors do not differ between men and women with chronic WAD. These findings imply little to no risk for sex bias in studies investigating psychosocial issues in patients with chronic WAD.
Urea persistence in floodwater and soil used for flooded rice production
Authors: Daigh A. L. , Savin M. C. , Brye K. , Norman R. , Miller D. 
Published: September 2014

AbstractUrea is a common fertilizer in delayed‐flood rice production in the United States, and its use worldwide has increased dramatically in recent decades. This study aimed to directly quantify urea‐N persistence in floodwater and soil used for rice production. We conducted a set of three laboratory experiments to investigate urea‐N presence in the floodwater and soil. Untreated urea was applied to dry or wet soil and flooded immediately or urea treated with the urease inhibitor N‐(n‐butyl)‐thiophosphoric triamide (NBPT), or untreated urea was applied to dry soil and flooded after a 5‐day delay. Urea‐N was analysed colorimetrically (using the microplate‐adapted, diacetyl monoxime method) in the floodwater, and at 2‐cm intervals in soil after 10‐cm long, silt‐loam soil columns were flooded for 12, 24, 48 and 96 h. The only management practice that led to insignificant urea‐N concentrations in floodwaters was the application of urea followed by a 5‐day delay before flooding. Urea‐N can persist in floodwaters for an estimated 98 and 120 h after immediately flooding dry‐soil‐applied or wet‐soil‐applied untreated urea, respectively. Urea‐N concentrations in floodwaters were up to 33 times less when dry‐soil‐applied than wet‐soil‐applied. Average NBPT‐treated urea‐N concentrations in soil ranged up to 63 mg/kg after 24 h of flooding and were <1 mg/kg after 96 h of flooding. The 5‐day delay resulted in ≤1 mg urea‐N/kg soil when untreated urea was applied. Generally, the threat of N entering adjacent waterways in the form of urea is likely to be limited because of its short‐term persistence (≤120 h) in rice floodwater.
Endothelial nitric oxide synthase mediates the nitric oxide component of reflex cutaneous vasodilatation during dynamic exercise in humans
Authors: McNamara Tanner C. , Keen Jeremy T. , Simmons Grant H. , Alexander Lacy M. , Wong Brett J. 
Published: September 2014

Key points

Increases in skin blood flow and sweating also occur during exercise; however, it is not known if the mechanisms controlling these responses are the same during passive heat stress and exercise.

The prevailing thought has been that mechanisms of cutaneous vasodilatation during passive heat stress and sustained dynamic exercise are the same, or very similar.

Nitric oxide (NO) has been shown to be important for increasing skin blood flow during passive heat stress but it is unknown if this molecule is also involved during sustained dynamic exercise.

The findings from our study suggest NO is involved in increasing skin blood flow during sustained dynamic exercise in humans but the NO is produced from a different enzyme compared to passive heat stress.

These findings may help us better understand and aid individuals who have difficulty regulating their body temperature during sustained dynamic exercise (e.g. ageing).

AbstractRecent data suggests neuronal nitric oxide synthase (nNOS) mediates the NO component of reflex cutaneous vasodilatation with passive heat stress. We tested the hypothesis that nNOS inhibition would attenuate reflex cutaneous vasodilatation during sustained dynamic exercise in young healthy humans. All subjects first performed an incremental test to exhaustion on a custom‐built supine cycle ergometer. On a separate day, subjects were instrumented with four intradermal microdialysis fibres on the forearm and each randomly assigned as: (1) lactated Ringer's (control); (2) 20 mm Nω‐nitro‐l‐arginine methyl ester hydrochloride (non‐selective NOS inhibitor); (3) 5 mm N‐propyl‐l‐arginine (nNOS inhibitor); and (4) 10 mm N5‐(1‐iminoethyl)‐l‐ornithine dihydrochloride [endothelial NOS (eNOS) inhibitor]. Following microdialysis placement, subjects performed supine cycling with the experimental arm at heart level at 60% for a period sufficient to raise core temperature 0.8°C. At the end of cycling, all microdialysis sites were locally heated to 43°C and sodium nitroprusside was perfused to elicit maximal vasodilatation. Mean arterial pressure, skin blood flow via laser‐Doppler flowmetry and core temperature via ingestible telemetric pill were measured continuously; cutaneous vascular conductance (CVC) was calculated as laser‐Doppler flowmetry/mean arterial pressure and normalized to maximum. There was no significant difference between control (58 ± 2%CVCmax) and nNOS‐inhibited (56 ± 3%CVCmax) sites in response to exercise‐induced hyperthermia. The increase in CVC at eNOS‐inhibited (41 ± 3%CVCmax) and non‐selective NOS‐inhibited (40 ± 4%CVCmax) sites were significantly attenuated compared to control and nNOS‐inhibited (P < 0.001 all conditions) but there was no difference between eNOS‐inhibited and non‐selective NOS‐inhibited sites. These data suggest eNOS, not nNOS, mediate NO synthesis during reflex cutaneous vasodilatation with sustained dynamic exercise.
Modulation of enteric neurons by interleukin‐6 and corticotropin‐releasing factor contributes to visceral hypersensitivity and altered colonic motility in a rat model of irritable bowel syndrome
Authors: Buckley Maria M. , O'Halloran Ken D. , Rae Mark G. , Dinan Timothy G. , O'Malley Dervla 
Published: September 2014

Key points

Hyperactivity of the stress system and low‐grade immune activation characterize the functional bowel disorder irritable bowel syndrome (IBS).

These studies show that interleukin (IL)‐6 and IL‐8 and the stress hormone corticotropin‐releasing factor (CRF), present in IBS plasma, have functional effects on gastrointestinal activity by stimulating myenteric neurons and colonic contractions.

Moreover, in the Wistar Kyoto rat model of IBS, which exhibits altered gastrointestinal motility and visceral pain sensitivity, blocking IL‐6 and/or CRF1 receptors alleviates these IBS‐like symptoms.

Underlying these effects are altered colonic protein expression of tight junction proteins which regulate gut barrier function and the T‐type calcium channel CaV3.2, which has been linked to visceral pain.

These findings demonstrate the importance of the enteric nervous system and intestinal physiology in bowel dysfunction.

AbstractThe search for effective therapeutic strategies for irritable bowel syndrome (IBS) is hampered by an incomplete understanding of its underlying pathophysiology. Stress and altered plasma cytokine profiles indicative of immune activation are characteristic of the disorder. The neuromodulatory effects of interleukin‐6 (IL‐6) and corticotropin‐releasing factor receptor (CRFR) 1 in visceral pain and stress‐induced defecation in the Wistar Kyoto (WKY) rat model of IBS were investigated. Sprague Dawley and WKY rats were administered anti‐IL‐6 receptor antibodies (xIL‐6R, 0.5 mg kg−1 i.p) with or without the CRFR1 antagonist antalarmin (10 mg kg−1 i.p). Post‐intervention, the pain threshold to colorectal distension and stress‐induced faecal output were compared and changes in colonic mucosal protein expression were investigated. The neuro‐stimulatory effects of IBS plasma on the myenteric plexus is mediated by IL‐6, IL‐8 and CRF. The stimulatory effects of these soluble factors on myenteric neuron excitability and colonic contractility were additive. Moreover, inhibition of IL‐6 and CRF1 receptors in vivo in the WKY IBS rat model normalized stress‐induced defecation (P < 0.01) and visceral pain sensitivity (P < 0.001) with associated changes in protein expression of the tight junction proteins occludin and claudin 2, the visceral pain‐associated T‐type calcium channel CaV3.2 and intracellular signalling molecules STAT3, SOCS3 and ERK1/2. These studies demonstrate the additive effects of immune and stress factors on myenteric neuronal excitability. Moreover, combined targeting of peripheral IL‐6 and CRF1 receptors is effective in alleviating IBS‐like symptoms in the WKY rat. Thus, crosstalk between stress and immune factors during IBS flares may underlie symptom exacerbation.
Charge at the 46th residue of connexin 50 is crucial for the gap‐junctional unitary conductance and transjunctional voltage‐dependent gating
Authors: Tong Xiaoling , Aoyama Hiroshi , Tsukihara Tomitake , Bai Donglin 
Published: September 2014

Key points
Gap‐junction (GJ) channels provide direct intercellular communication and are twice the length of most membrane channels, yet they often have high efficiency in permeation of ions, which is reflected by large unitary channel conductance (γj).
To reveal the key factors in determining the γj of a lens GJ channel, we studied connexin 50 mutant GJ channels, where a negatively or positively charged residue was introduced into a pore‐lining domain.
The results indicate that the pore surface electrostatic potential is a dictating factor for the connexin 50 GJ channel γj.
A change in the local resistance of the channel pore associated with these mutant channels is an important factor for their voltage‐dependent gating properties.
The combination of dual patch clamp and homology structure modelling is a powerful approach in revealing molecular mechanisms of GJ gating and ion permeation.
AbstractGap‐junction (GJ) channels are twice the length of most membrane channels, yet they often have large unitary channel conductance (γj). What factors make this possibly the longest channel so efficient in passing ions are not fully clear. Here we studied the lens connexin (Cx) 50 GJs, which display one of the largest γj and the most sensitive transjunctional voltage‐dependent gating (Vj gating) among all GJ channels. Introduction of charged residues into a putative pore‐lining domain (the first transmembrane and the first extracellular loop border) drastically altered the apparent γj. Specifically, G46D and G46E increased the Cx50 γj from 201 to 256 and 293 pS, respectively and the G46K channel showed an apparent γj of only 20 pS. G46K also drastically altered Vj gating properties in homotypic G46K and heterotypic Cx50/G46K channels, causing an apparent loss of fast Vj‐dependent gating transitions and leaving only loop gating transitions at the single channel current records. Both macroscopic and single channel currents of heterotypic Cx50/G46K channels showed a prominent rectification. Our homology structural models indicate that the pore surface electrostatic potentials are a dictating factor in determining the γj. Our data demonstrate, at the whole GJ channel level, a crucial role of the surface charge properties in the first transmembrane/first extracellular border domain in determining the efficiency of ion permeation and the Vj gating of Cx50 and possibly other GJ channels.
An Experimental Study of Smart Waterflooding on Fractured Carbonate Reservoirs
Authors: Awolayo Adedapo , AlSumaiti Ali M. , Sarma Hemanta 
Published: September 2014

Wetting state in many fractured carbonate reservoirs exists between mixed-wet to oil-wet. Interaction of negatively charged carboxylic molecules in the crude oil with the rock surface, and high capillary pressure encountered during oil migration into the reservoir rock frequently render the rock oil-wet. Similarly, the existence of fractures solitarily governs the fluid flow dynamics in the porous media. Therefore, oil recovery from oil-wet fractured reservoirs is extremely tasking due to complex mechanisms involved in interactions between the double porosity system and the reservoir fluids.
Waterflooding seems to be an economical technique to recover oil from fractured (water-wet) reservoirs where the rate of oil recovery is controlled by the water imbibition into the matrix from the fracture network. While for oil-wet reservoirs, waterflooding appears feeble and smart waterflooding looks very promising through varying of ions in the injection water. Hence changes the properties of the rock and improves waterflood performance.
Middle East carbonate cores, dead crude oil, and smart water of different salinity were used in both static imbibition cells and centrifuge experiments. In order to gain better understanding of the relative contribution of oil recovery between fracture and matrix, different core configurations were used. The tests were carried out initially with formation brine and followed by different slugs of smart water. Presented in this work are the results obtained from the formation brine-oil imbibition tests and smart water-oil imbibition tests in fractured and unfractured cores. Results showed that waterflood recovery from fractured carbonate cores was about 50% of the OOIC while incremental displacement for smart water imbibition was observed nearly as high as 13%.
Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling
Authors: Salipante Stephen J. , Kawashima Toana , Rosenthal Christopher , Hoogestraat Daniel R. , Cummings Lisa A. , Sengupta Dhruba J. , Harkins Timothy T. , Cookson Brad T. , Hoffman Noah G. 
Published: September 2014

ABSTRACT
High-throughput sequencing of the taxonomically informative 16S rRNA gene provides a powerful approach for exploring microbial diversity. Here we compare the performances of two common “benchtop” sequencing platforms, Illumina MiSeq and Ion Torrent Personal Genome Machine (PGM), for bacterial community profiling by 16S rRNA (V1-V2) amplicon sequencing. We benchmarked performance by using a 20-organism mock bacterial community and a collection of primary human specimens. We observed comparatively higher error rates with the Ion Torrent platform and report a pattern of premature sequence truncation specific to semiconductor sequencing. Read truncation was dependent on both the directionality of sequencing and the target species, resulting in organism-specific biases in community profiles. We found that these sequencing artifacts could be minimized by using bidirectional amplicon sequencing and an optimized flow order on the Ion Torrent platform. Results of bacterial community profiling performed on the mock community and a collection of 18 human-derived microbiological specimens were generally in good agreement for both platforms; however, in some cases, results differed significantly. Disparities could be attributed to the failure to generate full-length reads for particular organisms on the Ion Torrent platform, organism-dependent differences in sequence error rates affecting classification of certain species, or some combination of these factors. This study demonstrates the potential for differential bias in bacterial community profiles resulting from the choice of sequencing platform alone.
Evidence for the Cooccurrence of Nitrite-Dependent Anaerobic Ammonium and Methane Oxidation Processes in a Flooded Paddy Field
Authors: Shen Li-dong , Liu Shuai , Huang Qian , Lian Xu , He Zhan-fei , Geng Sha , Jin Ren-cun , He Yun-feng , Lou Li-ping , Xu Xiang-yang , Zheng Ping , Hu Bao-lan 
Published: September 2014

ABSTRACT

Anaerobic ammonium oxidation (anammox) and nitrite-dependent anaerobic methane oxidation (n-damo) are two of the most recent discoveries in the microbial nitrogen cycle. In the present study, we provide direct evidence for the cooccurrence of the anammox and n-damo processes in a flooded paddy field in southeastern China. Stable isotope experiments showed that the potential anammox rates ranged from 5.6 to 22.7 nmol N
2
g
−1
(dry weight) day
−1
and the potential n-damo rates varied from 0.2 to 2.1 nmol CO
2
g
−1
(dry weight) day
−1
in different layers of soil cores. Quantitative PCR showed that the abundance of anammox bacteria ranged from 1.0 × 10
5
to 2.0 × 10
6
copies g
−1
(dry weight) in different layers of soil cores and the abundance of n-damo bacteria varied from 3.8 × 10
5
to 6.1 × 10
6
copies g
−1
(dry weight). Phylogenetic analyses of the recovered 16S rRNA gene sequences showed that anammox bacteria affiliated with “
Candidatus
Brocadia” and “
Candidatus
Kuenenia” and n-damo bacteria related to “
Candidatus
Methylomirabilis oxyfera” were present in the soil cores. It is estimated that a total loss of 50.7 g N m
−2
per year could be linked to the anammox process, which is at intermediate levels for the nitrogen flux ranges of aerobic ammonium oxidation and denitrification reported in wetland soils. In addition, it is estimated that a total of 0.14 g CH
4
m
−2
per year could be oxidized via the n-damo process, while this rate is at the lower end of the aerobic methane oxidation rates reported in wetland soils.