bluuebunny/crossref_metadata_2025_split huggingface dataset:
Delayed liver regeneration in C3H/HeJ mice: possible involvement of haemodynamic and structural changes in the hepatic microcirculation
Authors: Marlini Muhamad , Mabuchi Ayako , Mallard Beth L. , Hairulhisyam Ngatiman , Akashi‐Takamura Sachiko , Harper Jacquie L. , Wheatley Antony M. 
Published: September 2016

New Findings
What is the central question of this study?
The liver regenerative process is complex and involves a sequence of signalling events, but the possible involvement of structural and haemodynamic changes in vivo during this process has never been explored.

What is the main finding and its importance?
Normal sinusoidal blood flow and velocity are crucial for a normal regenerative response, and delays in these haemodynamic events resulted in impaired liver regeneration in lipopolysaccharide‐insensitive, C3H/HeJ mice. Toll‐like receptor 4 signalling is required for restoration of normal liver architecture during the liver regenerative process.

Liver regeneration is delayed in mice with a defective Toll‐like receptor 4 (TLR4; C3H/HeJ mice) but is normal in TLR4 knockouts (TLR4−/−). Here, we investigated the possible involvement of structural and haemodynamic changes in vivo in the underlying mechanism. In lipopolysaccharide‐sensitive (C3H/HeN and C57BL/6) and lipopolysaccharide‐insensitive (C3H/HeJ and TLR4−/−) mice, a 70% partial hepatectomy (PH) was performed under inhalational anaesthesia. At days 3 and 7 after PH, the hepatic microcirculation was interrogated using intravital microscopy. Delayed liver regeneration was confirmed in C3H/HeJ, but not in C3H/HeN, C57BL/6 (WT) or TLR4−/− mice by liver weight‐to‐body‐weight ratio, the percentage of proliferating cell nuclear antigen (PCNA)‐positive cells and mitotic index data. At day 3 after PH, sinusoidal red blood cell velocity increased by 100% in C3H/HeN mice, but by only 40% in C3H/HeJ mice. Estimated sinusoidal blood flow was significantly higher at day 7 after PH in C3H/HeN than in C3H/HeJ mice. The hepatic cord width was significantly larger in C3H/HeN than in C3H/HeJ mice at day 3 and it was significantly larger in TLR4−/− than in C57BL/6 WT mice at day 7 after PH. Hepatocyte nucleus density and functional sinusoidal density was significantly reduced at days 3 and 7 after PH in all mouse strains compared with their zero‐time controls. Functional sinusoidal density was significantly lower in C3H/HeJ compared with C3H/HeN mice at day 7 after PH. The present study indicates that altered sinusoidal blood flow and velocity in C3H/HeJ mice may contribute to the observed delay in the regenerative response in these mice. In addition, restoration of normal liver architecture may be delayed in TLR4−/− mice.
Accumulation of K+ in the synaptic cleft modulates activity by influencing both vestibular hair cell and calyx afferent in the turtle
Authors: Contini Donatella , Price Steven D. , Art Jonathan J. 
Published: September 2016

Key points
In the synaptic cleft between type I hair cells and calyceal afferents, K+ ions accumulate as a function of activity, dynamically altering the driving force and permeation through ion channels facing the synaptic cleft.
High‐fidelity synaptic transmission is possible due to large conductances that minimize hair cell and afferent time constants in the presence of significant membrane capacitance.
Elevated potassium maintains hair cells near a potential where transduction currents are sufficient to depolarize them to voltages necessary for calcium influx and synaptic vesicle fusion.
Elevated potassium depolarizes the postsynaptic afferent by altering ion permeation through hyperpolarization‐activated cyclic nucleotide‐gated (HCN) channels, and contributes to depolarizing the afferent to potentials where a single EPSP (quantum) can generate an action potential.
With increased stimulation, hair cell depolarization increases the frequency of quanta released, elevates [K+]cleft and depolarizes the afferent to potentials at which smaller and smaller EPSPs would be sufficient to trigger APs.
AbstractFast neurotransmitters act in conjunction with slower modulatory effectors that accumulate in restricted synaptic spaces found at giant synapses such as the calyceal endings in the auditory and vestibular systems. Here, we used dual patch‐clamp recordings from turtle vestibular hair cells and their afferent neurons to show that potassium ions accumulating in the synaptic cleft modulated membrane potentials and extended the range of information transfer. High‐fidelity synaptic transmission was possible due to large conductances that minimized hair cell and afferent time constants in the presence of significant membrane capacitance. Increased potassium concentration in the cleft maintained the hair cell near potentials that promoted the influx of calcium necessary for synaptic vesicle fusion. The elevated potassium concentration also depolarized the postsynaptic neuron by altering ion permeation through hyperpolarization‐activated cyclic nucleotide‐gated (HCN) channels. This depolarization enabled the afferent to reliably generate action potentials evoked by single AMPA‐dependent EPSPs. Depolarization of the postsynaptic afferent could also elevate potassium in the synaptic cleft, and would depolarize other hair cells enveloped by the same neuritic process increasing the fidelity of neurotransmission at those synapses as well. Collectively, these data demonstrate that neuronal activity gives rise to potassium accumulation, and suggest that potassium ion action on HCN channels can modulate neurotransmission, preserving the fidelity of high‐speed synaptic transmission by dynamically shifting the resting potentials of both presynaptic and postsynaptic cells.
First Draft Genome Sequence of a UK Strain (UK99) of
Fusarium culmorum
Authors: Urban Martin , King Robert , Andongabo Ambrose , Maheswari Uma , Pedro Helder , Kersey Paul , Hammond-Kosack Kim 
Published: September 2016

ABSTRACT

Fusarium culmorum
is a soilborne fungal plant pathogen that causes foot and root rot and
Fusarium
head blight on small-grain cereals, in particular on wheat and barley. We report herein the draft genome sequence of a 1998 field strain called FcUK99 adapted to the temperate climate found in England.
Draft Genome Sequence of the
Bactrocera oleae
Symbiont “
Candidatus
Erwinia dacicola”
Authors: Blow Frances , Gioti Anastasia , Starns David , Ben-Yosef Michael , Pasternak Zohar , Jurkevitch Edouard , Vontas John , Darby Alistair C. 
Published: September 2016

ABSTRACT

“
Candidatus
Erwinia dacicola” is a
Gammaproteobacterium
that forms a symbiotic association with the agricultural pest
Bactrocera oleae
. Here, we present a 2.1-Mb draft hybrid genome assembly for “
Ca.
Erwinia dacicola” generated from single-cell and metagenomic data.
Draft Genome Sequence of Two Monosporidial Lines of the Karnal Bunt Fungus
Tilletia indica
Mitra (PSWKBGH-1 and PSWKBGH-2)
Authors: Sharma Pradeep , Tiwari Ratan , Saharan M. S. , Sharma Indu , Kumar Jitender , Mishra Shefali , Muthusamy Senthilkumar K. , Gupta R. K. , Jaiswal Sarika , Iquebal M. A. , Angadi U. B. , Kumar Neeraj , Fatma Samar , Rai Anil , Kumar Dinesh 
Published: September 2016

ABSTRACT

Karnal bunt disease caused by the fungus
Tilletia indica
Mitra is a serious concern due to strict quarantines affecting international trade of wheat. We announce here the first draft assembly of two monosporidial lines, PSWKBGH-1 and -2, of this fungus, having approximate sizes of 37.46 and 37.21 Mbp, respectively.
Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2
Authors: Uchimura Yasuhiro , Wyss Madeleine , Brugiroux Sandrine , Limenitakis Julien P. , Stecher Bärbel , McCoy Kathy D. , Macpherson Andrew J. 
Published: September 2016

ABSTRACT
We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species.
Genome Sequence of the Facultative Anaerobe Oerskovia enterophila DFA-19 (DSM 43852
T
)
Authors: Jag Vanessa , Poehlein Anja , Bengelsdorf Frank R. , Daniel Rolf , Dürre Peter 
Published: September 2016

ABSTRACT

Here, we report the draft genome sequence of
Oerskovia enterophila
DFA-19 (DSM 43852
T
), a facultative anaerobe soil bacterium, which was originally isolated from millipede feces and first described as
Promicromonospora enterophila
. The genome consists of a circular chromosome comprising approximately 4.65 Mb and 4,044 predicted protein-encoding genes.
Complete Genome Sequences of Bordetella pertussis Vaccine Reference Strains 134 and 10536
Authors: Weigand Michael R. , Peng Yanhui , Loparev Vladimir , Batra Dhwani , Burroughs Mark , Johnson Taccara , Juieng Phalasy , Rowe Lori , Tondella M. Lucia , Williams Margaret M. 
Published: September 2016

ABSTRACT

Vaccine formulations and vaccination programs against whooping cough (pertussis) vary worldwide. Here, we report the complete genome sequences of two divergent
Bordetella pertussis
reference strains used in the production of pertussis vaccines.
Complete Mitochondrial Genome Sequence of Sunflower (
Helianthus annuus
L.)
Authors: Grassa Christopher J. , Ebert Daniel P. , Kane Nolan C. , Rieseberg Loren H. 
Published: September 2016

ABSTRACT

This is the first complete mitochondrial genome sequence for sunflower and the first complete mitochondrial genome for any member of
Asteraceae
, the largest plant family, which includes over 23,000 named species. The master circle is 300,945-bp long and includes 27 protein-coding sequences, 18 tRNAs, and the 26S, 5S, and 18S rRNAs.
Complete Genome Sequence of the Filamentous Fungus Aspergillus westerdijkiae Reveals the Putative Biosynthetic Gene Cluster of Ochratoxin A
Authors: Chakrabortti Alolika , Li Jinming , Liang Zhao-Xun 
Published: September 2016

ABSTRACT

Ochratoxin A (OTA) is a common mycotoxin that contaminates food and agricultural products. Sequencing of the complete genome of
Aspergillus westerdijkiae
, a major producer of OTA
,
reveals more than 50 biosynthetic gene clusters, including a putative OTA biosynthetic gene cluster that encodes a dozen of enzymes, transporters, and regulatory proteins.
Draft Genome Sequence of the Heavy-Metal-Tolerant Marine Yeast Debaryomyces hansenii J6
Authors: Berrocal Camille A. , Rivera-Vicens Ramon E. , Nadathur Govind S. 
Published: September 2016

ABSTRACT

Debaryomyces hansenii
J6 is a heavy-metal-tolerant, flavinogenic yeast isolated from a Swedish estuary. We present here the 11.63-Mb genome of this organism containing 5,717 open reading frames. Comparison with available
Debaryomyces
genomes demonstrated that J6 is closer to
D. hansenii
MTCC234 than
D. fabry
CBS789 and
D. hansenii
CBS767.
Draft Genome Sequences of Microbacterium hominis LCDC-84-0209
T
Isolated from a Human Lung Aspirate and Microbacterium laevaniformans LCDC 91-0039 Isolated from a Human Blood Culture
Authors: Bernier Anne-Marie , Bernard Kathryn 
Published: September 2016

ABSTRACT

Draft genomes for
Microbacterium hominis
84-0209
T
and
M. laevaniformans
91-0039 were studied. Genome sizes (bps, [G+C contents]) were 3,506,522 (70.96%) and 2,999,965 (69.51%), respectively. Annotation revealed: (
M. hominis
) three rRNA sequences, 45 tRNA genes, and 3,218 coding sequences; (
M. laevaniformans
) three rRNA sequences, 49 tRNA genes, and 2,874 coding sequences.
Complete Genome Sequences of 17 Canadian Isolates of Salmonella enterica subsp.
enterica
Serovar Heidelberg from Human, Animal, and Food Sources
Authors: Labbé Geneviève , Ziebell Kim , Bekal Sadjia , Macdonald Kimberley A. , Parmley E. Jane , Agunos Agnes , Desruisseau Andrea , Daignault Danielle , Slavic Durda , Hoang Linda , Ramsay Danielle , Pollari Frank , Robertson James , Nash John H. E. , Johnson Roger P. 
Published: September 2016

ABSTRACT

Salmonella enterica
subsp.
enterica
serovar Heidelberg is a highly clonal serovar frequently associated with foodborne illness. To facilitate subtyping efforts, we report fully assembled genome sequences of 17 Canadian
S
. Heidelberg isolates including six pairs of epidemiologically related strains. The plasmid sequences of eight isolates contain several drug resistance genes.
Draft Genome Sequences of Histamine-Producing Morganella psychrotolerans Strains
Authors: Bjornsdottir-Butler Kristin , Leon Maria Sanchez , Benner Ronald A. 
Published: September 2016

ABSTRACT

Histamine-producing bacteria are responsible for scombrotoxin (histamine) fish poisoning, a leading cause of fish poisoning in the United States. We report here the first draft genomes of three histamine-producing
Morganella psychrotolerans
strains, isolated from tuna and mahi-mahi.
Complete Genome Sequences of the Plasmid-Bearing Campylobacter coli Strains HC2-48, CF2-75, and CO2-160 Isolated from Retail Beef Liver
Authors: Marasini Daya , Fakhr Mohamed K. 
Published: September 2016

ABSTRACT

The complete genome sequences of
Campylobacter coli
strains HC2-48, CF2-75, and CO2-160, isolated from retail beef liver, showed the presence of 1,663,782-, 1,711,393-, and 1,683,224-bp circular chromosomes and 44,064-, 44,233-, and 44,228-bp circular plasmids, respectively. This is the first reported
Campylobacter coli
genome sequence isolated from retail beef liver.
Draft Genome Sequence of Legionella jamestowniensis Isolated from a Patient with Chronic Respiratory Disease
Authors: Prochazka Birgit , Indra Alexander , Hasenberger Petra , Blaschitz Marion , Wagner Laura , Wewalka Günther , Sorschag Sieglinde , Schmid Daniela , Ruppitsch Werner 
Published: September 2016

ABSTRACT

Legionella jamestowniensis
can be found in the environment in various water samples, in wet soil, and in compost facilities, but evidence of its human pathogenicity has not yet been demonstrated. Here, we report the first draft genome sequence of an
L. jamestowniensis
isolate, derived from a patient suffering from a chronic respiratory disease.
Proterozoic geology of the Baraboo Interval
Authors: Bjørnerud Marcia 
Published: September 2016

Abstract
The Proterozoic Baraboo Quartzite was laid down by braided rivers and in near-shore marine environments on the southern edge of Paleo–North America during a period of tectonic stability following a prolonged interval of orogenic activity. The exceptional chemical maturity of the Quartzite points to warm, wet, tropical climate conditions, and its distinctive maroon to pink and purple color marks it as one of the earliest “red beds” on Earth. Detrital zircons from the base of the Quartzite constrain its depositional age to be younger than ca. 1710 Ma. The Quartzite is overlain by two other units known only from subsurface exploration: the Seeley Slate, interpreted as a shallow marine deposit, and the Freedom Formation, which has the physical and mineralogical characteristics of classic Superior-type iron formations but is younger than any of these by at least 150 m.y. The folding event at Baraboo was previously thought to have occurred at ca. 1630 Ma, based on indirect regional arguments. However, a growing number of 40Ar/39Ar ages in the range of 1450–1480 Ma have been obtained from occurrences of muscovite in hydrothermal veins in the Quartzite and from tectonic cleavage surfaces in the Seeley Slate, and these suggest a possible connection with the Wolf River Batholith igneous interval. The remarkable topographic relief that existed in the Baraboo Range at the time of the late Cambrian marine transgression, one billion years after the folding event, is another aspect of the regional geologic history that remains incompletely understood.
Baraboo Quartzite
Authors: Davis Richard A. 
Published: September 2016

Abstract
The Baraboo Quartzite contains numerous well-preserved sedimentary structures that enable interpretation of environments of deposition. Included are various types of cross-stratification, reactivation surfaces, and tidal bedding. The bulk of the Baraboo was deposited under tidal influence. The remainder represents deposition in a braided stream system. The origin of the tremendous volume of quartz sand remains somewhat unknown.
Quaternary geology of the Baraboo area
Authors: Davis Richard A. 
Published: September 2016

Abstract
The surficial geology of the Baraboo area is very important because it includes the transition from a glaciated region to the Driftless Area. The eastern portion of this area was glaciated as part of the Green Bay lobe of the ice sheet in this area. The terminal moraine is present and is characterized by sandy till. No valid information that substantiates glacial activity exists west of the city of Baraboo. The Driftless Area includes a site of the earliest Wisconsin habitation.
Utility of clinical tests to diagnose MRI-confirmed gluteal tendinopathy in patients presenting with lateral hip pain
Authors: Grimaldi Alison , Mellor Rebecca , Nicolson Phillipa , Hodges Paul , Bennell Kim , Vicenzino Bill 
Published: September 2016

PurposeGluteal tendinopathy (GT) is a source of lateral hip pain, yet common clinical diagnostic tests have limited validity. Patients with GT are often misdiagnosed, resulting in inappropriate management, including surgery. This study determined the diagnostic utility of clinical tests for GT, using MRI as the reference standard.Methods65 participants with lateral hip pain were examined to evaluate the ability of clinical tests to detect MRI-determined GT (an increase in intratendinous signal intensity on T2-weighted images). Palpation of the greater trochanter and several clinical pain provocation tests applying compressive and tensile loads on the gluteal tendons were investigated. MRI of the painful hip was examined by a radiologist, blind to clinical findings.ResultsPain reported within 30 s of standing on the affected limb conclusively moves a (nominal) 50% pretest probability of GT presence on MRI to a post-test probability of 98% (specificity 100%, positive likelihood ratio ∼12), whereas no pain on palpation (80% sensitivity) would rule out its presence. 20 participants (31%) had GT on MRI but clinically negative (ie, not positive on palpation and another test).ConclusionsKeeping in mind that the sample size was small (ie, possibly underpowered for indices of diagnostic utility with low precision), the results of this study indicate that a patient who reports lateral hip pain within 30 s of single-leg-standing is very likely to have GT. Patients with lateral hip pain who are not palpably tender over the greater trochanter are unlikely to have MRI-detected GT.
Can the UNAIDS 90-90-90 target be achieved? A systematic analysis of national HIV treatment cascades
Authors: Levi Jacob , Raymond Alice , Pozniak Anton , Vernazza Pietro , Kohler Philipp , Hill Andrew 
Published: September 2016

BackgroundIn 2014, the Joint United Nations Programme on HIV and AIDS (UNAIDS) and partners set the ‘90-90-90 targets’; aiming to diagnose 90% of all HIV positive people, provide antiretroviral therapy (ART) for 90% of those diagnosed and achieve viral suppression for 90% of those treated, by 2020. This results in 81% of all HIV positive people on treatment and 73% of all HIV positive people achieving viral suppression. We aimed to analyse how effective national HIV treatment programmes are at meeting these targets, using HIV care continuums or cascades.MethodsWe searched for HIV treatment cascades for 196 countries in published papers, conference presentations, UNAIDS databases and national reports. Cascades were constructed using reliable, generalisable, recent data from national, cross-sectional and longitudinal study cohorts. Data were collected for four stages; total HIV positive people, diagnosed, on treatment and virally suppressed. The cascades were categorised as complete (four stages) or partial (3 stages), and analysed for ‘break points’ defined as a drop >10% in coverage between consecutive 90-90-90 targets.Results69 country cascades were analysed (32 complete, 37 partial). Diagnosis (target one—90%) ranged from 87% (the Netherlands) to 11% (Yemen). Treatment coverage (target two—81% on ART) ranged from 71% (Switzerland) to 3% (Afghanistan). Viral suppression (target three—73% virally suppressed) was between 68% (Switzerland) and 7% (China).ConclusionsNo country analysed met the 90-90-90 targets. Diagnosis was the greatest break point globally, but the most frequent key break point for individual countries was providing ART to those diagnosed. Large disparities were identified between countries. Without commitment to standardised reporting methodologies, international comparisons are complex.
Small-for-gestational age and its association with maternal blood glucose, body mass index and stature: a perinatal cohort study among Chinese women
Authors: Leng Junhong , Hay John , Liu Gongshu , Zhang Jing , Wang Jing , Liu Huihuan , Yang Xilin , Liu Jian 
Published: September 2016

ObjectiveTo examine whether maternal low blood glucose (BG), low body mass index (BMI) and small stature have a joint effect on the risk of delivery of a small-for-gestational age (SGA) infant.DesignWomen from a perinatal cohort were followed up from receiving perinatal healthcare to giving birth.SettingBeichen District, Tianjin, China between June 2011 and October 2012.Participants1572 women aged 19–39 years with valid values of stature, BMI and BG level at gestational diabetes mellitus screening (gestational weeks 24–28), glucose challenge test <7.8 mmol/L and singleton birth (≥37 weeks’ gestation).Main outcome measuresSGA was defined as birth weight <10th centile for gender separated gestational age of Tianjin singletons.Results164 neonates (10.4%) were identified as SGA. From multiple logistic regression models, the ORs (95% CI) of delivery of SGA were 0.84 (0.72 to 0.98), 0.61 (0.49 to 0.74) and 0.64 (0.54 to 0.76) for every 1 SD increase in maternal BG, BMI and stature, respectively. When dichotomises, maternal BG (<6.0 vs ≥6.0 mmol/L), BMI (<24 vs ≥24 kg/m2) and stature (<160.0 vs ≥160.0 cm), those with BG, BMI and stature all in the lower categories had ∼8 times higher odds of delivering an SGA neonate (OR (95% CI) 8.01 (3.78 to 16.96)) relative to the reference that had BG, BMI and stature all in the high categories. The odds for an SGA delivery among women who had any 2 variables in the lower categories were ∼2–4 times higher.ConclusionsLow maternal BG is associated with an increased risk of having an SGA infant. The risk of SGA is significantly increased when the mother is also short and has a low BMI. This may be a useful clinical tool to identify women at higher risk for having an SGA infant at delivery.