bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the postglacial spread of human commensal Arabidopsis thaliana: journey to the East
Authors: Hsu Che‐Wei , Lo Cheng‐Yu , Lee Cheng‐Ruei 
Published: January 2019

Summary

With more sequenced genomes, our understanding of the demographic history of Arabidopsis thaliana is rapidly expanding. However, no‐one has yet compiled previous data to investigate patterns of genetic variation across Eurasia.

While sub‐Saharan accessions have been reported to be the most divergent group, in the nuclear genome we found accessions from Yunnan, China to be genetically closest to the sub‐Saharan group. In chloroplast, several deeply diverged haplogroups exist only in Eurasia, and African populations have lower variation in many haplogroups that they share with the Eurasian populations. These patterns cannot be easily explained by a single out‐of‐Africa event suggested previously.

For more recent demographic history, we dated the nonrelict expansion to 10 ka. In the Chinese Yangtze nonrelicts, we found clear traces of gene flow with local relicts, and genes under strong selection were enriched for traces of relict introgression, especially those related to biotic and immune responses. The results suggest the ability of nonrelicts to obtain locally adaptive alleles through admixture with relicts is important for the expansion across environmental gradients of Eurasia.

Our re‐analyses provide another model for the early history as well as elucidating factors contributing to the recent demographic turnover event of this species.
Inside out: root cortex‐localized LHK1 cytokinin receptor limits epidermal infection of Lotus japonicus roots by Mesorhizobium loti
Authors: Miri Mandana , Janakirama Preetam , Huebert Terry , Ross Loretta , McDowell Tim , Orosz Kathleen , Markmann Katharina , Szczyglowski Krzysztof 
Published: January 2019

Summary

During Lotus japonicus–Mesorhizobium loti symbiosis, the LOTUS HISTIDINE KINASE1 (LHK1) cytokinin receptor regulates both the initiation of nodule formation and the scope of root infection. However, the exact spatiotemporal mechanism by which this receptor exerts its symbiotic functions has remained elusive.

In this study, we performed cell type‐specific complementation experiments in the hyperinfected lhk1‐1 mutant background, targeting LHK1 to either the root epidermis or the root cortex. We also utilized various genetic backgrounds to characterize expression of several genes regulating symbiotic infection.

We show here that expression of LHK1 in the root cortex is required and sufficient to regulate both nodule formation and epidermal infections. The LHK1‐dependent signalling that restricts subsequent infection events is triggered before initial cell divisions for nodule primordium formation. We also demonstrate that AHK4, the Arabidopsis orthologue of LHK1, is able to regulate M. loti infection in L. japonicus, suggesting that an endogenous cytokinin receptor could be sufficient for engineering nitrogen‐fixing root nodule symbiosis in nonlegumes.

Our data provide experimental evidence for the existence of an LHK1‐dependent root cortex‐to‐epidermis feedback mechanism regulating rhizobial infection. This root‐localized regulatory module functionally links with the systemic autoregulation of nodulation (AON) to maintain the homeostasis of symbiotic infection.
Adjustments and coordination of hydraulic, leaf and stem traits along a water availability gradient
Authors: Rosas Teresa , Mencuccini Maurizio , Barba Josep , Cochard Hervé , Saura‐Mas Sandra , Martínez‐Vilalta Jordi 
Published: January 2019

SummaryTrait variability in space and time allows plants to adjust to changing environmental conditions. However, we know little about how this variability is distributed and coordinated at different organizational levels.For six dominant tree species in northeastern Spain (three Fagaceae and three Pinaceae) we quantified the inter‐ and intraspecific variability of a set of traits along a water availability gradient. We measured leaf mass per area (LMA), leaf nitrogen (N) concentration, carbon isotope composition in leaves (δ13C), stem wood density, the Huber value (Hv, the ratio of cross‐sectional sapwood area to leaf area), sapwood‐specific and leaf‐specific stem hydraulic conductivity, vulnerability to xylem embolism (P50) and the turgor loss point (Ptlp).Differences between families explained the largest amount of variability for most traits, although intraspecific variability was also relevant. Species occupying wetter sites showed higher N,P50andPtlp, and lower LMA, δ13C and Hv. However, when trait relationships with water availability were assessed within species they held only for Hv andPtlp.Overall, our results indicate that intraspecific adjustments along the water availability gradient relied primarily on changes in resource allocation between sapwood and leaf area and in leaf water relations.
Cross‐compartment metabolic coupling enables flexible photoprotective mechanisms in the diatomPhaeodactylum tricornutum
Authors: Broddrick Jared T. , Du Niu , Smith Sarah R. , Tsuji Yoshinori , Jallet Denis , Ware Maxwell A. , Peers Graham , Matsuda Yusuke , Dupont Chris L. , Mitchell B. Greg , Palsson Bernhard O. , Allen Andrew E. 
Published: January 2019

SummaryPhotoacclimation consists of short‐ and long‐term strategies used by photosynthetic organisms to adapt to dynamic light environments. Observable photophysiology changes resulting from these strategies have been used in coarse‐grained models to predict light‐dependent growth and photosynthetic rates. However, the contribution of the broader metabolic network, relevant to species‐specific strategies and fitness, is not accounted for in these simple models.We incorporated photophysiology experimental data with genome‐scale modeling to characterize organism‐level, light‐dependent metabolic changes in the model diatomPhaeodactylum tricornutum. Oxygen evolution and photon absorption rates were combined with condition‐specific biomass compositions to predict metabolic pathway usage for cells acclimated to four different light intensities.Photorespiration, an ornithine‐glutamine shunt, and branched‐chain amino acid metabolism were hypothesized as the primary intercompartment reductant shuttles for mediating excess light energy dissipation. Additionally, simulations suggested that carbon shunted through photorespiration is recycled back to the chloroplast as pyruvate, a mechanism distinct from known strategies in photosynthetic organisms.Our results suggest a flexible metabolic network inP. tricornutumthat tunes intercompartment metabolism to optimize energy transport between the organelles, consuming excess energy as needed. Characterization of these intercompartment reductant shuttles broadens our understanding of energy partitioning strategies in this clade of ecologically important primary producers.
Variance in biomass‐allocation fractions is explained by distribution in European trees
Authors: Veresoglou Stavros D. , Peñuelas Josep 
Published: January 2019

SummaryIntraspecific variability in ecological traits confers the ability of a species to adapt to an ever‐changing environment. Fractions of biomass allocation in plants (BAFs) represent both ecological traits and direct expressions of investment strategies and so have important implications on plant fitness, particularly under current global change.We combined data on BAFs of trees in > 10 000 forest plots with their distributions in Europe. We aimed to test whether plant species with wider distributions have more or less variable intraspecific variance of the BAFs foliage–woody biomass and shoot–root ratios than species with limited distribution.Irrespective of corrections for tree age and phylogenetic relatedness, the standard deviation in BAFs was up to three times higher in species with the most extensive distributions than in those with the least extensive distribution due to a higher genetic diversity. Variance in BAFs also increased with latitude.We show that a combination of 36% tree genetic diversity and 64% environmental variability explains variance in BAFs and implies that changes in genetic diversity occur quickly. Genetic diversity should thus play a key role in regulating species responses to future climate change. Loss of habitat, even if transient, could induce a loss of genetic diversity and hinder species survival.
Comparative genomics of Rhizophagus irregularis, R. cerebriforme, R. diaphanus and Gigaspora rosea highlights specific genetic features in Glomeromycotina
Authors: Morin Emmanuelle , Miyauchi Shingo , San Clemente Hélène , Chen Eric C. H. , Pelin Adrian , de la Providencia Ivan , Ndikumana Steve , Beaudet Denis , Hainaut Mathieu , Drula Elodie , Kuo Alan , Tang Nianwu , Roy Sébastien , Viala Julie , Henrissat Bernard , Grigoriev Igor V. , Corradi Nicolas , Roux Christophe , Martin Francis M. 
Published: January 2019

Summary

Glomeromycotina is a lineage of early diverging fungi that establish arbuscular mycorrhizal (AM) symbiosis with land plants. Despite their major ecological role, the genetic basis of their obligate mutualism remains largely unknown, hindering our understanding of their evolution and biology.

We compared the genomes of Glomerales (Rhizophagus irregularis, Rhizophagus diaphanus, Rhizophagus cerebriforme) and Diversisporales (Gigaspora rosea) species, together with those of saprotrophic Mucoromycota, to identify gene families and processes associated with these lineages and to understand the molecular underpinning of their symbiotic lifestyle.

Genomic features in Glomeromycotina appear to be very similar with a very high content in transposons and protein‐coding genes, extensive duplications of protein kinase genes, and loss of genes coding for lignocellulose degradation, thiamin biosynthesis and cytosolic fatty acid synthase. Most symbiosis‐related genes in R. irregularis and G. rosea are specific to Glomeromycotina. We also confirmed that the present species have a homokaryotic genome organisation.

The high interspecific diversity of Glomeromycotina gene repertoires, affecting all known protein domains, as well as symbiosis‐related orphan genes, may explain the known adaptation of Glomeromycotina to a wide range of environmental settings. Our findings contribute to an increasingly detailed portrait of genomic features defining the biology of AM fungi.
Retention of osteocytic micromorphology by sclerostin antibody in a concurrent ovariectomy and functional disuse model
Authors: Zhang Dongye , Miranda Mariana , Li Xiaofei , Han Jiangmeng , Sun Yueli , Rojas Nancy , He Shan , Hu Minyi , Lin Liangjun , Li Xiaodong , Ke Hua Zhu , Qin Yi‐Xian 
Published: January 2019

AbstractProlonged mechanical unloading in bedridden patients and concurrent hormonal dysregulation represents the cause of one of the severest forms of osteoporosis, a condition for which there are very few efficacious interventions available to date. Sclerostin, a Wnt antagonist, acts as a negative regulator of bone formation. Sclerostin antibody (Scl‐Ab)–mediated blockade of sclerostin can dramatically enhance bone formation and reduce bone resorption. This study was designed to investigate the therapeutic effect of the Scl‐Ab on severe bone loss induced by concurrent mechanical unloading and estrogen deficiency in a hindlimb‐suspended and ovariectomized rat model, and to study the cellular mechanisms underlying severe osteoporosis and Scl‐Ab action. Unloading and ovariectomy resulted in severe loss of trabecular and cortical bone mass and strength; Scl‐Ab can significantly counteract the deterioration of bone in unloaded and/or ovariectomized rats, with noticeably increased cortical bone formation. Scanning electron microscopy analysis revealed that unloading and ovariectomy lead to multiple morphological and structural abnormalities of osteocytes in cortical bone and the abnormalities were abolished by Scl‐Ab administration. This study extends our previous conclusion that Scl‐Ab represents a promising therapeutic approach for severe bone loss that occurs after being exposed to estrogen deficiency and prolonged mechanical unloading.
Impact of chest radiography‐based definition of bronchopulmonary dysplasia
Authors: Arai Hirokazu , Ito Tomoo , Ito Masato , Ota Syozo , Takahashi Tsutomu ,   The Neonatal Research Network of Japan
Published: January 2019

AbstractBackgroundBubbly/cystic appearance on chest radiograph is an important factor in severe‐type bronchopulmonary dysplasia (BPD) in Japan. The aim of this study was to determine the perinatal characteristics and neonatal complications of the bubbly/cystic(+) group in extremely preterm infants with BPD, that is, oxygen dependency at day 28 after birth (BPD28).MethodsThis was a multicenter retrospective cohort study of population data from infants (birthweight, <1,500 g) enrolled in the Neonatal Research Network of Japan. Of the 15 480 infants born at <28 weeks’ gestational age (GA) between 2003 and 2012, 8,979 met the BPD28 criteria. The BPD28 infants were classified according to bubbly/cystic appearance on radiograph (±) at >28 postnatal days.ResultsThe bubbly/cystic(+) group had lower GA and birthweight and required longer mechanical ventilation and oxygen dependency than the bubbly/cystic(−) group. After adjustment for confounding factors, bubbly/cystic appearance was an independent risk factor for home oxygen therapy at discharge.ConclusionBubbly/cystic appearance on chest radiograph was a predictor of short‐term respiratory outcomes in infants with BPD28, which is diagnosed much earlier (≥28 postnatal days), and has a potentially different etiology to BPD36 (oxygen and/or positive pressure respiratory support dependency at 36 weeks’ postmenstrual age).
Problematic alcohol use and depression in secondary school students in Miri, Malaysia
Authors: Chhoa Keng Hong , Zakaria Hazli , Abd Rahman Fairuz Nazri 
Published: January 2019

AbstractBackgroundAlcohol consumption in the under‐aged is one of the main concerns regarding Malaysian adolescents. There is no previous study on problematic alcohol use (PAU) in adolescents in Sarawak. The aim of this study was to determine the prevalence of PAU, its associated variables and its relationship with depression.MethodsThis was a cross‐sectional study. A total of 327 secondary school students completed the Alcohol Use Disorder Identification Test and Children's Depression Inventory, and a sociodemographic questionnaire. Binary and multivariable logistic regression were used to examine the relationship between the different variables.ResultsA total of 42.2% of adolescents had PAU. Urban adolescents had a higher prevalence compared with rural adolescents (OR, 1.612; 95% CI: 1.036–2.508P = 0.034). Female adolescents (56.8%) andBumiputeraSarawak adolescents (76.8%) comprised a large proportion of the respondents with PAU. Cultural norm (78.3%) and curiosity (68.1%) were the two main reasons for PAU. Only family history of alcohol use (OR, 2.273; 95% CI: 1.013–5.107;P = 0.047), ever consumed alcohol (OR, 57.585; 95% CI: 21.885–151.525;P < 0.001) and ever consumed beer (OR, 2.564; 95% CI: 1.032–6.372;P = 0.043) were significantly associated with PAU. The prevalence of depression was 21.4%. A significant relationship between PAU and depression was seen (OR, 2.557; 95% CI: 1.479–4.420;P = 0.001).ConclusionThere is a high prevalence of PAU in adolescents in Miri, Malaysia. More effort is needed to implement policies for this vulnerable group, with collaboration between agencies to ensure their mental and physical wellbeing and prevent a negative impact later. Clinicians should be more vigilant in detecting depression in adolescents with PAU to enable early intervention.
Somatic mutations and immune checkpoint biomarkers
Authors: Parris Brielle A. , Shaw Eloise , Pang Brendan , Soong Richie , Fong Kwun , Soo Ross A. 
Published: January 2019

ABSTRACTThe development of molecular testing for identifying somatic mutations and immune checkpoint biomarkers has directed treatment towards personalized medicine for patients with non‐small cell lung cancer. The choice of molecular testing in a clinical setting is influenced by cost, expertise in the technology, instrumentation setup and sample type availability. The molecular techniques described in this review include immunohistochemistry (IHC), fluorescent in situ hybridization, direct sequencing, real‐time polymerase chain reaction (PCR), denaturing high‐performance liquid chromatography, matrix‐assisted laser desorption/ionization time of flight mass spectrometry and next‐generation sequencing (NGS). IHC is routinely used in clinical practice for the classification, differentiation, histology and identification of targetable alterations of epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK) and programmed death ligand‐1 (PD‐L1). Recently, the PD‐L1 pathway was identified as being exploited by tumour cells, allowing immune resistance and tumour evasion. The development of immune checkpoint inhibitors as treatment for tumours expressing checkpoints has highlighted the need for standardized IHC assays to inform treatment decisions for patients. Direct sequencing was historically the gold standard for mutation testing for EGFR, KRAS (Kirsten rat sarcoma viral oncogene homologue) and BRAF (v‐Raf murine sarcoma viral oncogene homologue B1) requiring a high ratio of tumour to normal cells, but this has been superseded by more sensitive methods. NGS is a new emerging technique, which allows high‐throughput coverage of frequently mutated genes, including less common BRAF and MET mutations and alterations in tumour suppressor genes. When an NGS platform is unavailable, PCR‐based technologies offer an efficient and cost‐effective single gene test to guide patient treatment. This article will review these techniques and discuss the future of molecular platforms underpinning clinical management decisions.
Benefits of non‐invasive ventilation in acute hypercapnic respiratory failure
Authors: Comellini Vittoria , Pacilli Angela Maria Grazia , Nava Stefano 
Published: January 2019

ABSTRACTNon‐invasive ventilation (NIV) with bilevel positive airway pressure is a non‐invasive technique, which refers to the provision of ventilatory support through the patient's upper airway using a mask or similar device. This technique is successful in correcting hypoventilation. It has become widely accepted as the standard treatment for patients with hypercapnic respiratory failure (HRF). Since the 1980s, NIV has been used in intensive care units and, after initial anecdotal reports and larger series, a number of randomized trials have been conducted. Data from these trials have shown that NIV is a valuable treatment for HRF. This review aims to explore the principal areas in which NIV can be useful, focusing particularly on patients with acute HRF (AHRF). We will update the evidence base with the goal of supporting clinical practice. We provide a practical description of the main indications for NIV in AHRF and identify the group of patients with hypercapnic failure who will benefit most from the application of NIV.
The team effect on doping in professional male road cycling (2005‐2016)
Authors: Aubel Olivier , Lefèvre Brice , Le Goff Jean Marie , Taverna Natascia 
Published: January 2019

This article questions organizations’ (clubs, teams, etc) responsibility in doping use from the case of anti‐doping rules violations (ADRVs) sanctioned by the Union Cycliste Internationale in professional cycling. We built a database with 271 caught riders among 10 551 professional riders employed from 2005 to 2016 in the three first world divisions. We developed a time‐discrete event history model with a multilevel perspective to consider if the ADRV is related to the characteristic of a rider's career path (level 1) and/or the team by which the rider is employed (level 2). Our results confirm two hypotheses: Beginning a career before 2005 or after the age of 22 increased the risk of being caught. Each additional year in the pack increased the risk, despite the fact that a sanctioned rider's career duration average is 7.8 years (3.9 for the others). These caught riders have experienced a more tumultuous career with team changes and an interrupted path. A 2.45 Median Odds Ratio led us to assert a team effect on ADRV. By a team residual effect calculation, we identify 17 teams with a significant effect within the 129 that experienced an ADRV. Our results allow us to emphasize that to understand doping we must take into account work and employment condition, as well as team's organization. This approach completes the dominant “methodological individualism” perspective that considers athletes as analytical units and provides guidelines to the anti‐doping bodies that focus their action on individuals.
Therapeutic drug concentrations of isavuconazole following the administration of isavuconazonium sulfate capsules via gastro‐jejunum tube: A case report
Authors: Adamsick Meagan L. , Elshaboury Ramy H. , Gift Thais , Mansour Michael K. , Kotton Camille N. , Gandhi Ronak G. 
Published: January 2019

AbstractInvasive fungal infections are a common complication in immunocompromised patients, such as organ transplant recipients. Isavuconazole is a broad‐spectrum azole antifungal for the treatment of aspergillosis and mucormycosis. The package insert for isavuconazole recommends against opening the capsule for administration through enteral feeding tubes. We describe the case of a 68‐year‐old man with a complex post‐lung transplant course receiving isavuconazole for presumed invasive aspergillosis (bronchial alveolar lavage galactomannan index of >3.75) therapy administered through a gastrostomy‐jejunostomy tube (G‐J tube). Therapeutic drug monitoring was performed to ensure appropriate absorption. Peak and trough concentrations were measured in the early and late phases of the treatment course and resulted in trough levels of 2.7 mcg/mL and 4.0 mcg/mL, which is consistent with previously published trough concentrations of isavuconazole when the capsule was administered intact. This case report suggests that opening isavuconazole capsules and administration through a G‐J tube results in appropriate absorption and serum drug levels comparable to intact capsules.
Domestic value chains as stepping stones to global value chain integration
Authors: Beverelli Cosimo , Stolzenburg Victor , Koopman Robert B. , Neumueller Simon 
Published: January 2019

AbstractIdentifying the determinants of global value chain (GVC) integration is essential to understand the past expansion and current slowdown in GVCs. In this paper, we study the role of domestic value chains (DVCs) for GVC integration. In the presence of industry‐specific fixed costs of fragmenting production and of switching across input suppliers, DVCs can either be stepping stones or stumbling blocks for subsequent GVC entry. Focusing on backward linkages, that is, the sourcing of intermediates, we provide robust empirical evidence in favour of the stepping‐stone hypothesis. In our benchmark specification, a one standard deviation increase in DVC integration raises subsequent GVC integration by about 0.4%. To identify the mechanisms at work, we exploit two dimensions of industry‐level heterogeneity: product differentiation (a proxy of fragmentation costs) and relationship specificity (a proxy of the costs of switching between suppliers). We find that DVC integration is less conducive to GVC integration in industries that are characterised by relatively high switching costs and relatively low fragmentation costs.