bluuebunny/crossref_metadata_2025_split huggingface dataset:
Differential Tolerance of Glyphosate-Susceptible and Glyphosate-Resistant Biotypes of Junglerice (Echinochloa colona) to Environments during Germination, Growth, and Intraspecific Competition
Authors: Shrestha Anil , deSouza Larissa L. , Yang Pahoua , Sosnoskie Lynn , Hanson Bradley D. 
Published: January 2018

AbstractMuch of the agricultural area in California’s southwestern San Joaquin Valley (SJV) is prone to moisture stress and high soil-salinity conditions. Increased prevalence of glyphosate-resistant (GR) biotypes of junglerice [Echinochloa colona (L.) Link] in these environments and their ecological implications need to be further explored. Studies were conducted on GR and glyphosate-susceptible (GS) biotypes of E. colona to compare the effects of moisture and salinity stress on seed germination and salinity stress alone on growth and seed production. Intraspecific competition between the GR and GS plants was also assessed in a replacement series design experiment. With respect to germination, both biotypes were tolerant to moisture and salinity stress at germination; however, the GR biotype was more tolerant than the GS biotype. Water potential and electrical conductivity (EC) levels that reduced germination by 50% were estimated as −1.5 and −2.3 MPa and 8.5 and 12 dS m−1 for the GS and GR biotypes, respectively. The EC levels that reduced aboveground biomass by 50% were estimated as 9 and 11.5 dS m−1 for the GS and GR biotypes, respectively. Seed production was generally greater in the GR than the GS plants below 10 dS m−1. All plants produced up to 140 seeds plant−1, even at 20 dS m−1. The GR plants were more competitive and produced more aboveground dry biomass and seeds than the GS plants when grown together or alone. In conclusion, differences between these particular GR and GS biotypes to environmental stresses and intraspecific competition were noted that could have ecological implications for their prevalence in the southwestern SJV. The results also suggested that there could be high genetic variability and phenotypic plasticity in E. colona populations in the SJV and further population shifts could occur due to selection pressure from glyphosate.
Cell death-based treatment of glioblastoma
Authors: Fulda Simone 
Published: January 2018

Abstract
Cancer cells including glioblastoma have typically evolved multiple mechanisms to escape programmed cell death in order to maintain their survival. Defects in cell death mechanisms not only facilitate tumorigenesis but also ensure resistance to current anticancer therapies. This emphasizes that targeting cell death pathways may provide a means to tackle one of the Achilles’ heels of cancer. Over the last decades several approaches have been developed to selectively target cell death pathways for therapeutic purposes. Some of these concepts have already been transferred into clinical application in oncology and may open new perspectives for the treatment of cancer.
Cell death-based treatment of neuroblastoma
Authors: Valter Kadri , Zhivotovsky Boris , Gogvadze Vladimir 
Published: January 2018

AbstractNeuroblastoma (NB) is the most common solid childhood tumor outside the brain and causes 15% of childhood cancer-related mortality. The main drivers of NB formation are neural crest cell-derived sympathoadrenal cells that undergo abnormal genetic arrangements. Moreover, NB is a complex disease that has high heterogeneity and is therefore difficult to target for successful therapy. Thus, a better understanding of NB development helps to improve treatment and increase the survival rate. One of the major causes of sporadic NB is known to be MYCN amplification and mutations in ALK (anaplastic lymphoma kinase) are responsible for familial NB. Many other genetic abnormalities can be found; however, they are not considered as driver mutations, rather they support tumor aggressiveness. Tumor cell elimination via cell death is widely accepted as a successful technique. Therefore, in this review, we provide a thorough overview of how different modes of cell death and treatment strategies, such as immunotherapy or spontaneous regression, are or can be applied for NB elimination. In addition, several currently used and innovative approaches and their suitability for clinical testing and usage will be discussed. Moreover, significant attention will be given to combined therapies that show more effective results with fewer side effects than drugs targeting only one specific protein or pathway.
Cellular stressors contribute to the expansion of hematopoietic clones of varying leukemic potential
Authors: Wong Terrence N. , Miller Christopher A. , Jotte Matthew R. M. , Bagegni Nusayba , Baty Jack D. , Schmidt Amy P. , Cashen Amanda F. , Duncavage Eric J. , Helton Nichole M. , Fiala Mark , Fulton Robert S. , Heath Sharon E. , Janke Megan , Luber Kierstin , Westervelt Peter , Vij Ravi , DiPersio John F. , Welch John S. , Graubert Timothy A. , Walter Matthew J. , Ley Timothy J. , Link Daniel C. 
Published: January 2018

AbstractHematopoietic clones harboring specific mutations may expand over time. However, it remains unclear how different cellular stressors influence this expansion. Here we characterize clonal hematopoiesis after two different cellular stressors: cytotoxic therapy and hematopoietic transplantation. Cytotoxic therapy results in the expansion of clones carrying mutations in DNA damage response genes, including TP53 and PPM1D. Analyses of sorted populations show that these clones are typically multilineage and myeloid-biased. Following autologous transplantation, most clones persist with stable chimerism. However, DNMT3A mutant clones often expand, while PPM1D mutant clones often decrease in size. To assess the leukemic potential of these expanded clones, we genotyped 134 t-AML/t-MDS samples. Mutations in non-TP53 DNA damage response genes are infrequent in t-AML/t-MDS despite several being commonly identified after cytotoxic therapy. These data suggest that different hematopoietic stressors promote the expansion of distinct long-lived clones, carrying specific mutations, whose leukemic potential depends partially on the mutations they harbor.
Chemical durability of peraluminous glasses for nuclear waste conditioning
Authors: Piovesan Victor , Bardez-Giboire Isabelle , Fournier Maxime , Frugier Pierre , Jollivet Patrick , Montouillout Valérie , Pellerin Nadia , Gin Stéphane 
Published: January 2018

AbstractFor the handling of high level nuclear waste (HLW), new glass formulations with a high waste capacity and an enhanced thermal stability, chemical durability, and processability are under consideration. This study focuses on the durability of peraluminous glasses in the SiO2–Al2O3–B2O3–Na2O–CaO–La2O3 system, defined by an excess of Al3+ ions compared with the network-modifying cations Na+ and Ca2+. To qualify the behavior of such a peraluminous glass in a geological storage situation, its chemical durability was studied in various environments (pure water, groundwater, and alkaline solutions related to a cement environment) and glass alteration regimes (initial rate, residual rate, and resumption of alteration). The alteration solution was characterized by inductively coupled plasma, and the altered glass by scanning electron microscopy, X-ray diffraction and secondary ion mass spectrometry. A comparative study of the chemical durability of these and reference glasses (ISG and SON68) over all timescales highlights the remarkable properties of the former. While their initial dissolution rate is of the same order as the reference glasses, the gel formed under silica saturation conditions is more passivating, making its dissolution rate at least one order of magnitude lower, while its low alkalinity makes it less susceptible to clayey groundwater and highly alkaline solutions.
Quantum key distribution with an efficient countermeasure against correlated intensity fluctuations in optical pulses
Authors: Yoshino Ken-ichiro , Fujiwara Mikio , Nakata Kensuke , Sumiya Tatsuya , Sasaki Toshihiko , Takeoka Masahiro , Sasaki Masahide , Tajima Akio , Koashi Masato , Tomita Akihisa 
Published: January 2018

AbstractQuantum key distribution (QKD) allows two distant parties to share secret keys with the proven security even in the presence of an eavesdropper with unbounded computational power. Recently, GHz-clock decoy QKD systems have been realized by employing ultrafast optical communication devices. However, security loopholes of high-speed systems have not been fully explored yet. Here we point out a security loophole at the transmitter of the GHz-clock QKD, which is a common problem in high-speed QKD systems using practical band-width limited devices. We experimentally observe the inter-pulse intensity correlation and modulation pattern-dependent intensity deviation in a practical high-speed QKD system. Such correlation violates the assumption of most security theories. We also provide its countermeasure which does not require significant changes of hardware and can generate keys secure over 100 km fiber transmission. Our countermeasure is simple, effective and applicable to wide range of high-speed QKD systems, and thus paves the way to realize ultrafast and security-certified commercial QKD systems.
Biomaterials-enabled cornea regeneration in patients at high risk for rejection of donor tissue transplantation
Authors: Islam M. Mirazul , Buznyk Oleksiy , Reddy Jagadesh C. , Pasyechnikova Nataliya , Alarcon Emilio I. , Hayes Sally , Lewis Philip , Fagerholm Per , He Chaoliang , Iakymenko Stanislav , Liu Wenguang , Meek Keith M. , Sangwan Virender S. , Griffith May 
Published: January 2018

AbstractThe severe worldwide shortage of donor organs, and severe pathologies placing patients at high risk for rejecting conventional cornea transplantation, have left many corneal blind patients untreated. Following successful pre-clinical evaluation in mini-pigs, we tested a biomaterials-enabled pro-regeneration strategy to restore corneal integrity in an open-label observational study of six patients. Cell-free corneal implants comprising recombinant human collagen and phosphorylcholine were grafted by anterior lamellar keratoplasty into corneas of unilaterally blind patients diagnosed at high-risk for rejecting donor allografts. They were followed-up for a mean of 24 months. Patients with acute disease (ulceration) were relieved of pain and discomfort within 1–2 weeks post-operation. Patients with scarred or ulcerated corneas from severe infection showed better vision improvement, followed by corneas with burns. Corneas with immune or degenerative conditions transplanted for symptom relief only showed no vision improvement overall. However, grafting promoted nerve regeneration as observed by improved touch sensitivity to near normal levels in all patients tested, even for those with little/no sensitivity before treatment. Overall, three out of six patients showed significant vision improvement. Others were sufficiently stabilized to allow follow-on surgery to restore vision. Grafting outcomes in mini-pig corneas were superior to those in human subjects, emphasizing that animal models are only predictive for patients with non-severely pathological corneas; however, for establishing parameters such as stable corneal tissue and nerve regeneration, our pig model is satisfactory. While further testing is merited, we have nevertheless shown that cell-free implants are potentially safe, efficacious options for treating high-risk patients.
Angiogenesis and evading immune destruction are the main related transcriptomic characteristics to the invasive process of oral tongue cancer
Authors: Pérez-Valencia Juan Alberto , Prosdocimi Francisco , Cesari Italo M. , da Costa Igor Rodrigues , Furtado Carolina , Agostini Michelle , Rumjanek Franklin David 
Published: January 2018

AbstractMetastasis of head and neck tumors is responsible for a high mortality rate. Understanding its biochemistry may allow insights into tumorigenesis. To that end we carried out RNA-Seq analyses of 5 SCC9 derived oral cancer cell lines displaying increased invasive potential. Differentially expressed genes (DEGs) were annotated based on p-values and false discovery rate (q-values). All 292 KEGG pathways related to the human genome were compared in order to pinpoint the absolute and relative contributions to the invasive process considering the 8 hallmarks of cancer plus 2 new defined categories, as well as we made with our transcriptomic data. In terms of absolute contribution, the highest correlations were associated to the categories of evading immune destruction and energy metabolism and for relative contributions, angiogenesis and evading immune destruction. DEGs were distributed into each one of all possible modes of regulation, regarding up, down and continuum expression, along the 3 stages of metastatic progression. For p-values twenty-six genes were consistently present along the tumoral progression and 4 for q-values. Among the DEGs, we found 2 novel potentially informative metastatic markers: PIGG and SLC8B1. Furthermore, interactome analysis showed that MYH14, ANGPTL4, PPARD and ENPP1 are amenable to pharmacological interventions.
Proposed mechanism of HCP → FCC phase transition in titianium through first principles calculation and experiments
Authors: Yang Jia Xi , Zhao Heng Lv , Gong Hao Ran , Song Min , Ren Qing Qiang 
Published: January 2018

AbstractBy means of first principles calculation and experiments, a detailed mechanism is proposed to include the stages of slip, adjustment, and expansion for the HCP → FCC phase transformation with the prismatic relation of $${{\{}{10}\bar{{1}}{0}{\}}}_{{hcp}}{\parallel }{\{}{1}\bar{{1}}{0}{{\}}}_{{fcc}}$$

{
10

1
¯

0
}

hcp

∥
{
1

1
¯

0

}

fcc

and $${{[}{0001}{]}}_{{hcp}}{\parallel }{[}{001}{{]}}_{{fcc}}$$

[
0001
]

hcp

∥
[
001

]

fcc

in titanium. It is revealed that the formation of four FCC layers is preferable after the slip of Shockley partial dislocations of 1/6 $$\langle {1}\bar{{2}}{10}\rangle $$
〈
1

2
¯

10
〉
on $${\{}{10}\bar{{1}}{0}{\}}$$
{
10

1
¯

0
}
planes, and that the adjustment of interplanar spacing and the volume expansion are energetically favorable and could happen spontaneously without any energy barrier. It is also found that the transformed FCC lattice first follows the c/a ratio (1.583) of HCP and then becomes an ideal FCC structure (c/a = √2). The proposed mechanism could not only provide a deep understanding to the process of HCP → FCC prismatic transformation in titanium, but also clarify the controversy regarding volume expansion of HCP-FCC phase transition of titanium in the literature.
HPViewer: sensitive and specific genotyping of human papillomavirus in metagenomic DNA
Authors: Hao Yuhan , Yang Liying , Galvao Neto Antonio , Amin Milan R , Kelly Dervla , Brown Stuart M , Branski Ryan C , Pei Zhiheng 
Published: January 2018

Abstract

Motivation
Shotgun DNA sequencing provides sensitive detection of all 182 HPV types in tissue and body fluid. However, existing computational methods either produce false positives misidentifying HPV types due to shared sequences among HPV, human and prokaryotes, or produce false negative since they identify HPV by assembled contigs requiring large abundant of HPV reads.

Results
We designed HPViewer with two custom HPV reference databases masking simple repeats and homology sequences respectively and one homology distance matrix to hybridize these two databases. It directly identified HPV from short DNA reads rather than assembled contigs. Using 100 100 simulated samples, we revealed that HPViewer was robust for samples containing either high or low number of HPV reads. Using 12 shotgun sequencing samples from respiratory papillomatosis, HPViewer was equal to VirusTAP, and Vipie and better than HPVDetector with the respect to specificity and was the most sensitive method in the detection of HPV types 6 and 11. We demonstrated that contigs-based approaches had disadvantages of detection of HPV. In 1573 sets of metagenomic data from 18 human body sites, HPViewer identified 104 types of HPV in a body-site associated pattern and 89 types of HPV co-occurring in one sample with other types of HPV. We demonstrated HPViewer was sensitive and specific for HPV detection in metagenomic data.

Availability and implementation
HPViewer can be accessed at https://github.com/yuhanH/HPViewer/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Pro- versus Antinociceptive Nongenomic Effects of Neuronal Mineralocorticoid versus Glucocorticoid Receptors during Rat Hind Paw Inflammation
Authors: Li Xiongjuan , Shaqura Mohammed , Mohamed Doaa , Beyer Antje , Yamada Shunji , Mousa Shaaban A. , Schäfer Michael 
Published: January 2018

Abstract

Background
In naive rats, corticosteroids activate neuronal membrane–bound glucocorticoid and mineralocorticoid receptors in spinal cord and periphery to modulate nociceptive behavior by nongenomic mechanisms. Here we investigated inflammation-induced changes in neuronal versus glial glucocorticoid and mineralocorticoid receptors and their ligand-mediated nongenomic impact on mechanical nociception in rats.

Methods
In Wistar rats (n = 5 to 7/group) with Freund’s complete adjuvant hind paw inflammation, we examined glucocorticoid and mineralocorticoid receptor expression in spinal cord and peripheral sensory neurons versus glial using quantitative reverse transcription-polymerase chain reaction (qRT-PCR), Western blot, immunohistochemistry, and radioligand binding. Moreover, we explored the expression of mineralocorticoid receptors protecting enzyme 11-betahydroxysteroid dehydrogenase type 2 as well as the nociceptive behavioral changes after glucocorticoid and mineralocorticoid receptors agonist or antagonist application.

Results
Hind paw inflammation resulted in significant upregulation of glucocorticoid receptors in nociceptive neurons of spinal cord (60%) and dorsal root ganglia (15%) as well as mineralocorticoid receptors, while corticosteroid plasma concentrations remained unchanged. Mineralocorticoid (83 ± 16 fmol/mg) but not glucocorticoid (104 ± 20 fmol/mg) membrane binding sites increased twofold in dorsal root ganglia concomitant with upregulated 11-betahydroxysteroid dehydrogenase type 2 (43%). Glucocorticoid and mineralocorticoid receptor expression in spinal microglia and astrocytes was small. Importantly, glucocorticoid receptor agonist dexamethasone or mineralocorticoid receptor antagonist canrenoate-K rapidly and dose-dependently attenuated nociceptive behavior. Isobolographic analysis of the combination of both drugs showed subadditive but not synergistic or additive effects.

Conclusions
The enhanced mechanical sensitivity of inflamed hind paws accompanied with corticosteroid receptor upregulation in spinal and peripheral sensory neurons was attenuated immediately after glucocorticoid receptor agonist and mineralocorticoid receptor antagonist administration, suggesting acute nongenomic effects consistent with detected membrane-bound corticosteroid receptors.
What is the optimal target for treat-to-target strategies in rheumatoid arthritis?
Authors: Bergstra Sytske Anne , Allaart Cornelia F. 
Published: January 2018

Purpose of review
There has been a trend over time to aim for stricter treatment targets in the treatment of rheumatoid arthritis (RA). We reviewed recent literature to attempt to identify the optimal target in treat-to-target strategies in RA.

Recent findings
Achieving lower disease activity was shown to be beneficial, but few studies directly compared the effect of aiming for different treatment targets. Based on the limited available evidence, aiming for remission seems to result in more patients achieving (drug-free) remission than aiming for low disease activity (LDA), but it does not seem to result in better physical functioning. There are indications that adherence to a remission targeted protocol can be lower. In randomized trials in which LDA or remission were compared with ultrasound remission targets, treatment targeted at ultrasound remission was associated with more intensive treatment, but it did not result in better clinical or imaging outcomes.

Summary
There were no benefits of aiming for ultrasound remission in RA-patients. To decide whether remission or LDA is the best target in the treatment of RA-patients, a randomized clinical trial comparing both targets would be needed. On an individual level, cotargets such as functional ability should be considered.
Staged Prone/Supine Fixation of High-Energy Multicolumnar Tibial Plateau Fractures: A Multicenter Analysis
Authors: Row Elliot R. , Komatsu David E. , Watson J. Tracy , Jones Clifford , Kottmeier Stephen 
Published: January 2018

Purpose:
We present a surgical strategy to manage multicolumnar tibial plateau fracture variants by addressing the predominant posterior fragment employing a Lobenhoffer approach in the prone position followed by supine patient repositioning for anterolateral column access.

Design:
Multicenter retrospective analysis.

Setting:
Three academic Level 1 trauma centers.

Patients/Methods:
Twenty-eight cases (28 patients/28 knees) met inclusion criteria between 2003 and 2014. Patient demographic information was retrospectively reviewed with a mean follow-up time of 16.6 months (range 12–34 months). Postoperative radiographic analysis, physical examination findings, and patient outcome scores from the Knee Injury and Osteoarthritis Outcome Score questionnaire were recorded.

Results:
The average time to union was 3.6 months (range 3–9 months). Eighty-two percent of patients had satisfactory articular reduction (less than 2 mm articular step off). All patients demonstrated satisfactory coronal (medial proximal tibia angle 87 ± 5 degrees) and sagittal alignment (posterior proximal tibia angle 9 ± 4 degrees). Condylar width averaged 2.2 mm. Twenty percent of cases required posterior lateral columnar plating (in addition to posterior medial columnar plating), with none of these cases requiring an extensile exposure modification (medial gastrocnemius origin detachment) to expose posterior laterally. In 12 cases, the posterior approach was staged to allow for anterior soft tissue recovery before subsequent staged supine positioning and lateral column fixation. The knee range of motion averaged 123 degrees (ranged from 2 degrees of extension to 125 degrees flexion). The average Knee Injury and Osteoarthritis Outcome Score was 78/100 (range 29–95). Eleven percent of the patients in the series developed a surgical site infection (n = 3) with 2 requiring formal irrigation and debridement. The most common aseptic complication was radiographic posttraumatic arthrosis (18%). Clinically, 1 patient eventually required a total knee arthroplasty.

Conclusions:
High-energy multicolumnar tibial plateau fractures with significant posterior articular surface involvement may be predictably addressed with prone positioning, exposure, and fixation followed by supine repositioning and the inclusion of an anterior approach. This study demonstrates excellent postoperative radiographic results and acceptable clinical outcomes resulting from the described staged protocol.

Level of Evidence:
Therapeutic Level IV. See Instructions for Authors for a complete description of levels of evidence.