bluuebunny/crossref_metadata_2025 huggingface dataset:
Genomewide analysis of small RNAs in nonembryogenic and embryogenic tissues of citrus: microRNA‐and siRNA‐mediated transcript cleavage involved in somatic embryogenesis
Authors: Wu Xiao‐Meng , Kou Shu‐Jun , Liu Yuan‐Long , Fang Yan‐Ni , Xu Qiang , Guo Wen‐Wu
Published: January 2015

Somatic embryogenesis (SE) is a process of somatic cells becoming dedifferentiated and generating embryos. SE has been widely used in biotechnology as a powerful way of regeneration and a model system for studying plant embryogenesis, but the controlling mechanisms of SE are far from clear. Here, we show the genomewide profiles of miRNAs/siRNAs and their target genes in nonembryogenic and embryogenic tissues of ‘Valencia’ sweet orange. By high‐throughput sequencing (HTS) of small RNAs and RNA degradome tags, we identified 50 known and 45 novel miRNAs, 130 miniature inverted‐repeat transposable elements (MITEs) derived, 94 other and 235 phased small interfering RNAs (siRNAs), as well as 203 target genes. The majority of the abundantly expressed miRNAs/siRNAs exhibit lower expression levels in embryogenic callus (EC) or during SE process than in nonembryogenic callus (NEC), which is supposed to derepress the target genes that are involved in development and stress response, thus to activate the biological processes required for cell differentiation. However, the conserved csi‐miR156a/b, miR164b and 171c directed suppression of specific transcription factors (TFs) are supposed to inactivate the postembryonic growth thus to maintain normal SE. In this study, miRNA‐ and siRNA‐mediated silencing of target genes was found under sophisticated regulation in citrus SE system; the enhancement effect of specific conserved miRNAs on SE was discussed, providing new clues for future investigation of mechanisms that control SE.
Long noncoding RNA transcriptome of plants
Authors: Liu Jun , Wang Huan , Chua Nam‐Hai
Published: January 2015

Since their discovery more than two decades ago, animal long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes. Recently, a large number of lncRNAs have also been identified in higher plants, and here, we review their identification, classification and known regulatory functions in various developmental events and stress responses. Knowledge gained from a deeper understanding of this special group of noncoding RNAs may lead to biotechnological improvement of crops. Some possible examples in this direction are discussed.
Salt sensitivity in chickpea (Cicer arietinum L.): ions in reproductive tissues and yield components in contrasting genotypes
Authors: KOTULA LUKASZ , KHAN HAMMAD A. , QUEALY JOHN , TURNER NEIL C. , VADEZ VINCENT , SIDDIQUE KADAMBOT H. M. , CLODE PETA L. , COLMER TIMOTHY D.
Published: January 2015

The reproductive phase in chickpea (Cicer arietinum L.) is affected by salinity, but little is known about the underlying cause. We investigated whether high concentrations of Na+ and Cl– in the reproductive structures influence reproductive processes. Chickpea genotypes contrasting in tolerance were subjected to 0, 35 or 50 mm NaCl applied to soil in pots. Flower production and abortion, pod number, percentage of empty pods, seed number and size were evaluated. The concentrations of Na+, K+ and Cl– were measured in various plant tissues and, using X‐ray microanalysis, in specific cells of developing reproductive structures. Genotypic variation in reproductive success measured as seed yield in saline conditions was associated with better maintenance of flower production and higher numbers of filled pods (and thus seed number), whereas seed size decreased in all genotypes. Despite the variation in reproductive success, the accumulation of Na+ and Cl– in the early reproductive tissues of developing pods did not differ between a tolerant (Genesis836) and a sensitive (Rupali) genotype. Similarly, salinity tolerance was not associated with the accumulation of salt ions in leaves at the time of reproduction or in seeds at maturity.
Studies on cocktails of 31‐kDa, 36‐kDa and 51‐kDa antigens of Leishmania donovani along with saponin against murine visceral leishmaniasis
Authors: Kaur H. , Thakur A. , Kaur S.
Published: January 2015

A substantial number of antigens of Leishmania donovani have been described in the past. However, identifying candidate antigens is not enough. Appropriate antigen delivery to induce the right type of immune response against leishmaniasis (i.e. induction of a strong antigen‐specific Th1 type of immune response) is another crucial component of an effective vaccine. Therefore, ‘cocktail’ vaccines are proposed based on the assumption that such cocktails will show enhanced efficacy. Studies have been carried out on LD31 and LD51 polypeptides from L. donovani promastigotes, which have proven to be potential vaccine candidates. This study was designed to check the protective efficacy of various cocktails of low molecular weight antigens alone and along with saponin as adjuvant. Mice were sacrificed on different post‐challenge days for evaluation of parasite load and other immunological parameters. Protective efficacy of different vaccine formulations was revealed by significant decline in parasite burden and increased DTH Delayed Type Hypersenstivity responses. The antibody response was of IgG type with elevated IgG2a and decreased production of IgG1, whereas cytokine levels pointed towards the generation of protective Th1 type of immune response. Among all vaccine formulations, cocktail of 31+51+saponin was found to be highly immunogenic and imparted maximum protection.
Male poplars have a stronger ability to balance growth and carbohydrate accumulation than do females in response to a short‐term potassium deficiency
Authors: Yang Yanni , Jiang Hao , Wang Maolin , Korpelainen Helena , Li Chunyang
Published: January 2015

Potassium (K) deficiency influences plant performance, such as ion uptake and carbohydrate transport. However, little is known about differences between males and females in response to K deficiency. In this study, dry matter accumulation, photosynthetic capacity, allocation patterns of K+, Na+ and carbohydrates, and ultrastructural changes in males and females of Populus cathayana exposed to K deficiency were investigated. The results indicated that males maintained a significantly higher K+ content and K+/Na+ ratio in leaves and stems than did females under K deficiency. Moreover, K deficiency significantly increased the sucrose content of females, whereas no significant effect on males was detected. In addition, a comparative analysis showed that males allocated more resources to roots, while females allocated more to leaves, which resulted in sexually different root/shoot (R/S) ratios. Transmission electron microscopic (TEM) observations showed that males suffered fewer injuries than did females. These results suggested that males have a better ability to cope with K deficiency. In addition, the combined effects of salinity and K deficiency on poplars were studied. The results indicated that salt stress aggravates the negative effects caused by K deficiency. Taken together, our study provided evidence for gender‐specific strategies in ion and carbohydrate allocation in poplars exposed to a short‐term K deficiency. In leaves and stems, the lower K+ accumulation inhibited sucrose translocation and resulted in a decreased R/S ratio, which may contribute to males having a stronger ability to balance growth and carbohydrate accumulation when compared with females.
Re‐forestation restores native dominance in an island beetle fauna
Authors: Gardner‐Gee Robin , Stanley Margaret C. , Beggs Jacqueline R.
Published: January 2015

Native re‐forestation is a widely used restoration tool, typically undertaken with the expectation that planting native trees will initiate succession processes (including the re‐establishment of native fauna) that will eventually return the ecosystem to a native‐dominated state. Invertebrate groups can be used to assess restoration progress, as their life history traits enable them to respond more rapidly to environmental change than many other organisms. In this study, we assessed beetle responses to re‐forestation. Using two trapping methods (flight intercept traps and pitfall traps), we compared beetle assemblages in exotic pasture (pre‐restoration state), <10‐year‐old planted native forest (restoration intervention) and approximately 40‐year‐old unmanaged regenerating native forest (reference state). Analysis of the flight intercept‐trapped beetles suggests that re‐forestation has initiated a transition from an exotic‐dominated pasture fauna toward a native‐dominated fauna: in planted forests, 75% of all flight‐intercept‐trapped beetles were native (compared with 22% in pasture and 87% in unmanaged forest). Flight intercept‐trapped beetles also had higher native diversity and abundance in both forest types than in pasture. Pitfall‐trapped beetle species were predominantly native in both forest types, but there were few statistically significant differences between the forests and pasture in the pit‐fall trap data set. Both trapping methods detected significant compositional differences between the beetle assemblages in planted forest and unmanaged forest. Replanting native forest has increased native beetle diversity, abundance, and dominance (compared with the pre‐restoration state), but convergence with the unmanaged reference forest has not yet been achieved.
ST analysis for intrapartum fetal monitoring
Authors: Sacco Adalina , Muglu Javaid , Navaratnarajah Ramesan , Hogg Matthew
Published: January 2015

Key content

ST analysis (STAN) involves a combination of fetal heart rate interpretation and analysis of the fetal electrocardiogram.

STAN has been available for over 5 years in the UK and is used in some, but not all, maternity units.

STAN aims to reduce the incidence of fetal acidaemia and hypoxia by identifying these earlier and with greater sensitivity than cardiotocography (CTG) alone.

Learning objectives

To be familiar with the background theory and evidence for the use of STAN.

To learn the principles for interpretation of the STAN trace.

To review practical tips for STAN application and use of STAN monitors.

Ethical issues

STAN interpretation is currently not part of the RCOG curriculum for obstetrics and gynaecology trainees.

Trainees may rotate to a unit that uses STAN routinely and be expected to participate in its use with minimal training.
Disease‐Associated Mutations of TREM2 Alter the Processing of N‐Linked Oligosaccharides in the Golgi Apparatus
Authors: Park Ji‐Seon , Ji In Jung , An Hyun Joo , Kang Min‐Ji , Kang Sang‐Wook , Kim Dong‐Hou , Yoon Seung‐Yong
Published: January 2015

The triggering receptor expressed on myeloid cells 2 (TREM2) is an immune‐modulatory receptor involved in phagocytosis and inflammation. Mutations of Q33X, Y38C and T66M cause Nasu‐Hakola disease (NHD) which is characterized by early onset of dementia and bone cysts. A recent, genome‐wide association study also revealed that single nucleotide polymorphism of TREM2, such as R47H, increased the risk of Alzheimer's disease (AD) similar to ApoE4. However, how these mutations affect the trafficking of TREM2, which may affect the normal functions of TREM2, was not known. In this study, we show that TREM2 with NHD mutations are impaired in the glycosylation with complex oligosaccharides in the Golgi apparatus, in the trafficking to plasma membrane and further processing by γ‐secretase. Although R47H mutation in AD affected the glycosylation and normal trafficking of TREM2 less, the detailed pattern of glycosylated TREM2 differs from that of the wild type, thus suggesting that precise regulation of TREM2 glycosylation is impaired when arginine at 47 is mutated to histidine. Our results suggest that the impaired glycosylation and trafficking of TREM2 from endoplasmic reticulum/Golgi to plasma membrane by mutations may inhibit its normal functions in the plasma membrane, which may contribute to the disease.
Trafficking of Acetyl‐C16‐Ceramide‐NBD with Long‐Term Stability and No Cytotoxicity into the Golgi Complex
Authors: Makiyama Tomohiko , Nakamura Hiroyuki , Nagasaka Nobuo , Yamashita Hisahiro , Honda Takuya , Yamaguchi Naoto , Nishida Atsushi , Murayama Toshihiko
Published: January 2015

The Golgi complex plays a prominent role in the modification and sorting of lipids and proteins, and is a highly dynamic organelle that is dispersed and rearranged before and after mitosis. Several reagents including 4‐nitrobenzo‐2‐oxa‐1,3‐diazole‐labeled C6‐ceramide (NBD‐C6‐ceramide, a ceramide having an NBD‐bound C6‐N‐acyl chain) and Golgi‐specific proteins that emit fluorescence are used as Golgi markers. In the present study, we synthesized a new ceramide analog, acetyl‐C16‐ceramide‐NBD (a ceramide having an acetylated C‐1 hydroxyl group, C16‐N‐acyl chain, and NBD‐bound C15‐sphingosine), and showed that it preferentially accumulated in the Golgi complex without cytotoxicity for over 24 h. Pathways for cellular uptake and interorganelle trafficking of acetyl‐C16‐ceramide‐NBD were investigated. Acetyl‐C16‐ceramide‐NBD was transported to the Golgi complex via ceramide transport proteins. In contrast to NBD‐C6‐ceramide, acetyl‐C16‐ceramide‐NBD was resistant to ceramide metabolic enzymes such as sphingomyelin synthase and glucosylceramide synthase. Because of its weaker cytotoxicity and resistance to ceramide metabolic enzymes, the localization of the Golgi complex could be observed in acetyl‐C16‐ceramide‐NBD‐labeled cells before and after mitosis.
A Comparison of Optimal Tariffs and Welfare under No Lobbying, Domestic Lobbying and Domestic‐foreign Lobbying
Authors: Huang Xianhai , Jiang Mobing , Li Jie
Published: January 2015

Whether and what type of the lobbying‐induced trade policies can improve the domestic welfare? We show that as compared to the case of no lobbying and the case of domestic lobbying, the domestic‐foreign lobbying may achieve the lowest tariff and may also realise the highest welfare for the domestic country. Our finding provides a theoretical explanation to the prevalent lobbying competition between Asian firms and US firms in USA recently. We argue that the domestic‐foreign lobbying may contribute to a freer trade in the domestic country, and lobbying competition may be one of the strongest forces pushing for trade liberalisation.
A View through the Trade Window: North Korean Exports as an Indicator of Economic Capabilities
Authors: Jing Ran , Lovely Mary E.
Published: January 2015

This study uses detailed information on Democratic People's Republic of Korea exports to assess the state of its indigenous industrial (civilian‐use) capability. The view through the trade window is sobering. We find that most North Korean exports reflect the capabilities of foreign investors and do not reflect the factor abundance of North Korea other than its mineral endowments. While some capability emerged in aquaculture and export processing, there is little evidence of indigenous manufacturing activity that meets international standards. Moreover, most trade is facilitated either at the border or through foreign companies or special cooperative programmes. This lack of domestic trading experience indicates a low capability for finding and serving foreign markets.
Weed eradication feasibility: lessons of the 21st century
Authors: Panetta F D
Published: January 2015

The past decade has seen strong controversy concerning the upper bounds for weed eradication. Over this period, two of the most ambitious weed eradication attempts ever have failed. These have, however, provided rich data sets that have supported a productive and highly collaborative research effort. I review this research and present a new algorithm for assessing eradication feasibility, based upon time to maturation, seedbank persistence and membership of one of two contrasting dispersal functional groups. Eight ‘eradication syndromes’ are identified and their relative eradication feasibilities indicated. The syndrome with the highest feasibility includes species that combine long juvenile periods and low seedbank persistence with short‐distance and/or human‐mediated dispersal. At first glance, this may not be a common syndrome. The syndrome with the lowest feasibility comprises plants that combine a short juvenile period and high seedbank persistence with abiotic or non‐human‐mediated biotic dispersal. It includes a number of aquatic perennials that can be dispersed over large distances by floodwaters. Projected costs for a programme targeting a plant species should reflect its syndrome membership. Improved cost estimates will support better decision‐making with regard to programme initiation, maintenance and termination; models are available that can provide estimates of eradication programme duration and cost. Whether eradication has much of a future as a weed invasion management strategy will likely rest upon more timely, better‐informed and shrewder target selection.
Parent–Adolescent Patterns of Physical Activity, Sedentary Behaviors and Sleep Among a Sample of Overweight and Obese Adolescents
Authors: Tu Andrew W. , Watts Allison W. , Masse Louise C.
Published: January 2015

Background:

The purpose of this study was to examine the association between parent and adolescent levels of physical activity, sedentary behaviors, and sleep among a group of overweight and obese adolescents.

Methods:

Baseline data of parent–adolescent pairs who enrolled in a lifestyle modification intervention were analyzed for this study (n = 176). Participants completed questionnaires about their screen time (TV, video game, and computer time), wore an accelerometer for 8 days, and completed a sleep diary for 1 week. In total, 98 parent–adolescent dyads provided valid data for the analyses. Multivariable regression analyses were conducted to assess the relationship between parent and adolescent’s moderate-to-vigorous activity (MVPA), step counts, sedentary behaviors, and sleep duration. Analyses were split by weekday, weekday evening and weekend.

Results:

Parent–adolescent MVPA was significantly associated on weekdays (b = 0.18; SE = 0.08; β = 0.26), weekday evenings (b = 0.21; SE = 0.08; β = 0.28), and weekends (b = 0.29; SE = 0.12; β = 0.27). This study found associations between parent–child video game time on weekends (b = 1.10; SE = 0.49; β = 0.24) and computer time on weekdays (b = 0.42; SE = 0.19; β = 0.23). Adolescent sleep was associated with parental sleep on weekdays only (b = 0.38; SE = 0.09; β = 0.46).

Conclusions:

The findings warrant further investigation into the direction and mechanism of the relationship between parent and adolescent weight related behaviors.
Complete Genome Sequence of Classical Swine Fever Virus Subgenogroup 2.1 from Assam, India
Authors: Ahuja Anuj , Bhattacharjee Uttaran , Chakraborty Amit Kumar , Karam Amarjit , Ghatak Sandeep , Puro Kekungu , Das Samir , Shakuntala Ingudam , Srivastava Nidhi , Ngachan S. V. , Sen Arnab
Published: January 2015

We report the complete genome sequence of a classical swine fever virus (genogroup 2.1), isolated from an outbreak in Assam, India. This particular isolate showed a high degree of genetic variation within the subgenogroup 2.1 and may serve as a potential reference strain of the 2.1 genogroup of classical swine fever virus (CSFV) in the Indian subcontinent.
Draft Genome Sequence of Enterobacter sp. Strain UCD-UG_FMILLET (Phylum
Proteobacteria
)
Authors: Ettinger Cassandra L. , Mousa Walaa M. , Raizada Manish N. , Eisen Jonathan A.
Published: January 2015

Here, we present the draft genome of Enterobacter sp. strain UCD-UG_FMILLET. This strain is an endophyte isolated from the roots of finger millet, an Afro-Indian cereal crop. The genome contains 4,801,411 bp in 53 scaffolds.
Draft Genome Sequence of Burkholderia gladioli Strain UCD-UG_CHAPALOTE (Phylum
Proteobacteria
)
Authors: Ettinger Cassandra L. , Shehata Hanan R. , Johnston-Monje David , Raizada Manish N. , Eisen Jonathan A.
Published: January 2015

Here, we present the draft genome of
Burkholderia gladioli
strain UCD-UG_CHAPALOTE. This strain is an endophyte isolated from surface sterilized seeds of an ancient Mexican landrace of corn, Chapalote. The genome contains 8,527,129 bp in 109 scaffolds.
Long-term efficacy of deep sclerectomy in Posner-Schlossman syndrome
Authors: Campana Fiamma , Caramello Guido , Dallorto Laura , Rolle Teresa
Published: January 2015

The Posner-Schlossman syndrome (PSS) is an elusive disease that can lead to serious consequences such as glaucomatous damage. Deep sclerectomy has been proven thus far to be the most effective surgical intervention to keep intraocular pressure (IOP) elevation under control compared with other surgical techniques, because it presents the least amount of postoperative complications. The aim of this case report is to demonstrate the efficacy of deep sclerectomy with T-Flux and the long-lasting effects that persist after 7 years in an eye affected by PSS. This case report demonstrates that an intervention of deep sclerectomy can lead to excellent results in terms of visual acuity as well as IOP lowering early in the history of the patient affected by PSS so that it can preclude establishment of glaucomatous damage.
Clinician-friendly lower extremity physical performance tests in athletes: a systematic review of measurement properties and correlation with injury. Part 2—the tests for the hip, thigh, foot and ankle including the star excursion balance test
Authors: Hegedus Eric J , McDonough Suzanne M , Bleakley Chris , Baxter David , Cook Chad E
Published: January 2015

Objective

To review the quality of literature and measurement properties of physical performance tests (PPTs) of the lower extremity in athletes.

Methods

Using the PICOS method we established our research question as to whether individual PPTs of the lower extremity have any relationship to injury in competitive athletes ages 12 years to adult (no limit). A search strategy was constructed by combining the terms ‘lower extremity’ and synonyms for ‘performance test’ and names of performance tests with variants of the term ‘athlete’. After examining the knee in part 1 of this 2 part series, the current report focuses on findings in the rest of the lower extremity. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed and the Consensus-based Standards for the selection of health Measurement Instruments (COSMIN) checklist was used to critique the methodological quality of each paper. A second measure was used to analyse the quality of the measurement properties of each test.

Results

Thirty-one articles examined the measurement properties of 14 PPTs pertaining to the lower extremity. The terminology used to name and describe the tests and methodology by which the tests were conducted was inconsistent.

The star excursion balance test performed in three directions (anterior, posteromedial, and posterolateral) appears to be the only test to be associated with increased injury risk. There is moderate evidence that the one leg hop for distance and the hexagon hop can distinguish between normal and unstable ankles. There is also moderate evidence that the medial hop can distinguish between painful and normal hips in dancers.

Conclusions

Currently, there is relatively limited research-backed information on PPTs of the lower extremity in athletes. We would suggest convening an international consortium comprised of experts in sports to standardise the descriptions and methodologies, and to set forth a research agenda to establish definitively the measurement properties of the most common PPTs.
The contribution of primary prevention medication and dietary change in coronary mortality reduction in England between 2000 and 2007: a modelling study
Authors: Guzman-Castillo M , Ahmed R , Hawkins N , Scholes S , Wilkinson E , Lucy J , Capewell S , O'Flaherty M
Published: January 2015

Objective

To analyse the falls in coronary heart disease (CHD) mortality in England between 2000 and 2007 and quantify the relative contributions from preventive medications and population-wide changes in blood pressure (BP) and cholesterol levels, particularly by exploring socioeconomic inequalities.

Design

A modelling study.

Setting

Sources of data included controlled trials and meta-analyses, national surveys and official statistics.

Participants

English population aged 25+ in 2000–2007.

Main outcome measures

Number of deaths prevented or postponed (DPPs) in 2007 by socioeconomic status. We used the IMPACTSECmodel which applies the relative risk reduction quantified in previous randomised controlled trials and meta-analyses to partition the mortality reduction among specific treatments and risk factor changes.

Results

Between 2000 and 2007, approximately 20 400 DPPs were attributable to reductions in BP and cholesterol in the English population. The substantial decline in BP was responsible for approximately 13 000 DPPs. Approximately 1800 DPPs came from medications and some 11 200 DPPs from population-wide changes. Reduction in population BP prevented almost twofold more deaths in the most deprived quintile compared with the most affluent. Reduction in cholesterol resulted in approximately 7400 DPPs; approximately 5300 DPPs were attributable to statin use and approximately 2100 DPPs to population-wide changes. Statins prevented almost 50% more deaths in the most affluent quintile compared with the most deprived. Conversely, population-wide changes in cholesterol prevented threefold more deaths in the most deprived quintile compared with the most affluent.

Conclusions

Population-wide secular changes in systolic blood pressure (SBP) and cholesterol levels helped to substantially reduce CHD mortality and the associated socioeconomic disparities. Mortality reductions were, in absolute terms, greatest in the most deprived quintiles, mainly reflecting their bigger initial burden of disease. Statins for high-risk individuals also made an important contribution but maintained socioeconomic inequalities. Our results strengthen the case for greater emphasis on preventive approaches, particularly population-based policies to reduce SBP and cholesterol.
Carbon monoxide poisoning and risk of deep vein thrombosis and pulmonary embolism: a nationwide retrospective cohort study
Authors: Chung Wei-Sheng , Lin Cheng-Li , Kao Chia-Hung
Published: January 2015

Background

Few studies have investigated the relationship between carbon monoxide (CO) poisoning and risk of deep vein thrombosis (DVT) and pulmonary embolism (PE). Therefore, we conducted a nationwide longitudinal cohort study in Taiwan to determine whether patients with CO poisoning are associated with increased risk of developing DVT and PE.

Methods

This study investigated the incidence and risk factors for DVT and PE in 8316 patients newly diagnosed with CO poisoning from the Taiwan National Health Insurance Research Database between 2000 and 2011. The comparison cohort contained 33 264 controls without CO poisoning from the general population. Follow-up was initiated on the date of initial diagnosis of CO poisoning and continued until the date of a DVT or PE event, censoring or December 31, 2011. Cox proportional hazard regression models were used to analyse the risk of DVT and PE according to sex, age and comorbidities.

Results

The incidences of DVT and PE were higher in the patients with CO poisoning than in the controls (5.67 vs 1.47/10 000 person-years and 1.97 vs 1.02/10 000 person-years, respectively). After adjusting for age, sex and comorbidities, the patients with CO poisoning were associated with a 3.85-fold higher risk of DVT compared with the comparison cohort, and non-significantly associated with risk of PE. CO poisoning patients with a coexisting comorbidity or acute respiratory failure were associated with significantly and substantially increased risk of DVT.

Conclusion

Risk of DVT is significantly higher in patients with CO poisoning than in the general population.
Cyclophilin D disruption attenuates lipopolysaccharide-induced inflammatory response in primary mouse macrophages
Authors: Priber Janos , Fonai Fruzsina , Jakus Peter Balazs , Racz Boglarka , Chinopoulos Christos , Tretter Laszlo , Gallyas Ferenc , Sumegi Balazs , Veres Balazs
Published: January 2015

According to recent results, various mitochondrial processes can actively regulate the immune response. In the present report, we studied whether mitochondrial permeability transition (mPT) has such a role. To this end, we compared bacterial lipopolysaccharide (LPS)-induced inflammatory response in cyclophilin D (CypD) knock-out and wild-type mouse resident peritoneal macrophages. CypD is a regulator of mPT; therefore, mPT is damaged in CypD−/−cells. We chose this genetic modification-based model because the mPT inhibitor cyclosporine A regulates inflammatory processes by several pathways unrelated to the mitochondria. The LPS increased mitochondrial depolarisation, cellular and mitochondrial reactive oxygen species production, nuclear factor-κB activation, and nitrite- and tumour necrosis factor α accumulation in wild-type cells, but these changes were diminished or absent in the CypD-deficient macrophages. Additionally, LPS enhanced Akt phosphorylation/activation as well as FOXO1 and FOXO3a phosphorylation/inactivation both in wild-type and CypD−/−cells. However, Akt and FOXO phosphorylation was significantly more pronounced in CypD-deficient compared to wild-type macrophages. These results provide the first pieces of experimental evidence for the functional regulatory role of mPT in the LPS-induced early inflammatory response of macrophages.
Matrix-valued quantum lattice Boltzmann method
Authors: Mendl Christian B.
Published: January 2015

We devise a lattice Boltzmann method (LBM) for a matrix-valued quantum Boltzmann equation, with the classical Maxwell distribution replaced by Fermi–Dirac functions. To accommodate the spin density matrix, the distribution functions become 2 × 2 matrix-valued. From an analytic perspective, the efficient, commonly used BGK approximation of the collision operator is valid in the present setting. The numerical scheme could leverage the principles of LBM for simulating complex spin systems, with applications to spintronics.
A review on non-minimal universal extra dimensions
Authors: Flacke Thomas , Kong Kyoungchul , Park Seong Chan
Published: January 2015

We report on the current status of non-minimal universal extra dimension (NMUED) models. Our emphasis is on the possible extension of the minimal UED (MUED) model by allowing bulk masses and boundary localized terms. We take into account the data from the Large Hadron Collider (LHC) as well as direct and indirect searches of dark matter (DM) and electroweak (EW) precision measurements.
String-inspired infinite-derivative theories of gravity: A brief overview
Authors: Biswas Tirthabir , Talaganis Spyridon
Published: January 2015

In String Theory, there often appears a rather interesting class of higher derivative theories containing an infinite set of derivatives in the form of an exponential. These theories may provide a way to tame ultraviolet (UV) divergences without introducing ghost-like states. Here we provide a brief overview on the progress that has been made over the last decade to construct such infinite-derivative theories of gravity (IDG) which may be able to address the singularity problems in gravity. In the process, we will present some general results that applies to covariant torsion-free metric theories of gravity.
Scalar and electromagnetic quasinormal modes of an extended black hole in F(R) gravity
Authors: Sebastian Saneesh , Kuriakose V. C.
Published: January 2015

In this paper, we study the scalar and electromagnetic perturbations of an extended black hole in F(R) gravity. The quasinormal modes in two cases are evaluated and studied their behavior by plotting graphs in each case. To study the quasinormal mode, we use the third-order WKB method. The present study shows that the absolute value of imaginary part of complex quasinormal modes increases in both cases, thus the black hole is stable against these perturbations. As the mass of the scalar field increases the imaginary part of the frequency decreases. Thus, damping slows down with increasing mass of the scalar field.
A Multi-Output on-Chip Switched-Capacitor DC–DC Converter with Unequal Flying Capacitors for Different Power Modes
Authors: Yang Yintang , Zhao Yingbo , Dong Gang
Published: January 2015

This paper presents a multi-output on-chip switched-capacitor (SC) DC–DC converter simultaneously providing two output voltages (2VDD/3 and VDD/3, in addition to the available full VDD) that enables the use of three different power modes for optimizing system power/performance trade-offs: super-threshold (full VDD), near-threshold (2VDD/3) and sub-threshold (VDD/3). Unlike some previously proposed multi-output SC converters, the multiple conversion ratios of the proposed converter are achieved without changing the topology of the circuit, thus fewer components being needed to support multiple voltages. The paper also presents an optimization method by using unequal flying capacitors for different regions of the circuit by taking advantage of the different levels of expected power consumption in the various power modes. Above 84% and 70% efficiencies are obtained in simulation over a range of load currents from 0.4 to 5 mA, and from 0.4 to 1 mA, with conversion ratios of 2/3 and 1/3, respectively. The target application for the proposed converter is for circuits with discrete power modes and for systems that use dithering to emulate a continuous range of voltages such as the panoptic dynamic voltage scaling (PDVS).
Phenomenology of theories of gravity without Lorentz invariance: The preferred frame case
Authors: Blas Diego , Lim Eugene
Published: January 2015

Theories of gravitation without Lorentz invariance are candidates of low-energy descriptions of quantum gravity. In this paper, we will describe the phenomenological consequences of the candidates associated to the existence of a preferred time direction.
Sulfonated Reduced Graphene Oxide: A High Performance Anode Material for Lithium Ion Battery
Authors: Li Haibo , Niu Rui , Liang Sen , Ma Yulong , Luo Min , Li Jin , He Lijun
Published: January 2015

In this work, the sulfonated reduced graphene oxide (SRGO) was synthesized and proposed as an enhanced anode material for lithium ion battery (LIB). The result shows that the SRGO has an improved battery performance (i.e., ∼341.7 mAh/g and ∼190.6 mAh/g corresponds to SRGO and RGO at the 100th cycle with a current density of 200 mA/g) and superior cycling stability compared with pristine reduced graphene oxide (RGO). These are attributed to the improved specific surface area (448.35 m2/g) and conductivity (2.5 × 10-4 S/m). Further, the SRGO exhibits good rate capability and excellent energy density at various current densities ranging from 50 mAh/g to 2000 mAh/g, suggesting that SRGO could be a promising anode material for high capacity LIB.
Exploratory data analysis of the Large Scale Gas Injection Test (Lasgit) dataset, focusing on ‘second-order’ events around macro-scale gas flows
Authors: Bennett D. P. , Cuss R. J. , Vardon P. J. , Harrington J. F. , Sedighi M. , Thomas H. R.
Published: January 2015

The Large Scale Gas Injection Test (Lasgit) is a field-scale experiment designed to study the impact of gas build-up and subsequent migration through an engineered barrier system (EBS). Lasgit has a substantial experimental dataset containing in excess of 26 million datum points. The dataset is anticipated to contain a wealth of information, ranging from long-term trends and system behaviours to small-scale or ‘second-order’ features. In order to interrogate the Lasgit dataset, a bespoke computational toolkit, designed to expose and quantify difficult to observe phenomena in large, non-uniform datasets, has been developed and applied. Presented results focus on the investigation and interpretation of second-order events occurring in close proximity (temporally and spatially) to a known macro-scale gas flow event that occurred during the second gas injection test. The similarity of the investigated event to dilatant flow observed in laboratory experiments is noted, as is the evidence for localized flow pathways in the bentonite EBS. The sensitivity of the toolkit's ability to highlight second-order events is also evaluated.
Ethics to protect groundwater from depletion in India
Authors: Datta Partha Sarathi
Published: January 2015

In India, demand for water has increased due to population growth and the competition induced by economic aspirations for developmental activities. Despite abundant rainfall, a few crucial issues for the water crisis are as follows: erratic rainfall and zonal disparity in the distribution of the available water and its inefficient use across different regions, unregulated groundwater extraction, worsening water quality, inefficient management and implementation of the regulations, lack of an ethical framework, and so on. Over 70% of the surface water is polluted and is unsafe for drinking/farming. More than 65% of irrigated agriculture and 80–85% of the rural and urban water supply and drinking water supply depend on groundwater. However, people have inadequate knowledge and awareness and different perceptions of this vital natural resource and how vulnerable it is. Geoscientists have a significant role to play to increase public awareness on the topic of ‘groundwater ethics’ and its interaction with people, their habits and the water in order to control indiscriminate water extraction and its wasteful utilization. To protect groundwater from depletion, emphasis should be placed on community-focused groundwater use, the price of water extraction and the costs and benefits of water allocation for irrigation needs where consumptive use is high compared to all other uses with relatively smaller water needs.
Ultrasound reveals negligible cocontraction during isometric plantar flexion and dorsiflexion despite the presence of antagonist electromyographic activity
Authors: Raiteri Brent J. , Cresswell Andrew G. , Lichtwark Glen A.
Published: January 2015

Because of the approximate linear relationship between muscle force and muscle activity, muscle forces are often estimated during maximal voluntary isometric contractions (MVICs) from torque and surface electromyography (sEMG) measurements. However, sEMG recordings from a target muscle may contain cross-talk originating from nearby muscles, which could lead to erroneous force estimates. Here we used ultrasound imaging to measure in vivo muscle fascicle length ( Lf) changes and sEMG to measure muscle activity of the tibialis anterior, medial gastrocnemius, lateral gastrocnemius, and soleus muscles during ramp MVICs in plantar and dorsiflexion directions ( n = 8). After correcting longitudinal Lfchanges for ankle rotation, the antagonist Lfat peak antagonist root-mean-square (RMS) amplitude were significantly longer than the agonist Lfat this sEMG-matched level. On average, Lfshortened from resting length by 1.29 to 2.90 mm when muscles acted as agonists and lengthened from resting length by 0.43 to 1.16 mm when muscles acted as antagonists (depending on the muscle of interest). The lack of fascicle shortening when muscles acted as antagonists indicates that cocontraction was likely to be negligible, despite cocontraction as determined by sEMG of between 7 and 23% MVIC across all muscles. Different interelectrode distances (IEDs) over the plantar flexors revealed significantly higher antagonist RMS amplitudes for the 4-cm IEDs compared with the 2-cm IEDs, which further indicates that cross-talk was present. Consequently, investigators should be wary about performing agonist torque corrections for isometric plantar flexion and dorsiflexion based on the antagonist sEMG trace and predicted antagonist moment.
Peripheral chemoreceptor control of cardiovascular function at rest and during exercise in heart failure patients
Authors: Edgell Heather , McMurtry M. Sean , Haykowsky Mark J. , Paterson Ian , Ezekowitz Justin A. , Dyck Jason R. B. , Stickland Michael K.
Published: January 2015

Peripheral chemoreceptor activity/sensitivity is enhanced in chronic heart failure (HF), and sensitivity is linked to greater mortality. This study aimed to determine the role of the peripheral chemoreceptor in cardiovascular control at rest and during exercise in HF patients and controls. Clinically stable HF patients ( n = 11; ejection fraction: 39 ± 5%) and risk-matched controls ( n = 10; ejection fraction: 65 ± 2%) performed randomized trials with or without dopamine infusion (2 μg·min−1·kg−1) at rest and during 40% maximal voluntary contraction handgrip (HG) exercise, and a resting trial of 2 min of inspired 100% oxygen. Both dopamine and hyperoxia were used to inhibit the peripheral chemoreceptor. At rest in HF patients, dopamine decreased ventilation ( P = 0.02), decreased total peripheral resistance index ( P = 0.003), and increased cardiac and stroke indexes ( P ≤ 0.01), yet there was no effect of dopamine on these variables in controls ( P ≥ 0.7). Hyperoxia lowered ventilation in HF ( P = 0.01), but not in controls ( P = 0.9), indicating suppression of the peripheral chemoreceptors in HF. However, no decrease of total peripheral resistance index was observed in HF. As expected, HG increased heart rate, ventilation, and brachial conductance of the nonexercising arm in controls and HF patients. During dopamine infusion, there were no changes in mean arterial pressure, heart rate, or ventilation responses to HG in either group ( P ≥ 0.26); however, brachial conductance increased with dopamine in the control group ( P = 0.004), but decreased in HF ( P = 0.02). Our findings indicate that the peripheral chemoreceptor contributes to cardiovascular control at rest in HF patients and during exercise in risk-matched controls.
Association between C-Reactive Protein, Incident Liver Cancer, and Chronic Liver Disease Mortality in the Linxian Nutrition Intervention Trials: A Nested Case–Control Study
Authors: Chen Wen , Wang Jian-Bing , Abnet Christian C. , Dawsey Sanford M. , Fan Jin-Hu , Yin Liang-Yu , Yin Jian , Taylor Philip R. , Qiao You-Lin , Freedman Neal D.
Published: January 2015

Background: C-reactive protein (CRP) is a marker of systemic inflammation that has been associated with the incidence and prognosis for a number of different cancers. Recent data suggest that CRP may be a prognostic factor for liver cancer and cirrhosis. However, few long-term studies are available.

Methods: We prospectively examined associations between serum CRP and subsequent risk of liver cancer incidence or chronic liver disease mortality in a nested case–control study performed in the Linxian Nutrition Intervention Trials cohort. Baseline serum CRP was measured for 220 incident liver cancer cases, 276 participants who died of chronic liver disease, and 1,018 age-, sex-, and trial-matched controls. Unconditional logistical regression models were used to estimate ORs and 95% confidence intervals (CI).

Results: Compared with the lowest quartile, subjects in the fourth quartile of serum CRP had a higher risk of liver cancer incidence (OR, 1.63; 95% CI, 1.06–2.51), with a significant Ptrend across quartiles (P = 0.01). The association with liver cancer was only significant among men (Q4 vs. Q1; OR, 2.00; 1.10–3.62), but not among women (Q4 vs. Q1; OR, 1.15; 0.60–2.22). For chronic liver disease deaths, the corresponding risk estimate in men and women was 2.95 (1.90–4.57), with a monotonic trend (P < 0.001).

Conclusions: Higher serum CRP concentrations at baseline were associated with subsequent incidence of liver cancer and death from chronic liver disease.

Impact: Our findings suggest that levels of systemic inflammation may serve as a long-term marker of liver cancer and liver disease. Cancer Epidemiol Biomarkers Prev; 24(2); 386–92. ©2015 AACR.
Association of Nonsteroidal Anti-Inflammatory Drugs with Colorectal Cancer by Subgroups in the VITamins and Lifestyle (VITAL) Study
Authors: Wang Xiaoliang , Peters Ulrike , Potter John D. , White Emily
Published: January 2015

Background: There is substantial evidence that use of NSAIDs reduces the risk of colorectal cancer, but no subgroup has been identified for which the chemoprevention effect outweighs the risk of side effects.

Methods: We tested the interaction between NSAID use and multiple risk factors on colorectal cancer risk in the VITAL cohort. A total of 73,458 individuals ages 50 to 76 years completed a questionnaire between 2000 and 2002, and 674 incidental colorectal cancer cases were identified through 2010.

Results: In stratified analysis, high use of any type of NSAIDs (4+ days/week for 4+ years) was statistically significantly associated with a lower risk of colorectal cancer across all subgroups stratified by sex, body mass index, physical activity, smoking, alcohol intake, screening, and dietary factors. There was a suggestion of stronger associations among men, obese individuals, and heavier drinkers; however, none of these tests for interaction reached statistical significance. The associations were almost identical for subjects with higher overall colorectal cancer risk scores [HR, 0.62; 95% confidence interval (CI), 0.49–0.79] and those with lower risk scores (HR, 0.61; 95% CI, 0.42–0.88). Differential effects by cancer subsites and stages were tested. NSAID use was associated with a greater risk reduction of proximal colon cancer versus distal (P for difference = 0.06) and distant stage versus local (P for difference = 0.04).

Conclusion: The association between high use of NSAIDs and colorectal cancer risk does not differ significantly among subgroups.

Impact: Our results suggest that NSAIDs have a generally beneficial role in colorectal cancer prevention, largely unmodified by other exposures. Cancer Epidemiol Biomarkers Prev; 24(4); 727–35. ©2015 AACR.
Targeting Three Distinct HER2 Domains with a Recombinant Antibody Mixture Overcomes Trastuzumab Resistance
Authors: Pedersen Mikkel W. , Jacobsen Helle J. , Koefoed Klaus , Dahlman Anna , Kjær Ida , Poulsen Thomas T. , Meijer Per-Johan , Nielsen Lars S. , Horak Ivan D. , Lantto Johan , Kragh Michael
Published: January 2015

HER2 plays an important role in the development and maintenance of the malignant phenotype of several human cancers. As such, it is a frequently pursued therapeutic target and two antibodies targeting HER2 have been clinically approved, trastuzumab and pertuzumab. It has been suggested that optimal inhibition of HER2 is achieved when utilizing two or more antibodies targeting nonoverlapping epitopes. Superior clinical activity of the trastuzumab plus pertuzumab combination in metastatic breast cancer supports this hypothesis. Because trastuzumab and pertuzumab were not codeveloped, there may be potential for further optimizing HER2 targeting. The study herein evaluated functional activity of anti-HER2 antibody combinations identifying optimal epitope combinations that provide efficacious HER2 inhibition. High-affinity antibodies to all four extracellular domains on HER2 were identified and tested for ability to inhibit growth of different HER2-dependent tumor cell lines. An antibody mixture targeting three HER2 subdomains proved to be superior to trastuzumab, pertuzumab, or a combination in vitro and to trastuzumab in two in vivo models. Specifically, the tripartite antibody mixture induced efficient HER2 internalization and degradation demonstrating increased sensitivity in cell lines with HER2 amplification and high EGFR levels. When compared with individual and clinically approved mAbs, the synergistic tripartite antibody targeting HER2 subdomains I, II, and IV demonstrates superior anticancer activity. Mol Cancer Ther; 14(3); 669–80. ©2015 AACR.