bluuebunny/crossref_metadata_2025 huggingface dataset:
Whirly 3-interval exchange transformations
Authors: WU YUE
Published: October 2015

Irreducible interval exchange transformations are studied with regard to the whirly property, a condition for a non-trivial spatial factor. A uniformly whirly transformation is defined and is further studied. An equivalent condition is introduced for the whirly transformation. We will prove that almost all 3-interval exchange transformations are whirly, using a combinatorics approach with application of the Rauzy–Veech induction. It is still an open question whether the whirly property is a generic property for $m$-interval exchange transformations for $m\geq 4$.
The Earliest Irrigation in Turkmenia
Authors: Lisitsina G. N.
Published: October 2015

It has long been known that irrigation agriculture played a significant role in the history of civilization in the Near East, and it is not surprising, therefore, that many researchers have concentrated their efforts on the study of problems connected with early irrigation, based both on the evidence of literary sources (Jacobsen, 1960), and that provided by archaeology and palaeogeography. Probably the most interesting work of this kind is the systematic research which has been carried out in the Diyala river basin, which covers a wide chronological range (Adams, 1965). However, the thick sedimentary deposits in the Tigris and Euphrates valleys, and on the foothill plains and intermontane valleys in many regions of the Near East, have resulted, in most cases, in the ancient irrigation systems lying deeply buried and inaccessible. Very recently, as a result of joint archaeological and palaeogeographical investigations in southern Turkmenia, we have succeeded in discovering very early irrigation constructions in the region, where, in the 6th-2nd millennium BC were situated sites belonging to the painted pottery cultures-the Dieitun culture (Berdyev, 1965) and the so-called Anau culturewhich comprise the northern limits of the Near Eastern cultural world (FIG. I) (Pumpelly, 1908; Kuphtin, 1954; Masson, 1962, 1966 ; Sarianidi, 1965; Khlopin, 1963).
Folate and vitamin B12status and dietary intake of anaemic adolescent schoolgirls in the delta region of Myanmar
Authors: Htet Min Kyaw , Fahmida Umi , Thurnham David I. , Hlaing Lwin Mar , Akib Arwin , Utomo Budi , Houghton Lisa A.
Published: October 2015

The aim of the present study was to assess the prevalence of deficiency of folate and vitamin B12and, simultaneously, the nutrient intake adequacy of folate, vitamin B12, iron, vitamin A, vitamin C, vitamin B6and calcium in 391 adolescent anaemic (Hb<120 g/l) schoolgirls living in the delta region of Myanmar (Burma). Dietary intakes were assessed using a 3 d estimated food record. The distribution of observed intakes calculated from the food records were adjusted for usual intakes, and the prevalence of inadequacy was estimated using the estimated average requirement cut-point method. Median (first, third quartile) serum folate and vitamin B12concentrations were 6·5 (4·6, 8·5) nmol/l and 612·8 (443·2, 795·2) pmol/l, respectively. The prevalence of folate deficiency defined as <6·8 nmol/l was 54 %; however, vitamin B12deficiency defined as <148 pmol/l was negligible (<1 %). The prevalence of inadequate intake of folate was high (100 %) as was the prevalence of inadequate intakes of vitamin A, vitamin C, vitamin B6and calcium, ranging from 60 to 100 %. Red meat or poultry was rarely consumed, but fish was consumed on a daily basis. Green leafy vegetables were also consumed frequently but consumption of dairy products was uncommon. Folate deficiency was high, and the prevalence of inadequate intake of folate among other key micronutrients was relatively common in this sample of anaemic adolescent schoolgirls. Appropriate strategies such as food fortification and dietary diversification are needed to improve the micronutrient status of these young women to ensure optimal health and future reproductive success.
Specific serum carotenoids are inversely associated with breast cancer risk among Chinese women: a case–control study
Authors: Yan Bo , Lu Min-Shan , Wang Lian , Mo Xiong-Fei , Luo Wei-Ping , Du Yu-Feng , Zhang Cai-Xia
Published: October 2015

Previous epidemiological studies have revealed the anti-cancer effect of dietary circulating carotenoids. However, the protective role of specific individual circulating carotenoids has not been elucidated. The purpose of this study was to examine whether serum carotenoids, includingα-carotene,β-carotene,β-cryptoxanthin, lycopene and lutein/zeaxanthin, could lower the risk for breast cancer among Chinese women. A total of 521 women with breast cancer and age-matched controls (5-year interval) were selected from three teaching hospitals in Guangzhou, China. Concentrations ofα-carotene,β-carotene,β-cryptoxanthin, lycopene and lutein/zeaxanthin were measured using HPLC. Unconditional logistic regression models were used to calculate OR and 95 % CI using quartiles defined in the control subjects. Significant inverse associations were observed between serumα-carotene,β-carotene, lycopene, lutein/zeaxanthin and the risk for breast cancer. The multivariate OR for the highest quartile of serum concentration compared with the lowest quartile were 0·44 (95 % CI 0·30, 0·65) forα-carotene, 0·27 (95 % CI 0·18, 0·40) forβ-carotene, 0·41 (95 % CI 0·28, 0·61) for lycopene and 0·26 (95 % CI 0·17, 0·38) for lutein/zeaxanthin. However, no significant association was found between serumβ-cryptoxanthin and the risk for breast cancer. Stratified analysis by menopausal status and oestrogen receptor (ER)/progesterone receptor (PR) showed that serumα-carotene,β-carotene, lycopene and lutein/zeaxanthin were inversely associated with breast cancer risk among premenopausal women and among all subtypes of ER or PR status. The results suggest a protective role ofα-carotene,β-carotene, lycopene and lutein/zeaxanthin, but notβ-cryptoxanthin, in breast cancer risk.
Entomopathogenic nematodes for the control of the codling moth (Cydia pomonellaL.) in field and laboratory trials
Authors: Odendaal D. , Addison M.F. , Malan A.P.
Published: October 2015

Three commercially available entomopathogenic nematode (EPN) strains (Steinernema feltiaeandHeterorhabditis bacteriophoraHb1 and Hb2) and two local species (S.jeffreyenseandS. yirgalemense) were evaluated for the control of the codling moth (Cydia pomonella). In field spray trials, the use ofS. jeffreyenseresulted in the most effective control (67%), followed byH. bacteriophora(Hb1) (42%) andS. yirgalemense(41%). Laboratory bioassays using spray application in simulated field conditions indicateS. feltiaeto be the most virulent (67%), followed byS. yirgalemense(58%). A laboratory comparison of the infection and penetration rate of the different strains showed that, at 14°C, all EPN strains resulted in slower codling moth mortality than they did at 25°C. After 48 h, < 15% mortality was recorded for all species, whereas, at the warmer temperature, >98% mortality was recorded for all species involved. However, the washed codling moth larvae, cool-treated (at 14°C) withS. feltiaeorS. yirgalemense, resulted in 100% mortality 24 h later at room temperature, whereas codling moth larvae treated with the twoH. bacteriophorastrains resulted in 68% and 54% control, respectively. At 14°C,S. feltiaehad the highest average penetration rate of 20 IJs/larva, followed byS. yirgalemense, with 14 IJs/larva. At 25°C,S. yirgalemensehad the highest penetration rate, with 39 IJs/larva, followed byS. feltiae, with 9 IJs/larva. This study highlights the biocontrol potential ofS. jeffreyense, as well as confirming thatS. feltiaeis a cold-active nematode, whereas the other three EPN isolates tested prefer warmer temperatures.
Can community midwives prevent antenatal depression? An external pilot study to test the feasibility of a cluster randomized controlled universal prevention trial
Authors: Brugha T. S. , Smith J. , Austin J. , Bankart J. , Patterson M. , Lovett C. , Morgan Z. , Morrell C. J. , Slade P.
Published: October 2015

Background

Repeated epidemiological surveys show no decline in depression although uptake of treatments has grown. Universal depression prevention interventions are effective in schools but untested rigorously in adulthood. Selective prevention programmes have poor uptake. Universal interventions may be more acceptable during routine healthcare contacts for example antenatally. One study within routine postnatal healthcare suggested risk of postnatal depression could be reduced in non-depressed women from 11% to 8% by giving health visitors psychological intervention training. Feasibility and effectiveness in other settings, most notably antenatally, is unknown.

Method

We conducted an external pilot study using a cluster trial design consisting of recruitment and enhanced psychological training of randomly selected clusters of community midwives (CMWs), recruitment of pregnant women of all levels of risk of depression, collection of baseline and outcome data prior to childbirth, allowing time for women ‘at increased risk’ to complete CMW-provided psychological support sessions.

Results

Seventy-nine percent of eligible women approached agreed to take part. Two hundred and ninety-eight women in eight clusters participated and 186 termed ‘at low risk’ for depression, based on an Edinburgh Perinatal Depression Scale (EPDS) score of <12 at 12 weeks gestation, provided baseline and outcome data at 34 weeks gestation. All trial protocol procedures were shown to be feasible. Antenatal effect sizes in women ‘at low risk’ were similar to those previously demonstrated postnatally. Qualitative work confirmed the acceptability of the approach to CMWs and intervention group women.

Conclusion

A fully powered trial testing universal prevention of depression in pregnancy is feasible, acceptable and worth undertaking.
By the sweat of their brow? The effects of starting work again after pension age on life satisfaction in Germany and the United Kingdom
Authors: LUX THOMAS , SCHERGER SIMONE
Published: October 2015

In recent years, the employment rates of people of pension age have increased considerably. However, longitudinal evidence on the effects of this employment on wellbeing which might contribute to an evaluation of this late-life work is scarce. Based on empirical findings so far and on theoretical approaches to wellbeing, work and retirement, both negative and positive effects of post-retirement work on life satisfaction are plausible. In this paper, we investigate the effects of taking up work again between the ages of 65 and 75 on life satisfaction in different occupational classes in Germany and the United Kingdom. We expect that not only the heterogeneous conditions and experiences of working are crucial for the consequences that post-retirement work has for life satisfaction, but also the institutional arrangements surrounding this form of work. We use data from the German Socio-Economic Panel and the British Household Panel Survey, covering the 1990s and 2000s. Based on fixed-effects regression modelling, we find positive effects of working in both countries, although not all effects are significant. Differentiating by the class of the job in which the older person works, we find mainly positive effects and no significant differences between those who work in a lower-class job and all others. In addition, we find that the positive effect of working on life satisfaction is partly explained by increased satisfaction with household income for those working in a lower-class job in the United Kingdom. We conclude that many of the pessimistic assumptions about people working after pension age cannot be confirmed for our time of observation. However, there are several reasons for believing that the results will be different in the future or for differently defined populations of people working past pension age.
Diabetes diagnosis and nutrition facts label use among US adults, 2005–2010
Authors: An Ruopeng
Published: October 2015

Objective

To assess the role of diabetes diagnosis as a potential teachable moment in nutrition facts label use among US adults.

Design

Logistic regression analyses were conducted to examine the relationship between diabetes diagnosis status (diagnosed diabetes, undiagnosed diabetes, diagnosed prediabetes, undiagnosed prediabetes, no diabetes or prediabetes) and self-reported nutrition facts label use, adjusted by individual characteristics and survey design.

Setting

Study sample came from the National Health and Nutrition Examination Survey 2005–2010 waves.

Subjects

A total of 5110 US adults aged 20 years and older were included in the analyses. Diabetes/prediabetes was identified by fasting plasma glucose and glycated Hb testing.

Results

People with diagnosed diabetes/prediabetes were substantially more likely to report nutrition facts label use when making daily food purchase decisions compared with those with undiagnosed diabetes/prediabetes, whereas the prevalence of nutrition facts label use was similar between people with undiagnosed diabetes/prediabetes and those without diabetes/prediabetes. The adjusted prevalence (95 % CI) of any and regular nutrition facts label use was 85·93 (82·91, 88·95) % and 55·60 (50·04, 61·16) % among those with diagnosed diabetes, respectively, in comparison to 71·50 (59·64, 83·37) % and 32·88 (19·11, 46·65) % among those with undiagnosed diabetes. Analogously, the adjusted prevalence (95 % CI) of any and regular nutrition facts label use was 81·16 (75·27, 87·06) % and 45·28 (37·28, 53·29) % among those with diagnosed prediabetes, respectively, in comparison to 72·83 (68·06, 77·59) % and 39·95 (34·02, 45·89) % among those with undiagnosed prediabetes.

Conclusions

As a potential teachable moment, diabetes diagnosis may positively impact nutrition facts label use and motivate diabetic patients to manage their condition through making healthier food choices.
Frequency, intensity, and correlates of spiritual pain in advanced cancer patients assessed in a supportive/palliative care clinic
Authors: Delgado-Guay Marvin Omar , Chisholm Gary , Williams Janet , Frisbee-Hume Susan , Ferguson Andrea O. , Bruera Eduardo
Published: October 2015

Objective:

Regular assessments of spiritual distress/spiritual pain among patients in a supportive/palliative care clinic (SCPC) are limited or unavailable. We modified the Edmonton Symptom Assessment Scale (ESAS) by adding spiritual pain (SP) to the scale (0 = best, 10 = worst) to determine the frequency, intensity, and correlates of self-reported SP (≥1/10) (pain deep in your soul/being that is not physical) among these advanced cancer patients.

Method:

We reviewed 292 consecutive consults of advanced cancer patients (ACPs) who were evaluated at our SCPC between October of 2012 and January of 2013. Symptoms were assessed using the new instrument (termed the ESAS–FS).

Results:

The median age of patients was 61 (range = 22–92). Some 53% were male; 189 (65%) were white, 45 (15%) African American, and 34 (12%) Hispanic. Some 123 of 282 (44%) of ACPs had SP (mean (95% CI) = 4(3.5–4.4). Advanced cancer patients with SP had worse pain [mean (95% CI) = 5.3(4.8, 5.8) vs. 4.5(4.0, 5.0)] (p = 0.02); depression [4.2(3.7, 4.7) vs. 2.1(1.7, 2.6), p < 0.0001]; anxiety [4.2(3.6, 4.7) vs. 2.5(2.0, 3.0), p < 0.0001]; drowsiness [4.2(3.7, 4.7) vs. 2.8(2.3, 3.2), p < 0.0001]; well-being [5.4(4.9, 5.8) vs. 4.5(4.1, 4.9), p = 0.0136]; and financial distress (FD) [4.4(3.9, 5.0) vs. 2.2(1.8, 2.7), p < 0.0001]. Spiritual pain correlated (Spearman) with depression (r = 0.45, p < 0.0001), anxiety (r = 0.34, p < 0.0001), drowsiness (r = 0.26, p < 0.0001), and FD (r = 0.44, p < 0.0001). Multivariate analysis showed an association with FD [OR (95% Wald CI) = 1.204(1.104–1.313), p < 0.0001] and depression [1.218(1.110–1.336), p < 0.0001]. The odds that patients who had SP at baseline would also have SP at follow-up were 182% higher (OR = 2.82) than for patients who were SP-negative at baseline (p = 0.0029). SP at follow-up correlated with depression (r = 0.35, p < 0.0001), anxiety (r = 0.25, p = 0.001), well-being (r = 0.27, p = 0.0006), nausea (r = 0.29, p = 0.0002), and financial distress (r = 0.42, p < 0.0001).

Significance of results:

Spiritual pain, which is correlated with physical and psychological distress, was reported in more than 40% of ACPs. Employment of the ESAS–FS allows ACPs with SP to be identified and evaluated in an SCPC. More research is needed.
High-level construal benefits, meaning making, and posttraumatic growth in cancer patients
Authors: Wang Yu , Gan Yiqun , Miao Miao , Ke Qin , Li Wenju , Zhang Zijin , Cheng Gang
Published: October 2015

Objective:

The present study sought to explore the role of meaning making and high-level construal in the relationship between meaning discrepancy and posttraumatic growth among Chinese cancer patients.

Method:

The participants were 193 individuals diagnosed with cancer. Meaning discrepancy, meaning making, high-level construal in meaning making, and posttraumatic growth were measured. Bootstrapping and structural equation modeling were performed to test the mediation effects of high-level construal on the meaning-making process.

Results:

Mediation analysis revealed that perceived discrepancies were associated with individuals' meaning-making efforts. Meaning-making efforts prompted participants to adopt a high-level construal orientation, which in turn enhanced posttraumatic growth.

Significance of results:

Our study empirically tested construal level theory in a population suffering from severe chronic trauma. The results demonstrate the important role of high-level construal in the meaning-making process of cancer patients, suggesting a specific effective strategy to foster posttraumatic growth. It seems encouraging to indicate that adopting such high-level construal may be included as part of psychological interventions for cancer patients.
Optimal design of a bonus-malus system: linear relativities revisited
Authors: Tan Chong It
Published: October 2015

In this paper, we revisit the determination of optimal relativities under the linear form of relativities that is more viable in designing a commercial bonus-malus system. We derive the analytical formulae for the optimal linear relativities subject to a financial balanced inequality constraint. We also numerically investigate the impact of different a priori risk classification towards the effectiveness of transition rules. Our results show that the a priori risk segmentation is not a sensitive factor for the effectiveness of transition rules. Furthermore, relative to the general relativities, we find that the restriction of linear relativities only produces a small amount of deterioration towards the numerical value of the optimised objective function.
Erkennen von Rechenschwäche durch LehrerInnen und Testungen im Klassenverband
Authors: Fischer Ursula , Rösch Stephanie , Nuerk Hans-Christoph , Moeller Korbinian
Published: October 2015

Zusammenfassung. In den letzten Jahren wächst in den Schulen stetig das Bewusstsein für Rechenschwäche. Um einem Kind schulische Maßnahmen wie Förderunterricht zukommen zu lassen, ist dabei nach wie vor das LeherInnenurteil von zentraler Bedeutung. Testbasierte Diagnostik kann jedoch helfen, die Förderung in der Schule zu optimieren, indem konkrete Problembereiche der jeweiligen Kinder aufgedeckt werden. Zu diesem Zweck kooperiert unsere Arbeitsgruppe seit mehreren Jahren mit einer Grundschule, in der die Kinder nicht nur von den Lehrkräften für die Förderung ausgewählt werden, sondern auch eine Klassentestung numerischer Fähigkeiten durch PsychologInnen unserer Arbeitsgruppe stattfindet. Kinder, die in dieser Testung die niedrigsten Werte erreichen, werden dementsprechend von uns für die Förderung vorgeschlagen. Die Qualität dieser gemeinsamen Einschätzung haben wir nun auf die Probe gestellt, indem wir die Kinder, die von den LehrerInnen oder unserer Testung als förderbedürftig eingeschätzt wurden, einer umfangreichen Rechenschwächediagnostik unterzogen haben. Wir wollten wissen, ob es uns gemeinsam mit den Lehrkräften gelingt, Kinder mit Rechenschwäche zuverlässig zu erkennen. Generell zeigte sich eine gute Übereinstimmung zwischen der LehrerInneneinschätzung und unseren Testergebnissen. Der vorliegende Beitrag soll als ein erster Erfahrungsbericht beschreiben, wie eine solche gemeinsame Einschätzung durch LehrerInnen und PsychologInnen zur besseren Erkennung rechenschwacher Grundschüler beitragen kann.
Follicular regulatory T cells impair follicular T helper cells in HIV and SIV infection
Authors: Miles Brodie , Miller Shannon M. , Folkvord Joy M. , Kimball Abigail , Chamanian Mastooreh , Meditz Amie L. , Arends Tessa , McCarter Martin D. , Levy David N. , Rakasz Eva G. , Skinner Pamela J. , Connick Elizabeth
Published: October 2015

Human and simian immunodeficiency viruses (HIV and SIV) exploit follicular lymphoid regions by establishing high levels of viral replication and dysregulating humoral immunity. Follicular regulatory T cells (TFR) are a recently characterized subset of lymphocytes that influence the germinal centre response through interactions with follicular helper T cells (TFH). Here, utilizing both human and rhesus macaque models, we show the impact of HIV and SIV infection on TFR number and function. We find that TFR proportionately and numerically expand during infection through mechanisms involving viral entry and replication, TGF-β signalling, low apoptosis rates and the presence of regulatory dendritic cells. Further, TFR exhibit elevated regulatory phenotypes and impair TFH functions during HIV infection. Thus, TFR contribute to inefficient germinal centre responses and inhibit HIV and SIV clearance.
Structural analysis of hierarchically organized zeolites
Authors: Mitchell Sharon , Pinar Ana B. , Kenvin Jeffrey , Crivelli Paolo , Kärger Jörg , Pérez-Ramírez Javier
Published: October 2015

Advances in materials synthesis bring about many opportunities for technological applications, but are often accompanied by unprecedented complexity. This is clearly illustrated by the case of hierarchically organized zeolite catalysts, a class of crystalline microporous solids that has been revolutionized by the engineering of multilevel pore architectures, which combine unique chemical functionality with efficient molecular transport. Three key attributes, the crystal, the pore and the active site structure, can be expected to dominate the design process. This review examines the adequacy of the palette of techniques applied to characterize these distinguishing features and their catalytic impact.
Erratum: Screening for recombinants of Crambe abyssinica after transformation by the pMF1 marker-free vector based on chemical selection and meristematic regeneration
Authors: Qi Weicong , Tinnenbroek-Capel Iris E. M. , Salentijn Elma M. J. , Schaart Jan G. , Cheng Jihua , Denneboom Christel , Zhang Zhao , Zhang Xiaolin , Zhao Han , Visser Richard G. F. , Huang Bangquan , Van Loo Eibertus N. , Krens Frans A.
Published: October 2015

The T-DNA region of pMF1 vector of marker-free system developed by Wageningen UR, has Recombinase R-LBD gene fusion and nptII and codA gene fusion between two recombination sites. After transformation applying dexamethasone (DEX) can activate the recombinase to remove the T-DNA fragment between recombination sites. The recombinant ought to be selected on 5-fluorocytocine (5-FC) because of codA converting 5-FC into 5-fluorouracil the toxic. A PMF1 vector was transformed into hexaploid species Crambe abyssinica. Two independent transformants were chosen for DEX-induced recombination and later 5-FC selection. In contrast to earlier pMF1 experiments, the strategy of stepwise selection based on meristematic regeneration was engaged. After a long period of 5-FC selection, recombinants were obtained successfully, but most of the survivors were wildtype and non-recombinant. The results revealed when applying the PMF1 marker-free system on C. abyssinica, 1) Increasing in the DEX concentration did not correspondingly enhance the success of recombination; 2) both of the DEX-induced recombination and 5-FC negative selection were apparently insufficient which was leading to the extremely high frequency in chimerism occurring for recombinant and non-recombinant cells in tissues; 3) the strategy of stepwise selection based on meristem tissue regeneration was crucial for successfully isolating the recombinant germplasm from the chimera.
Unraveling Quantum Annealers using Classical Hardness
Authors: Martin-Mayor Victor , Hen Itay
Published: October 2015

Recent advances in quantum technology have led to the development and manufacturing of experimental programmable quantum annealing optimizers that contain hundreds of quantum bits. These optimizers, commonly referred to as ‘D-Wave’ chips, promise to solve practical optimization problems potentially faster than conventional ‘classical’ computers. Attempts to quantify the quantum nature of these chips have been met with both excitement and skepticism but have also brought up numerous fundamental questions pertaining to the distinguishability of experimental quantum annealers from their classical thermal counterparts. Inspired by recent results in spin-glass theory that recognize ‘temperature chaos’ as the underlying mechanism responsible for the computational intractability of hard optimization problems, we devise a general method to quantify the performance of quantum annealers on optimization problems suffering from varying degrees of temperature chaos: A superior performance of quantum annealers over classical algorithms on these may allude to the role that quantum effects play in providing speedup. We utilize our method to experimentally study the D-Wave Two chip on different temperature-chaotic problems and find, surprisingly, that its performance scales unfavorably as compared to several analogous classical algorithms. We detect, quantify and discuss several purely classical effects that possibly mask the quantum behavior of the chip.
Membrane vesicle-mediated release of bacterial RNA
Authors: Sjöström Annika E. , Sandblad Linda , Uhlin Bernt Eric , Wai Sun Nyunt
Published: October 2015

Many Gram-negative bacterial species release outer membrane vesicles (OMVs) that interact with the host by delivering virulence factors. Here, we report for the first time that RNA is among the wide variety of bacterial components that are associated with OMVs. To characterize the RNA profiles of bacterial OMVs, we performed RNA deep sequencing analysis using OMV samples isolated from a wild type Vibrio cholerae O1 El Tor strain. The results showed that RNAs originating from intergenic regions were the most abundant. Our findings reveal a hitherto unrecognised feature of OMVs mimicking eukaryotic exosomes and highlight a need to evaluate the potential role of RNA-containing bacterial membrane vesicles in bacteria-host interactions.
Protein array identification of protein markers for serodiagnosis of Mycobacterium tuberculosis infection
Authors: Zhou Fangbin , Xu Xindong , Wu Sijia , Cui Xiaobing , Fan Lin , Pan Weiqing
Published: October 2015

The lack of effective and accurate diagnostic tools contributes to the high prevalence of tuberculosis (TB) worldwide. The current serodiagnostics for TB are inadequate mainly due to lack of TB-specific antigens with highly accurate diagnosis. In the current study, we aimed to identify novel diagnostic antigens using glutathione S-transferase (GST)-fusion protein technique. We determined the reactivity of these recombinant proteins arrayed in solution and on GSH-immobilized microplates with TB patient sera. Of 409 TB proteins produced, ninety-two yielded seropositive reactions, fourteen including eight novel proteins showed strong immunoreactivity. Further, six were selected and constructed as a multiple-antigen combination set through analysis of various combinations. A comparative study of the multiple-antigen combination set and a commercially available kit revealed that the combination set showed 66.3% (95% CI 60.5–71.8) sensitivity, which was significantly higher than that of the commercial kit [31.6% (95% CI 26.3–37.3)]. The specificity of both methods was similar at 89.6% (95% CI 83.3–95.4) and 90.6% (95% CI 83.0–95.6), respectively. This study provides a set of novel diagnostic protein markers with great potential for the development of novel diagnostic tools for active TB.
Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation and marker discovery
Authors: Singh Harpal , Rai Krishan Mohan , Upadhyay Santosh Kumar , Pant Poonam , Verma Praveen Chandra , Singh Ajit Pratap , Singh Pradhyumna Kumar
Published: October 2015

Bryophytes are the first land plants but are scarcely studied at the molecular level. Here, we report transcriptome sequencing and functional annotation of Dumortiera hirsuta, as a representative bryophyte. Approximately 0.5 million reads with ~195 Mb data were generated by sequencing of mRNA using 454 pyrosequencer. De novo assembly of reads yielded 85,240 unigenes (12,439 contigs and 72,801 singletons). BlastX search at NCBI-NR database showed similarity of 33,662 unigenes with 10-10 e-value. A total of 23,685 unigenes were annotated at TAIR10 protein database. The annotated unigenes were further classified using the Gene Ontology. Analysis at Kyoto Encyclopedia of Genes and Genomes pathway database identified 95 pathways with significant scores, among which metabolic and biosynthesis of secondary metabolite were the major ones. Phenylpropanoid pathway was elucidated and selected genes were characterized by real time qPCR. We identified 447 transcription factors belonging to 41 families and 1594 eSSRs in 1479 unigenes. D. hirsuta unigenes showed homology across the taxa from algae to angiosperm indicating their role as the connecting link between aquatic and terrestrial plants. This could be a valuable genomic resource for molecular and evolutionary studies. Further, it sheds light for the isolation and characterization of new genes with unique functions.
Systems assessment of intercalated combination of chemotherapy and EGFR TKIs versus chemotherapy or EGFR TKIs alone in advanced NSCLC patients
Authors: Yan Han , Li Qin , Wang Wei , Zhen Hongchao , Cao Bangwei
Published: October 2015

Both chemotherapy and epidermal growth factor receptor tyrosine kinase inhibitors (EGFR TKIs) are widely applied for the treatment of non-small cell lung cancer (NSCLC), but the efficacy of these two treatments in combination is not yet clear. Thus, we sought to evaluate the efficacy of the intercalated combination of these two treatments in NSCLC. The PubMed database, EMBASE, Cochrane Controlled Trials Register and Chinese Biomedical Database were systematically searched by two researchers for randomized clinical trials (RCTs) that examined the intercalated combination of chemotherapy and EGFR TKIs in NSCLC. Ten studies involving 1,660 patients were included in this systematic review. The statistical results showed that the intercalated combination of chemotherapy and EGFR TKIs significantly improved overall survival (OS) (hazard ratio (HR) = 0.83, 95% confidence interval (CI): 0.70–0.98), progression-free survival (PFS) (HR = 0.65, 95% CI: 0.51–0.84) and the objective response rate (ORR) (risk ratio (RR) = 1.90, 95% CI: 1.22–2.98) compared to chemotherapy alone. Similarly, compared to EGFR TKIs monotherapy, the intercalated combination of chemotherapy and EGFR TKIs seemed superior to EGFR TKIs alone in terms of PFS, ORR and DCR (PFS: HR = 0.75, 95% CI: 0.62–0.91, ORR: RR = 1.49, 95% CI: 1.12–2.00 and DCR: RR = 1.33, 95% CI: 1.15–1.54) in advanced NSCLC therapy.
Histidine provides long-term neuroprotection after cerebral ischemia through promoting astrocyte migration
Authors: Liao Ru-jia , Jiang Lei , Wang Rong-rong , Zhao Hua-wei , Chen Ying , Li Ya , Wang Lu , Jie Li-Yong , Zhou Yu-dong , Zhang Xiang-nan , Chen Zhong , Hu Wei-wei
Published: October 2015

The formation of glial scar impedes the neurogenesis and neural functional recovery following cerebral ischemia. Histamine showed neuroprotection at early stage after cerebral ischemia, however, its long-term effect, especially on glial scar formation, hasn’t been characterized. With various administration regimens constructed for histidine, a precursor of histamine, we found that histidine treatment at a high dose at early stage and a low dose at late stage demonstrated the most remarkable long-term neuroprotection with decreased infarct volume and improved neurological function. Notably, this treatment regimen also robustly reduced the glial scar area and facilitated the astrocyte migration towards the infarct core. In wound-healing assay and transwell test, histamine significantly promoted astrocyte migration. H2 receptor antagonists reversed the promotion of astrocyte migration and the neuroprotection provided by histidine. Moreover, histamine upregulated the GTP-bound small GTPase Rac1, while a Rac1 inhibitor, NSC23766, abrogated the neuroprotection of histidine and its promotion of astrocyte migration. Our data indicated that a dose/stage-dependent histidine treatment, mediated by H2 receptor, promoted astrocyte migration towards the infarct core, which benefited long-term post-cerebral ischemia neurological recovery. Therefore, targeting histaminergic system may be an effective therapeutic strategy for long-term cerebral ischemia injury through its actions on astrocytes.
Coupling and electrical control of structural, orbital and magnetic orders in perovskites
Authors: Varignon Julien , Bristowe Nicholas C. , Bousquet Eric , Ghosez Philippe
Published: October 2015

Perovskite oxides are already widely used in industry and have huge potential for novel device applications thanks to the rich physical behaviour displayed in these materials. The key to the functional electronic properties exhibited by perovskites is often the so-called Jahn-Teller distortion. For applications, an electrical control of the Jahn-Teller distortions, which is so far out of reach, would therefore be highly desirable. Based on universal symmetry arguments, we determine new lattice mode couplings that can provide exactly this paradigm and exemplify the effect from first-principles calculations. The proposed mechanism is completely general, however for illustrative purposes, we demonstrate the concept on vanadium based perovskites where we reveal an unprecedented orbital ordering and Jahn-Teller induced ferroelectricity. Thanks to the intimate coupling between Jahn-Teller distortions and electronic degrees of freedom, the electric field control of Jahn-Teller distortions is of general relevance and may find broad interest in various functional devices.
Genome-wide DNA methylation detection by MethylCap-seq and Infinium HumanMethylation450 BeadChips: an independent large-scale comparison
Authors: De Meyer Tim , Bady Pierre , Trooskens Geert , Kurscheid Sebastian , Bloch Jocelyne , Kros Johan M. , Hainfellner Johannes A. , Stupp Roger , Delorenzi Mauro , Hegi Monika E. , Van Criekinge Wim
Published: October 2015

Two cost-efficient genome-scale methodologies to assess DNA-methylation are MethylCap-seq and Illumina’s Infinium HumanMethylation450 BeadChips (HM450). Objective information regarding the best-suited methodology for a specific research question is scant. Therefore, we performed a large-scale evaluation on a set of 70 brain tissue samples, i.e. 65 glioblastoma and 5 non-tumoral tissues. As MethylCap-seq coverages were limited, we focused on the inherent capacity of the methodology to detect methylated loci rather than a quantitative analysis. MethylCap-seq and HM450 data were dichotomized and performances were compared using a gold standard free Bayesian modelling procedure. While conditional specificity was adequate for both approaches, conditional sensitivity was systematically higher for HM450. In addition, genome-wide characteristics were compared, revealing that HM450 probes identified substantially fewer regions compared to MethylCap-seq. Although results indicated that the latter method can detect more potentially relevant DNA-methylation, this did not translate into the discovery of more differentially methylated loci between tumours and controls compared to HM450. Our results therefore indicate that both methodologies are complementary, with a higher sensitivity for HM450 and a far larger genome-wide coverage for MethylCap-seq, but also that a more comprehensive character does not automatically imply more significant results in biomarker studies.
Cavity enhanced atomic magnetometry
Authors: Crepaz Herbert , Ley Li Yuan , Dumke Rainer
Published: October 2015

Atom sensing based on Faraday rotation is an indispensable method for precision measurements, universally suitable for both hot and cold atomic systems. Here we demonstrate an all-optical magnetometer where the optical cell for Faraday rotation spectroscopy is augmented with a low finesse cavity. Unlike in previous experiments, where specifically designed multipass cells had been employed, our scheme allows to use conventional, spherical vapour cells. Spherical shaped cells have the advantage that they can be effectively coated inside with a spin relaxation suppressing layer providing long spin coherence times without addition of a buffer gas. Cavity enhancement shows in an increase in optical polarization rotation and sensitivity compared to single-pass configurations.
Effects of random rewiring on the degree correlation of scale-free networks
Authors: Qu Jing , Wang Sheng-Jun , Jusup Marko , Wang Zhen
Published: October 2015

Random rewiring is used to generate null networks for the purpose of analyzing the topological properties of scale-free networks, yet the effects of random rewiring on the degree correlation are subject to contradicting interpretations in the literature. We comprehensively analyze the degree correlation of randomly rewired scale-free networks and show that random rewiring increases disassortativity by reducing the average degree of the nearest neighbors of high-degree nodes. The effect can be captured by the measures of the degree correlation that consider all links in the network, but not by analogous measures that consider only links between degree peers, hence the potential for contradicting interpretations. We furthermore find that random and directional rewiring affect the topology of a scale-free network differently, even if the degree correlation of the rewired networks is the same. Consequently, the network dynamics is changed, which is proven here by means of the biased random walk.
Constitutional de novo deletion of the FBXW7 gene in a patient with focal segmental glomerulosclerosis and multiple primitive tumors
Authors: Roversi Gaia , Picinelli Chiara , Bestetti Ilaria , Crippa Milena , Perotti Daniela , Ciceri Sara , Saccheri Fabiana , Collini Paola , Poliani Pietro L. , Catania Serena , Peissel Bernard , Pagni Fabio , Russo Silvia , Peterlongo Paolo , Manoukian Siranoush , Finelli Palma
Published: October 2015

Multiple primary malignant neoplasms are rare entities in the clinical setting, but represent an important issue in the clinical management of patients since they could be expression of a genetic predisposition to malignancy. A high resolution genome wide array CGH led us to identify the first case of a de novo constitutional deletion confined to the FBXW7 gene, a well known tumor suppressor, in a patient with a syndromic phenotype characterized by focal segmental glomerulosclerosis and multiple primary early/atypical onset tumors, including Hodgkin’s lymphoma, Wilms tumor and breast cancer. Other genetic defects may be associated with patient’s phenotype. In this light, constitutional mutations at BRCA1, BRCA2, TP53, PALB2 and WT1 genes were excluded by performing sequencing and MLPA analysis; similarly, we ruled out constitutional abnormalities at the imprinted 11p15 region by methylation specific -MLPA assay. Our observations sustain the role of FBXW7 as cancer predisposition gene and expand the spectrum of its possible associated diseases.
Vaccination Programs for Endemic Infections: Modelling Real versus Apparent Impacts of Vaccine and Infection Characteristics
Authors: Ragonnet Romain , Trauer James M. , Denholm Justin T. , Geard Nicholas L. , Hellard Margaret , McBryde Emma S.
Published: October 2015

Vaccine effect, as measured in clinical trials, may not accurately reflect population-level impact. Furthermore, little is known about how sensitive apparent or real vaccine impacts are to factors such as the risk of re-infection or the mechanism of protection. We present a dynamic compartmental model to simulate vaccination for endemic infections. Several measures of effectiveness are calculated to compare the real and apparent impact of vaccination and assess the effect of a range of infection and vaccine characteristics on these measures. Although broadly correlated, measures of real and apparent vaccine effectiveness can differ widely. Vaccine impact is markedly underestimated when primary infection provides partial natural immunity, when coverage is high and when post-vaccination infectiousness is reduced. Despite equivalent efficacy, ‘all or nothing’ vaccines are more effective than ‘leaky’ vaccines, particularly in settings with high risk of re-infection and transmissibility. Latent periods result in greater real impacts when risk of re-infection is high, but this effect diminishes if partial natural immunity is assumed. Assessments of population-level vaccine effects against endemic infections from clinical trials may be significantly biased and vaccine and infection characteristics should be considered when modelling outcomes of vaccination programs, as their impact may be dramatic.
Highly photosensitive graphene field-effect transistor with optical memory function
Authors: Ishida Shohei , Anno Yuki , Takeuchi Masato , Matsuoka Masaya , Takei Kuniharu , Arie Takayuki , Akita Seiji
Published: October 2015

Graphene is a promising material for use in photodetectors for the ultrawide wavelength region: from ultraviolet to terahertz. Nevertheless, only the 2.3% light absorption of monolayer graphene and fast recombination time of photo-excited charge restrict its sensitivity. To enhance the photosensitivity, hybridization of photosensitive material and graphene has been widely studied, where the accumulated photo-excited charge adjacent to the graphene channel modifies the Fermi level of graphene. However, the charge accumulation process slows the response to around a few tens of seconds to minutes. In contrast, a charge accumulation at the contact would induce the efficient light-induced modification of the contact resistance, which would enhance its photosensitivity. Herein, we demonstrate a highly photosensitive graphene field-effect transistor with noise-equivalent power of ~3 × 10−15 W/Hz1/2 and with response time within milliseconds at room temperature, where the Au oxide on Au electrodes modulates the contact resistance because of the light-assisted relaxation of the trapped charge at the contact. Additionally, this light-induced relaxation imparts an optical memory function with retention time of ~5 s. These findings are expected to open avenues to realization of graphene photodetectors with high sensitivity toward single photon detection with optical memory function.
InSAR analysis of surface deformation over permafrost to estimate active layer thickness based on one-dimensional heat transfer model of soils
Authors: Li Zhiwei , Zhao Rong , Hu Jun , Wen Lianxing , Feng Guangcai , Zhang Zeyu , Wang Qijie
Published: October 2015

This paper presents a novel method to estimate active layer thickness (ALT) over permafrost based on InSAR (Interferometric Synthetic Aperture Radar) observation and the heat transfer model of soils. The time lags between the periodic feature of InSAR-observed surface deformation over permafrost and the meteorologically recorded temperatures are assumed to be the time intervals that the temperature maximum to diffuse from the ground surface downward to the bottom of the active layer. By exploiting the time lags and the one-dimensional heat transfer model of soils, we estimate the ALTs. Using the frozen soil region in southern Qinghai-Tibet Plateau (QTP) as examples, we provided a conceptual demonstration of the estimation of the InSAR pixel-wise ALTs. In the case study, the ALTs are ranging from 1.02 to 3.14 m and with an average of 1.95 m. The results are compatible with those sparse ALT observations/estimations by traditional methods, while with extraordinary high spatial resolution at pixel level (~40 meter). The presented method is simple and can potentially be used for deriving high-resolution ALTs in other remote areas similar to QTP, where only sparse observations are available now.
Genome editing of CXCR4 by CRISPR/cas9 confers cells resistant to HIV-1 infection
Authors: Hou Panpan , Chen Shuliang , Wang Shilei , Yu Xiao , Chen Yu , Jiang Meng , Zhuang Ke , Ho Wenzhe , Hou Wei , Huang Jian , Guo Deyin
Published: October 2015

Genome editing via CRISPR/Cas9 has become an efficient and reliable way to make precise, targeted changes to the genome of living cells. CXCR4 is a co-receptor for the human immunodeficiency virus type 1 (HIV-1) infection and has been considered as an important therapeutic target for AIDS. CXCR4 mediates viral entry into human CD4+ cells by binding to envelope protein, gp120. Here, we show that human CXCR4 gene is efficiently disrupted by CRISPR/Cas9-mediated genome editing, leading to HIV-1 resistance of human primary CD4+ T cells. We also show that the Cas9-mediated ablation of CXCR4 demonstrated high specificity and negligible off-target effects without affecting cell division and propagation. The precise and efficient genome editing of CXCR4 will provide a new strategy for therapeutic application against HIV-1 infection.
Increased abundance of translation machinery in stem cell–derived neural progenitor cells from four schizophrenia patients
Authors: Topol A , English J A , Flaherty E , Rajarajan P , Hartley B J , Gupta S , Desland F , Zhu S , Goff T , Friedman L , Rapoport J , Felsenfeld D , Cagney G , Mackay-Sim A , Savas J N , Aronow B , Fang G , Zhang B , Cotter D , Brennand K J
Published: October 2015

The genetic and epigenetic factors contributing to risk for schizophrenia (SZ) remain unresolved. Here we demonstrate, for the first time, perturbed global protein translation in human-induced pluripotent stem cell (hiPSC)-derived forebrain neural progenitor cells (NPCs) from four SZ patients relative to six unaffected controls. We report increased total protein levels and protein synthesis, together with two independent sets of quantitative mass spectrometry evidence indicating markedly increased levels of ribosomal and translation initiation and elongation factor proteins, in SZ hiPSC NPCs. We posit that perturbed levels of global protein synthesis in SZ hiPSC NPCs represent a novel post-transcriptional mechanism that might contribute to disease progression.