bluuebunny/crossref_metadata_2025 huggingface dataset:
In Vitro
Assessment of the Antimicrobial Efficacy of Optimized Nitroglycerin-Citrate-Ethanol as a Nonantibiotic, Antimicrobial Catheter Lock Solution for Prevention of Central Line-Associated Bloodstream Infections
Authors: Reitzel Ruth A. , Rosenblatt Joel , Hirsh-Ginsberg Cheryl , Murray Kimberly , Chaftari Anne-Marie , Hachem Ray , Raad Issam
Published: June 2016

The rapid, broad-spectrum, biofilm-eradicating activity of the combination of 0.01% nitroglycerin, 7% citrate, and 20% ethanol and its potential as a nonantibiotic, antimicrobial catheter lock solution (ACLS) were previously reported. Here, a nitroglycerin-citrate-ethanol (NiCE) ACLS optimized for clinical assessment was developed by reducing the nitroglycerin and citrate concentrations and increasing the ethanol concentration. Biofilm-eradicating activity was sustained when the ethanol concentration was increased from 20 to 22% which fully compensated for reducing the citrate concentration from 7% to 4% as well as the nitroglycerin concentration from 0.01% to 0.0015% or 0.003%. The optimized formulations demonstrated complete and rapid (2 h) eradication of methicillin-resistant
Staphylococcus aureus
(MRSA), vancomycin-intermediate
Staphylococcus aureus
(VISA), methicillin-resistant
Staphylococcus epidermidis
(MRSE), vancomycin-resistant enterococci (VRE), multidrug-resistant (MDR)
Pseudomonas aeruginosa
, MDR
Klebsiella pneumoniae
, MDR
Enterobacter cloacae
, MDR
Acinetobacter baumannii
, MDR
Escherichia coli
, MDR
Stenotrophomonas maltophilia
,
Candida albicans
, and
Candida glabrata
biofilms. The optimized NiCE lock solutions demonstrated anticoagulant activities comparable to those of heparin lock solutions. NiCE lock solution was significantly more effective than taurolidine-citrate-heparin lock solution in eradicating biofilms of
Staphylococcus aureus
and
Candida glabrata
. The optimized, nonantibiotic, heparin-free NiCE lock solution demonstrates rapid broad-spectrum biofilm eradication as well as effective anticoagulant activity, making NiCE a high-quality ACLS candidate for clinical assessment.
Therapeutic Potential of the Mycobacterium tuberculosis Mycolic Acid Transporter, MmpL3
Authors: Li Wei , Obregón-Henao Andrés , Wallach Joshua B. , North E. Jeffrey , Lee Richard E. , Gonzalez-Juarrero Mercedes , Schnappinger Dirk , Jackson Mary
Published: June 2016

In recent years, whole-cell-based screens for novel small molecule inhibitors active against
Mycobacterium tuberculosis
in culture followed by the whole-genome sequencing of spontaneous resistant mutants have identified multiple chemical scaffolds thought to kill the bacterium through the inactivation of the mycolic acid transporter, MmpL3. Consistent with the fact that MmpL3 is required for the formation of the mycobacterial outer membrane, we have conclusively shown in this study, using conditionally regulated knockdown mutants, that
mmpL3
is required for the replication and viability of
M. tuberculosis
, both under standard laboratory growth conditions and during the acute and chronic phases of infection in mice. Speaking for the vulnerability of this target, silencing
mmpL3
had a rapid bactericidal effect on actively replicating cells
in vitro
and reduced by 3 to 5 logs in less than 4 weeks the bacterial loads of acutely and chronically infected mouse lungs, respectively. Depletion of MmpL3 further rendered
M. tuberculosis
hypersusceptible to MmpL3 inhibitors. The exquisite vulnerability of MmpL3 at all stages of the infection establishes this transporter as an attractive new target with the potential to improve and shorten current drug-susceptible and drug-resistant tuberculosis chemotherapies.
Targeting the Cytochrome
bc
1
Complex of Leishmania Parasites for Discovery of Novel Drugs
Authors: Ortiz Diana , Forquer Isaac , Boitz Jan , Soysa Radika , Elya Carolyn , Fulwiler Audrey , Nilsen Aaron , Polley Tamsen , Riscoe Michael K. , Ullman Buddy , Landfear Scott M.
Published: June 2016

Endochin-like quinolones (ELQs) are potent and specific inhibitors of cytochrome
bc
1
from
Plasmodium falciparum
and
Toxoplasma gondii
and show promise for novel antiparasitic drug development. To determine whether the mitochondrial electron transport chain of
Leishmania
parasites could be targeted similarly for drug development, we investigated the activity of 134 structurally diverse ELQs. A cohort of ELQs was selectively toxic to amastigotes of
Leishmania mexicana
and
L. donovani
, with 50% inhibitory concentrations (IC
50
s) in the low micromolar range, but the structurally similar hydroxynaphthoquinone buparvaquone was by far the most potent inhibitor of electron transport, ATP production, and intracellular amastigote growth. Cytochrome
bc
1
is thus a promising target for novel antileishmanial drugs, and further improvements on the buparvaquone scaffold are warranted for development of enhanced therapeutics.
Microfilariae of Brugia malayi Inhibit the mTOR Pathway and Induce Autophagy in Human Dendritic Cells
Authors: Narasimhan Prakash Babu , Bennuru Sasisekhar , Meng Zhaojing , Cotton Rachel N. , Elliott Kathleen R. , Ganesan Sundar , McDonald-Fleming Renee , Veenstra Timothy D. , Nutman Thomas B. , Tolouei Semnani Roshanak
Published: June 2016

Immune modulation is a hallmark of patent filarial infection, including suppression of antigen-presenting cell function and downmodulation of filarial antigen-specific T cell responses. The mammalian target of rapamycin (mTOR) signaling pathway has been implicated in immune regulation, not only by suppressing T cell responses but also by regulating autophagy (through mTOR sensing amino acid availability). Global proteomic analysis (liquid chromatography-tandem mass spectrometry) of microfilaria (mf)-exposed monocyte-derived dendritic cells (DC) indicated that multiple components of the mTOR signaling pathway, including mTOR, eIF4A, and eIF4E, are downregulated by mf, suggesting that mf target this pathway for immune modulation in DC. Utilizing Western blot analysis, we demonstrate that similar to rapamycin (a known mTOR inhibitor), mf downregulate the phosphorylation of mTOR and its regulatory proteins, p70S6K1 and 4E-BP1, a process essential for DC protein synthesis. As active mTOR signaling regulates autophagy, we examined whether mf exposure alters autophagy-associated processes. mf-induced autophagy was reflected in marked upregulation of phosphorylated Beclin 1, known to play an important role in both autophagosome formation and autolysosome fusion, in induction of LC3II, a marker of autophagosome formation, and in induced degradation of p62, a ubiquitin-binding protein that aggregates protein in autophagosomes and is degraded upon autophagy that was reduced significantly by mf exposure and by rapamycin. Together, these results suggest that
Brugia malayi
mf employ mechanisms of metabolic modulation in DC to influence the regulation of the host immune response by downregulating mTOR signaling, resulting in increased autophagy. Whether this is a result of the parasite-secreted rapamycin homolog is currently under study.
NLRP3 Inflammasome Activation in THP-1 Target Cells Triggered by Pathogenic Naegleria fowleri
Authors: Kim Jong-Hyun , Sohn Hae-Jin , Yoo Jong-Kyun , Kang Heekyoung , Seong Gi-Sang , Chwae Yong-Joon , Kim Kyongmin , Park Sun , Shin Ho-Joon
Published: June 2016

Naegleria fowleri
, known as the brain-eating amoeba, causes acute primary amoebic meningoencephalitis. During swimming and other recreational water activities,
N. fowleri
trophozoites penetrate the nasal mucosa and invade the olfactory bulbs, resulting in intense inflammatory reactions in the forebrain tissue. To investigate what kinds of inflammasome molecules are expressed in target cells due to
N. fowleri
infection, human macrophage cells (THP-1 cells) were cocultured with
N. fowleri
trophozoites in a noncontact system, and consequently, interleukin-1β (IL-1β) production was estimated. Caspase-1 activation and IL-1β production from THP-1 cells by Western blotting and the culture supernatant by enzyme-linked immunosorbent assay analysis were observed at 3 h after cocultivation. In addition, the increased expression of ASC and NLRP3, which make up an inflammasome complex, was also observed at 3 h after cocultivation. To confirm the caspase-1 activation and IL-1β production via the NLRP3 inflammasome in THP-1 cells triggered by
N. fowleri
trophozoites, THP-1 cells were pretreated with several inhibitors. The inhibition assay showed that CA-074 (a cathepsin B inhibitor), glybenclamide (an NLRP3 molecule inhibitor), and
N
-benzyloxycarbony-Val-Ala-Asp(
O
-methyl)-fluoromethylketone (Z-VAD-FMK; a caspase-1 inhibitor) reduced the levels of caspase-1 activation and IL-1β production from THP-1 cells. This study suggests that
N. fowleri
infection induces the NLRP3 inflammasome, which activates caspase-1 and subsequently produces IL-1β, thus resulting in inflammation.
Interleukin-8, CXCL1, and MicroRNA miR-146a Responses to Probiotic Escherichia coli Nissle 1917 and Enteropathogenic E. coli in Human Intestinal Epithelial T84 and Monocytic THP-1 Cells after Apical or Basolateral Infection
Authors: Sabharwal Harshana , Cichon Christoph , Ölschläger Tobias A. , Sonnenborn Ulrich , Schmidt M. Alexander
Published: June 2016

Bacterium-host interactions in the gut proceed via directly contacted epithelial cells, the host's immune system, and a plethora of bacterial factors. Here we characterized and compared exemplary cytokine and microRNA (miRNA) responses of human epithelial and THP-1 cells toward the prototype enteropathogenicEscherichia coli(EPEC) strain E2348/69 (O127:H6) and the probiotic strainEscherichia coliNissle 1917 (EcN) (O6:K5:H1). Human T84 and THP-1 cells were used as cell culture-based model systems for epithelial and monocytic cells. Polarized T84 monolayers were infected apically or basolaterally. Bacterial challenges from the basolateral side resulted in more pronounced cytokine and miRNA responses than those observed for apical side infections. Interestingly, the probiotic EcN also caused a pronounced transcriptional increase of proinflammatory CXCL1 and interleukin-8 (IL-8) levels when human T84 epithelial cells were infected from the basolateral side. miR-146a, which is known to regulate adaptor molecules in Toll-like receptor (TLR)/NF-κB signaling, was found to be differentially regulated in THP-1 cells between probiotic and pathogenic bacteria. To assess the roles of flagella and flagellin, we employed several flagellin mutants of EcN. EcN flagellin mutants induced reduced IL-8 as well as CXCL1 responses in T84 cells, suggesting that flagellin is an inducer of this cytokine response. Following infection with an EPEC type 3 secretion system (T3SS) mutant, we observed increased IL-8 and CXCL1 transcription in T84 and THP-1 cells compared to that in wild-type EPEC. This study emphasizes the differential induction of miR-146a by pathogenic and probioticE. colistrains in epithelial and immune cells as well as a loss of probiotic properties in EcN interacting with cells from the basolateral side.
Key Enzymes of the Semiphosphorylative Entner-Doudoroff Pathway in the Haloarchaeon Haloferax volcanii: Characterization of Glucose Dehydrogenase, Gluconate Dehydratase, and 2-Keto-3-Deoxy-6-Phosphogluconate Aldolase
Authors: Sutter Jan-Moritz , Tästensen Julia-Beate , Johnsen Ulrike , Soppa Jörg , Schönheit Peter
Published: June 2016

The halophilic archaeon
Haloferax volcanii
has been proposed to degrade glucose via the semiphosphorylative Entner-Doudoroff (spED) pathway. So far, the key enzymes of this pathway, glucose dehydrogenase (GDH), gluconate dehydratase (GAD), and 2-keto-3-deoxy-6-phosphogluconate (KDPG) aldolase (KDPGA), have not been characterized, and their functional involvement in glucose degradation has not been demonstrated. Here we report that the genes HVO_1083 and HVO_0950 encode GDH and KDPGA, respectively. The recombinant enzymes show high specificity for glucose and KDPG and did not convert the corresponding C
4
epimers galactose and 2-keto-3-deoxy-6-phosphogalactonate at significant rates. Growth studies of knockout mutants indicate the functional involvement of both GDH and KDPGA in glucose degradation. GAD was purified from
H. volcanii
, and the encoding gene,
gad
, was identified as HVO_1488. GAD catalyzed the specific dehydration of gluconate and did not utilize galactonate at significant rates. A knockout mutant of GAD lost the ability to grow on glucose, indicating the essential involvement of GAD in glucose degradation. However, following a prolonged incubation period, growth of the Δ
gad
mutant on glucose was recovered. Evidence is presented that under these conditions, GAD was functionally replaced by xylonate dehydratase (XAD), which uses both xylonate and gluconate as substrates. Together, the characterization of key enzymes and analyses of the respective knockout mutants present conclusive evidence for the
in vivo
operation of the spED pathway for glucose degradation in
H. volcanii
.

IMPORTANCE
The work presented here describes the identification and characterization of the key enzymes glucose dehydrogenase, gluconate dehydratase, and 2-keto-3-deoxy-6-phosphogluconate aldolase and their encoding genes of the proposed semiphosphorylative Entner-Doudoroff pathway in the haloarchaeon
Haloferax volcanii
. The functional involvement of the three enzymes was proven by analyses of the corresponding knockout mutants. These results provide evidence for the
in vivo
operation of the semiphosphorylative Entner-Doudoroff pathway in haloarchaea and thus expand our understanding of the unusual sugar degradation pathways in the domain
Archaea
.
Clostridium difficile
Infection
Authors: Shin Jae Hyun , Chaves-Olarte Esteban , Warren Cirle A.
Published: June 2016

Clostridium difficile
is an anaerobic, Gram-positive, spore-forming, toxin-secreting bacillus that has long been recognized to be the most common etiologic pathogen of antibiotic-associated diarrhea.
C. difficile
infection (CDI) is now the most common cause of health care–associated infections in the United States and accounts for 12% of these infections (Magill SS et al.,
N Engl J Med
370:
1198–1208, 2014). Among emerging pathogens of public health importance in the United States, CDI has the highest population-based incidence, estimated at 147 per 100,000 (Lessa FC et al.,
N Engl J Med
372:
825–834, 2015). In a report on antimicrobial resistance,
C. difficile
has been categorized by the Centers for Disease Control and Prevention as one of three “urgent” threats (
http://www.cdc.gov/drugresistance/threat-report-2013/
). Although
C. difficile
was first described in the late 1970s, the past decade has seen the emergence of hypertoxigenic strains that have caused increased morbidity and mortality worldwide. Pathogenic strains, host susceptibility, and other regional factors vary and may influence the clinical manifestation and approach to intervention. In this article, we describe the global epidemiology of CDI featuring the different strains in circulation outside of North America and Europe where strain NAP1/027/BI/III had originally gained prominence. The elderly population in health care settings has been disproportionately affected, but emergence of CDI in children and healthy young adults in community settings has, likewise, been reported. New approaches in management, including fecal microbiota transplantation, are discussed.
Mobilization of Carbapenemase-Mediated Resistance in
Enterobacteriaceae
Authors: Mathers Amy
Published: June 2016

There has been a dramatic increase in the last decade in the number of carbapenem-resistant
Enterobacteriaceae
, often leaving patients and their providers with few treatment options and resultant poor outcomes when an infection develops. The majority of the carbapenem resistance is mediated by bacterial acquisition of one of three carbapenemases (
Klebsiella pneumoniae
carbapenemase [KPC], oxacillinase-48-like [OXA-48], and the New Delhi metallo-β-lactamase [NDM]). Each of these enzymes has a unique global epidemiology and microbiology. The genes which encode the most globally widespread carbapenemases are typically carried on mobile pieces of DNA which can be freely exchanged between bacterial strains and species via horizontal gene transfer. Unfortunately, most of the antimicrobial surveillance systems target specific strains or species and therefore are not well equipped for examining genes of drug resistance. Examination of not only the carbapenemase gene itself but also the genetic context which can predispose a gene to mobilize within a diversity of species and environments will likely be central to understanding the factors contributing to the global dissemination of carbapenem resistance. Using the three most prevalent carbapenemase genes as examples, this chapter highlights the potential impact the associated genetic mobile elements have on the epidemiology and microbiology for each carbapenemase. Understanding how a carbapenemase gene mobilizes through a bacterial population will be critical for detection methods and ultimately inform infection control practices. Understanding gene mobilization and tracking will require novel approaches to surveillance, which will be required to slow the spread of this emerging resistance.
Emerging Fungal Infections in the Pacific Northwest: The Unrecognized Burden and Geographic Range of
Cryptococcus gattii
and
Coccidioides immitis
Authors: Lockhart Shawn R. , McCotter Orion Z. , Chiller Tom M.
Published: June 2016

Both
Cryptococcus gattii
and
Coccidioides
can cause debilitating diseases if not identified early. It is imperative that clinicians recognize these diseases and begin treatment quickly when necessary. In order to have these two mycoses in their differential diagnosis, clinicians, microbiologists, and public health officials must be aware of the expanding geographic boundary in the case of
Coccidioides immitis
and the new emergence in the case of
C. gattii
. Accordingly, there is now mandatory reporting for cases of
C. gattii
and
C. immitis
in both Washington and Oregon, and the Centers for Disease Control and Prevention keeps a repository of available isolates. Through the One Health initiative, clinicians, veterinarians, and public health officials are collaborating to better understand the emergence and expanding geographic range of these extremely important fungal diseases.
Increasing access to care for sick newborns: evidence from the Ghana Newhints cluster-randomised controlled trial
Authors: Manu Alexander , Hill Zelee , ten Asbroek Augustinus HA , Soremekun Seyi , Weobong Benedict , Gyan Thomas , Tawiah-Agyemang Charlotte , Danso Samuel , Amenga-Etego Seeba , Owusu-Agyei Seth , Kirkwood Betty R
Published: June 2016

Objectives

To evaluate the impact of Newhints community-based surveillance volunteer (CBSV) assessments and referrals on access to care for sick newborns and on existing inequities in access.

Design

We evaluated a prospective cohort nested within the Newhints cluster-randomised controlled trial.

Setting

Community-based intervention involving more than 750 000, predominantly rural, population in seven contiguous districts in the Brong-Ahafo Region, Ghana.

Participants

Participants were recently delivered women (from more than 120 000 women under surveillance) and their 16 168 liveborn babies. Qualitative in-depth interviews with referral narratives (IDIs) were conducted with 92 mothers, CBSVs and health facility front-desk and maternity/paediatrics ward staff.

Interventions

Newhints trained and effectively supervised 475 CBSVs (existing within the Ghana Health Service) in 49 of 98 supervisory zones (clusters) to assess and refer newborns with any of the 10-key-danger signs to health facilities within the first week after birth; promote independent care seeking for sick newborns and problem-solve around barriers between November 2008 and December 2009.

Primary outcomes

The main evaluation outcomes were rates of compliance with referrals and independent care seeking for newborn illnesses.

Results

Of 4006 sampled, 2795 (69.8%) recently delivered women received CBSV assessment visits and 279 (10.0%) newborns were referred with danger signs. Compliance with referrals was unprecedentedly high (86.0%) with women in the poorest quintile (Q1) complying better than the least poor (Q5):87.5%(Q1) vs 69.7%(Q5); p=0.038. Three-quarters went to hospitals; 18% were admitted and 58% received outpatient treatment. Some (24%) mothers were turned away at facilities and follow-on IDIs showed that some of these untreated babies subsequently died. Independent care seeking for severe newborn illness increased from 55.4% in control to 77.3% in Newhints zones, especially among Q1 where care seeking almost doubled (95.0% vs 48.6%; RR=1.94 (1.32, 2.84); p=0.001). Rates were the highest among rural residents but urban residents complied quicker.

Conclusions

Home visits are feasible and a potentially pro-poor approach to link sick newborns to facilities. Its effectiveness in improving survival hinges on matched improvement in facility quality of care.

Trial registration number

NCT00623337.
Latest trends in ADHD drug prescribing patterns in children in the UK: prevalence, incidence and persistence
Authors: Beau-Lejdstrom Raphaelle , Douglas Ian , Evans Stephen J W , Smeeth Liam
Published: June 2016

Objectives

To investigate attention deficit and hyperactivity disorder (ADHD) drug prescribing in children under 16 years old in the UK between 1992 and 2013.

Methods

All patients under 16 registered in the Clinical Practice Research Datalink (CPRD) with a minimum of 1 year of observation time and who received at least one prescription of any ADHD drug between 1 January 1992 and 31 December 2013.Trends in prevalence and incidence of use of ADHD drugs in children were calculated between 1995 and 2013 and persistence in new users was estimated.

Results

The prevalence of ADHD drug use in children under 16 increased 34-fold overall, rising from 1.5 95% CI (1.1 to 2.0) per 10 000 children in 1995 to 50.7 95% CI (49.2 to 52.1) per 10 000 children in 2008 then stabilising to 51.1 95% CI (49.7 to 52.6) per 10 000 children in 2013. The rate of new users increased eightfold reaching 10.2 95% CI (9.5 to 10.9) per 10 000 children in 2007 then decreasing to 9.1 95% CI (8.5 to 9.7) per 10 000 children in 2013. Although prevalence and incidence increased rather steeply after 1995, this trend seems to halt from 2008 onwards. We identified that 77%, 95% CI (76% to 78%) of children were still under treatment after 1 year and 60% 95% CI (59% to 61%) after 2 years.

Conclusions

There was a marked increase in ADHD drug use among children in the UK from 1992 until around 2008, with stable levels of use since then. UK children show relatively long persistence of treatment with ADHD medications compared to other countries.
Identification of depression in women during pregnancy and the early postnatal period using the Whooley questions and the Edinburgh Postnatal Depression Scale: protocol for the Born and Bred in Yorkshire: PeriNatal Depression Diagnostic Accuracy (BaBY PaNDA) study
Authors: Littlewood Elizabeth , Ali Shehzad , Ansell Pat , Dyson Lisa , Gascoyne Samantha , Hewitt Catherine , Keding Ada , Mann Rachel , McMillan Dean , Morgan Deborah , Swan Kelly , Waterhouse Bev , Gilbody Simon
Published: June 2016

Introduction

Perinatal depression is well recognised as a mental health condition but <50% of cases are identified by healthcare professionals in routine clinical practice. The Edinburgh Postnatal Depression Scale (EPDS) is often used to detect symptoms of postnatal depression in maternity and child services. The National Institute for Health and Care Excellence (NICE) recommends 2 ‘ultra-brief’ case-finding questions (the Whooley questions) to aid identification of depression during the perinatal period, but this recommendation was made in the absence of any validation studies in a perinatal population. Limited research exists on the acceptability of these depression case-finding instruments and the cost-effectiveness of routine screening for perinatal depression.

Methods and analysis

The diagnostic accuracy of the Whooley questions and the EPDS will be determined against a reference standard (the Client Interview Schedule—Revised) during pregnancy (around 20 weeks) and the early postnatal period (around 3–4 months post partum) in a sample of 379 women. Further outcome measures will assess a range of psychological comorbidities, health-related quality of life and resource utilisation. Women will be followed up 12 months postnatally. The sensitivity, specificity and predictive values of the Whooley questions and the EPDS will be calculated against the reference standard at 20 weeks pregnancy and 3–4 months post partum. Acceptability of the depression case-finding instruments to women and healthcare professionals will involve in-depth qualitative interviews. An existing decision analytic model will be adapted to determine the cost-effectiveness of routine screening for perinatal depression.

Ethics and dissemination

This study is considered low risk for participants. Robust protocols will deal with cases where risk of depression, self-harm or suicide is identified. The protocol received favourable ethical opinion from the North East—York Research Ethics Committee (reference: 11/NE/0022). The study findings will be published in peer-reviewed journals and presented at relevant conferences.
Clinical Stage and Risk of Recurrence and Mortality: Interaction of Dna Methylation Factors in Patients with Colorectal Cancer
Authors: Chang Hsien-Feng , Wu Chang-Chieh , Sun Chien-An , Chu Chi-Ming , Lin Fu-Gong , Hsieh Jih-Fu , Hsu Chih-Hsiung , Huang Chi-Hua , Yang Tsan , Tsai Yang-Ming , Kuan Jen-Chun , Chou Yu-Ching
Published: June 2016

Aberrant DNA methylation plays a crucial role in cancer development; however, prospective evidence of an interaction between molecular biomarkers and cancer staging for predicting the prognosis of colorectal cancer (CRC) is still limited. We examined DNA methylation in tumors and adjacent normal tissues from patients who underwent CRC surgical resection, and evaluated the interaction between cancer staging (advanced vs local) and DNA methylation to predict the prognosis of CRC. We recruited 132 patients with CRC from Tri-Service General Hospital in Taiwan and used the candidate gene approach to select 3 tumor suppressor genes involved in carcinogenesis pathways. ORs and 95% CIs were computed using logistic regression analyses while adjusting for potential covariates. Advanced cancer stage was correlated with cancer recurrence (OR 7.22, 95% CI 2.82 to 18.45; p<0.001). In addition, after stratification by promoter methylation in 3 combined genes in the matched normal tissues, we observed a joint effect after adjusting for sex, age at surgery, and adjuvant chemotherapy, yielding a significant OR of 20.35 (95% CI 4.16 to 99.57; p<0.001). DNA methylation status would significantly increase the recurrence risk of CRC with a significant impact on joint effect between DNA methylation and clinical stage, particularly in matched normal tissues. This was attributed to molecular changes that could not be examined on the basis of clinical pathology. Our interaction results may serve as a reference marker for evaluating the risk of recurrence in future studies.
Termitarium-inhabitingBacillus endophyticusTSH42 andBacillus cereusTSH77 colonizingCurcuma longaL.: isolation, characterization, and evaluation of their biocontrol and plant-growth-promoting activities
Authors: Chauhan Ankit Kumar , Maheshwari Dinesh Kumar , Kim Kangmin , Bajpai Vivek K.
Published: June 2016

Bacillus strains were isolated from termitarium soil and screened for their antifungal activity through the production of diffusible and volatile metabolites. Further, the bacterial strains that showed antifungal activity were evaluated for their biocontrol potential on the basis of their plant-growth-promoting attributes. Termitarium-inhabiting Bacillus strains TSH42 and TSH77 significantly reduced the growth of pathogenic fungus Fusarium solani, controlled the symptoms of rhizome rot in turmeric (Curcuma longa L.), and demonstrated various plant-growth-promoting traits in different in vitro assays. On the basis of morphological, physiological, biochemical, and 16S rDNA characteristics, isolates TSH42 and TSH77 were identified as Bacillus endophyticus (KT379993) and Bacillus cereus (KT379994), respectively. Through liquid chromatography – mass spectrometry analysis, acidified cell-free culture filtrate (CFCF) of B. cereus TSH77 was shown to contain surfactin and fengycin, while CFCF of B. endophyticus TSH42 contained iturin in addition to surfactin and fengycin. Treatment of the turmeric (C. longa L.) plants with TSH42 and TSH77 significantly reduced the percentage incidence of rhizome rot disease caused by F. solani. The same treatment also increased the fresh rhizome biomass and plant growth in greenhouse conditions.
E-msNSP: Efficient Negative Sequential Patterns Mining Based on Multiple Minimum Supports
Authors: Xu Tiantian , Dong Xiangjun , Xu Jianliang , Gong Yongshun
Published: June 2016

Mining negative sequential patterns (NSP) has been an important research area in data mining and knowledge discovery and it is much more challenging than mining positive sequential patterns (PSP) due to the computational complexity and search space. Only a few methods have been proposed to mine NSP and most of them only use single minimum support, which implicitly assumes that all items in the database are of the same nature or of similar frequencies in the database. This is often not the case in real-life applications. There are several methods to mine sequential patterns with multiple minimum supports (MMS), but these methods only consider PSP and do not handle NSP. So in this paper, we propose a new method, called e-msNSP, to mine NSP with multiple minimum supports. We also solve the problem of how to set up the minimum support to a sequence with negative item(s). E-msNSP consists of three major steps: (i) using the improved MS-GSP method to mine PSP with multiple minimum supports and storing all positive sequential candidates’ (PSC) related information simultaneously; (ii) using the same method in e-NSP to generate negative sequential candidates (NSC) based on above mined PSP; (iii) calculating the support of these NSC based only on the corresponding PSP and then getting NSP. To the best of our knowledge, e-msNSP is the first method to mine NSP with MMS and does not impose strict constraints. Experimental results show that the e-msNSP is highly effective and efficient.
Multiple Object Detection and Tracking in Complex Background
Authors: Ma Yingdong , Liu Yuchen , Liu Shuai , Zhang Zhibin
Published: June 2016

Multiple object tracking is a fundamental step for many computer vision applications. However, detecting and tracking objects in complex background is still a challenging task. This paper proposes an approach, which combines an improved Gaussian mixture modeling (GMM) with multiple particle filters (MPFs) for automatic multiple targets detecting and tracking. For GMM, we make improvement on GMM in the phase of model updating by using the expectation maximization algorithm and [Formula: see text] recent frames with weight parameters of Gaussian distributions. In the tracking stage, we integrate multiple features of targets, including color, edge and depth, into MPFs to improve the performance of object tracking. By comparing with various particle filter approaches, the experimental results show that our approach can track multiple targets in complex backgrounds automatically and accurately.
Quadratic normalization in monoids
Authors: Dehornoy Patrick , Guiraud Yves
Published: June 2016

In the general context of presentations of monoids, we study normalization process that are determined by their restriction to length-two words. Garside’s greedy normal forms and quadratic convergent rewriting systems, in particular those associated with the plactic monoids, are typical examples. Having introduced a parameter, called the class and measuring the complexity of the normalization of length-three words, we analyze the normalization of longer words and describe a number of possible behaviors. We fully axiomatize normalizations of class [Formula: see text], show the convergence of the associated rewriting systems, and characterize those deriving from a Garside family.
On algebras with many symmetric operations
Authors: Carvalho Catarina , Krokhin Andrei
Published: June 2016

An [Formula: see text]-ary operation [Formula: see text] is called symmetric if, for all permutations [Formula: see text] of [Formula: see text], it satisfies the identity [Formula: see text]. We show that, for each finite algebra [Formula: see text], either it has symmetric term operations of all arities or else some finite algebra in the variety generated by [Formula: see text] has two automorphisms without a common fixed point. We also show this two-automorphism condition cannot be replaced by a single fixed-point-free automorphism.
Deciding absorption
Authors: Barto Libor , Kazda Alexandr
Published: June 2016

We characterize absorption in finite idempotent algebras by means of Jónsson absorption and cube term blockers. As an application we show that it is decidable whether a given subset is an absorbing subuniverse of an algebra given by the tables of its basic operations.
Monoid and group of pseudo braids
Authors: Bardakov Valeriy G. , Jablan Slavik , Wang Hang
Published: June 2016

In this paper, we introduce pseudo braid monoids and show that, such a monoid is isomorphic to a singular braid monoid. We also prove an analogue of Markov’s Theorem for pseudo braids.
Fractal simplices
Authors: Carter J. Scott
Published: June 2016

There are three constructions of which I know that yield higher dimensional analogues of Sierpinski’s triangle. The most obvious is to remove the open convex hull of the midpoints of the edges of the [Formula: see text]-simplex. The complement is a union of simplices. Continue the removal recursively in each of the remaining sub-simplices. The result is an uncountably infinite figure in [Formula: see text]-dimensional space that is Cantor-like in a manner analogous to the Sierpinski triangle. A countable analogue is obtained by means of playing the chaos game in the [Formula: see text]-simplex. In this “game” one chooses a random [Formula: see text]-ary sequence; starting from the initial point (that is identified with a vertex of the simplex), one continues to plot points by moving half-again as much towards the next point in the sequence. The resulting plot converges to the figure described above. Similarly, coloring the multinomial coefficients black or white according to their parity results in a similar figure, when the [Formula: see text]-dimensional analogue of the Pascal triangle is rescaled and embedded in space.
On the link invariants from the Yokonuma–Hecke algebras
Authors: Chmutov S. , Jablan S. , Karvounis K. , Lambropoulou S.
Published: June 2016

In this paper, we study properties of the Markov trace tr[Formula: see text] and the specialized trace [Formula: see text] on the Yokonuma–Hecke algebras, such as behavior under inversion of a word, connected sums and mirror imaging. We then define invariants for framed, classical and singular links through the trace [Formula: see text] and also invariants for transverse links through the trace tr[Formula: see text]. In order to compare the invariants for classical links with the Homflypt polynomial, we develop computer programs and we evaluate them on several Homflypt-equivalent pairs of knots and links. Our computations lead to the result that these invariants are topologically equivalent to the Homflypt polynomial on knots. However, they do not demonstrate the same behavior on links.
Determinant of links, spanning trees, and a theorem of Shank
Authors: Ge Jun , Zhang Lianzhu
Published: June 2016

In this note, we first give an alternative elementary proof of the relation between the determinant of a link and the spanning trees of the corresponding Tait graph. Then, we use this relation to give an extremely short, knot theoretical proof of a theorem due to Shank stating that a link has component number one if and only if the number of spanning trees of its Tait graph is odd.
Plaited polyhedra: A knot theory point of view
Authors: Radović Ljiljana , Gerdes Paulus , Jablan Slavik , Sazdanovic Radmila
Published: June 2016

Plaited polyhedra, discovered by P. Gerdes in African dance rattle capsules are analyzed from the knot-theory point of view. Every plaited polyhedron can be derived from a knot or link diagram as its dual. In the attempt to classify obtained plaited polyhedra, we propose different methods based on families of knots and links in Conway notation or their corresponding braid families, both leading to the notion of families of plaited polyhedra.
Unknotting and maximum unknotting numbers
Authors: Zeković Ana , Jablan Slavik , Kauffman Louis , Sazdanovic Radmila , Stošić Marko
Published: June 2016

We introduce concepts of the maximum unknotting number and the mixed unknotting number, taking into consideration the Bernhard–Jablan Conjecture about computing the unknotting number based only on minimal knot diagrams. The existence of Kauffman knots (alternating knots, such that a crossing change does not change their minimal crossing number) was first suggested by Kauffman. We extend the concept and offer three related classes of knots named: Kauffman knots, Zeković knots and Taniyama knots.
An explicit formula for the A-polynomial of the knot with Conway’s notation C(2n,3)
Authors: Ham Ji-Young , Lee Joongul
Published: June 2016

An explicit formula for the [Formula: see text]-polynomial of the knot with Conway’s notation [Formula: see text] is obtained from the explicit Riley–Mednykh polynomial of it.
Algorithmic simplification of knot diagrams: New moves and experiments
Authors: Petronio Carlo , Zanellati Adolfo
Published: June 2016

This paper has an experimental nature and contains no new theorems. We introduce certain moves for classical knot diagrams that for all examples we have tested them on give a monotonic complete simplification. A complete simplification of a knot diagram [Formula: see text] is a sequence of moves that transform [Formula: see text] into a diagram [Formula: see text] with the minimal possible number of crossings for the isotopy class of the knot represented by [Formula: see text]. The simplification is monotonic if the number of crossings never increases along the sequence. Our moves are certain [Formula: see text] generalizing the classical Reidemeister moves [Formula: see text], and another one [Formula: see text] (together with a variant [Formula: see text]) aimed at detecting whether a knot diagram can be viewed as a connected sum of two easier ones. We present an accurate description of the moves and several results of our implementation of the simplification procedure based on them, publicly available on the web.
On invariants of link maps in dimension four
Authors: Lightfoot Ash
Published: June 2016

We fill a gap in the proof that the proposed link homotopy invariant [Formula: see text] of Li is well defined. It is also shown that if the homotopy invariant [Formula: see text] of Schneiderman–Teichner is to be adapted to a link homotopy invariant of link maps, the result coincides with [Formula: see text].
Stability and phase space analysis in f(R) theory with generalized exponential f(R) model
Authors: Boko R. D. , Houndjo M. J. S. , Tossa J.
Published: June 2016

We have studied in this paper, the stability of dynamical system in [Formula: see text] gravity. We have considered the [Formula: see text] [Formula: see text]-gravity and explored its dynamical analysis. We found six critical points among which only one describes a universe filled of both matter and dominated dark energy. It is shown that these critical points present specific phase spaces described by the corresponding fluids. Furthermore, we have investigated the stability conditions of these critical points and find that these conditions are dependent of the model parameters. We also study the stability of a new power-law [Formula: see text] model with de Sitter and power law solutions.
QCD gluon vertices from the string-inspired formalism
Authors: Ahmadiniaz Naser , Schubert Christian
Published: June 2016

The Bern–Kosower formalism, developed around 1990 as a novel way of obtaining QCD amplitudes as the limit of infinite string tension of the corresponding string amplitudes, was originally designed as an on-shell formalism. Building on early work by Strassler, the authors have recently shown that this “string-inspired formalism” is extremely efficient also as a tool for the study of off-shell amplitudes in QCD, and in particular for achieving compact form factor decompositions of the [Formula: see text]-gluon vertices. Among other things, this formalism allows one to achieve a manifestly gauge invariant decomposition of these vertices by way of integration-by-parts, rather than the usual tedious analysis of the non-abelian off-shell Ward identities, and to combine the spin zero, half and one cases. Here, we will provide a summary of the method, as well as its application to the three- and four-gluon vertices.
Gauge theory by canonical transformations
Authors: Koenigstein Adrian , Kirsch Johannes , Stoecker Horst , Struckmeier Juergen , Vasak David , Hanauske Matthias
Published: June 2016

Electromagnetism, the strong and the weak interactions are commonly formulated as gauge theories in a Lagrangian description. In this paper, we present an alternative formal derivation of [Formula: see text]-gauge theory in a manifestly covariant Hamilton formalism. We make use of canonical transformations as our guiding tool to formalize the gauging procedure. The introduction of the gauge field, its transformation behavior and a dynamical gauge field Lagrangian/Hamiltonian are unavoidable consequences of this formalism, whereas the form of the free gauge Lagrangian/Hamiltonian depends on the selection of the gauge dependence of the canonically conjugate gauge fields.
Viscosity to entropy ratio of QGP in relativistic heavy ion collision: Hard thermal loop corrections
Authors: Pari Sharareh Mehrabi , Javidan Kurosh , Shahri Fatemeh Taghavi
Published: June 2016

In this work, we report on our computation results for the best value of the shear viscosity to entropy ratio of quark–gluon plasma produced in the relativistic Au–Au collisions at [Formula: see text][Formula: see text]GeV. Time evolution of heavy quarks distribution functions is calculated by solving the Fokker–Planck evolution equation using the new technique: Iterative Laplace transform method. We compute the drag and diffusion coefficients by considering the hard thermal loop corrections and also temperature dependence running strong coupling, up to complete interactions of leading order.
ON THE HESTON MODEL WITH STOCHASTIC CORRELATION
Authors: TENG LONG , EHRHARDT MATTHIAS , GÜNTHER MICHAEL
Published: June 2016

The degree of relationship between financial products and financial institutions, e.g. must be considered for pricing and hedging. Usually, for financial products modeled with the specification of a system of stochastic differential equations, the relationship is represented by correlated Brownian motions (BMs). For example, the BM of the asset price and the BM of the stochastic volatility in the Heston model correlates with a deterministic constant. However, market observations clearly indicate that financial quantities are correlated in a strongly nonlinear way, correlation behaves even stochastically and unpredictably. In this work, we extend the Heston model by imposing a stochastic correlation given by the Ornstein–Uhlenbeck and the Jacobi processes. By approximating nonaffine terms, we find the characteristic function in a closed-form which can be used for pricing purposes. Our numerical results and experiment on calibration to market data validate that incorporating stochastic correlations improves the performance of the Heston model.
Academic Research and the Strategic Interaction of Scholars and Editors: A Two-Stage Game
Authors: Besancenot Damien , Faria João Ricardo , Mixon Franklin G.
Published: June 2016

This paper presents a two-stage game in order to explore the strategic interaction between the editor of an academic journal and a representative scholar. At the outset of the game, the editor chooses the “characteristics” of the journal, which encompass its rejection rate and other facets of the journal’s profile. Next, the scholar decides whether or not to submit a paper to the journal. We show that scholars’ behavior precludes the possibility of low-quality journals. As such, editors have only the choice between managing high-quality journals with few issues or second-tier journals publishing many papers. Moreover, if our two-stage game suggests that higher costs for scholars contribute to journal quality, numerical simulation shows that the effect of these costs on journal quality may be low. Lastly, our game-theoretic approach points out that it is difficult for journal editors to define optimal rejection rates.
Multiple solutions for semi-linear corner degenerate elliptic equations with singular potential term
Authors: Chen Hua , Tian Shuying , Wei Yawei
Published: June 2016

The present paper is concern with the Dirichlet problem for semi-linear corner degenerate elliptic equations with singular potential term. We first give the preliminary of the framework and then discuss the weighted corner type Hardy inequality. By using the variational method, we prove the existence of multiple solutions for the Dirichlet boundary-value problem.
On a determinantal inequality arising from diffusion tensor imaging
Authors: Lin Minghua
Published: June 2016

In comparing geodesics induced by different metrics, Audenaert formulated the following determinantal inequality [Formula: see text] where [Formula: see text] are [Formula: see text] positive semidefinite matrices. We complement his result by proving [Formula: see text] Our proofs feature the fruitful interplay between determinantal inequalities and majorization relations. Some related questions are mentioned.
Homotopy composition of cospans
Authors: Kock Joachim , Spivak David I.
Published: June 2016

It is well known that the category of finite sets and cospans, composed by pushout, contains the universal special commutative Frobenius algebra. In this paper, we observe that the same construction yields also general commutative Frobenius algebras, if just the pushouts are changed to homotopy pushouts.
The Hirzebruch χy-genus and Poincaré polynomial revisited
Authors: Li Ping
Published: June 2016

The Hirzebruch [Formula: see text]-genus and Poincaré polynomial share some similar features. In this paper, we investigate two of their similar features simultaneously. Through this process we shall derive several new results as well as reprove and improve some known results.
Quasilinear elliptic problems with concave–convex nonlinearities
Authors: Carvalho M. L. M. , da Silva Edcarlos D. , Goulart C.
Published: June 2016

In this paper, the existence and multiplicity of solutions for a quasilinear elliptic problem driven by the [Formula: see text]-Laplacian operator is established. These solutions are also built as ground state solutions using the Nehari method. The main difficulty arises from the fact that the [Formula: see text]-Laplacian operator is not homogeneous and the nonlinear term is indefinite.