bluuebunny/crossref_metadata_2025_split huggingface dataset:
Crop–weed competition rather than temperature limits the population establishment of two annual C4 weeds at the edge of their northern range
Authors: Hyvönen T , Ramula S 
Published: February 2014

SummaryClimate change is predicted to affect range expansion of harmful C4 weeds into the boreal region, given that they are able to successfully colonise both C3 and C4 crops. We studied the impact of a 3°C elevation in temperature on the establishment and maintenance of populations of two annual C4 weeds (Amaranthus retroflexus and Echinochloa crus‐galli) with and without a competing C3 (barley) or C4 (maize) crop. Data obtained from field and glasshouse experiments were modelled using a periodic matrix population model. Competition of a weed with a crop appeared to be a more important factor for limiting the maintenance of weed populations than elevation in temperature, as neither of the weed species was able to maintain populations in competition with crops. Even an increase in the frequency of warm years did not result in viable weed populations establishing. However, A. retroflexus was able to form persistent populations in competition with maize when released from competition every fifth year. Simulations parameterised from glasshouse data predicted that both weed species would persist without competition in the current climate, whereas simulations parameterised from field data suggested only A. retroflexus to be able to persist. These results demonstrate that competition affects the range expansion of arable weed species more than elevation in temperature, necessitating the inclusion of crop–weed interactions in models of range shifts as a consequence of climate change.
Climate warming alters competition between two highly invasive alien plant species and dominant native competitors
Authors: Verlinden M , De Boeck H J , Nijs I 
Published: February 2014

SummaryBiological invasions and climate warming are two major threats to the world's biodiversity. To date, their impacts have largely been considered independently, despite indications that climate warming may increase the success of many invasive alien species. We therefore set up an experiment to study competition between native and invasive alien plant species and the effects of climate warming thereon. Two highly invasive alien plant species in Belgium, each with a native competitor that dominated in invaded sites, were grown either together (1:1 mixtures) or in isolation (monocultures) at ambient and elevated temperature (+3°C) in climate‐controlled chambers. To detect possible mechanisms underlying the effects of competition and elevated temperature, we conducted a combined growth and nitrogen uptake analysis. In one pair, Senecio inaequidens – Plantago lanceolata (alien invasive – native), the alien species dominated in mixture, while in the other pair, Solidago gigantea – Epilobium hirsutum, the native species dominated. Climate warming reduced the invader dominance in the first species pair, but stimulated the suppressed invader in the latter. Many of the biomass responses for these two species pairs could be traced to the root‐specific nitrogen uptake capacity. The responses of the native‐invasive interaction to warming could not always be extrapolated from the monoculture responses, pointing to the necessity for experiments that take into account species interactions.
Experiences and Attitudes Towards Evidence‐Informed Policy‐Making Among Research and Policy Stakeholders in the Canadian Agri‐Food Public Health Sector
Authors: Young I. , Gropp K. , Pintar K. , Waddell L. , Marshall B. , Thomas K. , McEwen S.A. , Rajić A. 
Published: February 2014

SummaryPolicy‐makers working at the interface of agri‐food and public health often deal with complex and cross‐cutting issues that have broad health impacts and socio‐economic implications. They have a responsibility to ensure that policy‐making based on these issues is accountable and informed by the best available scientific evidence. We conducted a qualitative descriptive study of agri‐food public health policy‐makers and research and policy analysts in Ontario, Canada, to understand their perspectives on how the policy‐making process is currently informed by scientific evidence and how to facilitate this process. Five focus groups of 3–7 participants and five‐one‐to‐one interviews were held in 2012 with participants from federal and provincial government departments and industry organizations in the agri‐food public health sector. We conducted a thematic analysis of the focus group and interview transcripts to identify overarching themes. Participants indicated that the following six key principles are necessary to enable and demonstrate evidence‐informed policy‐making (EIPM) in this sector: (i) establish and clarify the policy objectives and context; (ii) support policy‐making with credible scientific evidence from different sources; (iii) integrate scientific evidence with other diverse policy inputs (e.g. economics, local applicability and stakeholder interests); (iv) ensure that scientific evidence is communicated by research and policy stakeholders in relevant and user‐friendly formats; (V) create and foster interdisciplinary relationships and networks across research and policy communities; and (VI) enhance organizational capacity and individual skills for EIPM. Ongoing and planned efforts in these areas, a supportive culture, and additional education and training in both research and policy realms are important to facilitate evidence‐informed policy‐making in this sector. Future research should explore these findings further in other countries and contexts.
Paraphyly and budding speciation in the hairy snail (Pulmonata, Hygromiidae)
Authors: Kruckenhauser Luise , Duda Michael , Bartel Daniela , Sattmann Helmut , Harl Josef , Kirchner Sandra , Haring Elisabeth 
Published: February 2014

Delimitation of species is often complicated by discordance of morphological and genetic data. This may be caused by the existence of cryptic or polymorphic species. The latter case is particularly true for certain snail species showing an exceptionally high intraspecific genetic diversity. The present investigation deals with the Trochulus hispidus complex, which has a complicated taxonomy. Our analyses of the COI sequence revealed that individuals showing a T. hispidus phenotype are distributed in nine highly differentiated mitochondrial clades (showing p‐distances up to 19%). The results of a parallel morphometric investigation did not reveal any differentiation between these clades, although the overall variability is quite high. The phylogenetic analyses based on 12S, 16S and COI sequences show that the T. hispidus complex is paraphyletic with respect to several other morphologically well‐defined Trochulus species (T. clandestinus, T. villosus, T. villosulus and T. striolatus) which form well‐supported monophyletic groups. The nc marker sequence (5.8S–ITS2–28S) shows only a clear separation of T. o. oreinos and T. o. scheerpeltzi, and a weakly supported separation of T. clandestinus, whereas all other species and the clades of the T. hispidus complex appear within one homogeneous group. The paraphyly of the T. hispidus complex reflects its complicated history, which was probably driven by geographic isolation in different glacial refugia and budding speciation. At our present state of knowledge, it cannot be excluded that several cryptic species are embedded within the T. hispidus complex. However, the lack of morphological differentiation of the T. hispidus mitochondrial clades does not provide any hints in this direction. Thus, we currently do not recommend any taxonomic changes. The results of the current investigation exemplify the limitations of barcoding attempts in highly diverse species such as T. hispidus.
Whole-Genome Sequencing of the Nonproteolytic Bacillus anthracis V770-NP1-R Strain Reveals Multiple Mutations in Peptidase Loci
Authors: Cohen-Gihon Inbar , Israeli Ofir , Beth-Din Adi , Levy Haim , Cohen Ofer , Shafferman Avigdor , Zvi Anat , Chitlaru Theodor 
Published: February 2014

ABSTRACT

We report the draft whole-genome sequence of the nonproteolytic
Bacillus anthracis
V770-NP1-R strain. Compared to those of other
B. anthracis
strains, the genome exhibits unique mutations in multiple targets potentially affecting proteolytic functions. One of these mutations is a deletion that disrupts the NprR quorum-sensing regulator of the NprA protease.
Metastatic signet ring cell carcinoma of unknown primary source
Authors: O'Kane Dermot , Dean Kylie , Nightingale Rachael , Carlotto Simone 
Published: February 2014

An elderly man presented to the emergency department following a motorbike accident. He had sustained chest injuries and a grade 1 splenic laceration. He had a moderate amount of free fluid and some omental standing on trauma CT, which was concerning for occult malignancy. A follow-up CT 4 weeks later showed a marked progression of the ascites and omental stranding. Ascitic tap was negative for malignancy. Tumour markers were normal. The patient developed a proximal small bowel obstruction which appeared to be related to this omental caking in the left upper quadrant on CT. Gastroduodenoscopy did not display any mass lesion. There was an external compression of the duodenum which could not be traversed with the scope. Laparoscopy showed a widespread peritoneal carcinomatosis. Biopsies of the omentum and peritoneum confirmed metastatic signet ring cell carcinoma (cytokeratin 7 and cytokeratin 20 positive). The patient was palliated but died 2 weeks after his diagnosis.
Republished: Recent advances: personalised use of current Crohn’s disease therapeutic options
Authors: Vermeire Séverine , Ferrante Marc , Rutgeerts Paul 
Published: February 2014

Abstract
Several aspects of the management of Crohn’s disease (CD) are shared between patients. The goal of all therapies should be to achieve clinical and endoscopic remission in a timely manner to avoid disease progression and abdominal resections. The way this goal is achieved may differ and predicting how the disease will evolve, what the most appropriate therapy with the highest chance of success will be, how long a therapy needs to be continued, and what the intensity of follow-up should be are more difficult questions and require an individualised approach. Clinical parameters have been suggested to aid in the therapeutic decision process but lack specificity. Although much promise has been put in molecular markers, these have not yet found their way to the clinic. More recently, clinicians have started to gain interest in drug level monitoring to adapt doses of immunomodulators and/or anti-tumour necrosis factor antibodies in an individualised manner. An increasing number of studies show that therapeutic drug monitoring can help physicians to improve and personalise the management of their patients. What is needed now are pharmaco-economic studies showing that personalised management of CD is cost effective.
LDsplit: screening for cis-regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms
Authors: Yang Peng , Wu Min , Guo Jing , Kwoh Chee Keong , Przytycka Teresa M , Zheng Jie 
Published: February 2014

Abstract

Background
As a fundamental genomic element, meiotic recombination hotspot plays important roles in life sciences. Thus uncovering its regulatory mechanisms has broad impact on biomedical research. Despite the recent identification of the zinc finger protein PRDM9 and its 13-mer binding motif as major regulators for meiotic recombination hotspots, other regulators remain to be discovered. Existing methods for finding DNA sequence motifs of recombination hotspots often rely on the enrichment of co-localizations between hotspots and short DNA patterns, which ignore the cross-individual variation of recombination rates and sequence polymorphisms in the population. Our objective in this paper is to capture signals encoded in genetic variations for the discovery of recombination-associated DNA motifs.

Results
Recently, an algorithm called “LDsplit” has been designed to detect the association between single nucleotide polymorphisms (SNPs) and proximal meiotic recombination hotspots. The association is measured by the difference of population recombination rates at a hotspot between two alleles of a candidate SNP. Here we present an open source software tool of LDsplit, with integrative data visualization for recombination hotspots and their proximal SNPs. Applying LDsplit on SNPs inside an established 7-mer motif bound by PRDM9 we observed that SNP alleles preserving the original motif tend to have higher recombination rates than the opposite alleles that disrupt the motif. Running on SNP windows around hotspots each containing an occurrence of the 7-mer motif, LDsplit is able to guide the established motif finding algorithm of MEME to recover the 7-mer motif. In contrast, without LDsplit the 7-mer motif could not be identified.

Conclusions
LDsplit is a software tool for the discovery of cis-regulatory DNA sequence motifs stimulating meiotic recombination hotspots by screening and narrowing down to hotspot associated SNPs. It is the first computational method that utilizes the genetic variation of recombination hotspots among individuals, opening a new avenue for motif finding. Tested on an established motif and simulated datasets, LDsplit shows promise to discover novel DNA motifs for meiotic recombination hotspots.
Public and private pregnancy care in Reggio Emilia Province: an observational study on appropriateness of care and delivery outcomes
Authors: Bonvicini Laura , Candela Silvia , Evangelista Andrea , Bertani Daniela , Casoli Morena , Lusvardi Annarella , Messori Antonella , Giorgi Rossi Paolo 
Published: February 2014

Abstract

Background
In industrialized countries, improvements have been made in both maternal and newborn health. While attention to antenatal care is increasing, excessive medicalization is also becoming more common.
The aim of this study is to compare caesarean section (CS) frequency and ultrasound scan utilization in a public model of care involving both midwives and obstetricians with a private model in which care is provided by obstetricians only.

Methods
Design: Observational population-based study. Setting: Reggio Emilia Province. Population: 5957 women resident in the province who delivered between October 2010 and November 2011. Main outcome measures: CS frequency and ultrasound scan utilization, stillbirths, and other negative perinatal outcomes. Women in the study were searched in the public family and reproductive health clinic medical records to identify those cared for in the public system. Outcomes of the two antenatal care models were compared through multivariate logistic regression adjusting for maternal characteristics and, for CS only, by stratifying by Robson’s Group.

Results
Compared to women cared for in private services (N = 3,043), those in public service (N = 2,369) were younger, less educated, more frequently non-Italian, and multiparous. The probability of CS was slightly higher for women cared for by private obstetricians than for those cared for in the public system (31.8% vs. 27.1%; adjusted odds ratio: 1.10; 95% CI: 0.93–1.29): The probability of having more than 3 ultrasound scans was higher in private care (89.6% vs. 49.8%; adjusted odds ratio: 5.11; 95% CI: 4.30–6.08). CS frequency was higher in private care for all Robson’s classes except women who underwent CS during spontaneous labour. Among negative perinatal outcomes only a higher risk of pre-term birth was observed for pregnancies cared for in private services.

Conclusions
The public model provides less medicalized and more guidelines-oriented care than does the private model, with no increase in negative perinatal outcomes.
Regulation of Mcl-1 by constitutive activation of NF-kappaB contributes to cell viability in human esophageal squamous cell carcinoma cells
Authors: Liu Haidan , Yang Jinfu , Yuan Yunchang , Xia Zhenkun , Chen Mingjiu , Xie Li , Ma Xiaolong , Wang Jian , Ouyang Sufeng , Wu Qin , Yu Fenglei , Zhou Xinmin , Yang Yifeng , Cao Ya , Hu Jianguo , Yin Bangliang 
Published: February 2014

Abstract

Background
Esophageal squamous cell carcinoma (ESCC) is one of the most lethal malignancies with a 5-year survival rate less than 15%. Understanding of the molecular mechanisms involved in the pathogenesis of ESCC becomes critical to develop more effective treatments.

Methods
Mcl-1 expression was measured by reverse transcription (RT)-PCR and Western blotting. Human Mcl-1 promoter activity was evaluated by reporter gene assay. The interactions between DNA and transcription factors were confirmed by electrophoretic mobility shift assay (EMSA) in vitro and by chromatin immunoprecipitation (ChIP) assay in cells.

Results
Four human ESCC cell lines, TE-1, Eca109, KYSE150 and KYSE510, are revealed increased levels of Mcl-1 mRNA and protein compare with HaCaT, an immortal non-tumorigenic cell line. Results of reporter gene assays demonstrate that human Mcl-1 promoter activity is decreased by mutation of kappaB binding site, specific NF-kappaB inhibitor Bay11-7082 or dominant inhibitory molecule DNMIkappaBalpha in TE-1 and KYSE150 cell lines. Mcl-1 protein level is also attenuated by Bay11-7082 treatment or co-transfection of DNMIkappaBalpha in TE-1 and KYSE150 cells. EMSA results indicate that NF-kappaB subunits p50 and p65 bind to human Mcl-1-kappaB probe in vitro. ChIP assay further confirm p50 and p65 directly bind to human Mcl-1 promoter in intact cells, by which regulates Mcl-1 expression and contributes to the viability of TE-1 cells.

Conclusions
Our data provided evidence that one of the mechanisms of Mcl-1 expression in human ESCC is regulated by the activation of NF-kappaB signaling. The newly identified mechanism might provide a scientific basis for developing effective approaches to treatment human ESCC.
Syndemics of syphilis, HCV infection, and methamphetamine use along the east coast of China
Authors: Liao Meizhen , Kang Dianmin , Tao Xiaorun , Cox Catherine , Qian Yuesheng , Wang Guoyong , Yang Cui , Zhu XiaoYan , Zhang Na , Bi Zhenqiang , Jia Yujiang 
Published: February 2014

Abstract

Background
An upsurge in club drug use has been observed in recent years in some cities of China, especially methamphetamine, which is quickly replacing heroin to become the most widespread drug across the nation. This study investigated the type of drugs used, syphilis and hepatitis C virus (HCV) infection and the correlates for syphilis, HCV and unprotected commercial sex behavior among drug users in two cities along the east coast of China.

Methods
A cross-sectional survey conducted in 2010 provided demographics, sexual and drug use behaviors, HIV knowledge and the utilization of intervention services among drug users. Blood samples were tested for HIV, syphilis, and HCV infection.

Results
Of 805 eligible participants, 0.2% were infected with HIV, 3.7% with HCV, and 9.6% with syphilis. Of the participants, 96.6% were methamphetamine users, 11.9% reported ever having used ≥2 types of these drugs, and 11.4% reported ever injecting drugs. In the multivariable logistic regression analysis, participants infected with syphilis were more likely to be female (adjusted odds ratio (AOR)=2.8, 95% confidence interval (CI): 1.2-6.5), have ever had commercial sex in the past 12 months (AOR=2.0, 95% CI: 1.0-3.9), be infected with HCV (AOR=12.1, 95% CI: 4.1-20.3) and less likely to have ever had sex with regular partners in the past 12 months (AOR=0.2, 95% CI: 0.1-0.6). Participants infected with HCV were more likely to have ever injected drugs (AOR=2.7, 95% CI: 1.1-6.5) and be infected with syphilis (AOR=8.0, 95% CI: 3.5-18.0). Participants who had unprotected sex with commercial sex partners in the last sexual encounter were more likely to be female (AOR=2.9, 95% CI:1.7-4.9), have middle school or lower level education (AOR=3.4, 95% CI:2.0-5.5), never have received intervention in the last year (AOR=2.1, 95%CI:1.2-3.6) and be infected with syphilis (AOR=4.2, 95% CI:2.4-7.4).

Conclusions
Methamphetamine is the predominant drug used among the drug users, the prevalence of syphilis and HCV infection are alarmingly high, and unprotected commercial sex was common among this group. The findings highlight the need for effective, multifaceted interventions addressing sexual and drug use-related risky behaviors among this group. Further research is needed to better understand the causal pathway of the syndemics.
Motivations and perceptions of community advisory boards in the ethics of medical research: the case of the Thai-Myanmar border
Authors: Maung Lwin Khin , Cheah Phaik Yeong , Cheah Phaik Kin , White Nicholas J , Day Nicholas P J , Nosten Francois , Parker Michael 
Published: February 2014

Abstract

Background
Community engagement is increasingly promoted as a marker of good, ethical practice in the context of international collaborative research in low-income countries. There is, however, no widely agreed definition of community engagement or of approaches adopted. Justifications given for its use also vary. Community engagement is, for example, variously seen to be of value in: the development of more effective and appropriate consent processes; improved understanding of the aims and forms of research; higher recruitment rates; the identification of important ethical issues; the building of better relationships between the community and researchers; the obtaining of community permission to approach potential research participants; and, the provision of better health care. Despite these diverse and potentially competing claims made for the importance of community engagement, there is very little published evidence on effective models of engagement or their evaluation.

Methods
In this paper, drawing upon interviews with the members of a Community Advisory Board on the Thai-Myanmar border, we describe and critically reflect upon an approach to community engagement which was developed in the context of international collaborative research in the border region.

Results and conclusions
Drawing on our analysis, we identify a number of considerations relevant to the development of an approach to evaluating community engagement in this complex research setting. The paper also identifies a range of important ways in which the Community Advisory Board is in practice understood by its members (and perhaps by community members beyond this) to have morally significant roles and responsibilities beyond those usually associated with the successful and appropriate conduct of research.