bluuebunny/crossref_metadata_2025_split huggingface dataset:
Refugees in Greece: Facing a Multifaceted Labyrinth
Authors: Tsitselikis Konstantinos 
Published: June 2018

AbstractThe years after 2015 were remarkable for the reception and accommodation schemes of refugees fleeing Syria, Iraq and Afghanistan. The EU‐Turkey common statement of March 2016 and, most of all, the sealing of the Balkan corridor, blocked the flow of refugees towards central Europe through Greece, testing the readiness of the Greek authorities to take action to meet a series of urgent needs (accommodation, nutrition, asylum procedures, health) and social integration processes (education, training, access to labour). Approximately 45,000 refugees are settled in refugee camps or urban settlements all over the country. Those entrapped in the Eastern Aegean islands should be returned to Turkey, which is considered a “safe third country”. The purpose of this article is to shed light on a phenomenon that is ongoing and challenges a series of policies and legal principles both in Greece and the EU.
Media Violence and the General Aggression Model
Authors: Anderson Craig A. , Bushman Brad J. 
Published: June 2018

AbstractThe General Aggression Model (GAM) is a meta‐theory that considers the role of personal and situational variables on aggressive behavior, ranging from the biological to the cultural. Possible mediating variables include internal states (e.g., aggressive thoughts, angry feelings, increased physiological arousal) and the results of appraisal and decision processes (automatic and controlled). In this article, we focus on one situational variable—exposure to violent media—and how it can influence a wide array of cognitive, developmental, emotional, and social processes that can increase likelihood of aggression. Previous research has shown that exposure to violent media can increase aggression through all three internal state paths, and by increasing hostile appraisals. In this article, we use GAM as a theoretical framework to explain a wide variety of violent media effects. We also add some clarifications and extensions to GAM that research in the past 15 years has shown to be needed in the model. We also suggest new research directions in the media violence domain that we believe will be especially useful in the future.
Chloroplast phylogenomics of the New World grape species (Vitis, Vitaceae)
Authors: Wen Jun , Harris AJ , Kalburgi Yash , Zhang Ning , Xu Yuan , Zheng Wei , Ickert‐Bond Stefanie M. , Johnson Gabriel , Zimmer Elizabeth A. 
Published: June 2018

AbstractVitis L. (the grape genus) is the economically most important fruit crop, as the source of grapes and wine. Phylogenetic relationships within the genus have been highly controversial. Herein, we employ sequence data from whole plastomes to attempt to enhance Vitis phylogenetic resolution. The results support the New World Vitis subgenus Vitis as monophyletic. Within the clade, V. californica is sister to the remaining New World Vitis subgenus Vitis. Furthermore, within subgenus Vitis, a Eurasian clade is robustly supported and is sister to the New World clade. The clade of Vitis vinifera ssp. vinifera and V. vinifera ssp. sylvestris is sister to the core Asian clade of Vitis. Several widespread species in North America are found to be non‐monophyletic in the plastome tree, for example, the broadly defined Vitis cinerea and V. aestivalis each needs to be split into several species. The non‐monophyly of some species may also be due to common occurrences of hybridizations in North American Vitis. The classification of North American Vitis by Munson into nine series is discussed based on the phylogenetic results. Analyses of divergence times and lineage diversification support a rapid radiation of Vitis in North America beginning in the Neogene.
How to Measure Field‐of‐Study Mismatch? A Comparative Analysis of the Different Methods
Authors: Sellami Sana , Verhaest Dieter , Van Trier Walter 
Published: June 2018

AbstractWe compare the different methods used to measure field‐of‐study mismatch. A first part reviews the literature, detailing, and discussing the different approaches. A second part uses a dataset allowing one to investigate whether these different approaches result in differences with respect to the incidence and determinants of field‐of‐study mismatch. As substantial differences do indeed exist, even among variants of similar approaches, we conclude that empirical results should be interpreted with caution. While making several recommendations concerning the measurement of field‐of‐study mismatch, we also call for more focused research on the validity and reliability of field‐of‐study mismatch measures.
Tonle Sap Lake: Current status and important research directions for environmental management
Authors: Uk Sovannara , Yoshimura Chihiro , Siev Sokly , Try Sophal , Yang Heejun , Oeurng Chantha , Li Shangshang , Hul Seingheng 
Published: June 2018

AbstractTonle Sap Lake (TSL) in Cambodia is the largest freshwater body in South‐East Asia and one of the most productive ecosystems in the world. The lake and its ecosystems are widely under threat, however, due to anthropogenic activities occurring inside and outside its basin (e.g., water infrastructure development; land use change), being poorly understood in most aspects. This study provides an updated review of the state of knowledge of the TSL ecosystem, as well as important research directions for sustainable lake environmental management of Tonle Sap Lake by focusing on four major topics, including climate change and hydrology, sediment dynamics, nutrient dynamics and primary and secondary production. The findings of this study suggest anthropogenic activities in the TSL basin, as well as the Mekong, in combination together with climate changes, are key contributing factors in the degradation of the TSL ecosystem. Insufficient accurate data, however, precludes quantitative assessment of such impacts, making it difficult to quantitatively assess and accurately understand the ecosystem process in the lake ecosystem. More efforts are recommended in regard to environmental monitoring in all sub‐basins around TSL, assessing seasonal changes in nutrient and sediment inputs corresponding to water level and flow changes, assessing cumulative impacts of water infrastructure and climate change on the ecosystem dynamics, and elucidation of ecosystem processes within the lake's internal system.
Comment on “Composition and origin of holotype Al‐Cu‐Zn minerals in relation to quasicrystals in the Khatyrka meteorite” by M. Ivanova et al. (2017)
Authors: Andronicos C. L. , Bindi L. , Distler V. V. , Hollister L. S. , Lin C. , MacPherson G. J. , Steinhardt P. J. , Yudovskaya M. 
Published: June 2018

AbstractIvanova et al. () proposed that the aluminides we described in the Khatyrka meteorite fragments, both crystal and quasicrystal metal phases, were derived from industrial materials used during placer gold mining and that these had been shredded and blast‐propelled into natural meteoritic material that happened to be at the site. The blast hypothesis was not supported by evidence that metal shrapnel or metal parts from mining operations (or from any other industrial use) occur at the site that are similar in composition to the aluminides that we described in Khatyrka; we doubt such compositions would exist because alloys with the compositions we reported have no known industrial applications. We further show that this hypothesis cannot be reconciled geologically, chemically, or physically with our observations. These observations demonstrate that the fragments central to our study have been embedded below gold‐bearing fluvial gravels in undisturbed sediment for at least ~6670 to 8004 14C years before mining operations commenced. The case presented here thus specifically rules out the blast hypothesis and also presents a challenge to other anthropogenic explanations. We also address each of Ivanova et al.'s points challenging our conclusion that the silicates attached to the aluminides were CV3 chondritic minerals.
Two‐needle knitting and cross‐knit looping: early bronze age pottery imprints from anatolia and the caucasus
Authors: Sagona Claudia 
Published: June 2018

SummaryThere is ample evidence for the use of prehistoric loom‐woven, tabby fabric (made by plain warp and weft technique) in the construction of pottery. Ancient potters from the steppe regions of central Asia through to Anatolia and in some parts of Europe sometimes built their wares aided by old fragments of cloth and basketry, which left impressions on and in the walls of their vessels. In the highlands of eastern Turkey at the site of Sos Höyük and at Chobareti, in Georgia, the impressions on Early Bronze Age pottery include an array of textiles and, notably, what appears to be the earliest known evidence for two‐needle knitting and for the continued use of the single‐element, cross‐knit looping (also known as Coptic ‘nalbinding’) made using an eyed‐needle, a craft which has been found in Pre‐Pottery Neolithic contexts of the Levant. Various basketry techniques are also represented.
Transcriptome analysis of Porphyromonas gingivalis and Acinetobacter baumannii in polymicrobial communities
Authors: Miller D.P. , Wang Q. , Weinberg A. , Lamont R.J. 
Published: June 2018

SummaryAcinetobacter baumannii is a nosocomial, opportunistic pathogen that causes several serious conditions including meningitis, septicemia, endocarditis, and pneumonia. It can be found in the oral biofilm, which may be a reservoir for pneumonia and chronic obstructive pulmonary disease. Subgingival colonization by A. baumannii is associated with chronic and aggressive periodontitis as well as refractory periodontal disease. Porphyromonas gingivalis, a keystone periodontal pathogen localized to subgingival plaque, is also implicated in several chronic conditions including aspiration pneumonia. Although both bacteria are found together in subgingival plaque and can cause multiple polymicrobial infections, nothing is known about the interactions between these two important human pathogens. In this study, we used RNA sequencing to understand the transcriptional response of both species as they adapt to heterotypic communities. Among the differentially regulated genes were those encoding a number of important virulence factors for both species including adhesion, biofilm formation, and protein secretion. Additionally, the presence of A. baumannii increased the abundance of P. gingivalis in model dual‐species communities. Collectively these results suggest that both P. gingivalis and A. baumannii adapt to each other and have synergistic potential for increased pathogenicity. In identifying the mechanisms that promote pathogenicity and refractory disease, novel approaches to mitigate polymicrobial synergistic interactions may be developed to treat or prevent associated diseases.
Pigmentation abnormalities in nucleotide excision repair disorders: Evidence and hypotheses
Authors: Kasraian Zeinab , Trompezinski Sandra , Cario‐André Muriel , Morice‐Picard Fanny , Ged Cécile , Jullie Marie‐Laure , Taieb Alain , Rezvani Hamid Reza 
Published: June 2018

AbstractSkin pigmentation abnormalities are manifested in several disorders associated with deficient DNA repair mechanisms such as nucleotide excision repair (NER) and double‐strand break (DSB) diseases, a topic that has not received much attention up to now. Hereditary disorders associated with defective DNA repair are valuable models for understanding mechanisms that lead to hypo‐ and hyperpigmentation. Owing to the UV‐associated nature of abnormal pigmentary manifestations, the outcome of the activated DNA damage response (DDR) network could be the effector signal for alterations in pigmentation, ultimately manifesting as pigmentary abnormalities in repair‐deficient disorders. In this review, the role of the DDR network in the manifestation of pigmentary abnormalities in NER and DSB disorders is discussed with a special emphasis on NER disorders.
Predictability of myometrial, lower uterine segment and cervical invasion with 3D transvaginal ultrasonography and magnetic resonance imaging in endometrial cancer patients: a prospective cohort study
Authors: Yildirim Nuri , Saatli Bahadir , Kose Semir , Sancar Ceren , Ulukus Cagnur , Koyuncuoglu Meral , Saygili Ugur , Obuz Funda 
Published: June 2018

Aims: The objective of this study is to identify the diagnostic performance of three-dimensional transvaginal ultrasonography (3D-US) and magnetic resonance imaging (MRI) in detecting myometrial, lower uterine segment and/or cervical invasion in endometrial cancer patients.Materials and methods: In this prospective study, 40 patients diagnosed with endometrial cancer were performed 3D-US and MRI, preoperatively. Deep myometrial, lower uterine segment and cervical invasion were evaluated subjectively and results were compared with the final histology as a gold standard.Results: Diagnostic accuracy of 3D-US for detecting deep myometrial, lower uterine segment and cervical invasion were 87.5%, 80% and 85%, respectively. The same results for MRI were 75%, 65% and 70%, respectively. For deep myometrial, lower uterine segment and/or cervical invasion in endometrial cancer, 3D-US had higher sensitivity, specificity, negative and positive predictive value and accuracy than MRI. The combination of these two imaging techniques had an increased sensitivity of detecting all parameters related with tumoral invasion but decreased specificity and the accuracy.Conclusion: 3D-US had better performance in detecting myometrial, lower uterine segment and/or cervical invasion than MRI in endometrial cancer patients. Combination of these techniques was not preferred according to this study.
Prenatal diagnosis of cleft lip and cleft lip palate – a case series
Authors: Marginean Claudiu , Sasarean Vladut , Marginean Cristina Oana , Melit Lorena Elena , Marginean Maria Oana 
Published: June 2018

Aim: Orofacial clefts comprise cleft lip (CL) or cleft lip-palate (CLP) and are the most frequently encountered malformation of the facial region, accounting for approximately 1-2.2/1,000 live births. The aim of this study was to reveal the particularities regarding the prenatal diagnosis of orofacial clefts in a series of 11 cases diagnosed in a tertiary center.Material and methods: The study was performed in a tertiary diagnostic center for a period of 8 years (January 2010 – December 2017), on8125 patients that were assessed for screening or suspicion of malformations.Results: During the assessed period a number of 11 fetuses (0.13%) were diagnosed by 2D and 3D ultrasound with CL (4 cases) or CLP (7 cases). The smallest gestational age at diagnosis was of 14 weeks, whereas the highest was 35 weeks. Of the 7 cases diagnosed with CLP, 4 presented also other associated anomalies that involved the central nervous system, the kidney, the skeleton and the stomach. All 4 cases of CL had identifiable associated anomalies. Termination of pregnancy was encountered in 3 cases with CLP.Conclusions: CLP can be diagnosed even at the end of the 1st trimester of pregnancy. CL is usually diagnosed during the 2nd trimester ultrasound exam and is commonly an isolated anomaly.
Identification of Host Factors Involved in Human Cytomegalovirus Replication, Assembly, and Egress Using a Two-Step Small Interfering RNA Screen
Authors: McCormick Dominique , Lin Yao-Tang , Grey Finn 
Published: June 2018

ABSTRACT
As obligate intracellular parasites, viruses are completely dependent on host factors for replication. Assembly and egress of complex virus particles, such as human cytomegalovirus (HCMV), are likely to require many host factors. Despite this, relatively few have been identified and characterized. This study describes a novel high-throughput, two-step small interfering RNA (siRNA) screen, which independently measures virus replication and virus production. By combining data from replication and virus production, multiple candidate genes were identified in which knockdown resulted in substantial loss of virus production with limited effect on primary replication, suggesting roles in later stages such as virus assembly and egress. Knockdown of the top candidates, ERC1, RAB4B, COPA, and COPB2, caused profound loss of virus production. Despite COPA and COPB2 being reported to function in the same complex, knockdown of these genes produced distinct phenotypes. Furthermore, knockdown of COPA caused increased expression of viral late genes despite substantial inhibition of viral DNA replication. This suggests that efficient viral genome replication is not required for late gene expression. Finally, we show that RAB4B relocates to the viral assembly compartment following infection with HCMV and knockdown of RAB4B reduces the release of intact virion particles, suggesting that it plays a role in virion assembly and egress. This study demonstrates a powerful high-throughput screen for identification of host-virus interactions, identifies multiple host genes associated with HCMV assembly and egress, and uncovers potentially independent functions for coatomer components COPA and COPB2 during infection.

IMPORTANCE
Human cytomegalovirus infection is a significant cause of disease in immunocompromised populations, individuals with heart disease, and recipients of solid organ and bone marrow transplants. HCMV is also the leading cause of infectious congenital birth defects. The majority of antivirals in clinical use target components of the virus to specifically inhibit replication. However, a major drawback of this approach is the emergence of resistance. An alternative approach is to target host factors that the virus requires for successful infection. In this study, multiple host factors were identified that were found to be essential for the production of newly infectious human cytomegalovirus. Identifying which host genes are necessary for virus replication extends our understanding of how viruses replicate and how cells function and provides potential targets for novel antivirals.
Trichomonas vaginalis
Macrophage Migration Inhibitory Factor Mediates Parasite Survival during Nutrient Stress
Authors: Chen Yi-Pei , Twu Olivia , Johnson Patricia J. 
Published: June 2018

ABSTRACT

Trichomonas vaginalis
is responsible for the most prevalent non-viral sexually transmitted disease worldwide, and yet the mechanisms used by this parasite to establish and maintain infection are poorly understood. We previously identified a
T. vaginalis
homologue (TvMIF) of a human cytokine, human macrophage migration inhibitory factor (huMIF). TvMIF mimics huMIF’s role in increasing cell growth and inhibiting apoptosis in human host cells. To interrogate a role of TvMIF in parasite survival during infection, we asked whether overexpression of TvMIF (TvMIF-OE) confers an advantage to the parasite under nutrient stress conditions by comparing the survival of TvMIF-OE parasites to that of empty vector (EV) parasites. We found that under conditions of serum starvation, overexpression of TvMIF resulted in increased parasite survival. Serum-starved parasites secrete 2.5-fold more intrinsic TvMIF than unstarved parasites, stimulating autocrine and paracrine signaling. Similarly, we observed that addition of recombinant TvMIF increased the survival of the parasites in the absence of serum. Recombinant huMIF likewise increased the parasite survival in the absence of serum, indicating that the parasite may use this host survival factor to resist its own death. Moreover, TvMIF-OE parasites were found to undergo significantly less apoptosis and reactive oxygen species (ROS) generation under conditions of serum starvation, consistent with increased survival being the result of blocking ROS-induced apoptosis. These studies demonstrated that a parasitic MIF enhances survival under adverse conditions and defined TvMIF and huMIF as conserved survival factors that exhibit cross talk in host-pathogen interactions.

IMPORTANCE
Macrophage migration inhibitory factor (MIF) is a conserved protein found in most eukaryotes which has been well characterized in mammals but poorly studied in other eukaryotes. The limited analyses of MIF proteins found in unicellular eukaryotes have focused exclusively on the effect of parasitic MIF on the mammalian host. This was the first study to assess the function of a parasite MIF in parasite biology. We demonstrate that the
Trichomonas vaginalis
MIF functions to suppress cell death induced by apoptosis, thereby enhancing parasite survival under adverse conditions. Our research reveals a conserved survival mechanism, shared by a parasite and its host, and indicates a role for a conserved protein in mediating cross talk in host-pathogen interactions.
A Proteolytic Complex Targets Multiple Cell Wall Hydrolases in Pseudomonas aeruginosa
Authors: Srivastava Disha , Seo Jin , Rimal Binayak , Kim Sung Joon , Zhen Stephanie , Darwin Andrew J. 
Published: June 2018

ABSTRACT

Carboxy-terminal processing proteases (CTPs) occur in all three domains of life. In bacteria, some of them have been associated with virulence. However, the precise roles of bacterial CTPs are poorly understood, and few direct proteolytic substrates have been identified. One bacterial CTP is the CtpA protease of
Pseudomonas aeruginosa
, which is required for type III secretion system (T3SS) function and for virulence in a mouse model of acute pneumonia. Here, we have investigated the function of CtpA in
P. aeruginosa
and identified some of the proteins it cleaves. We discovered that CtpA forms a complex with a previously uncharacterized protein, which we have named LbcA (
l
ipoprotein
b
inding partner of
C
tpA). LbcA is required for CtpA activity
in vivo
and promotes its activity
in vitro
. We have also identified four proteolytic substrates of CtpA, all of which are uncharacterized proteins predicted to cleave the peptide cross-links within peptidoglycan. Consistent with this, a
ctpA
null mutant was found to have fewer peptidoglycan cross-links than the wild type and grew slowly in salt-free medium. Intriguingly, the accumulation of just one of the CtpA substrates was required for some Δ
ctpA
mutant phenotypes, including the defective T3SS. We propose that LbcA-CtpA is a proteolytic complex in the
P. aeruginosa
cell envelope, which controls the activity of several peptidoglycan cross-link hydrolases by degrading them. Furthermore, based on these and other findings, we suggest that many bacterial CTPs might be similarly controlled by partner proteins as part of a widespread mechanism to control peptidoglycan hydrolase activity.

IMPORTANCE
Bacterial carboxy-terminal processing proteases (CTPs) are widely conserved and have been associated with the virulence of several species. However, their roles are poorly understood, and few direct substrates have been identified in any species.
Pseudomonas aeruginosa
is an important human pathogen in which one CTP, known as CtpA, is required for type III secretion system function and for virulence. This work provides an important advance by showing that CtpA works with a previously uncharacterized binding partner to degrade four substrates. These substrates are all predicted to hydrolyze peptidoglycan cross-links, suggesting that the CtpA complex is an important control mechanism for peptidoglycan hydrolysis. This is likely to emerge as a widespread mechanism used by diverse bacteria to control some of their peptidoglycan hydrolases. This is significant, given the links between CTPs and virulence in several pathogens and the importance of peptidoglycan remodeling to almost all bacterial cells.