bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of techniques used for superimposition of maxillary and mandibular 3D surface models to evaluate tooth movement: a systematic review
Authors: Stucki Sven , Gkantidis Nikolaos 
Published: August 2019

Summary

Background
Superimposition of three-dimensional (3D) digital models offers great opportunities to assess tooth movement during time. In the literature, several superimposition techniques are described.

Objectives
To summarize and critically assess the available evidence from studies on serial digital 3D dental model superimposition.

Search methods
MEDLINE via Ovid and PubMed, EMBASE via Ovid, Cochrane Register of Diagnostic Test Accuracy Studies, and Google Scholar were searched with no time limit (last update: December 2018). Hand and unpublished literature searches were also performed.

Selection criteria
Studies of any design that had a sample size ≥5 and tested superimposition of serial 3D digital dental models to assess tooth movement were included.

Data collection and analysis
Study selection, data extraction, and risk of bias assessment were performed independently by the authors.

Results
Twelve studies met the eligibility criteria. The total risk of bias (QUADAS-2 tool) of 10 studies was high, whereas only 2 studies had unclear bias. Ten studies had high and two studies low overall applicability concerns. From these, one study tested the mandibular alveolar bone area, three studies the rugae area, nine studies a larger palatal area, and two studies the incisive papilla area. The high heterogeneity in samples, outcomes, and methods did not allow for synthesis of a considerable amount of studies in any case.

Limitations
The high heterogeneity among studies and the limited evidence did not allow for solid conclusions.

Conclusions and implications
The following areas of the maxilla could provide reliable outcomes: (1) the medial two-thirds of the third rugae and the area 5 mm dorsal to them and (2) an area including all rugae, with the lateral margins located at least 5 mm from the gingival margins and a distal margin that does not extend beyond the first molars. No recommendation is possible for other regions of the mouth. There is an urgent need for further research in the field.

Registration
PROSPERO (CRD42019124365).
Yeast prion-based metabolic reprogramming induced by bacteria in fermented foods
Authors: Watanabe Daisuke , Takagi Hiroshi 
Published: August 2019

ABSTRACT
Microbial communities of yeast and bacterial cells are often observed in the manufacturing processes of fermented foods and drinks, such as sourdough bread, cheese, kefir, wine and sake. Community interactions and dynamics among microorganisms, as well as their significance during the manufacturing processes, are central issues in modern food microbiology. Recent studies demonstrated that the emergence of a yeast prion termed [GAR+] in Saccharomyces cerevisiae is induced by coculturing with bacterial cells, resulting in the switching of the carbon metabolism. In order to facilitate mutualistic symbiosis among microorganisms, this mode of microbial interaction is induced between yeasts and lactic acid bacteria species used in traditional sake making. Thus, yeast prions have attracted much attention as novel platforms that govern the metabolic adaptation of cross-kingdom ecosystems. Our minireview focuses on the plausible linkage between fermented-food microbial communication and yeast prion-mediated metabolic reprogramming.
Protection Deficit: The Failure of Australia’s Offshore Processing Arrangements to Guarantee ‘Protection Elsewhere’ in the Pacific
Authors: Gleeson Madeline 
Published: August 2019

Abstract
In 2012, Australia reintroduced arrangements for ‘offshore processing’ in the Pacific, which forcibly transferred asylum seekers arriving by boat to the Republic of Nauru and Papua New Guinea (PNG), purportedly for refugee status determination (RSD). Previous studies have focused on the detention of asylum seekers transferred to these States in ‘regional processing centres’ (RPCs). This article instead provides a factual foundation for more current inquiries into the content and scope of each State’s protection obligations under international law, which have increased in importance since the end of closed detention in the RPCs in 2015 and 2017. The formal legal and diplomatic arrangements established in and between the three States for the transfer of asylum seekers; processing of their claims; and provision of durable solutions will be examined, with reference to the minimum standards required. The article identifies a protection deficit in the legal architecture and bilateral arrangements underpinning offshore processing. Since their inception, the arrangements have lacked clarity regarding the respective obligations of the three States; involved transfers even in the absence of fair and efficient procedures for RSD in Nauru and PNG; and failed to ensure timely access to appropriate outcomes for all transferees (whether determined to be in need of international protection or not). The article therefore concludes that Australia should facilitate readmission to its territory for all people in Nauru and PNG who do not have access to an appropriate alternative outcome. It also suggests that any future attempts to establish third country transfer procedures will require radically different legal and diplomatic arrangements to enhance responsibility sharing and cooperation on refugee protection, and to comply with international law.
The Dark Side of Cooperation: International Organizations and Member Corruption
Authors: Hafner-Burton Emilie M , Schneider Christina J 
Published: August 2019

AbstractPolitical corruption is rampant in—and destructive to—many parts of the world. A growing number of international organizations (IOs) claim to address the problem by encouraging good governance norms and rules, such as anti-corruption standards and practices. Whether membership in IOs dampens corruption, however, is unclear. Our central argument is that the characteristics of IO membership determine both whether corruption is tolerated and the extent to which formal anti-corruption rules effectively combat the problem. First, groups of corrupt states are reticent to enforce good governance norms or rules against other IO members, rendering punishment for corruption incredible. Second, leaders may witness the value of corruption to their IO peers and learn to act the same way. Using a variety of data sources and estimation strategies, including new data on IO anti-corruption mandates, we demonstrate that: (1) countries that participate in member-corrupted IOs are significantly more likely to engage in corruption themselves—and experience an increase in corruption over time—than are countries that participate in less corrupt IOs; and (2) this tolerance for corruption occurs even within IOs that have adopted formal anti-corruption mandates, rendering good governance rules largely cheap talk among organizations governed by corrupt principles.
Extended-spectrum resistance to β-lactams/β-lactamase inhibitors (ESRI) evolved from low-level resistant Escherichia coli
Authors: Rodríguez-Villodres Ángel , Gil-Marqués María Luisa , Álvarez-Marín Rocío , Bonnin Rémy A , Pachón-Ibáñez María Eugenia , Aguilar-Guisado Manuela , Naas Thierry , Aznar Javier , Pachón Jerónimo , Lepe José Antonio , Smani Younes 
Published: August 2019

Abstract

Objectives
Escherichia coli is characterized by three resistance patterns to β-lactams/β-lactamase inhibitors (BLs/BLIs): (i) resistance to ampicillin/sulbactam and susceptibility to amoxicillin/clavulanic acid and piperacillin/tazobactam (RSS); (ii) resistance to ampicillin/sulbactam and amoxicillin/clavulanic acid, and susceptibility to piperacillin/tazobactam (RRS); and (iii) resistance to ampicillin/sulbactam, amoxicillin/clavulanic acid and piperacillin/tazobactam (RRR). These resistance patterns are acquired consecutively, indicating a potential risk of developing resistance to piperacillin/tazobactam, but the precise mechanism of this process is not completely understood.

Methods
Clinical isolates incrementally pressured by piperacillin/tazobactam selection in vitro and in vivo were used. We determined the MIC of piperacillin/tazobactam in the presence and absence of piperacillin/tazobactam pressure. We deciphered the role of the blaTEM genes in the new concept of extended-spectrum resistance to BLs/BLIs (ESRI) using genomic analysis. The activity of β-lactamase was quantified in these isolates.

Results
We show that piperacillin/tazobactam resistance is induced in E. coli carrying blaTEM genes. This resistance is due to the increase in copy numbers and transcription levels of the blaTEM gene, thus increasing β-lactamase activity and consequently increasing piperacillin/tazobactam MICs. Genome sequencing of two blaTEM-carrying representative isolates showed that piperacillin/tazobactam treatment produced two types of duplications of blaTEM (8 and 60 copies, respectively). In the clinical setting, piperacillin/tazobactam treatment of patients infected by E. coli carrying blaTEM is associated with a risk of therapeutic failure.

Conclusions
This study describes for the first time the ESRI in E. coli. This new concept is very important in the understanding of the mechanism involved in the acquisition of resistance to BLs/BLIs.
Molecular and Functional Characterization of One Odorant-Binding Protein Gene OBP3 in Bemisia tabaci (Hemiptera: Aleyrodidae)
Authors: Wang Ran , Hu Yuan , Wei Peiling , Qu Cheng , Luo Chen 
Published: August 2019

Abstract
Odorant binding proteins (OBPs) of insects play a critical role in chemical perceptions and choice of insect host plant. Bemisia tabaci is a notorious insect pest which can damage more than 600 plant species. In order to explore functions of OBPs in B. tabaci, here we investigated binding characteristics and function of odorant-binding protein 3 in B. tabaci (BtabOBP3). The results indicated that BtabOBP3 shows highly similar sequence with OBPs of other insects, including the typical signature motif of six cysteines. The recombinant BtabOBP3 protein was obtained, and the evaluation of binding affinities to tested volatiles of host plant was conducted, then the results indicated that β-ionone had significantly higher binding to BtabOBP3 among other tested plant volatiles. Furthermore, silencing of BtabOBP3 significantly altered choice behavior of B. tabaci to β-ionone. In conclusion, it has been demonstrated that BtabOBP3 exerts function as one carrier of β-ionone and the results could be contributed to reveal the mechanisms of choosing host plant in B. tabaci.
Climate Change and the Risk of Malaria Transmission in Iran
Authors: Hanafi-Bojd Ahmad Ali , Vatandoost Hassan , Yaghoobi-Ershadi Mohammad Reza 
Published: August 2019

Abstract
Climate change is an important factor affecting the dynamics of the vectors population and, hence, the risk of vector-borne diseases. This study aimed to predict the environmental suitability for malaria vectors in Iran under climate change scenarios in 2030s and 2050s. Literature search was performed to find documents on the spatial distribution of Anopheles stephensi Liston, 1901, Anopheles culicifacies s.l. Giles, 1901, Anopheles fluviatilis s.l. James, 1902, Anopheles superpictus s.l. Grassi, 1899, Anopheles dthali Patton, 1905, Anopheles maculipennis s.l. Meigen, 1818, and Anopheles sacharovi Favre, 1903 (Diptera: Culicidae) published between 1970 and 2017. The bioclimatic data under three climate change scenarios (representative concentration pathway 2.6 [RCP2.6], RCP4.5, and RCP8.5) and MaxEnt model were used to predict the ecological niches for each species. Comparison between the two study periods under the three scenarios for each species revealed that RCP8.5 would reduce the area at risk for An. culicifacies s.l., An. dthali and An. superpictus s.l. in the 2050s compared to the 2030s, but the reverse will be induced by RCP2.6 and RCP4.5 scenarios. For An. fluviatilis s.l., RCP2.6 will reduce the risk areas in the 2050s, whereas an increase is expected under the two other scenarios. Moreover, all scenarios would decrease the high-risk areas of An. maculipennis s.l. in the 2050s. For An. sacharovi, RCP2.6 would increase its high-risk areas, whereas RCP4.5 and RCP8.5 would decrease its exposure. The high-risk area of An. stephensi is expected to increase under RCP8.5 in the 2030s and RCP4.5 in 2050s, but it will be almost unchanged or reduced under other scenarios.
Evaluating Clonal Hematopoiesis in Tumor-Infiltrating Leukocytes in Breast Cancer and Secondary Hematologic Malignancies
Authors: Comen Elizabeth A , Bowman Robert L , Selenica Pier , Kleppe Maria , Farnoud Noushin R , Pareja Fresia , Weigelt Britta , Hill Corinne E , Alon Abigail , Geyer Felipe C , Akturk Guray , Reis-Filho Jorge S , Norton Larry , Levine Ross L 
Published: August 2019

Abstract
Chemotherapy and radiation therapy are the foundations of adjuvant therapy for early-stage breast cancer. As a complication of cytotoxic regimens, breast cancer patients are at risk for therapy-related myeloid neoplasms (t-MNs). These t-MNs are commonly refractory to antileukemic therapies and result in poor patient outcomes. We previously demonstrated that somatic mutations in leukemia-related genes are present in the tumor-infiltrating leukocytes (TILeuks) of a subset of early breast cancers. Here, we performed genomic analysis of microdissected breast cancer tumor cells and TILeuks from seven breast cancer patients who subsequently developed leukemia. In four patients, mutations present in the leukemia were detected in breast cancer TILeuks. This finding suggests that TILeuks in the primary breast cancer may harbor the ancestor of the future leukemogenic clone. Additional research is warranted to ascertain whether infiltrating mutant TILeuks could constitute a biomarker for the development of t-MN and to determine the functional consequences of mutant TILeuks.
Case Study of a Breacher: Investigation of Neurotrauma Biomarker Levels, Self-reported Symptoms, and Functional MRI Analysis Before and After Exposure to Measured Low-Level Blast
Authors: Eonta Stephanie E , Kamimori Gary H , Wang Kevin K W , Carr Walter , LaValle Christina R , Egnoto Michael J , Tate Charmaine M 
Published: August 2019

Abstract
We report a case study on a single military member who received moderate blast overpressure (OP) exposure during routine breacher training. We extend previous research on blast exposure during training, which lacked sufficient data to assess symptom profiles and OP exposure. The present work was conducted because a subjective symptom profile similar to that seen in sports concussion has been reported by military personnel exposed to blast. Data collection for this study was carried out under a research protocol approved by the relevant Human Subjects Review Committees on one subject, who received the highest OP exposure during training. The volunteer was a 20-year-old male with no prior history of traumatic brain injury (TBI) or blast exposure. The volunteer was part of a breacher training team that completed a 2-week explosive entry course. The course included 3 classroom days and 9 days of practical training, held in the morning, afternoon, and evening sessions. Blast exposure occurred on five of the nine practical training days, with multiple exposures over the course of each day. Assessments of serum, self-reported symptoms, magnetic resonance imaging, and blast characterization were conducted. Results indicated changes in glial fibrillary acidic protein and ubiquitin C-terminal hydrolase-L1 postblast exposure but did not manifest changes in spectrin-derived breakdown product 150 or magnetic resonance imaging. No additional symptoms were reported by the subject. Objective markers of mild TBI remain elusive, but support for serum biomarkers as an early detection mechanism is promising. Additionally, this case study demonstrated an association between OP and high level of neurotrauma biomarker in an individual.
Unusual Patterns of Mitochondrial Inheritance in the Brown Alga Ectocarpus
Authors: Mignerot Laure , Nagasato Chikako , Peters Akira F , Perrineau Marie-Mathilde , Scornet Delphine , Pontheaux Florian , Djema Walid , Badis Yacine , Motomura Taizo , Coelho Susana M , Cock J Mark 
Published: August 2019

AbstractMost eukaryotes inherit their mitochondria from only one of their parents. When there are different sexes, it is almost always the maternal mitochondria that are transmitted. Indeed, maternal uniparental inheritance has been reported for the brown alga Ectocarpus but we show in this study that different strains of Ectocarpus can exhibit different patterns of inheritance: Ectocarpus siliculosus strains showed maternal uniparental inheritance, as expected, but crosses using different Ectocarpus species 7 strains exhibited either paternal uniparental inheritance or an unusual pattern of transmission where progeny inherited either maternal or paternal mitochondria, but not both. A possible correlation between the pattern of mitochondrial inheritance and male gamete parthenogenesis was investigated. Moreover, in contrast to observations in the green lineage, we did not detect any change in the pattern of mitochondrial inheritance in mutant strains affected in life cycle progression. Finally, an analysis of field-isolated strains provided evidence of mitochondrial genome recombination in both Ectocarpus species.
Spacer acquisition from RNA mediated by a natural reverse transcriptase-Cas1 fusion protein associated with a type III-D CRISPR–Cas system in Vibrio vulnificus
Authors: González-Delgado Alejandro , Mestre Mario Rodríguez , Martínez-Abarca Francisco , Toro Nicolás 
Published: August 2019

Abstract
The association of reverse transcriptases (RTs) with CRISPR–Cas system has recently attracted interest because the RT activity appears to facilitate the RT-dependent acquisition of spacers from RNA molecules. However, our understanding of this spacer acquisition process remains limited. We characterized the in vivo acquisition of spacers mediated by an RT-Cas1 fusion protein linked to a type III-D system from Vibrio vulnificus strain YJ016, and showed that the adaptation module, consisting of the RT-Cas1 fusion, two different Cas2 proteins (A and B) and one of the two CRISPR arrays, was completely functional in a heterologous host. We found that mutations of the active site of the RT domain significantly decreased the acquisition of new spacers and showed that this RT-Cas1-associated adaptation module was able to incorporate spacers from RNA molecules into the CRISPR array. We demonstrated that the two Cas2 proteins of the adaptation module were required for spacer acquisition. Furthermore, we found that several sequence-specific features were required for the acquisition and integration of spacers derived from any region of the genome, with no bias along the 5′and 3′ends of coding sequences. This study provides new insight into the RT-Cas1 fusion protein-mediated acquisition of spacers from RNA molecules.
Training-free measures based on algorithmic probability identify high nucleosome occupancy in DNA sequences
Authors: Zenil Hector , Minary Peter 
Published: August 2019

AbstractWe introduce and study a set of training-free methods of an information-theoretic and algorithmic complexity nature that we apply to DNA sequences to identify their potential to identify nucleosomal binding sites. We test the measures on well-studied genomic sequences of different sizes drawn from different sources. The measures reveal the known in vivo versus in vitro predictive discrepancies and uncover their potential to pinpoint high and low nucleosome occupancy. We explore different possible signals within and beyond the nucleosome length and find that the complexity indices are informative of nucleosome occupancy. We found that, while it is clear that the gold standard Kaplan model is driven by GC content (by design) and by k-mer training; for high occupancy, entropy and complexity-based scores are also informative and can complement the Kaplan model.
Imaging challenges of immunotherapy and targeted therapy in patients with brain metastases: response, progression, and pseudoprogression
Authors: Galldiks Norbert , Kocher Martin , Ceccon Garry , Werner Jan-Michael , Brunn Anna , Deckert Martina , Pope Whitney B , Soffietti Riccardo , Le Rhun Emilie , Weller Michael , Tonn Jörg C , Fink Gereon R , Langen Karl-Josef 
Published: August 2019

Abstract
The advent of immunotherapy using immune checkpoint inhibitors (ICIs) and targeted therapy (TT) has dramatically improved the prognosis of various cancer types. However, following ICI therapy or TT—either alone (especially ICI) or in combination with radiotherapy—imaging findings on anatomical contrast-enhanced MRI can be unpredictable and highly variable, and are often difficult to interpret regarding treatment response and outcome. This review aims at summarizing the imaging challenges related to TT and ICI monotherapy as well as combined with radiotherapy in patients with brain metastases, and to give an overview on advanced imaging techniques which potentially overcome some of these imaging challenges. Currently, major evidence suggests that imaging parameters especially derived from amino acid PET, perfusion-/diffusion-weighted MRI, or MR spectroscopy may provide valuable additional information for the differentiation of treatment-induced changes from brain metastases recurrence and the evaluation of treatment response.
Solutions for whole grain food development
Authors: Tan Bin , Wu Na-Na , Zhai Xiao-Tong 
Published: August 2019

AbstractOwing to the health benefits associated with whole grains, there has been a sustained global effort to increase their consumption, with many countries developing guidelines for recommended amounts of whole grain intake. In China, the consumption of whole grains is low. This is due, in part, to technical obstacles in the development of whole grain foods. This review focuses on possible solutions in the whole value chain and the application of new food technologies to develop whole grain foods that taste better, have more appealing texture, are safe to consume, and better retain bioactive compounds.
Clinical Characteristics and Outcome of Staphylococcus aureus Prostate Abscess From Ten Years of Experience at a Tertiary Care Center
Authors: Walker Bryan , Heidel Eric , Shorman Mahmoud 
Published: August 2019

Abstract

Objective
Prostatic abscess (PA) is an uncommon infection that is generally secondary to Escherichia coli and other members of the Enterobacteriaceae family. In recent years, although rare, more reports of Staphylococcus aureus (S. aureus) PA have been reported, especially with increasing reports of bacteremia associated with injection drug use (IDU).

Method
This was a retrospective review of adult patients admitted to a tertiary care hospital between 2008 and 2018 and who had a diagnosis of S. aureus PA.

Results
Twenty-one patients were included. The average age was 46 years. Fourteen (67%) patients presented with genitourinary concerns. Main risk factors included concurrent skin or soft tissue infections (52%), history of genitourinary disease or instrumentation (48%), IDU (38%), and diabetes mellitus (38%). Methicillin-resistant Staphylococcus aureus (MRSA) was identified in 57% and concomitant bacteremia in 81% of patients. Surgical or a radiologically guided drainage was performed in 81% of patients. Antibiotic treatment duration ranged from 3 to 8 weeks. Six patients were lost to follow-up. Clinical resolution was observed in the remaining 15 (81%) patients who had follow-up.

Conclusions
S. aureus PA continues to be a rare complication of S.aureus infections. In most published reports, MRSA is the culprit. In high risk patients with persistent bacteremia, physicians need to consider the prostate as a site of infection.