bluuebunny/crossref_metadata_2025_split huggingface dataset:
Helicobacter pylori antibiotic resistance in Portugal: Systematic review and meta‐analysis
Authors: Lopo Inês , Libânio Diogo , Pita Inês , Dinis‐Ribeiro Mário , Pimentel‐Nunes Pedro 
Published: June 2018

AbstractBackgroundPortugal presents both a high prevalence of Helicobacter pylori (Hp) infection and a high prevalence of antibiotic resistance. However, conclusive data on its magnitude are lacking. We aimed at summarizing the existing data.Materials and MethodsA systematic review was conducted after searching in two databases (PubMed and SciELO). Meta‐analysis was performed, and comparison of resistance rates between children and adults and by type of resistance (primary and secondary) was made.ResultsEight cross‐sectional studies assessing Hp resistance to antibiotics were included. Overall resistance rates were as follows: clarithromycin (CLA) 42% (95% CI: 30‐54), metronidazole (MTZ) 25% (95% CI: 15‐38), ciprofloxacin (CIP) 9% (95% CI: 3‐18), levofloxacin (LVX) 18% (95% CI: 2‐42), tetracycline (TTC) 0.2% (95% CI: 0‐1), and amoxicillin (AMX) 0.1% (95% CI: 0‐0.2). Multidrug resistance was also an important problem, with the following global resistance rates: CLA plus MTZ of 10% (adults 20% (95% CI: 15‐26) vs children 6% (95% CI: 4‐9)) and CLA plus CIP of 2% (primary resistance in children's group). High secondary resistance rates were found for all antibiotics. Resistance was higher among adults for all antibiotics, except CLA that had high resistance levels both among adults and children (42% 95% CI: 14‐71 and 40% 95% CI: 33‐47).ConclusionsHp resistance to the most widely used antibiotics is high in Portugal. Accordingly, our results suggest that the best therapeutic strategy for Hp in Portugal may be quadruple therapy with bismuth for adults and triple therapy including AMX plus MTZ or bismuth‐based therapy for children.
Improvement in the radio frequency method to pasteurise shell eggs by automation and cost reduction
Authors: Geveke David J. , Bigley Andrew B. W. , Brunkhorst Christopher D. , Jones Deana R. , Tilman Eric D. 
Published: June 2018

SummaryThe existing radio frequency (RF) shell egg pasteurisation method, while 60% faster than the industrial hot water method, requires manual rotation of the eggs and expensive deionised water. Therefore, the RF pasteurisation equipment was redesigned to automate egg rotation and use inexpensive tap water. A two‐step process heated eggs for 6 min with RF and then for 15 min with 56.7 °C water. The 21‐min combination process reduced Salmonella Typhimurium in eggs by 6.1 log without affecting the appearance of the albumen, whereas processing with 56.7 °C water alone required 60 min to reduce Salmonella by 5.0 log and clouded the albumen. Angel food cakes made from 21 min RF eggs had significantly greater volumes (P < 0.0001) than those from 60‐min hot water eggs. The improved RF process produced better eggs and cakes than those from the industrial hot water process and is now commercially feasible.
‘In some ways it all helps but in some ways it doesn't’: The complexities of service users’ experiences of inpatient mental health care in Australia
Authors: Isobel Sophie 
Published: June 2018

AbstractRecovery‐oriented mental health care requires active involvement of service users in the evaluation of care. While experience of care surveys is routinely given out upon discharge, capturing the depth and detail of service users’ experiences in such a way to meaningfully improve services may require more in‐depth and targeted approaches. This study aimed to gather voluntary and involuntary service users’ experiences of care during hospitalization in two acute adult mental health inpatient units, through the collaborative completion of a purpose designed tool. The purpose of the study was to examine broad experiences of care and to identify the utility of proactive approaches to ongoing service evaluation. Overall, 67 participants were interviewed. Findings highlight the complexity of experiences of care including how an admission can seemingly facilitate clinical recovery while not being recovery‐oriented. The findings also detail areas for improvement in the way that care is delivered and evaluated. The implications are particularly pertinent for mental health nurses to consider how, within the existing constraints of their roles, they can provide therapeutic care to all service users.
Spatio‐temporal cladoceran (Branchiopoda) responses to climate change and UV radiation in subarctic ecotonal lakes
Authors: Nevalainen Liisa , Rantala Marttiina V. , Rautio Milla , Luoto Tomi P. 
Published: June 2018

AbstractAimTo understand modern and past aquatic community responses to climate‐induced shifts in productivity and ultraviolet radiation (UV) exposure.LocationTree line ecotone from north boreal forest to subarctic tundra in northeastern Finnish Lapland.TaxonCladocera (Crustacea: Branchiopoda).MethodsThirty‐one small and shallow lakes were examined for summer epilimnetic communities (SEC) and surface sediment fossil integrative communities (FIC) of Cladocera for species distribution and their environmental correlations. A 700‐year down‐core sediment sequence from a tree line lake (Námmájávri) was analysed for FICs and cladoceran‐inferred UV absorbance (ABSUV, indicative of melanin pigmentation) for evidence of long‐term community and photoprotective responses and compared with records of palaeotemperature, solar intensity, and composite sediment biogeochemistry by variance partitioning analysis.ResultsThe SECs were primarily correlated with specific UV absorbance (indicative of UV exposure) and total phosphorus and FICs by mean July air temperature and total nitrogen. The Námmájávri FICs showed subtle changes with a directional shift between the 19th and 21st centuries and were mostly explained by solar intensity. ABSUV exhibited increases during the 18th and 20th centuries, being related to variation in sediment biogeochemistry, which was indicative of changes in auto‐ versus allochthonous production.Main conclusionsThe ecotonal distribution of cladocerans is sensitive to temperature, nutrients, and allochthonous carbon, which is closely linked with UV exposure. The long‐term community shifts and photoprotection have been governed by solar intensity and biogeochemical shifts through lake water optics, attributable to direct UV impact or climate‐mediated intensification in photodegradation of allochthonous carbon. Estimations of the dual effects and mechanisms of increasing temperatures and UV on subarctic lakes and their biota remain challenging as their individual impacts on key species were partly contradictory.
Effect of Monochromatic Light on Circadian Rhythm of Clock Genes in Chick Pinealocytes
Authors: Ma Shuhui , Wang Zixu , Cao Jing , Dong Yulan , Chen Yaoxing 
Published: June 2018

AbstractThe avian circadian system is a complex of mutually coupled pacemakers residing in pineal gland, retina and suprachiasmatic nucleus. In this study, the self‐regulation mechanism of pineal circadian rhythm was investigated by culturing chick primary pinealocytes exposed to red light (RL), green light (GL), blue light (BL), white light (WL) and constant darkness (DD), respectively. All illuminations were set up with a photoperiod of 12 light: 12 dark. The 24‐h expression profiles of seven core clock genes (cBmal1/2, cClock, cCry1/2 and cPer2/3), cAanat and melatonin showed significant circadian oscillation in all groups, except for the loss of cCry1 rhythm in BL. Compared to WL, GL increased the amplitudes and mesors of positive elements (cClock and cBmal1/2) and reduced those of negative elements (cCry1/2 and cPer2/3), in contrast to RL. The temporal patterns of cAanatmRNA and melatonin secretion have always been consistent with the positive genes. Besides, GL advanced the acrophases of the positive elements, cAanat and melatonin, but RL and BL showed the opposite effect. Thereby, GL could promote the secretion of melatonin by enhancing the expressions of positive clock genes and repressing the expressions of negative clock genes.
Diagnosis of invasive mold diseases in patients with hematological malignancies using Aspergillus, Mucorales, and panfungal PCR in BAL
Authors: Wehrle‐Wieland Elisabeth , Affolter Kristina , Goldenberger Daniel , Tschudin Sutter Sarah , Halter Joerg , Passweg Jakob , Tamm Michael , Khanna Nina , Stolz Daiana 
Published: June 2018

AbstractBackgroundAccurate diagnosis of invasive mold diseases (IMD) remains challenging. Here, the performance of panfungal PCR, Aspergillus and MucoralesPCR in bronchoalveolar lavage (BAL) was evaluated.MethodsWe conducted a single‐center study including 167 hematologic patients at risk for IMD with BAL performed 2011‐2014. Diagnostic performance of single tests (Aspergillus‐, Mucorales‐, and panfungal PCR, galactomannan (GM)≥0.5 and ≥1, culture/cytology) or in combination was calculated for predicting IMD comparing proven/probable or proven/probable/possible IMD vs no IMD, respectively.ResultsIMD was classified as proven (n = 6), probable (n = 31), possible (n = 29) and no IMD (n = 101) according to EORTC/MSG criteria. GM ≥ 0.5 in BAL showed the highest sensitivity with 81% for diagnosing IMD whereas the other tests only 5%‐35%. By contrast, specificity was highest for panfungal PCR with 99% and GM ≥ 1, Mucorales and AspergillusPCR reached specificity ≥91%. When combining the tests, GM ≥ 0.5 and panfungal PCR show a sensitivity and specificity of 87% and 78% for IMD or with AspergillusPCR a sensitivity and specificity of 88% and 72% for invasive pulmonary aspergillosis, respectively. Including possible IMD patients did not improve the sensitivity of PCRs. In probable/proven IMD patients, the addition of panfungal PCR resulted further in detection of Fusarium species and Alternaria species, and the MucoralesPCR was positive in 2 probable IMD cases.ConclusionThis study illustrates that the diagnosis of IMD is still very problematic and lacks objectivity. Together with GM in BAL, the PCRs may prove an addition to the current available diagnostic armamentarium in IMD because of their ability to identify molds on a species level.
Genotyping analysis of MNS blood group GP(B‐A‐B) hybrid glycophorins in the Chinese Southern Han population using a high‐resolution melting assay
Authors: Wei Ling , Lopez Genghis H. , Zhang Yang , Wen Jizhi , Wang Zhen , Fu Yongshui , Hyland Catherine A. , Flower Robert L. , Luo Guangping , Ji Yanli 
Published: June 2018

BACKGROUNDMNS hybrid GP(B‐A‐B) glycophorins are more commonly found in Southeast Asians and alloantibodies to antigens they carry are clinically significant. Detection of hybrid glycophorins by serologic techniques is limited due to lack of commercial reagents. In this study, a genotyping method for GP(B‐A‐B) hybrid glycophorins based on high‐resolution melting (HRM) analysis was applied for genotyping analysis in the Chinese Southern Han population.STUDY DESIGN AND METHODSDNA samples from 3104 Chinese Southern Han blood donors were collected. GYP(B‐A‐B) genotypes were analyzed by HRM assay. Parts of samples (n = 106) were also tested by multiplex ligation‐dependent probe amplification (MLPA) assay. Direct sequencing was conducted in samples with variant melting curve profiles.RESULTSA total of five GYP(B‐A‐B) genotypes (201/3104, 6.5%) were identified, which were GYP*Mur heterozygote (n = 194), GYP*Mur homozygote (n = 3), GYP*Bun heterozygote (n = 2), GYP*HF heterozygote (n = 1), and a novel GYP(B‐A‐B) hybrid allele (n = 1). Genotyping results for GYP*Mur and wild‐type GYPB samples obtained by HRM were consistent with MLPA, while GYP*Bun and GYP*HF heterozygote identified by HRM could only be identified to have one copy of 5′ inactive splice site of GYPB Pseudoexon 3 by MLPA. In addition, 10 single‐nucleotide polymorphisms (SNPs) including four known and six novel SNPs were identified in 31 samples. One sample was identified carrying both GYP*Mur and GYP*Sch alleles.CONCLUSIONThe HRM assay could distinguish the GYP(B‐A‐B) hybrid alleles successfully. Polymorphisms identified within the GYPB gene should be taken into consideration when developing GYP(B‐A‐B) genotyping kits for the Chinese population.
Does human leukocyte antigens sensitization matter for xenotransplantation?
Authors: Byrne Guerard W. 
Published: June 2018

AbstractThe major histocompatibility complex class I and class II human leukocyte antigens (HLA) play a central role in adaptive immunity but are also the dominant polymorphic proteins targeted in allograft rejection. Sensitized patients with high levels of panel‐reactive anti‐HLA antibody (PRA) are at risk of early allograft injury, rejection, reduced allograft survival and often experience prolonged waiting times prior to transplantation. Xenotransplantation, using genetically modified porcine organs, offers a unique source of donor organs for these highly sensitized patients if the anti‐HLA antibody, which places the allograft at risk, does not also enhance anti‐pig antibody reactivity responsible for xenograft rejection. Recent improvements in xenotransplantation efficacy have occurred due to improved immune suppression, identification of additional xenogeneic glycans, and continued improvements in donor pig genetic modification. Genetically engineered pig cells, devoid of the known xenogeneic glycans, minimize human antibody reactivity in 90% of human serum samples. For waitlisted patients, early comparisons of patient PRA and anti‐pig antibody reactivity found no correlation suggesting that patients with high PRA levels were not at increased risk of xenograft rejection. Subsequent studies have found that some, but not all, highly sensitized patients express anti‐HLA class I antibody which cross‐reacts with swine leukocyte antigen (SLA) class I proteins. Recent detailed antigen‐specific analysis suggests that porcine‐specific anti‐SLA antibody from sensitized patients binds cross‐reactive groups present in a limited subset of HLA antigens. This suggests that using modern genetic methods, a program to eliminate specific SLA alleles through donor genetic engineering or stringent donor selection is possible to minimize recipient antibody reactivity even for highly sensitized individuals.
The ethics of organ donation, donation after circulatory determination of death, and xenotransplantation from an Islamic perspective
Authors: Padela Aasim I. , Duivenbode Rosie 
Published: June 2018

AbstractDonation after circulatory determination of death (DCDD) and xenotransplantation are advanced as possible solutions to the growing gap between the number of individuals in need of organ transplantation and the pool of donors. Investigating how various publics, including religious leaders, might view these “therapies” is essential for broad public and professional support and will be needed in order to make these solutions viable. This study, therefore, presents normative Islamic bioethical perspectives on donation after circulatory determination of death and xenotransplantation. First, we will discuss foundational Islamic ethico‐legal debates regarding organ donation. These debates can be grouped into three broad positions, those who consider organ donation categorically impermissible as a violation of human dignity (ḥurma and karāma), those who agree that organ donation is impermissible in principle, but allow it conditionally on the basis of dire necessity (ḍarūra), and those who permit organ donation based on notions of public interest (maṣlaḥa). Next, we will reflect upon the additional ethical dimensions DCDD and xenotransplantation add to these debates. We contend that the condition of minimal harm to the donor and the definition of death need to be accounted for within Islamic perspectives on DCDD. Xenotransplantation, on the other hand, highlights concerns about using pigs for therapeutic purposes. We conclude by commenting on additional questions that remain to be addressed in the Islamic bioethical debate over these practices and with recommendations for further research.
Powassan virus, a scoping review of the global evidence
Authors: Corrin Tricia , Greig Judy , Harding Shannon , Young Ian , Mascarenhas Mariola , Waddell Lisa A. 
Published: June 2018

AbstractBackgroundPowassan virus (POWV), a flavivirus discovered in 1958, causes sporadic but severe cases of encephalitis in humans. Since 2007, the number of human Powassan cases diagnosed each year in the USA has steadily increased. This is in agreement with predictions that Powassan cases may increase in North America as a result of increased exposure to infected ticks. However, the increase may also reflect improved diagnostics and reporting among other factors.MethodsA scoping review was prioritized to identify and characterize the global literature on POWV. Following an a priori developed protocol, a comprehensive search strategy was implemented. Two reviewers screened titles and abstracts for relevant research and the identified full papers were used to characterize the POWV literature using a predetermined data characterization tool.ResultsOne hundred and seventy‐eight articles were included. The majority of the studies were conducted in North America (88.2%) between 1958 and 2017. Both genotypes of POWV (Powassan lineage 1 and Deer Tick virus) were isolated or studied in vitro, in vectors, nonhuman hosts and human populations. To date, POWV has been reported in 147 humans in North America. The virus has also been isolated from five tick species, and several animals have tested positive for exposure to the virus. The relevant articles identified in this review cover the following eight topics: epidemiology (123 studies), pathogenesis (66), surveillance (33), virus characterization (22), POWV transmission (8), diagnostic test accuracy (8), treatment (4) and mitigation strategies (3).ConclusionThe literature on POWV is relatively small compared with other vector‐borne diseases, likely because POWV has not been prioritized due to the small number of severe sporadic human cases. With the projected impact of climate change on tick populations, increases in the number of human cases are expected. It is recommended that future research efforts focus on closing some of the important knowledge gaps identified in this scoping review.
Global Proteomic Changes Induced by the Epstein-Barr Virus Oncoproteins Latent Membrane Protein 1 and 2A
Authors: DeKroon Robert M. , Gunawardena Harsha P. , Edwards Rachel , Raab-Traub Nancy 
Published: June 2018

ABSTRACT
The Epstein-Barr virus (EBV) oncoproteins latent membrane protein 1 (LMP1) and LMP2A constitutively activate multiple signaling pathways, and both have been shown to interact with cellular ubiquitin ligases and affect cellular ubiquitination. To detect the LMP1- and LMP2A-mediated effects on the global cellular proteome, epithelial cell lines expressing LMP1 or LMP2A were analyzed using label-free quantitative proteomics. To identify proteins whose ubiquitination is affected by the viral proteins, the cells were cultured in the presence and absence of deubiquitinase (DUB) and proteasome inhibitors. More than 7,700 proteins were identified with high confidence and considerably more proteins showed significant differences in expression in the presence of inhibitors. Few of the differentially expressed proteins with or without inhibitors were common between LMP1 and LMP2A, confirming that the viral proteins induce unique changes in cell expression and function. However, ingenuity pathway analysis (IPA) of the data indicated that LMP1 and LMP2A modulate many of the same cellular regulatory pathways, including cell death and survival, cell movement, and actin filament dynamics. In addition, various proteasome subunits, ubiquitin-specific peptidases and conjugating enzymes, vesicle trafficking proteins, and NF-κB and mitogen-activated protein kinase signaling proteins were affected by LMP1 or LMP2A. These findings suggest that LMP1 and LMP2A may commonly target critical cell pathways through effects on distinct genes, with many cellular proteins modified by ubiquitination and/or degradation.

IMPORTANCE
The Epstein-Barr virus proteins latent membrane protein 1 and 2 have potent effects on cell growth and signaling. Both proteins bind to specific ubiquitin ligases and likely modulate the cellular proteome through ubiquitin-mediated effects on stability and intracellular location. In this study, a comprehensive proteomic analysis of the effects of LMP1 and LMP2A revealed that both proteins affected proteasome subunits, ubiquitin-specific conjugases and peptidases, and vesical trafficking proteins. The data suggest that the effects of these proteins on the abundance and ubiquitination of cellular proteins are in part responsible for their effects on cell growth regulation.
CRISPR Screen Reveals that EHEC’s T3SS and Shiga Toxin Rely on Shared Host Factors for Infection
Authors: Pacheco Alline R. , Lazarus Jacob E. , Sit Brandon , Schmieder Stefanie , Lencer Wayne I. , Blondel Carlos J. , Doench John G. , Davis Brigid M. , Waldor Matthew K. 
Published: June 2018

ABSTRACT

Enterohemorrhagic
Escherichia coli
(EHEC) has two critical virulence factors—a type III secretion system (T3SS) and Shiga toxins (Stxs)—that are required for the pathogen to colonize the intestine and cause diarrheal disease. Here, we carried out a genome-wide CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats with Cas9) loss-of-function screen to identify host loci that facilitate EHEC infection of intestinal epithelial cells. Many of the guide RNAs identified targeted loci known to be associated with sphingolipid biosynthesis, particularly for production of globotriaosylceramide (Gb3), the Stx receptor. Two loci (TM9SF2 and LAPTM4A) with largely unknown functions were also targeted. Mutations in these loci not only rescued cells from Stx-mediated cell death, but also prevented cytotoxicity associated with the EHEC T3SS. These mutations interfered with early events associated with T3SS and Stx pathogenicity, markedly reducing entry of T3SS effectors into host cells and binding of Stx. The convergence of Stx and T3SS onto overlapping host targets provides guidance for design of new host-directed therapeutic agents to counter EHEC infection.

IMPORTANCE
Enterohemorrhagic
Escherichia coli
(EHEC) has two critical virulence factors—a type III secretion system (T3SS) and Shiga toxins (Stxs)—that are required for colonizing the intestine and causing diarrheal disease. We screened a genome-wide collection of CRISPR mutants derived from intestinal epithelial cells and identified mutants with enhanced survival following EHEC infection. Many had mutations that disrupted synthesis of a subset of lipids (sphingolipids) that includes the Stx receptor globotriaosylceramide (Gb3) and hence protect against Stx intoxication. Unexpectedly, we found that sphingolipids also mediate early events associated with T3SS pathogenicity. Since antibiotics are contraindicated for the treatment of EHEC, therapeutics targeting sphingolipid biosynthesis are a promising alternative, as they could provide protection against both of the pathogen’s key virulence factors.