bluuebunny/crossref_metadata_2025 huggingface dataset:
Resource manipulation through experimental defoliation has legacy effects on allocation to reproductive and vegetative organs inQuercus ilex
Authors: Le Roncé Iris , Toïgo Maude , Dardevet Elia , Venner Samuel , Limousin Jean-Marc , Chuine Isabelle
Published: July 2020

Background and Aims

In plants, high costs of reproduction during some years can induce trade-offs in resource allocation with other functions such as growth, survival and resistance against herbivores or extreme abiotic conditions, but also with subsequent reproduction. Such trade-offs might also occur following resource shortage at particular moments of the reproductive cycle. Because plants are modular organisms, strategies for resource allocation to reproduction can also vary among hierarchical levels. Using a defoliation experiment, our aim was to test how allocation to reproduction was impacted by resource limitation.

Methods

We applied three levels of defoliation (control, moderate and intense) to branches of eight Quercus ilex trees shortly after fruit initiation and measured the effects of resource limitation induced by leaf removal on fruit development (survival, growth and germination potential) and on the production of vegetative and reproductive organs the year following defoliation.

Key Results

We found that defoliation had little impact on fruit development. Fruit survival was not affected by the intense defoliation treatment, but was reduced by moderate defoliation, and this result could not be explained by an upregulation of photosynthesis. Mature fruit mass was not affected by defoliation, nor was seed germination success. However, in the following spring defoliated branches produced fewer shoots and compensated for leaf loss by overproducing leaves at the expense of flowers. Therefore, resource shortage decreased resource allocation to reproduction the following season but did not affect sex ratio.

Conclusions

Our results support the idea of a regulation of resource allocation to reproduction beyond the shoot scale. Defoliation had larger legacy effects than immediate effects.
Longest incubation period of Mycobacterium chimaera infection after cardiac surgery
Authors: Vendramin Igor , Peghin Maddalena , Tascini Carlo , Livi Ugolino
Published: July 2020

Mycobacterium chimaera infections have been associated with contamination of a heater–cooler unit used during cardiopulmonary bypass procedures since 2006. Mycobacterium chimaera is a slow-growing non-tuberculous mycobacterium responsible for an infection, which is difficult to treat and has often a devastating course. Until now, M. chimaera infection has been shown to occur up to 8 years after operation. We report a patient presenting with an aortic pseudoaneurysm who developed M. chimaera infection 12 years after repair of an acute type A aortic dissection with graft replacement of the ascending aorta and stent-grafting of the arch. As far as we know, this is the case with the longest incubation period of M. chimaera infection. The present experience indicates that all patients who underwent open heart procedures since 2006 with such heater–cooler unit model should be closely followed up regardless of time of index surgery.
The Phenotypic Consequences of Genetic Divergence between Admixed Latin American Populations: Antioquia and Chocó, Colombia
Authors: Chande Aroon T , Rishishwar Lavanya , Ban Dongjo , Nagar Shashwat D , Conley Andrew B , Rowell Jessica , Valderrama-Aguirre Augusto E , Medina-Rivas Miguel A , Jordan I King
Published: July 2020

Genome-wide association studies have uncovered thousands of genetic variants that are associated with a wide variety of human traits. Knowledge of how trait-associated variants are distributed within and between populations can provide insight into the genetic basis of group-specific phenotypic differences, particularly for health-related traits. We analyzed the genetic divergence levels for 1) individual trait-associated variants and 2) collections of variants that function together to encode polygenic traits, between two neighboring populations in Colombia that have distinct demographic profiles: Antioquia (Mestizo) and Chocó (Afro-Colombian). Genetic ancestry analysis showed 62% European, 32% Native American, and 6% African ancestry for Antioquia compared with 76% African, 10% European, and 14% Native American ancestry for Chocó, consistent with demography and previous results. Ancestry differences can confound cross-population comparison of polygenic risk scores (PRS); however, we did not find any systematic bias in PRS distributions for the two populations studied here, and population-specific differences in PRS were, for the most part, small and symmetrically distributed around zero. Both genetic differentiation at individual trait-associated single nucleotide polymorphisms and population-specific PRS differences between Antioquia and Chocó largely reflected anthropometric phenotypic differences that can be readily observed between the populations along with reported disease prevalence differences. Cases where population-specific differences in genetic risk did not align with observed trait (disease) prevalence point to the importance of environmental contributions to phenotypic variance, for both infectious and complex, common disease. The results reported here are distributed via a web-based platform for searching trait-associated variants and PRS divergence levels at http://map.chocogen.com (last accessed August 12, 2020).
Rare deleterious BUB1B variants induce premature ovarian insufficiency and early menopause
Authors: Chen Qing , Ke Hanni , Luo Xuezhen , Wang Lingbo , Wu Yanhua , Tang Shuyan , Li Jinsong , Jin Li , Zhang Feng , Qin Yingying , Chen Xiaojun
Published: July 2020

Losing of ovarian functions prior to natural menopause age causes female infertility and early menopause. Premature ovarian insufficiency (POI) is defined as the loss of ovarian activity before 40 years of age. Known genetic causes account for 25–30% of POI cases, demonstrating the high genetic heterogeneity of POI and the necessity for further genetic explorations. Here we conducted genetic analyses using whole-exome sequencing in a Chinese non-syndromic POI family with the affected mother and at least four affected daughters. Intriguingly, a rare missense variant of BUB1B c.273A>T (p.Gln91His) was shared by all the cases in this family. Furthermore, our replication study using targeted sequencing revealed a novel stop-gain variant of BUB1B c.1509T>A (p.Cys503*) in one of 200 sporadic POI cases. Both heterozygous BUB1B variants were evaluated to be deleterious by multiple in silico tools. BUB1B encodes BUBR1, a crucial spindle assembly checkpoint component involved in cell division. BUBR1 insufficiency may induce vulnerability to oxidative stress. Therefore, we generated a mouse model with a loss-of-function mutant of Bub1b, and also employed D-galactose-induced aging assays for functional investigations. Notably, Bub1b+/− female mice presented late-onset subfertility, and they were more sensitive to oxidative stress than wild-type female controls, mimicking the clinical phenotypes of POI cases affected by deleterious BUB1B variants. Our findings in human cases and mouse models consistently suggest, for the first time, that heterozygous deleterious variants of BUB1B are involved in late-onset POI and related disorders.
Thoracoscopic sleeve segmentectomy for bipulmonal non-small-cell lung cancer with curative approach
Authors: Herrmann Dominik , Gencheva-Bozhkova Plamena , Oggiano Melanie , Hecker Erich
Published: July 2020

A patient with simultaneous bilateral non-small-cell lung cancer underwent a thoracoscopic sleeve segmentectomy on the right side to avoid lobectomy in curative approach. The patient also had a second, left-sided tumour requiring at least a left-sided sleeve upper lobectomy for complete resection. In anticipation of the second pulmonary resection in a patient whose lung function was already impaired by the first operation, we opted for a thoracoscopic approach with fast recovery. The left-sided operation was performed 60 days after the right-sided sleeve segmentectomy without any complications.
Proportional multistate lifetable modelling of preventive interventions: concepts, code and worked examples
Authors: Blakely Tony , Moss Rob , Collins James , Mizdrak Anja , Singh Ankur , Carvalho Natalie , Wilson Nick , Geard Nicholas , Flaxman Abraham
Published: July 2020

Burden of Disease studies—such as the Global Burden of Disease (GBD) Study—quantify health loss in disability-adjusted life-years. However, these studies stop short of quantifying the future impact of interventions that shift risk factor distributions, allowing for trends and time lags. This methodology paper explains how proportional multistate lifetable (PMSLT) modelling quantifies intervention impacts, using comparisons between three tobacco control case studies [eradication of tobacco, tobacco-free generation i.e. the age at which tobacco can be legally purchased is lifted by 1 year of age for each calendar year) and tobacco tax]. We also illustrate the importance of epidemiological specification of business-as-usual in the comparator arm that the intervention acts on, by demonstrating variations in simulated health gains when incorrectly: (i) assuming no decreasing trend in tobacco prevalence; and (ii) not including time lags from quitting tobacco to changing disease incidence. In conjunction with increasing availability of baseline and forecast demographic and epidemiological data, PMSLT modelling is well suited to future multiple country comparisons to better inform national, regional and global prioritization of preventive interventions. To facilitate use of PMSLT, we introduce a Python-based modelling framework and associated tools that facilitate the construction, calibration and analysis of PMSLT models.
Understanding the experiences of self-injurious behavior in autism spectrum disorder: Implications for monitoring technology design
Authors: Cantin-Garside Kristine D , Nussbaum Maury A , White Susan W , Kim Sunwook , Kim Chung Do , Fortes Diogo M G , Valdez Rupa S
Published: July 2020

Objective

Monitoring technology may assist in managing self-injurious behavior (SIB), a pervasive concern in autism spectrum disorder (ASD). Affiliated stakeholder perspectives should be considered to design effective and accepted SIB monitoring methods. We examined caregiver experiences to generate design guidance for SIB monitoring technology.

Materials and Methods

Twenty-three educators and 16 parents of individuals with ASD and SIB completed interviews or focus groups to discuss needs related to monitoring SIB and associated technology use.

Results

Qualitative content analysis of participant responses revealed 7 main themes associated with SIB and technology: triggers, emotional responses, SIB characteristics, management approaches, caregiver impact, child/student impact, and sensory/technology preferences.

Discussion

The derived themes indicated areas of emphasis for design at the intersection of monitoring and SIB. Systems design at this intersection should consider the range of manifestations of and management approaches for SIB. It should also attend to interactions among children with SIB, their caregivers, and the technology. Design should prioritize the transferability of physical technology and behavioral data as well as the safety, durability, and sensory implications of technology.

Conclusions

The collected stakeholder perspectives provide preliminary groundwork for an SIB monitoring system responsive to needs as articulated by caregivers. Technology design based on this groundwork should follow an iterative process that meaningfully engages caregivers and individuals with SIB in naturalistic settings.
Qualitative synthesis of temperate bat responses to silvicultural treatments—where do we go from here?
Authors: Loeb Susan C
Published: July 2020

Most bat species depend on forests for roosting, foraging, and drinking during part or all of their life cycles. Many of the world’s forests are managed using a variety of silvicultural treatments and, over the past 40 years, researchers have studied the responses of bats to these treatments. I carried out a qualitative synthesis of the literature on roosting and foraging responses of temperate insectivorous bats to silvicultural treatments at the stand level to determine what treatments may be most compatible with conservation and to guide future research. Eighty-eight studies from Canada, the United States, Europe, Australia, and New Zealand, met review criteria. Based on my results, foraging and commuting habitat use was less affected by changes in forest structure and composition than roost habitat use. Mid-rotation treatments that reduce clutter while retaining overstory structure (e.g., thinning and fire) had more neutral and positive effects than treatments that removed all or most of the overstory. Based on an examination of the methods and assumptions of the 88 studies included in this review, I conclude that future studies should: 1) strive to account for treatment effects on detection probability of bats when using acoustic detectors; 2) examine responses of bats to silvicultural treatments outside the maternity season; 3) examine demographic and physiological responses to silvicultural treatments in addition to habitat use to fully understand the effects of these treatments on bat populations; and 4) use stand-level data to model forest management effects across large landscapes and over long time periods.
Characterization of gamma irradiation-induced mutations in Arabidopsis mutants deficient in non-homologous end joining
Authors: Du Yan , Hase Yoshihiro , Satoh Katsuya , Shikazono Naoya
Published: July 2020

To investigate the involvement of the non-homologous end joining (NHEJ) pathway in plant mutagenesis by ionizing radiation, we conducted a genome-wide characterization of the mutations induced by gamma rays in NHEJ-deficient Arabidopsis mutants (AtKu70−/− and AtLig4−/−). Although both mutants were more sensitive to gamma rays than the wild-type control, the AtKu70−/− mutant was slightly more sensitive than the AtLig4−/− mutant. Single-base substitutions (SBSs) were the predominant mutations in the wild-type control, whereas deletions (≥2 bp) and complex-type mutations [i.e. more than two SBSs or short insertion and deletions (InDels) separated by fewer than 10 bp] were frequently induced in the mutants. Single-base deletions were the most frequent deletions in the wild-type control, whereas the most common deletions in the mutants were 11–30 bp. The apparent microhomology at the rejoined sites of deletions peaked at 2 bp in the wild-type control, but was 3–4 bp in the mutants. This suggests the involvement of alternative end joining and single-strand annealing pathways involving increased microhomology for rejoining DNA ends. Complex-type mutations comprising short InDels were frequently detected in the mutants, but not in the wild-type control. Accordingly, NHEJ is more precise than the backup pathways, and is the main pathway for rejoining the broken DNA ends induced by ionizing radiation in plants.
A blueberry MIR156a–SPL12 module coordinates the accumulation of chlorophylls and anthocyanins during fruit ripening
Authors: Li Xuyan , Hou Yanming , Xie Xin , Li Hongxue , Li Xiaodong , Zhu Yan , Zhai Lulu , Zhang Chunyu , Bian Shaomin
Published: July 2020

Color change is an important event during fruit maturation in blueberry, usually depending on chlorophyll degradation and anthocyanin accumulation. MicroRNA156 (miR156)–SPL modules are an important group of regulatory hubs involved in the regulation of anthocyanin biosynthesis. However, little is known regarding their roles in blueberry or in chlorophyll metabolism during color change. In this study, a MIR156 gene (VcMIR156a) was experimentally identified in blueberry (Vaccinium corymbosum). Overexpression of VcMIR156a in tomato (Solanum lycopersicum) enhanced anthocyanin biosynthesis and chlorophyll degradation in the stem by altering pigment-associated gene expression. Further investigation indicated that the VcSPL12 transcript could be targeted by miR156, and showed the reverse accumulation patterns during blueberry fruit development and maturation. Noticeably, VcSPL12 was highly expressed at green fruit stages, while VcMIR156a transcripts mainly accumulated at the white fruit stage when expression of VcSPL12 was dramatically decreased, implying that VcMIR156a–VcSPL12 is a key regulatory hub during fruit coloration. Moreover, VcSPL12 decreased the expression of several anthocyanin biosynthetic and regulatory genes, and a yeast two-hybrid assay indicated that VcSPL12 interacted with VcMYBPA1. Intriguingly, expression of VcSPL12 significantly enhanced chlorophyll accumulation and altered the expression of several chlorophyll-associated genes. Additionally, the chloroplast ultrastructure was altered by the expression of VcMIR156a and VcSPL12. These findings provide a novel insight into the functional roles of miR156–SPLs in plants, especially in blueberry fruit coloration.
Halakhic Flexibility and Communal Unity: R. Marcus Horovitz and the Schächtfrage
Authors: Skloot Joseph A
Published: July 2020

Unlike his mentor, R. Esriel Hildesheimer, and his chief antagonist, R. Samson Raphael Hirsch, R. Marcus Horovitz, the “communal Orthodox rabbi” (orthodoxer Gemeinderabbiner) of Frankfurt am Main at the end of the nineteenth century, has received relatively little scholarly attention. Horovitz was both a creative halakhic mind and a passionate communal leader devoted to Jewish unity at a time of intense ideological and political division. This article considers Horovitz’s analysis of the halakhic permissibility of stunning an animal with a blow to the head after slaughter, a practice that was being advanced by animal protection groups in Switzerland and Germany at the time. In a lengthy responsum on the topic, after a thorough reading of halakhic sources, Horovitz argued that the practice was permissible and called for a united Jewish response. The responsum illuminates both the virtuosity of its under-studied author and the complex social and political forces faced by Orthodox rabbis at the time of the Schächtfrage (the controversy over the legality of kosher animal slaughter in German-speaking lands).
Design, creation and in vitro testing of a reduced immunogenicity humanized anti-CD25 monoclonal antibody that retains functional activity
Authors: Stickler Marcia , Reddy Anita , Xiong Joanna M , Wong Melanie H , Akamatsu Yoshiko , Hinton Paul R , Harding Fiona A
Published: July 2020

Humanized and fully human sequence-derived therapeutic antibodies retain the capacity to induce anti-drug antibodies. Daclizumab (humanized version of the murine anti-Tac antibody; E.HAT) was selected for a proof of concept application of engineering approaches to reduce potential immunogenicity due to its demonstrated immunogenicity in the clinic. Reduced immunogenicity variants of E.HAT were created by identifying and modifying a CD4+ T cell epitope region in the VH region. Variant epitope region peptides were selected for their reduced capacity to induce CD4+ T cell proliferative responses in vitro. Variant antibody molecules were created, and CD25 affinity and potency were similar to the unmodified parent antibody. Fab fragments from the variant antibodies induced a lower frequency and magnitude of responses in human peripheral blood mononuclear cells proliferation tests. By the empirical selection of two amino acid mutations, fully functional humanized E.HAT antibodies with reduced potential to induce immune responses in vitro were created.
The distributions by foreign trusts to Italian tax residence beneficiaries: the new rules
Authors: Belluzzo Luigi
Published: July 2020

New rules in Italy are now reshaping years of discussion about the use of non-tax resident trusts. Although the new law places certain interpretative issues, in the following article, the author analyses the main concepts and the impact of Article 13 of Law Decree 124/2019 in connection with guidelines previously issued by the Italian Tax Office and circular newsletter 61/E/2010 in particular. For non-Italian resident trusts, the distinction between capital and income, within the Italian meaning and according to the new (tax) assumption also related to black-listed income, is of paramount importance as the new rules set the tax treatment for trust attributions to Italian tax resident trust beneficiaries.
When is a trustee's decision momentous and is momentousness sufficient?
Authors: Alexander Stephen , Hooper Katie
Published: July 2020

How should a trustee judge whether or not a decision is momentous, justifying an application for a blessing on Public Trustee v Cooper principles and what will the Court’s approach be if the decision put before it is, in fact, routine in nature? If a decision may be properly characterised as momentous, when will the court nonetheless refuse to bless it and to how much scrutiny will the decision be subject in this regard? These are questions with which the Royal Court of Jersey has had to grapple in two recent decisions, and those decisions provide useful lessons to trustees.
CE: PANDAS: Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infection
Authors: Pabst Christine , Subasic Kim
Published: July 2020

If undiagnosed and untreated, pediatric autoimmune neuropsychiatric disorders associated with streptococcal infection (PANDAS) can suddenly and drastically disrupt the lives of previously healthy children and their families. The key to prompt diagnosis of PANDAS and its appropriate treatment is provider awareness that streptococcal infection may present with neuropsychiatric symptoms. The authors discuss the signs and symptoms that characterize PANDAS, as well as its presumed pathogenesis, and illustrate, through a composite case history, a symptom presentation, diagnostic journey, treatment course, and recovery that is representative of many PANDAS cases.
Erythematous Geometric Patch on Back
Authors: Laborada Jennifer , Jacob Sharon E.
Published: July 2020

Teledermatology describes dermatologic medical services and study review provided through telecommunication technology. The following is a teledermatology case of an erythematous geometric patch on the middle and lower back.
Subungual Blue-Gray Linear Discoloration and the Curette Extraction Technique
Authors: Chung Michael Y. , Macknet Kenneth D. , Jacob Sharon E.
Published: July 2020

Teledermatology is a term to describe the provision of dermatologic medical services through telecommunication technology. This is a case of blue-gray linear discoloration under the nail of the little finger.
Hidradenitis Suppurativa and Scrotal Elephantiasis Case Report
Authors: Snyder Stephanie N. , Kolli Sree S. , Hughes Olivia B. , Pichardo Rita O.
Published: July 2020

Scrotal elephantiasis occasionally presents in conjunction with hidradenitis suppurativa (HS). A 39-year-old morbidly obese African American man, with a previous smoking history, has a 20-year history of HS complicated by a 3-year history of scrotal elephantiasis. His Hurley Stage III HS affects the scrotum, penis, lower abdomen, bilateral groin, and buttock regions. Although his scrotal edema is likely attributed to his history of HS, other causes were ruled out. A computed tomography scan of pelvis with intravenous contrast revealed edematous enlargement of the scrotum and multiple inflammatory abscesses consistent with HS. His condition was complicated by development of infection of the scrotal, perineal, and penile areas. He is currently on adalimumab 40 mg weekly and uses silvadene 1% cream topically. Improvement of his HS has been attributed to the current medical regimen and weight loss. He is responding well to implemented adalimumab for HS with no adverse effects reported. He has undergone several irrigation and debridement procedures for scrotal elephantiasis with success. He is currently preparing for gastric bypass surgery and lumpectomy after this procedure.
Development and Implementation of a Nurse-Led Home Phototherapy Program for Challenging Chronic Skin Conditions
Authors: Matthews Sarah W. , Sherman Karen J. , Chien Andy J.
Published: July 2020

Chronic skin conditions pose complex treatment challenges, and treatment adherence issues are a common problem. Home phototherapy is a well-documented, effective treatment for chronic skin conditions such as psoriasis and atopic dermatitis. Nonetheless, its effectiveness is dependent on patient self-management at home, and lack of adherence to complex prescribed treatment protocols occurs frequently. Additional problems that can occur include clinical teams failing to address patient concerns or treatment challenges with home phototherapy or failing to increase or modify therapy when treatments are not meeting therapeutic goals. This phenomenon is referred to as clinical inertia. The aims of this article are to (a) describe the development and implementation of a nurse-led home phototherapy program designed to both prevent clinical inertia and support patients' success in learning self-management for their chronic skin conditions at home and (b) outline the study protocol designed to evaluate the health outcomes and clinical resource utilization from the home phototherapy program.
Could It Be Pneumonia? Lung Ultrasound in Children With Low Clinical Suspicion for Pneumonia
Authors: Scheier Eric , Levick Nadine , Peled Julia , Balla Uri
Published: July 2020

Background:

Community-acquired pneumonia (CAP) is a significant cause of pediatric morbidity and mortality worldwide. Emergency department point of care ultrasound (POCUS) is a first-line modality for diagnosis of CAP. The current coronavirus disease 2019 pandemic creates a unique opportunity to incorporate lung POCUS into the evaluation of a broader range of children. It has increased the utility of lung POCUS in both evaluation and follow-up of pediatric coronavirus cases. An increased use of lung POCUS creates an opportunity for earlier diagnosis while allowing the opportunity for overdiagnosis of small infiltrates and atelectasis. We collated a case series to demonstrate the benefit of lung POCUS in a very broad range of children.

Methods:

We collected a case series of 5 patients between December 2018 and December 2019 who presented nonclassically and were diagnosed with CAP on POCUS by a pediatric emergency physician.

Conclusion:

Routine lung POCUS in ill children will allow treating physicians to identify and follow a pulmonary infiltrate consistent with CAP quickly. We anticipate that early and more frequent use of POCUS and earlier diagnosis of CAP may improve outcomes by decreasing healthcare encounters within the same illness and by reducing the incidence of late sequelae of pneumonia such as empyema and effusions. However, we acknowledge that this may come at the expense of the overtreatment of viral infiltrates and atelectasis. Further study is required to improve the specificity of lung POCUS in the evaluation of CAP.
Severe intimate partner violence is associated with all-cause mortality among women living with HIV
Authors: Closson Kalysha , McLinden Taylor , Parry Rebeccah , Lee Melanie , Gibbs Andrew , Kibel Mia , Wang Lu , Trigg Jason , Braitstein Paula , Pick Neora , Parashar Surita , Montaner Julio S.G. , Kaida Angela , Hogg Robert S.
Published: July 2020

Objective:

To examine the independent association between intimate partner violence (IPV) severity and all-cause mortality among women living with HIV (WLHIV).

Design:

Cross-sectional questionnaire linked to longitudinal vital statistics data.

Methods:

We examined the lifetime prevalence of IPV and age-standardized all-cause mortality rates by IPV severity reported by WLHIV. Lifetime IPV (emotional/verbal, physical, or sexual) severity was assessed as a categorical variable: no history of any IPV (none); experienced one or two forms of IPV (moderate); or experienced all three forms of IPV (severe IPV). Two separate logistic regression models examined associations between any IPV (vs. none) as well as IPV severity (none vs. moderate, severe) and all-cause mortality.

Results:

At the time of interview (2007–2010), 260 participants self-identified as women with a median (Q1–Q3) age of 41 years (35–46). Of these women, the majority were unemployed (85%), 59% reported any IPV and 24% reported severe IPV. Of the 252 women followed until 31 December 2017, 25% (n = 63) died. Age-standardized all-cause mortality rates for WLHIV who experienced severe IPV were two-times higher than women with no history of IPV (44.7 per 1000 woman-years vs. 20.9 per 1000 woman-years). After adjustment for confounding, experiences of severe IPV (vs. none) were significantly associated with all-cause mortality (aOR = 2.42, 95% CI = 1.03–5.70).

Conclusion:

Although we found that any lifetime experience of IPV was not associated with all-cause mortality, women ever experiencing severe IPV were significantly more likely to die during the study period. This may suggest a need for increased trauma- and violence-aware approaches.
Link prediction in real-world multiplex networks via layer reconstruction method
Authors: Abdolhosseini-Qomi Amir Mahdi , Jafari Seyed Hossein , Taghizadeh Amirheckmat , Yazdani Naser , Asadpour Masoud , Rahgozar Maseud
Published: July 2020

Networks are invaluable tools to study real biological, social and technological complex systems in which connected elements form a purposeful phenomenon. A higher resolution image of these systems shows that the connection types do not confine to one but to a variety of types. Multiplex networks encode this complexity with a set of nodes which are connected in different layers via different types of links. A large body of research on link prediction problem is devoted to finding missing links in single-layer (simplex) networks. In recent years, the problem of link prediction in multiplex networks has gained the attention of researchers from different scientific communities. Although most of these studies suggest that prediction performance can be enhanced by using the information contained in different layers of the network, the exact source of this enhancement remains obscure. Here, it is shown that similarity w.r.t. structural features (eigenvectors) is a major source of enhancements for link prediction task in multiplex networks using the proposed layer reconstruction method and experiments on real-world multiplex networks from different disciplines. Moreover, we characterize how low values of similarity w.r.t. structural features result in cases where improving prediction performance is substantially hard.
New material ofEpiaceratheriumand a new species ofMesaceratheriumclear up the phylogeny of early Rhinocerotidae (Perissodactyla)
Authors: Tissier Jérémy , Antoine Pierre-Olivier , Becker Damien
Published: July 2020

Reduction of the anterior dentition (i.e. incisors and canines) is a major adaptative trait of the Rhinocerotidae among Perissodactyla. However, the corresponding evolutionary sequence was lacking a robust phylogenetic frame to support it thus far. Here, we describe a new Oligocene species of Rhinocerotinae,Mesaceratheriumsp. nov. from the Swiss locality of Bumbach (MP25 reference level). In addition, we identify the only known complete mandible ofEpiaceratherium magnum, an early-branching rhinocerotid, as well as one of the earliest European rhinoceroses. We also compute a parsimony analysis based on morpho-anatomical characters to assess their phylogenetic position and elucidate the early evolution of the Rhinocerotidae. Our results allow to propose a new scenario for the reduction of the anterior dentition in which upper and lower dentitions would have undergone distinct evolutionary trajectories.
A family of T6SS antibacterial effectors related to L,D-transpeptidases targets the Peptidoglycan
Authors: Sibinelli de Sousa Stephanie , Takuno Hespanhol Julia , Matsuyama Bruno , Mesnage Stephane , Nicastro Gianlucca , Sanchez Limache Daniel Enrique , Francisco de Souza Robson , Bayer Santos Ethel
Published: July 2020

Type VI secretion systems (T6SSs) are contractile nanomachines widely used by bacteria to intoxicate competitors. Salmonella Typhimurium encodes a T6SS within the Salmonella pathogenicity island 6 (SPI-6) that is used during competition against species of the gut microbiota. We characterized a new SPI-6 T6SS antibacterial effector named Tlde1 (type VI L,D-transpeptidase effector 1). Tlde1 is toxic in target-cell periplasm and its toxicity is neutralized by co-expression with immunity protein Tldi1 (type VI L,D-transpeptidase immunity 1). Time-lapse microscopy revealed that intoxicated cells display altered cell division and lose cell envelope integrity. Bioinformatics analysis showed that Tlde1 is evolutionarily related to L,D-transpeptidases. Point mutations on conserved histidine121 and cysteine131 residues eliminated toxicity. Co-incubation of purified recombinant Tlde1 and peptidoglycan tetrapeptides showed that Tlde1 displays both L,D-carboxypeptidase activity by cleaving GM-tetrapeptides between meso-diaminopimelic acid3 and D-alanine4, and L,D-transpeptidase exchange activity by replacing D-alanine4 for a non-canonical D-amino acid. Tlde1 constitutes a new family of T6SS effectors widespread in Proteobacteria. This work increases our knowledge about the bacterial effectors used in interbacterial competitions and provides molecular insight into a new mechanism of bacterial antagonism.
Assessment of mosquito insecticidal activity of bacterial extracts produced by Colombian strains
Authors: Agudelo-Restrepo Manuela , Hernández‐Quesada Martha Lucia , Yonny Sanabria-Duran Edinson , Uribe-Soto Sandra Inés , Ortiz-Reyes Adriana , Romero-Tabarez Magally
Published: July 2020

Aedes aegypti and Aedes albopictus are the major vectors for the transmission of more than 30 disease-causing viruses as dengue fever, dengue hemorragic fever, zika, yellow fever and chikungunya. Vector control is one of the important strategies used in order to fight these diseases in tropical and subtropical countries. However, mosquito control is facing a threat because of the emergence of resistance to synthetic insecticides. The aim of this study was to identify larvicidal and adulticidal activity of secondary metabolites in extracts produced by bacteria isolated from different sources in Colombia. A total of 105 extracts produced from the same number of bacteria were evaluated for their activity against fourth instar larvae and adults of A. aegypti and A. albopictus using standard protocols defined for the WHO (World Health Organization) and CDC (Control Disease Centre, USA). Six extracts showed relevant activity (more than 50% of mosquito larvae were killed after 48 hours), two of them showed to be actives against larvae of Aedes aegypti and four against larvae of Aedes albopictus. None of the extracts showed activity against the mosquitoes in adult stage. The bacteria producing active extracts were identified using the biolog ® identification system as Serratia marcescens ss marcescens, Escherichia hermannii, Serratia marcescens ss marcescens, Bacillus marisflavi, Bacillus atropheus/subtilis and Pseudomonas chlororaphis subsp. aurantiaca. In conclusion, bacterial extracts are a good source for the search of new strategies in the control of mosquitoes. Further studies to determine the compound responsible for the insecticidal activity are in progress.
Screening for urinary tract infection-causing Klebsiella pneumoniae using CHROMagar
Authors: Bakhashween Rimah , Bawazeer Abeer , Aljaser Azizah , Alsuhemy Haya , Alsharif Ghadah
Published: July 2020

Introduction. Urinary tract infections (UTIs) are considered prevalent among humans. While Klebsiella pneumoniae and Escherichia coli are commonly isolated from patients with UTIs, K. pneumoniae is more frequently isolated from specimens isolated from hospital-acquired infections.

Aim. The current study aimed to characterise and evaluate pathogenic K. pneumoniae isolated from patients suspected with a UTI at King Abdulaziz University Hospital.

Methodology. Twenty-four urine samples obtained from patients, between 12 November 2018 and 11 January 2019, were included in the study, and the microbial content was analysed via urine culture and VITEK 2 analyses.

Results. Of the 24 urine specimens, 23 samples (95.8%) yielded significant microbial growth (> 105 CFU/mL K. pneumoniae), and one sample (4.2%) yielded non-pathogenic microbial growth (< 105 CFU/mL K. pneumoniae). Of the specimens with cell counts of >105 CFU/mL, 21 samples (87.5%) were pure cultures showing the growth of a single pathogen, and three samples (12.5%) were mixed cultures, showing the growth of two or more pathogens; 10 (41.7%) samples were extended-spectrum beta-lactamase (ESBL) producers. VITEK 2 analysis showed that the most effective antibiotic was piperacillin, with 87.5% of the strains isolated in this study showing sensitivity to it, followed by gentamicin (83.3%) and ciprofloxacin (79.2%). Antibiotic susceptibility studies identified resistance against ampicillin (45.83%), trimethoprim (41.67%), and amoxicillin (25%) in the study isolates. Differential chromogenic culture media CHROMagar ESBL and CHROMagar KPC (K. pneumoniae carbapenemase) were used for rapid screening of ESBL and KPC producers. Among the 24 K. pneumoniae isolates, six isolates (25%) formed metallic blue colonies on CHROMagar ESBL, five (20.3%) were inhibited, and nine (37.5%) showed weak pigmentation. Three isolates (12.5%) formed pink colonies on CHROMagar ESBL. Seventeen isolates (70.8%) were KPC-positive, four (16.7%) showed weak pigmentation, and three (12.5%) formed pink colonies on CHROMagar KPC. The results from CHROMagar cultures agreed with those of VITEK 2 analyses.

Conclusion. Various microbial detection methods have been used in medical microbiology laboratories to identify and screen for microbial resistance in clinical specimens. VITEK 2 and CHROMagar are amongst the commonly used methods. Here, we report a possible discrepancy between the detection techniques and that the data obtained by different methods need not be synergistic. However, the use of a chromogenic medium offers a quick and accurate method for detection, enumeration, and presumptive identification of urinary tract pathogens.
Coccus Pocus 2019: A microbiology-inspired scary story competition
Authors: Efthimiou Georgios
Published: July 2020

Antibiotic resistance by pathogenic microorganisms is a major threat of our times, leading to a significant rise of serious untreatable infections, especially in hospital environments. In addition, biofilms further protect the microbes against antibiotics, detergents and the attacks of our immune system. This Halloween, we launched an exciting scary story competition, named Coccus Pocus 2019. The participants were encouraged to write a short horror sci-fi story between 500 and 2,000 words, including antimicrobial resistance and microbial biofilms. The evaluation committee that was composed of eight academics and researchers from the University of Hull and other institutions, ranked the stories according to intrigue of their plot, use of language, character description and scientific soundness. The prizes (online gift vouchers) were awarded to the three winning stories, during an awards ceremony. Feedback questionnaires were completed by the participants, which showed that they all found the competition very interesting and useful, allowing them to sharpen their creative writing skills and explore key microbiology topics. The event was communicated in the social media and blogs were posted in university bulletins and on microbiology websites. It is our ambition that the competition will be held again and again around the country, aiming to increase public awareness about the important problem of antimicrobial resistance and biofilms and boost the enthusiasm of young people about the fascinating field of microbiology.
Plasmids and temperate phages influence each other’s transfer rates
Authors: Schwyter Lukas , Igler Claudia , Hall Alex , Wendling Carolin
Published: July 2020

Accessory genes, such as antibiotic resistance genes (ARGs) can spread horizontally by mobile genetic elements, including plasmids and (temperate) bacteriophages leading to increased bacterial fitness in particular environments. In contrast to plasmids, temperate phages i.e. viruses that can incorporate their own genetic material into their host bacteria (then called lysogen) can additionally increase their hosts’ fitness through their ability to kill phage-susceptible competitors. However, in contrast to ARG-transfer by plasmids (conjugation), which has been extensively studied, ARG-transfer by phages (lysogenization) has received far less attention. Here we combined experiments using E. coli, phage lambda and the Rp4 plasmid (phage and plasmid both with an ampicillin resistance gene) and mathematical models to test which mechanism (lysogenization or conjugation) dominates under which conditions.

In the absence of selection and in two-species experiments (Donor & Recipient), conjugation was significantly more common than lysogenization. However, in three-species experiments (DonorPlasmid, DonorPhage& Recipient) lysogenization rates increased by several orders of magnitude. By using phage-friendly environments that favour phage adsorption we were able to shift the ratio between lysogens and transconjugants even further towards lysogens and in extreme-events to the extinction of transconjugants. Mathematical models additionally allowed us to investigate how starting population sizes of both donors and the recipient influence conjugation and lysogenization dynamics. Taken together, our results suggest that plasmids and temperate phages can influence each other’s transfer rates which, in the present study system, seems to be largely driven by population size effects.
Safety and passivation of faecal contamination in waste
Authors: Takaya C. , Carpenter J. , Muir R. , Brittle S. , Sarker D.K. , Cooper I.
Published: July 2020

Absorbent hygiene wastes like nappies and incontinence pads are ubiquitous in municipal and healthcare waste streams around the world as they are convenient products used in child-care and adult incontinence management. Absorbent Hygiene Product (AHP) manufacturing is resource-intensive as the products are required to be of the highest value as they are in almost-constant contact with sensitive body parts. The potential for recovering such valuable resources such as cellulose-based fibres and super-absorbent polymers for reuse in non-food sectors like the construction and wastewater industries has been considered in this study. Appropriate decontamination via chemical methods have been examined using AHPs contaminated with human-associated bacteria.

Findings suggest that for simulated AHP wastes inoculated with 108–109 CFU g-1 of human-associated bacteria like Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis, and Streptococcus pyogenes, a 1:1 ratio of 0.5% calcium hypochlorite/AHP waste is adequate to inactivate the bacteria particularly when combined with an inorganic salt for at least 60 min. Specifically, 4 to 5 log10 reductions were observed. Following such disinfection, material storage and temperatures above 25ºC minimise incidences of microbial regrowth. The disinfection protocol was not found to adversely affect the AHP quality. Overall, such findings suggest that AHP recycling is a potential alternative to current AHP waste disposal practices like incineration (with or without energy recovery) and landfilling.
Household transmission and host immune evasion factors of LA-MRSA CC398
Authors: Niklaus Sieber Raphael , Ravnholt Urth Tinna , Rhod Larsen Anders , Leo Skov Robert , Stegger Marc , Larsen Jesper
Published: July 2020

Staphylococcus aureus uses several strategies to evade the host immune reaction including expression of the genes on the immune evasion cluster (IEC), which target the innate immune response, and tarP, which alters the structure of the bacterial wall teichoic acids to avoid binding of host antibodies. IEC is carried on an ΦSa3 prophage, while the tarP gene is found located on diverse prophages. Livestock-associated methicillin-resistant S. aureus of clonal complex 398 (LA-MRSA CC398) typically lacks the IEC, but a number of Danish isolates have been found to carry the elements regardless.

In this study, whole-genome sequences of 96 isolates from humans and 45 isolates from pigs from the North Denmark Region were used to establish a maximum-likelihood phylogeny from core-genome SNPs and to investigate the prevalence of IEC and tarP. Furthermore, epidemiological and national surveillance data were used to investigate household transmission and the prevalence of IEC in LA-MRSA CC398 isolates from the general population. The study documents several independent acquisitions of IEC on distinct ΦSa3 prophages in humans and an almost 3-fold higher human-to-human transmission rate of LA-MRSA CC398 in households with strains carrying IEC than in households with strains lacking it. No such effect was found for tarP, which is widespread among LA-MRSA CC398 isolates from both humans and pigs. Moreover, IEC also seems to promote spread of LA-MRSA CC398 in the general population. Thus, LA-MRSA CC398 is capable of re-adapting to the human host by acquisition of human-specific immune evasion factors encoded on mobile genetic elements.
Investigating the association between organic acids and phenotypic alterations of avian pathogenic Escherichia coli
Authors: Fallata Ghaith , Wall Doanl
Published: July 2020

The excessive use of antibiotics in agriculture is routinely described as a major contributor to bacterial resistance. Globally, antibiotics are widely used as growth supplements in livestock. This has led to concerns regarding human-use antibiotics in food and food-producing animals. Lately, organic acids (OAs) such as propionic acid (PA) and formic acid (FA) have been increasingly used as alternative antimicrobials or preservatives instead of antibiotics. These are particularly efficient at removing salmonella.

Recently, we have shown that exposure of a Crohn’s Disease associated bacterial pathotype, Adherent-invasive Escherichia coli (AIEC), to PA significantly alters its phenotype resulting in increased adhesion and invasion of epithelial cells and increased persistence through biofilm formation. AIEC are both evolutionarily and phylogenetically related to avian pathogenic Escherichia coli (APEC), however the virulence mechanisms of APEC in poultry remain unclear. The widespread use of OAs as growth supplements and antimicrobials in the poultry industry is a rising concern due to the ability of OAs to alter the bacterial pathotype. In this study, we examined the effect of FA on the phenotype of APEC. We observed that following FA-exposure, APEC showed an increased ability to adhere to and invade human intestinal epithelial cells and form better biofilms both aerobically and anaerobically. Worryingly, these isolates also showed an increased resistance to several antibiotics. These results suggest that the increasing use of alternative antimicrobial such as FA in the poultry industry may lead to APEC strains that are increasingly virulent towards human cells with a potential for increased horizontal transmission