bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of a Europe‐wide Survey on Paediatric Nutrition Training
Authors: Broekaert Ilse J. , Jahnel Joerg , Moes Nicolette , van der Doef Hubert , Hojsak Iva , Tzivinikos Christos
Published: February 2020

Commissioned by the European Society for Paediatric Gastroenterology, Hepatology and Nutrition (ESPGHAN), we investigated how European physicians training in these fields are educated in nutrition. A survey on time spent in nutrition training, composition of multidisciplinary nutrition teams, and topics covered during training enrolled 50 participants. A median of 20% of training time was spent on nutrition training during fellowship. Fourteen (28%) had regular nutrition teaching. Thirty‐four (68%) were part of a multidisciplinary nutrition team. Twelve (24%) used the ESPGHAN syllabus. Most frequent topics during nutrition training were diagnosis/investigation of failure to thrive, indications/contraindications for enteral feeds, and benefits/risks of enteral/parenteral nutrition. Twenty‐seven (54%) had taken a formal nutrition course. Nutrition training in Europe varies and the ESPGHAN training syllabus is not yet implemented Europe‐wide. ESPGHAN nutrition summer schools, and Web‐based learning may provide appropriate training. We suggest that all patients necessitating nutritional care be treated by multidisciplinary nutrition teams.
Microbiologically Documented Bloodstream Infection in Children With Malignancies: A Single-center Experience
Authors: Tang Yue-Jia , Su Ying , Cao Qing , Gao Yi-Jin
Published: February 2020

Background:

Bloodstream infection (BSI) remains a considerable cause of morbidity and mortality for cancer patients. With a better understanding of it, better methods can be used. The primary objective of this study was to describe the characteristics of BSIs in our institution, and the second was to determine the possible risk factors associated with them.

Materials and Methods:

Data of cancer patients from 2009 to 2015 at our institution were included. Medical information and blood cultures were analyzed to determine the BSI rate. The χ2 and Fisher exact tests were used for categorical data and to determine risk factors associated with BSIs and pathogens.

Results:

A total of 565 (8.6%) events were diagnosed with BSIs. Although Gram-negative bacteria (52.6%) were the most commonly isolated pathogens, Gram-positive microorganisms (45.0%) were also prevalent. Oral and gastrointestinal organisms were common. Pathogens were more likely to be identified in patients with central venous catheters and in patients with prolonged neutropenia (P<0.05).

Conclusions:

This study provides updated epidemiology in BSIs and helps with the prevention and management of suspected BSIs in vulnerable patients. Better anti-infection therapy could be provided to these patients based on the isolated pathogens.
Childhood Extracorporeal Membrane Oxygenation Survivors: Parents Highlight Need for Structured Follow-Up and Support After Hospital Discharge
Authors: Wray Jo , Kakat Suzan , Brown Katherine , O’Callaghan Maura , Thiruchelvam Timothy , Hoskote Aparna
Published: February 2020

Objectives:

To examine parental experiences of childhood extracorporeal membrane oxygenation survivors to understand: 1) the problems children faced and 2) the support received following hospital discharge.

Design:

Single-center descriptive study.

Setting:

Nationally commissioned center for neonatal and pediatric extracorporeal membrane oxygenation.

Patients:

All traceable survivors less than 18 years old who received extracorporeal membrane oxygenation from January 1998 to April 2013.

Intervention:

Anonymized postal questionnaire completed by parents of extracorporeal membrane oxygenation survivors.

Measurements and Main Results:

Parent-reported developmental problems, follow-up, and the degree of satisfaction with any follow-up experience. Parents of 89 of 366 extracorporeal membrane oxygenation survivors (24%) responded. Sixty-six (74%) reported having developmental concerns about their child, including speech and language (n = 32; 36%), concentration (n = 28; 31%), movement/physical difficulties (n = 26; 29%), and educational difficulties (n = 22; 25%); 46 (52%) indicated that their child had difficulties across multiple domains. Twenty-one (34%) of those with one or more reported developmental concerns were not receiving any follow-up. However, 57 (64%) attended our 1-year follow-up extracorporeal membrane oxygenation clinic and 54 of 57 (95%) found it very useful. Three themes related to perceived need were identified from parents’ free-text comments: the need for an expert point of contact and follow-up at the extracorporeal membrane oxygenation center; more information on extracorporeal membrane oxygenation and any long-term effects; and more support from, and easier access to, community specialist services.

Conclusions:

A proportion of children who have undergone extracorporeal membrane oxygenation treatment have needs that are not being met, with variable access to service provision. Structured follow-up after discharge would enable early identification of developmental concerns, permit early referral or intervention, and provide support to families. Education and sharing of information about extracorporeal membrane oxygenation with general practitioners/family physicians, community professionals, and schools are essential.
Outcomes of Children Who Present to the Emergency Department After Hematopoietic Cell Transplantation
Authors: Bergmann Kelly R. , Orchard Paul J. , Roback Mark G. , Gaillard Philippe , Furnival Ronald A.
Published: February 2020

Objectives

Our primary objective was to describe emergency department (ED) presentation, treatment, and outcomes for children after hematopoietic cell transplantation (HCT). Our secondary objective was to identify factors associated with serious infection in this population.

Methods

This is a retrospective review of HCT patients who presented to our university children's hospital ED from January 1, 2011, to June 30, 2013. Emergency department presentation, treatment, and outcomes were described. Descriptive statistics were used to compare children with definite serious infection with those without serious infection. Multiple binary logistic regression was performed for risk factors associated with definite serious infection.

Results

Fifty-four HCT patients (132 encounters) presented to our ED. Most were transplanted for a malignant (46%) or metabolic (36%) diagnosis and were recipients of bone marrow (51%) or umbilical cord blood (45%). Fever was the most common complaint (25%). Emergency department laboratory (64%) or imaging (58%) studies were frequently obtained. Admission was common (n = 70/132, 53%), with 79% (n = 55) of admissions to intensive care or bone marrow transplant units. Thirty-five encounters had definite serious infection, 5 had probable serious infection, and 92 had no serious infection. Fever (P < 0.001) and high-risk white blood cell (WBC) count of less than 5 or greater than 15 k/μL (P < 0.001) were associated with definite serious infection. Fever (odds ratio = 8.84, 95% confidence interval = 2.92–26.73) and high-risk WBC (odds ratio = 6.67, 95% confidence interval = 2.24–19.89) remained significantly associated with definite serious infection in our regression model.

Conclusions

Children presenting to the ED after HCT require extensive support and resources, with more than half requiring admission. Fever and high-risk WBC are associated with serious infection.
Physicians' Approach to Anaphylaxis in Childhood
Authors: Tuncel Tuba , Sancaklı Ozlem , Bag Ozlem , Cetin Hafize Selma , Özdoğru Emine Ece
Published: February 2020

Objectives

Anaphylaxis is a life-threatening, severe, generalized, or systemic hypersensitivity reaction. The incidence of anaphylaxis is increasing especially in pediatric age. Our aim in this study was to investigate the knowledge and attitudes of the physicians on the diagnosis and treatment of anaphylaxis.

Methods

A questionnaire form consisting of a total of 18 questions was prepared. Six questions concerned demographic data; 7 questions inquired about physician's knowledge level about treatment of anaphylaxis. In the last part, 5 different case scenarios were given, and their diagnoses and treatments were asked.

Results

A total of 120 physicians participated in the study. Of the participants, 66.7% were residents. The rate of correct answer about dose of epinephrine was 57.5%. The rates of making correct diagnoses in anaphylaxis case scenarios 1, 2, and 3 were 60%, 73.3%, and 91.7%, respectively, whereas epinephrine administration rates were 54%, 67.5%, and 92.5%, respectively. When the answers of all these questions given by the residents and specialists and among physicians who updated and did not update were compared, there were no statistically significant differences except epinephrine administration rate and its route (P < 0.05).

Conclusions

The results of the current study suggest that physicians' knowledge levels were inadequate in making the diagnosis of anaphylaxis, and physicians use epinephrine in conditions without hypotension or an undefined possible/known allergen contact. Information about epinephrine administration was partially correct. It is currently considered to be the simplest measure to have a written anaphylaxis action plan including diagnostic criteria for anaphylaxis.
Racial Disparities in Anal Cancer Screening Among Men Living With HIV: Findings From a Clinical Cohort Study
Authors: Gillis Jennifer L. , Grennan Troy , Grewal Ramandip , Ogilvie Gina , Gaspar Mark , Grace Daniel , Lofters Aisha , Raboud Janet M. , Saarela Olli , Rosenes Ron , Salit Irving E. , Burchell Ann N. ,   the OHTN Cohort Study Team
Published: February 2020

Background:

Our objective was to quantify the extent of anal cancer screening among men receiving HIV specialty care in Ontario, Canada, and evaluate factors associated with screening.

Setting:

Cross-sectional questionnaire within a multisite clinical HIV cohort.

Methods:

A questionnaire assessing knowledge and experience with human papillomavirus–associated diseases and their prevention was administered in 2016–2017 to 1677 men in the Ontario HIV Treatment Network Cohort Study. We used logistic regression to identify factors associated with having discussed screening with a health care provider and self-reported receipt of screening [digital anal rectal examinations (DARE); anal cytology or anoscopy]. Results reported as adjusted odds ratios (aORs) with 95% confidence intervals (CIs).

Results:

Forty percent of men reported ever having had anal cytology/anoscopy, and 70% had ever had DARE. After accounting for differences in age, sexual orientation, years since HIV diagnosis, previous diagnosis with AIDS, knowing someone with human papillomavirus–associated cancer, comfort discussing anal health, education, and income, the proportion screened differed by self-identified race. Compared with white men, Asian men were less likely to have discussed screening with a health care provider (aOR = 0.48; 95% CI: 0.29 to 0.80) or to have been screened by DARE (aOR = 0.27; 95% CI: 0.17 to 0.44) or anal cytology/anoscopy (aOR = 0.51; 95% CI: 0.31 to 0.83), and African, Caribbean, or black men (aOR = 0.47; 95% CI: 0.31 to 0.70) were less likely to have had DARE. Results were consistent when restricting the analyses to gay, bisexual, and other men who have sex with men.

Conclusion:

Our findings highlight the potential for disparities in anal cancer screening that need to be considered when developing guidelines and screening programs to reduce the burden of anal cancer among men living with HIV and ensure health equity.
Creating Options for Difficult-to-match Kidney Transplant Candidates
Authors: de Klerk Marry , Kal-van Gestel Judith A. , van de Wetering Jacqueline , Kho Marcia L. , Middel-de Sterke Sandra , Betjes Michiel G.H. , Zuidema Willij C. , Roelen Dave , Glorie Kristiaan , Roodnat Joke I.
Published: February 2020

Background.

Most transplantation centers recognize a small patient population that unsuccessfully participates in all available, both living and deceased donor, transplantation programs for many years: the difficult-to-match patients. This population consists of highly immunized and/or ABO blood group O or B patients.

Methods.

To improve their chances, Computerized Integration of Alternative Transplantation programs (CIAT) were developed to integrate kidney paired donation, altruistic/unspecified donation, and ABO and HLA desensitization. To compare CIAT with reality, a simulation was performed, including all patients, donors, and pairs who participated in our programs in 2015–2016. Criteria for inclusion as difficult-to-match, selected-highly immunized (sHI) patient were as follows: virtual panel reactive antibody >85% and participating for 2 years in Eurotransplant Acceptable Mismatch program. sHI patients were given priority, and ABO blood group incompatible (ABOi) and/or HLA incompatible (HLAi) matching with donor-specific antigen–mean fluorescence intensity (MFI) <8000 were allowed. For long-waiting blood group O or B patients, ABOi matches were allowed.

Results.

In reality, 90 alternative program transplantations were carried out: 73 compatible, 16 ABOi, and 1 both ABOi and HLAi combination. Simulation with CIAT resulted in 95 hypothetical transplantations: 83 compatible (including 1 sHI) and 5 ABOi combinations. Eight sHI patients were matched: 1 compatible, 6 HLAi with donor-specific antigen-MFI <8000 (1 also ABOi), and 1 ABOi match. Six/eight combinations for sHI patients were complement-dependent cytotoxicity cross-match negative.

Conclusions.

CIAT led to 8 times more matches for difficult-to-match sHI patients. This offers them better chances because of a more favorable MFI profile against the new donor. Besides, more ABO compatible matches were found for ABOi couples, while total number of transplantations was not hampered. Prioritizing difficult-to-match patients improves their chances without affecting the chances of regular patients.
Olanzapine-Associated Pisa Syndrome in an Autistic Adolescent
Authors: Guler Hasan Ali , Turkoglu Serhat , Cetin Fatih Hilmi , Ucar Halit Necmi , Erdogan Yakup
Published: February 2020

Objectives

The objective of this study is to report a case of Pisa syndrome due to olanzapine use in an autistic adolescent.

Methods

The patient was a 12-year-old adolescent girl who was taking olanzapine for autism-related behavioral problems. Abnormal posture and balance problems appeared in the third month of olanzapine treatment. The patient was diagnosed as having Pisa syndrome after clinical evaluation. Biperiden was started on the patient whose complaints continued despite olanzapine treatment was stopped. Patient's complaints regressed with biperiden treatment.

Results

According to our knowledge, there is no an autistic adolescent case of Pisa syndrome previously reported in the literature. Further studies are needed to clarify the etiology and treatment of Pisa syndrome.

Conclusions

In patients with balance problems and abnormal posture as a result of olanzapine use, the clinician should keep in mind Pisa syndrome.
A systematic review of studies with clinician-rated scales on the pharmacological treatment of delusional disorder
Authors: Muñoz-Negro José Eduardo , Gómez-Sierra Francisco José , Peralta Victor , González-Rodríguez Alexandre , Cervilla Jorge A.
Published: February 2020

To collect the best available evidence and to compare the first-generation antipsychotics (FGAs) vs. the second-generation antipsychotics (SGAs) in the treatment of delusional disorder (DD). Systematic review including studies evaluating treatment response in DD using clinician-rated scales appearing in PubMed and Web of Science databases from inception till September 2019. Those studies meeting inclusion criteria were selected. Outcomes were summarized into two response categories: (1) response to treatment equal to or greater than 50% and (2) response less than 50%. Biases and quality of the studies were evaluated, and relevant data were extracted. Finally, both narrative review and quantitative synthesis were performed. The final sample included six studies (437 patients, 318 on treatment with SGAs). Antipsychotics achieved a good response in 32.3% of patients. Effectiveness differences between FGA and SGA were only marginal favouring the former. Among the most used antipsychotics, risperidone and olanzapine showed, respectively, 34.3 and 33.7% good response. Pimozide (n = 35) demonstrated a higher response rates compared with other antipsychotics. Inpatients showed the best treatment outcomes. Antipsychotics appeared to be an effective treatment in patients with DD. FGA were slightly superior to SGA. Pimozide does not seem to provide any advantage in most DD subtypes.
Three-dimensional scaling laws of cetacean propulsion characterize the hydrodynamic interplay of flukes' shape and kinematics
Authors: Ayancik Fatma , Fish Frank E. , Moored Keith W.
Published: February 2020

Cetaceans convert dorsoventral body oscillations into forward velocity with a complex interplay between their morphological and kinematic features and the fluid environment. However, it is unknown to what extent morpho-kinematic features of cetaceans are intertwined to maximize their efficiency. By interchanging the shape and kinematic variables of five cetacean species, the interplay of their flukes morpho-kinematic features is examined by characterizing their thrust, power and propulsive efficiency. It is determined that the shape and kinematics of the flukes have considerable influence on force production and power consumption. Three-dimensional heaving and pitching scaling laws are developed by considering both added mass and circulatory-based forces, which are shown to closely model the numerical data. Using the scaling relations as a guide, it is determined that the added mass forces are important in predicting the trend between the efficiency and aspect ratio, however, the thrust and power are driven predominately by the circulatory forces. The scaling laws also reveal that there is an optimal dimensionless heave-to-pitch ratioh* that maximizes the efficiency. Moreover, the optimalh* varies with the aspect ratio, the amplitude-to-chord ratio and the Lighthill number. This indicates that the shape and kinematics of propulsors are intertwined, that is, there are specific kinematics that are tailored to the shape of a propulsor in order to maximize its propulsive efficiency.
Negative feedback: ants choose unoccupied over occupied food sources and lay more pheromone to them
Authors: Wendt Stephanie , Kleinhoelting Nico , Czaczkes Tomer J.
Published: February 2020

In order to make effective collective decisions, ants lay pheromone trails to lead nest-mates to acceptable food sources. The strength of a trail informs other ants about the quality of a food source, allowing colonies to exploit the most profitable resources. However, recruiting too many ants to a single food source can lead to over-exploitation, queuing, and thus decreased food intake for the colony. The nonlinear nature of pheromonal recruitment can also lead colonies to become trapped in suboptimal decisions, if the environment changes. Negative feedback systems can ameliorate these problems. We investigated a potential source of negative feedback: whether the presence of nest-mates makes food sources more or less attractive.Lasius nigerworkers were trained to food sources of identical quality, scented with different odours. Ants fed alone at one odour. At the other odour ants fed either with other feeding nest-mates, or with dummy ants (black surface lipid-coated glass beads). Ants tended to avoid food sources at which other nest-mates were present. They also deposited less pheromone to occupied food sources, suggesting an active avoidance behaviour, and potentiating negative feedback. This effect may prevent crowding at a single food source when other profitable food sources are available elsewhere, leading to a higher collective food intake. It could also potentially protect colonies from becoming trapped in local feeding optima. However, ants did not avoid the food associated with dummy ants, suggesting that surface lipids and static visual cues alone may not be sufficient for nest-mate recognition in this context.
Erythrobacter insulae sp. nov., isolated from a tidal flat
Authors: Park Sooyeon , Chen Siyu , Yoon Jung-Hoon
Published: February 2020

A Gram-staining-negative, aerobic, non-motile and coccoid, ovoid or rod-shaped bacterial strain, designated as JBTF-M21T, was isolated from a tidal flat sediment on the Yellow Sea, Republic of Korea. The neighbour-joining phylogenetic tree based on 16S rRNA gene sequences indicated that JBTF-M21T fell within the clade comprising the type strains of species of the genus

Erythrobacter

. JBTF-M21T exhibited 16S rRNA gene sequence similarities of 97.0–98.4 % to the type strains of

Erythrobacter longus

,

Erythrobacter aquimaris

,

Erythrobacter nanhaisediminis

,

Erythrobacter vulgaris

,

Erythrobacter seohaensis

,

Erythrobacter litoralis

and

Erythrobacter citreus

and 93.7–96.6 % to the type strains of the other species of the genus

Erythrobacter

. The ANI and dDDH values between JBTF-M21T and the type strains of

E. longus

,

E. nanhaisediminis

,

E. seohaensis

and

E. litoralis

were 70.83–72.93 % and 18.0–18.8 %, respectively. Mean DNA–DNA relatedness values between JBTF-M21T and the type strains of

E. aquimaris

,

E. vulgaris

and

E. citreus

were 12–24 %. The DNA G+C content of JBTF-M21T was 57.0 mol%. JBTF-M21T contained Q-10 as the predominant ubiquinone and C18 : 1ω7c and C17 : 1ω6c as the major fatty acids. The major polar lipids ofJBTF-M21T were phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and sphingoglycolipid. Distinguishing phenotypic properties, together with the phylogenetic and genetic distinctiveness, revealed that JBTF-M21T is separated from species of the genus

Erythrobacter

with validly published names. On the basis of the data presented, strain JBTF-M21T is considered to represent a novel species of the genus

Erythrobacter

, for which the name Erythrobacter insulae sp. nov. is proposed. The type strain is JBTF-M21T (=KACC 19864T=NBRC 113584T).
Bartonella kosoyi sp. nov. and Bartonella krasnovii sp. nov., two novel species closely related to the zoonotic Bartonella elizabethae, isolated from black rats and wild desert rodent-fleas
Authors: Gutiérrez Ricardo , Shalit Tali , Markus Barak , Yuan Congli , Nachum-Biala Yaarit , Elad Daniel , Harrus Shimon
Published: February 2020

The genusBartonella(Family:Bartonellaceae; Order:Rhizobiales;Class: Alphaproteobacteria) comprises facultative intracellular Gram-negative, haemotropic, slow-growing, vector-borne bacteria. Wild rodents and their fleas harbor a great diversity of species and strains of the genusBartonella, including several zoonotic ones. This genetic diversity coupled with a fastidious nature of the organism results in a taxonomic challenge that has led to a massive collection of uncharacterized strains. Here, we report the genomic and phenotypic characterization of two strains, members of the genusBartonella(namely Tel Aviv and OE 1–1), isolated fromRattus rattusrats andSynosternus cleopatraefleas, respectively. Scanning electron microscopy revealed rod-shaped bacteria with polar pili, lengths ranging from 1.0 to 2.0 µm and widths ranging from 0.3 to 0.6 µm. OE 1–1 and Tel Aviv strains contained one single chromosome of 2.16 and 2.23 Mbp and one plasmid of 29.0 and 41.5 Kbp, with average DNA G+C contents of 38.16 and 38.47 mol%, respectively. These strains presented an average nucleotide identity (ANI) of 89.9 %.Bartonella elizabethaewas found to be the closest phylogenetic relative of both strains (ANI=90.9–93.6 %). The major fatty acids identified in both strains were C18:1ω7c, C18 : 0and C16 : 0. They differ fromB. elizabethaein their C17 : 0and C15 : 0compositions. Both strains are strictly capnophilic and their biochemical profiles resembled those of species of the genusBartonellawith validly published names, whereas differences in arylamidase activities partially assisted in their speciation. Genomic and phenotypic differences demonstrate that OE 1–1 and Tel Aviv strains represent novel individual species, closely related toB. elizabethae, for which we propose the namesBartonella kosoyisp. nov. andBartonella krasnoviisp. nov.
Weissella sagaensis sp. nov., isolated from traditional Chinese yogurt
Authors: Li Yu Qin , Tian Wen Li , Gu Chun Tao
Published: February 2020

Three Gram-stain-positive bacterial strains, designated X0750T, X0278 and X0401, isolated from traditional yogurt in Tibet Autonomous Region, PR China, were characterized by a polyphasic approach, including sequence analyses of the 16S rRNA gene and three housekeeping genes (pheS, rpoA and recA), determination of average nucleotide identity (ANI) and average amino acid identity (AAI), in silico DNA–DNA hybridization (isDDH), fatty acid methyl ester (FAME) analysis and phenotypic characterization. Strain X0750T was phylogenetically related to the type strains of

Weissella hellenica

,

Weissella bombi

,

Weissella paramesenteroides

,

Weissella jogaejeotgali

,

Weissella thailandensis

,

Weissella oryzae

,

Weissella cibaria

and

Weissella confusa

, having 94.4–100 % 16S rRNA gene sequence similarities, 76.7–90.0 % pheS gene sequence similarities, 88.9–99.4 % rpoA gene sequence similarities and 77.6–92.8 % recA gene sequence similarities, respectively. ANI, isDDH and AAI values between strain X0750T and type strains of phylogenetically related species were less than 90.4, 40.9 and 92.8 % respectively, confirming that strain X0750T represents a novel species within the genus

Weissella

. Based upon the data obtained in the present study, a novel species, Weissella sagaensis sp. nov., is proposed and the type strain is X0750T(=NCIMB 15192T=CCM 8924T=LMG 31184T=CCTCC AB 2018403T).
Blue light emitting diodes enhance the antivirulence effects of Curcumin against Helicobacter pylori
Authors: Darmani Homa , Smadi Ehda A.M. , Bataineh Sereen M.B.
Published: February 2020

Introduction. Growing concern about the increasing frequency of resistance of

Helicobacter pylori

to the available antimicrobial agents worldwide has encouraged the search for new strategies in treating and eradicating

H. pylori

infections. Endoscopic blue-light therapy has been used in patients with

H. pylori

gastritis with limited success due to subsequent repopulation with

H. pylori

. Clinical trials using Curcumin could not eradicate infection either.

Aim. We studied the effect of blue light emitting diodes (LEDs) in conjunction with Curcumin on

H. pylori

, since this has not been previously reported.

Methodology. We examined the effect of Curcumin with and without irradiation with blue LEDs on the viability of

H. pylori

and four key factors important for colonization and establishment of

H. pylori

infection, namely urease production, motility, adhesion and biofilm formation.

Results. We found that a combination of Curcumin and blue LEDs caused significant reductions in viability, urease production, motility, haemagglutination activity, as well as increased disruption of mature preformed biofilms of

H. pylori

, in comparison to Curcumin alone (P<0.0001), at sublethal concentrations of Curcumin.

Conclusion. Targeting the virulence factors of

H. pylori

with blue LED photoactivated Curcumin would theoretically cripple this pathogen from colonizing and causing tissue damage and perhaps overcome the problem of repopulation with

H. pylori

that often occurs following endoscopic blue-light therapy.
A genuine mycobacterial thermophile: Mycobacterium hassiacum growth, survival and GpgS stability at near-pasteurization temperatures
Authors: Alarico Susana , Nunes-Costa Daniela , Silva Alexandra , Costa Mafalda , Macedo-Ribeiro Sandra , Empadinhas Nuno
Published: February 2020

Mycobacterium hassiacum

is so far the most thermophilic among mycobacteria as it grows optimally at 50 °C and up to 65 °C in a glycerol-based medium, as verified in this study. Since this and other nontuberculous mycobacteria (NTM) thrive in diverse natural and artificial environments, from where they may access and infect humans, we deemed essential to probe

M. hassiacum

resistance to heat, a strategy routinely used to control microbial growth in water-supply systems, as well as in the food and drink industries. In addition to possibly being a threat in its own right in rare occasions,

M. hassiacum

is also a good surrogate for studying other NTM species more often associated with opportunistic infection, namely

Mycobacterium avium

and

Mycobacterium abscessus

as well as their strictly pathogenic counterparts

Mycobacterium tuberculosis

and

Mycobacterium leprae

. In this regard, this thermophilic species is likely to be useful as a source of stable proteins that may provide more detailed structures of potential drug targets. Here, we investigate

M. hassiacum

growth at near-pasteurization temperatures and at different pHs and also characterize its thermostable glucosyl-3-phosphoglycerate synthase (GpgS), an enzyme considered essential for

M. tuberculosis

growth and associated with both nitrogen starvation and thermal stress in different NTM species.
Stocktaking the environmental coverage of a continental ecosystem observation network
Authors: Guerin Greg R. , Williams Kristen J. , Sparrow Ben , Lowe Andrew J.
Published: February 2020

Field-based sampling of terrestrial habitats at continental scales is required to build ecosystem observation networks. However, a key challenge for detecting change in ecosystem composition, structure and function is to obtain a representative sample of habitats. Representative sampling contributes to ecological validity when analysing large spatial surveys, but field resources are limited and representativeness may differ markedly from purely practical sampling strategies to statistically rigorous ones. Here, we report a post hoc assessment of the coverage of environmental gradients as a surrogate for ecological coverage by a continental-scale survey of the Australian Terrestrial Ecosystem Research Network (TERN). TERN’s surveillance program maintains a network of ecosystem observation plots that were init ially established in the rangelands through a stratification method (clustering of bioregions by environment) and Ausplots methodology. Subsequent site selection comprised gap filling combined with opportunistic sampling. Firstly, we confirmed that environmental coverage has been a good surrogate for ecological coverage. The cumulative sampling of environments and plant species composition over time were strongly correlated (based on mean multivariate dispersion; r = 0.93). We then compared the environmental sampling of Ausplots to 100,000 background points and a set of retrospective (virtual) sampling schemes: systematic grid, simple random, stratified random, and generalised random-tessellation stratified (GRTS). Differences were assessed according to sampling densities along environmental gradients, and multivariate dispersion (environmental space represented via multi-dimensional scaling). Ausplots outperformed systematic grid, simple random and GRTS in coverage of environmental space (Tukey HSD of mean dispersion, p < .001). GRTS site selection obtained similar coverage to Ausplots when employing the same bioregional stratification. Stratification by climatic zones generated the highest environmental coverage (p < .001), but the resulting sampling densities over-represented mesic coastal habitats. The Ausplots stratification by bioregions implemented under practical constraints represented complex environments well compared to statistically oriented or spatially even samples. However, potential statistical inference and power also depend on spatial and temporal replication, unbiased site selection, and accurate field measurements relative to the magnitude of change. A key conclusion is that environmental, rather than spatial, stratification is required to maximise ecological coverage across continental ecosystem observation networks.
Prognostic significance ofSOCS1andSOCS3tumor suppressors in hepatocellular carcinoma and its correlation to key oncogenic signaling pathways
Authors: Khan Md Gulam Musawwir , Ghosh Amit , Varia Bhavesh , Santharam Madanraj Appiya , Ihsan Awais Ullah , Ramanathan Sheela , Ilangumaran Subburaj
Published: February 2020

Suppressor of cytokine signaling (SOCS) proteins SOCS1 and SOCS3 are considered tumor suppressors in liver hepatocellular carcinoma (LIHC). To gain insight into the underlying molecular mechanisms, the expression ofSOCS1/ SOCS3was evaluated in The Cancer Genome Atlas LIHC dataset along with key oncogenic signaling pathway genes.SOCS1expression was not significantly reduced in HCC yet higher expression predicted favorable prognosis, whereasSOCS3lacked predictive potential despite lower expression. Only a small proportion of the cell cycle, receptor tyrosine kinase, growth factor and RAS-RAF-MEK-MAPK signaling genes negatively correlated withSOCS1orSOCS3, of which even fewer showed elevated expression in HCC and predicted survival. However, many PI3K-AKT-MTOR pathway genes showed mutual exclusivity withSOCS1/SOCS3and displayed independent predictive ability. Among genes that negatively correlated withSOCS1/SOCS3, CDK2, MLST8, AURKA, MAP3K4andRPTORshowed corresponding modulations in the livers of mice lackingSocs1orSocs3during liver regeneration and in experimental HCC, and in Hepa1-6 murine HCC cells overexpressing SOCS1/SOCS3. However, Cox proportional hazards model identifiedCXCL8, DAB2andPIK3R1as highly predictive in combination withSOCS1orSOCS3. These data suggest that developing prognostic biomarkers and precision treatment strategies based onSOCS1/SOCS3expression need careful testing in different patient cohorts.
Estimating indirect parental genetic effects on offspring phenotypes using virtual parental genotypes derived from sibling and half sibling pairs
Authors: Hwang Liang-Dar , Tubbs Justin D , Luong Justin , Lundberg Mischa , Moen Gunn-Helen , Sham Pak C , Cuellar-Partida Gabriel , Evans David M
Published: February 2020

Indirect parental genetic effects may be defined as the influence of parental genotypes on offspring phenotypes over and above that which results from the transmission of genes from parents to children. However, given the relative paucity of large-scale family-based cohorts around the world, it is difficult to demonstrate parental genetic effects on human traits, particularly at individual loci. In this manuscript, we illustrate how parental genetic effects on offspring phenotypes, including late onset diseases, can be estimated at individual loci in principle using large-scale genome-wide association study (GWAS) data, even in the absence of parental genotypes. Our strategy involves creating “virtual” mothers and fathers by estimating the genotypic dosages of parental genotypes using physically genotyped data from relative pairs. We then utilize the expected dosages of the parents, and the actual genotypes of the offspring relative pairs, to perform conditional genetic association analyses to obtain asymptotically unbiased estimates of maternal, paternal and offspring genetic effects. We develop a freely available web application that quantifies the power of our approach using closed form asymptotic solutions. We implement our methods in a user-friendly software packageIMPISH(IMputingParental genotypesInSiblings andHalf-Siblings) which allows users to quickly and efficiently impute parental genotypes across the genome in large genome-wide datasets, and then use these estimated dosages in downstream linear mixed model association analyses. We conclude that imputing parental genotypes from relative pairs may provide a useful adjunct to existing large-scale genetic studies of parents and their offspring.
A statistical modelling reveals bi-directional chromatin scanning by RAG in the human TCR-α locus
Authors: O’Connor Ciarán , McNamara Deirdre , Nakagome Shigeki
Published: February 2020

Rearrangements of germline variable (V), diversity (D), and joining (J) coding gene segments generate a diverse T cell receptor (TCR) repertoire. Two different molecular mechanisms govern a stochastic nature of gene choices by the recombination activating gene (RAG) protein complex. One is diffusion access in which a chromatin loop containing a coding gene bounces back and forth until the loop encounters a distant gene. The other is a linear chromatin scan, which extrudes chromatin loops to assemble a gene pair in a distance-dependent manner. However, the extent to which those two mechanisms underlie V(D)J recombination in human TCRs still remains unclear. Applying statistical modelling to TCR sequence data, we infer the stochastic process of gene choices during this recombination. The inferred usage of V and J gene segments vary from gene to gene. This pattern of gene usage is consistent across individuals, suggesting a fundamental bias in the gene choice. Our modelling shows the dependency of VJ pairing on their linear distance in the TCR-α locus; proximal-proximal and distal-distal VJ pairs are more preferred than proximal-distal or distal-proximal gene pairs. These results support bi-directional RAG scanning into proximal and distal sides of the TCR-α V gene locus.
Fmn2 regulates growth cone motility by mediating a molecular clutch to generate traction forces
Authors: Ghate Ketakee , Mutalik Sampada P. , Sthanam Lakshmi Kavitha , Sen Shamik , Ghose Aurnab
Published: February 2020

Growth cone - mediated axonal outgrowth and accurate synaptic targeting are central to brain morphogenesis. Translocation of the growth cone necessitates mechanochemical regulation of cell - extracellular matrix interactions and the generation of propulsive traction forces onto the growth environment. However, the molecular mechanisms subserving force generation by growth cones remain poorly characterized. The formin family member, Fmn2, has been identified earlier as a regulator of growth cone motility. Here, we explore the mechanisms underlying Fmn2 function in the growth cone. Evaluation of multiple components of the adhesion complexes suggests that Fmn2 regulates point contact stability. Analysis of F-actin retrograde flow reveals that Fmn2 functions as a clutch molecule and mediates the coupling of the actin cytoskeleton to the growth substrate, via point contact adhesion complexes. Using traction force microscopy, we show that the Fmn2-mediated clutch function is necessary for the generation of traction stresses by neurons. Our findings suggest that Fmn2, a protein associated with neurodevelopmental and neurodegenerative disorders, is a key regulator of a molecular clutch activity and consequently motility of neuronal growth cones.
R/UAStools::plotshpcreate: Create Multi-Polygon Shapefiles for Extraction of Research Plot Scale Agriculture Remote Sensing Data
Authors: Anderson Steven L. , Murray Seth C.
Published: February 2020

Agricultural researchers are embracing remote sensing tools to phenotype and monitor agriculture crops. Specifically, large quantities of data are now being collected on small plot research studies using Unoccupied Aerial Systems (UAS, aka drones), ground systems, or other technologies but, data processing and analysis lags behind. One major contributor to current data processing bottlenecks has been the lack of publicly available software tools tailored towards remote sensing of small plots, and usability for researchers inexperienced in remote sensing. To address these needs we created plot shapefile maker (R/UAS::plotshpcreate), an open source R function which rapidly creates ESRI polygon shapefiles to the desired dimensions of individual agriculture research plots areas of interest and associates plot specific information. Plotshpcreate was developed to utilize inputs containing experimental design, field orientation, and plot dimensions for easily creating a multi-polygon shapefile of an entire small plot experiment. Output shapefiles are based on the user inputs geolocation of the front left corner of the research field ensuring accurate overlay of polygons often without manual user adjustment. The output shapefile is useful in GIS software to extract plot level data tracing back to the unique IDs of the experimental plots. Plotshpcreate is available on GitHub (https://github.com/andersst91/UAStools).
A Novel Method for the Estimation of a Dynamic Effective Reproduction Number (Dynamic-R) in the CoViD-19 Outbreak
Authors: Chong Yi Chen
Published: February 2020

The CoViD-19 outbreak has escalated to a pandemic in the last few weeks, with no signs of stopping. Pharmaceutical solutions based upon virologic studies, at this point, remain inconclusive. In contrast, this paper looks towards epidemiological models during this phase of viral growth, in particular, by providing a responsive, timely model of the R value based on the previous few days’ results.

Such an R value, although bearing less statistical precision due to limited sampling, could allow R to become a more effective, responsive standalone measure of infectious transmission. It demonstrates that the R value can be used as a dynamic, time-dependent indicator without the use of curve-fitting, and also estimates the most recent R-value of the CoViD-19 outbreak to be about 4.29, based on the data from the previous 3 days.
Network-based Machine Learning Approach for Structural Domain Identification in Proteins
Authors: Tiwari Anirudh , Parekh Nita
Published: February 2020

In the era of structural genomics, with a large number of protein structures becoming available, identification of domains is an important problem in protein function analysis as it forms the first step in protein classification. Domain identification has been an active area of research for over four decades and a wide range of automated methods have been proposed. In the proposed network-based machine learning approach, NML-DIP, a combination of supervised (SVM) and unsupervised (k-means) machine learning techniques are used for domain identification in proteins. The algorithm proceeds by first representing protein structure as a protein contact network and using topological properties,viz., length, density, and interaction strength (that assesses inter- and intra-domain interactions) as feature vectors in the first SVM to distinguish between single and multi-domain proteins. A second SVM is used to identify the number of domains in multi-domain proteins. Thus, it does not require a prior information of the number of domains. Thek-means algorithm is then used to identify the domain boundaries that are assessed using CATH annotation. The performance of the proposed algorithm is evaluated on four benchmark datasets and compared with four state-of-the-art domain identification methods. The performance of the approach is comparable to other domain identification tools and works well even when the domains are formed with non-contiguous segments. The performance of the program is significantly improved for prior information about the number of domains. The algorithm is available at:https://bit.ly/NML-DIP.
Genomic profiling of cell lines reveals hidden research bias and caveats
Authors: Luo Yongwen , Ju Lingao , Zhang Yi , Xiao Yu , Wang Xinghuan
Published: February 2020

Cancer cell lines are extremely valuable tools for carcinoma research. Biodiversity of cell lines and continuous random mutation in cell lines during passage, however, might result in phenotypic inconsistency and lead to biased experimental conclusions. Using statistics based on known and inferred protein interaction networks, as well as public research literature database, our study shows that essential driver genotypes of cell lines might have hidden impact on research results. Furthermore, by comprehensive genomic profiling of 8 most common used urothelial cell lines and comparing them to previous publications, we found that regardless of similar short tandem repeat (STR) profile, driver gene loss in cell lines could happen by random mutation. Our results suggest that clinical research using urothelial carcinoma cell lines might be influenced by cell line genotypes which could only be determined by next-generation sequencing. Meanwhile, this study indicates that the conditionally reprogrammed cells (CRCs), which closely resemble original tumor tissue, might represent a better alternative for in vitro research, which may be better used for personalized medicine.
Cellular heterogeneity–adjusted clonal methylation (CHALM) provides better prediction of gene expression
Authors: Xu Jianfeng , Shi Jiejun , Cui Xiaodong , Cui Ya , Li Jingyi Jessica , Goel Ajay , Chen Xi , Su Jianzhong , Issa Jean-Pierre , Li Wei
Published: February 2020

Promoter DNA methylation is a well-established mechanism of transcription repression, but its global correlation with gene expression is surprisingly weak. This weak correlation is due in part to the failure of current methylation quantification methods to consider the heterogeneity among sequenced bulk cells. Here, we introduceCellHeterogeneity–Adjusted cLonalMethylation (CHALM) as a novel methylation quantification method. CHALM better explains the functional consequences of DNA methylation, such as its correlations with gene expression and H3K4me3. When applied to different methylation datasets, the CHALM method has uniquely detected differentially methylated genes that exhibit distinct biological functions supporting underlying mechanisms.
Lessons learnt from 288 COVID-19 international cases: importations over time, effect of interventions, underdetection of imported cases
Authors: Pinotti Francesco , Di Domenico Laura , Ortega Ernesto , Mancastroppa Marco , Pullano Giulia , Valdano Eugenio , Boëlle Pierre-Yves , Poletto Chiara , Colizza Vittoria
Published: February 2020

288 cases have been confirmed out of China from January 3 to February 13, 2020. We collected and synthesized all available information on these cases from official sources and media. We analyzed importations that were successfully isolated and those leading to onward transmission. We modeled their number over time, in relation to the origin of travel (Hubei province, other Chinese provinces, other countries) and interventions. We characterized importations timeline to assess the rapidity of isolation, and epidemiologically linked clusters to estimate the rate of detection. We found a rapid exponential growth of importations from Hubei, combined with a slower growth from the other areas. We predicted a rebound of importations from South East Asia in the upcoming weeks. Time from travel to detection has considerably decreased since the first importation, however 6 cases out of 10 were estimated to go undetected. Countries outside China should be prepared for the possible emergence of several undetected clusters of chains of local transmissions.