bluuebunny/crossref_metadata_2025 huggingface dataset:
piRNA Clusters Need a Minimum Size to Control Transposable Element Invasions
Authors: Kofler Robert
Published: March 2020

piRNA clusters are thought to repress transposable element (TE) activity in mammals and invertebrates. Here, we show that a simple population genetics model reveals a constraint on the size of piRNA clusters: The total size of the piRNA clusters of an organism must exceed 0.2% of a genome to repress TE invasions. Moreover, larger piRNA clusters accounting for up to 3% of the genome may be necessary when populations are small, transposition rates are high, and TE insertions are recessive. If piRNA clusters are too small, the load of deleterious TE insertions that accumulate during a TE invasion may drive populations extinct before an effective piRNA-based defense against the TE can be established. Our findings are solely based on three well-supported assumptions: 1) TEs multiply within genomes, 2) TEs are mostly deleterious, and 3) piRNA clusters act as transposon traps, where a single insertion in a cluster silences all TE copies in trans. Interestingly, the piRNA clusters of some species meet our observed minimum size requirements, whereas the clusters of other species do not. Species with small piRNA clusters, such as humans and mice, may experience severe fitness reductions during invasions of novel TEs, which is possibly even threatening the persistence of some populations. This work also raises the important question of how piRNA clusters evolve. We propose that the size of piRNA clusters may be at an equilibrium between evolutionary forces that act to expand and contract piRNA clusters.
Reflection on modern methods: trial emulation in the presence of immortal-time bias. Assessing the benefit of major surgery for elderly lung cancer patients using observational data
Authors: Maringe Camille , Benitez Majano Sara , Exarchakou Aimilia , Smith Matthew , Rachet Bernard , Belot Aurélien , Leyrat Clémence
Published: March 2020

Acquiring real-world evidence is crucial to support health policy, but observational studies are prone to serious biases. An approach was recently proposed to overcome confounding and immortal-time biases within the emulated trial framework. This tutorial provides a step-by-step description of the design and analysis of emulated trials, as well as R and Stata code, to facilitate its use in practice. The steps consist in: (i) specifying the target trial and inclusion criteria; (ii) cloning patients; (iii) defining censoring and survival times; (iv) estimating the weights to account for informative censoring introduced by design; and (v) analysing these data. These steps are illustrated with observational data to assess the benefit of surgery among 70–89-year-old patients diagnosed with early-stage lung cancer. Because of the severe unbalance of the patient characteristics between treatment arms (surgery yes/no), a naïve Kaplan-Meier survival analysis of the initial cohort severely overestimated the benefit of surgery on 1-year survival (22% difference), as did a survival analysis of the cloned dataset when informative censoring was ignored (17% difference). By contrast, the estimated weights adequately removed the covariate imbalance. The weighted analysis still showed evidence of a benefit, though smaller (11% difference), of surgery among older lung cancer patients on 1-year survival. Complementing the CERBOT tool, this tutorial explains how to proceed to conduct emulated trials using observational data in the presence of immortal-time bias. The strength of this approach is its transparency and its principles that are easily understandable by non-specialists.
HIV Modifies the Effect of Tobacco Smoking on Oral Human Papillomavirus Infection
Authors: Alli Babatunde Y , Burk Robert D , Fatahzadeh Mahnaz , Kazimiroff Julie , Grossberg Robert M , Smith Richard V , Ow Thomas J , Wiltz Mauricio , Polanco Jacqueline , Rousseau Marie-Claude , Nicolau Belinda , Schlecht Nicolas F
Published: March 2020

Background

People living with HIV (PLWH) are more likely to smoke and harbor oral human papillomavirus (HPV) infections, putting them at higher risk for head and neck cancer. We investigated effects of HIV and smoking on oral HPV risk.

Methods

Consecutive PLWH (n = 169) and at-risk HIV-negative individuals (n = 126) were recruited from 2 US health centers. Smoking history was collected using questionnaires. Participants provided oral rinse samples for HPV genotyping. We used multivariable logistic regression models with interaction terms for HIV to test for smoking effect on oral HPV.

Results

PLWH were more likely to harbor oral HPV than HIV-negative individuals, including α (39% vs 28%), β (73% vs 63%), and γ-types (33% vs 20%). HIV infection positively modified the association between smoking and high-risk oral HPV: odds ratios for smoking 3.46 (95% confidence interval [CI], 1.01–11.94) and 1.59 (95% CI, .32–8.73) among PLWH and HIV-negative individuals, respectively, and relative excess risk due to interaction (RERI) 3.34 (95% CI, −1.51 to 8.18). RERI for HPV 16 was 1.79 (95% CI, −2.57 to 6.16) and 2.78 for β1-HPV (95% CI, −.08 to 5.65).

Conclusion

Results show tobacco smoking as a risk factor for oral HPV among PLWH.
Combining Hepatitis B Virus RNA and Hepatitis B Core–Related Antigen: Guidance for Safely Stopping Nucleos(t)ide Analogues in Hepatitis B e Antigen–Positive Patients With Chronic Hepatitis B
Authors: Fan Rong , Peng Jie , Xie Qing , Tan Deming , Xu Min , Niu Junqi , Wang Hao , Ren Hong , Chen Xinyue , Wang Maorong , Sheng Jifang , Tang Hong , Bai Xuefan , Wu Yaobo , Zhou Bin , Sun Jian , Hou Jinlin ,   for the Chronic Hepatitis B Study Consortium, Ning Qin , Shi Guangfeng , Wan Mobin , Chen Shijun , Yu Yanyan , Ma Hong , Cheng Jun , Zhang Hongfei , Liu Huimin , Gao Zhiliang
Published: March 2020

Background

Safe nucleos(t)ide analogue discontinuation in chronic hepatitis B (CHB) is an unmet need. We aimed to investigate whether combining hepatitis B virus (HBV) RNA and hepatitis B core–related antigen (HBcrAg) could perform satisfactorily in predicting off-treatment outcomes.

Methods

The evaluation cohort included 127 hepatitis B e antigen (HBeAg)–positive patients from a multicenter prospective trial who stopped telbivudine-based therapy after achieving HBeAg seroconversion and HBV DNA < 50 IU/mL for > 48 weeks. As validation, 59 patients treated with entecavir or tenofovir before discontinuation were analyzed.

Results

At the end of treatment (EOT), HBV RNA and HBcrAg were significant independent predictors of the clinical relapse risk. In the evaluation cohort, no clinical relapse occurred among patients with negative HBV RNA and HBcrAg < 4 log10 U/mL at EOT (low-risk group), whereas 46.8% patients with positive HBV RNA and HBcrAg ≥ 4 log10 U/mL (high-risk group) experienced clinical relapse during 4-year posttreatment follow-up (P < .001); the corresponding incidences in the validation cohort were 0% and 69.4% (P < .001), respectively. More patients in the low-risk group achieved HBsAg loss than the other patients after treatment cessation (16.1% vs 1.3%, P = .002).

Conclusions

Combining HBV RNA and HBcrAg performed satisfactorily in predicting clinical relapse and HBsAg loss after treatment cessation in HBeAg-positive patients with CHB.

The combination of hepatitis B virus RNA and hepatitis B core–related antigen performed satisfactorily in predicting clinical relapse and hepatitis B surface antigen loss after stopping nucleos(t)ide analogue treatment among noncirrhotic hepatitis B e antigen–positive patients with chronic hepatitis B and could be used to guide safe discontinuation.
Using word embeddings to improve the privacy of clinical notes
Authors: Abdalla Mohamed , Abdalla Moustafa , Rudzicz Frank , Hirst Graeme
Published: March 2020

Objective

In this work, we introduce a privacy technique for anonymizing clinical notes that guarantees all private health information is secured (including sensitive data, such as family history, that are not adequately covered by current techniques).

Materials and Methods

We employ a new “random replacement” paradigm (replacing each token in clinical notes with neighboring word vectors from the embedding space) to achieve 100% recall on the removal of sensitive information, unachievable with current “search-and-secure” paradigms. We demonstrate the utility of this paradigm on multiple corpora in a diverse set of classification tasks.

Results

We empirically evaluate the effect of our anonymization technique both on upstream and downstream natural language processing tasks to show that our perturbations, while increasing security (ie, achieving 100% recall on any dataset), do not greatly impact the results of end-to-end machine learning approaches.

Discussion

As long as current approaches utilize precision and recall to evaluate deidentification algorithms, there will remain a risk of overlooking sensitive information. Inspired by differential privacy, we sought to make it statistically infeasible to recreate the original data, although at the cost of readability. We hope that the work will serve as a catalyst to further research into alternative deidentification methods that can address current weaknesses.

Conclusion

Our proposed technique can secure clinical texts at a low cost and extremely high recall with a readability trade-off while remaining useful for natural language processing classification tasks. We hope that our work can be used by risk-averse data holders to release clinical texts to researchers.
Brevipalpus Species Vectoring Citrus Leprosis Virus (Cilevirus and Dichorhavirus)
Authors: Ferreira Leticia M , Nunes Maria A , Sinico Thaís E , Soares Alex J , Novelli Valdenice M
Published: March 2020

Citrus leprosis (CL) is one of the most devastating viral diseases of orchards, and industries correspondingly invest highly in the management and control of the virus vector. In Brazil, the disease is caused most predominantly by the citrus leprosis virus C (CiLV-C, Kitaviridae: Cilevirus), and also by citrus leprosis virus N (CiLV-N, Rhabdoviridae: Dichorhavirus). Both viruses are transmitted by false spider mites and at least three different species, Brevipalpus yothersi Baker, B. papayensis Baker, and B. phoenicis (Geijskes) sensu stricto, have been reported in citrus orchards. The main goal of this study was to evaluate the capacity of three Brevipalpus species to transmit citrus leprosis virus (cytoplasmic and nuclear types). The capacity of false spider mites to acquire the virus was accomplished using RT–PCR and the ability to inoculation the virus to host plants (common bean and sweet orange) was assessed via viral transmission assays. Common beans infested with B. yothersi and B. papayensis showed symptoms of CiLV-C in 87.5 and 17% of the plants assessed, respectively. In sweet orange, B. yothersi was exclusively able to inoculate CiLV-C, and around 83% of samples were symptomatic. Host plants infected with CiLV-N showed symptoms only when infested with B. phoenicis sensu stricto (s.s.). All the Brevipalpus species (Acari: Tenuipalpidae) were able to acquire both viruses (CiLV-C and CiLV-N), but not infect plants. These results suggest the existence of virus-vector specificity in the leprosis pathosystem, and this information will be critical for enhancing our further understanding of epidemiological features and disease management.
National Socialist Medical Literature and the Censorship Practices in the Soviet Occupation Zone and Early East German State
Authors: Polianski Igor J
Published: March 2020

This study examines how medical discourse and culture were affected by the denazification policies of the Soviet occupation authorities in East Germany. Examining medical textbooks in particular, it reveals how the production and dissemination of medical knowledge was subject to a complex process of negotiation among authors, publishers, and censorship officials. Drawing on primary-source material produced by censorship authorities that has not been rigorously examined to date, it reveals how knowledge production processes were structured by broader ideological and political imperatives. It thus sheds new light on a unique chapter in the history of censorship.
Characterization of the Complete Mitochondrial Genome of Epicauta impressicornis (Coleoptera: Meloidae) and Its Phylogenetic Implications for the Infraorder Cucujiformia
Authors: Liu Yang-Yang , Zhou Zhi-Cheng , Chen Xiang-Sheng
Published: March 2020

The complete mitochondrial genome (mitogenome) of Epicauta impressicornis Pic (Coleoptera: Meloidae) was determined. The circular genome is 15,713-bp long, and encodes 13 protein-coding genes (PCGs), 2 ribosomal RNA (rRNA) genes, 22 transfer RNA (tRNA) genes, and a control region (CR). The 13 PCGs start with the typical ATN codon and terminate with the typical stop codon TAA (ND2, ND4L, ND6, ATP6, ATP8, and CYTB), TAG (ND1 and ND3), and T- (COX1, COX2, COX3, ND4, and ND5). The two rRNA genes (rrn12S and rrn16S) are encoded on the minority strand. All tRNAs genes except trnS1 (AGN) are predicted to fold into the typical cloverleaf structure. The longest overlap (10 bp) is observed between ATP8 and ATP6. CR mainly harbors a conserved poly-T stretch (15 bp), a short repeat unit (17 bp), some universal microsatellite-like repeats, and a canonical poly-A tail. Phylogenetic analysis using Bayesian inferences and maximum likelihood based on nucleotide and corresponding amino acid sequences of the 13 PCGs showed that E. impressicornis is closely related to E. chinensis, this relationship is and supported within Cucujiformia belonging to Meloidae (Tenebrionoidea). Our results further confirmed the monophyly of Tenebrionoidea, Lymexyloidea, Curculionoidea, Chrysomeloidea, Cucujoidea, Coccinelloidea, and Cleroidea within Cucujiformia, and revealed the sister relationships of (Cleroidea + Coccinelloidea), (Lymexyloidea + Tenebrionoidea), and ((Chrysomeloidea + Cucujoidea) + Curculionoidea). We believe that the complete mitogenome of E. impressicornis will contribute to further studies on molecular bases for the classification and phylogeny of Meloidae or even Cucujiformia.
Prognostic impact of sarcopenia in patients with metastatic hormone-sensitive prostate cancer
Authors: Ikeda Takashi , Ishihara Hiroki , Iizuka Junpei , Hashimoto Yasunobu , Yoshida Kazuhiko , Kakuta Yoichi , Takagi Toshio , Okumi Masayoshi , Ishida Hideki , Kondo Tsunenori , Tanabe Kazunari
Published: March 2020

Background

Cancer cachexia is associated with a poor prognosis. This study aimed to investigate the association between sarcopenia and survival in patients with metastatic hormone-sensitive prostate cancer.

Methods

We retrospectively evaluated 197 patients diagnosed with metastatic hormone-sensitive prostate cancer in our department and its affiliated institution between January 2008 and December 2015. Sarcopenia was diagnosed according to the sex-specific consensus definition. Castration-resistance prostate cancer-free survival, cancer-specific survival and overall survival from the metastatic hormone-sensitive prostate cancer diagnoses were calculated using the Kaplan–Meier method and compared using the log-rank test. Risk factors affecting the survival outcomes were analyzed using the Cox proportional regression analysis.

Results

In total, 163 patients (82.7%) had sarcopenia. Cancer-specific survival and overall survival were significantly shorter in sarcopenic patients than in non-sarcopenic patients (median cancer-specific survival: 77.0 months vs. not reached, P = 0.0099; overall survival: 72.0 months vs. not reached, P = 0.0465), whereas castration-resistance prostate cancer-free survival did not significantly differ between the groups (P = 0.6063). Multivariate analyses showed that sarcopenia was an independent factor for cancer-specific survival (hazard ratio: 2.18, P = 0.0451), together with the Gleason score (hazard ratio: 1.87, P = 0.0272) and LATITUDE risk classification (hazard ratio: 2.73, P = 0.0008). Moreover, the prognostic association of sarcopenia was remarkable in patients aged <73.0 years (cancer-specific survival: 82.0 months vs. not reached, P = 0.0027; overall survival: 72.0 months vs. not reached, P = 0.0078 in sarcopenic vs. non-sarcopenic patients), whereas the association was not significant in patients aged ≥73.0 years (cancer-specific survival: 76.0 and 75.0 months, respectively, P = 0.7879; overall survival: 67.0 and 52.0 months, respectively, P = 0.7263).

Conclusion

Sarcopenia was an independent risk factor of cancer-specific survival in patients with metastatic hormone-sensitive prostate cancer, especially in younger patients.
The Economics of Leasing
Authors: Merrill Thomas W
Published: March 2020

Leasing may be the most important legal institution that has received virtually no systematic scholarly attention. Real property leasing is familiar in the context of residential tenancies. But it is also widely used in commercial contexts, including office buildings and shopping centers. Personal property leasing, which was rarely encountered before World War II, has more recently exploded on a world-wide basis, with everything from autos to farm equipment to airplanes being leased. This article seeks to develop a composite picture of the defining features of leases and why leasing is such a widespread and highly successful economic institution. The reasons fall under three general headings. (i) Leasing is an attractive method of financing the acquisition of assets, especially for persons who have limited capital or would like to conserve their capital and cash flows for other purposes. (ii) Leasing is a device for minimizing the risks that either lessees or lessors associate with owning assets; although leasing also creates risks, various lease modifications have been developed to manage these derivative risks. (iii) By dividing the rights to an asset between lessor and lessee, leasing permits the parties to specialize in different functions and to solve various impediments to contracting that would be difficult to overcome among separate owners. Understanding the economic advantages of leasing is an important first step in considering possible legal reforms of leasing.
Moving Forward in Cervical Cancer: Enhancing Susceptibility to DNA Repair Inhibition and Damage, an NCI Clinical Trials Planning Meeting Report
Authors: Harkenrider Matthew M , Markham Merry Jennifer , Dizon Don S , Jhingran Anuja , Salani Ritu , Serour Ramy K , Lynn Jean , Kohn Elise C
Published: March 2020

Cervical cancer is the fourth most common cancer in women worldwide, and prognosis is poor for those who experience recurrence or develop metastatic disease, in part due to the lack of active therapeutic directions. The National Cancer Institute convened a Cervical Cancer Clinical Trials Planning Meeting in October 2018 to facilitate the design of hypothesis-driven clinical trials focusing on locally advanced, metastatic, and recurrent cervical cancer around the theme of enhancing susceptibility to DNA repair inhibition and DNA damage. Before the meeting, a group of experts in the field summarized available preclinical and clinical data to identify potentially active inducers and inhibitors of DNA. The goals of the Clinical Trials Planning Meeting focused on identification of novel experimental strategies capitalizing on DNA damage and repair (DDR) regulators and cell cycle aberrations, optimization of radiotherapy as a DDR agent, and design of clinical trials incorporating DDR regulation into the primary and recurrent or metastatic therapies for cervical carcinoma. Meeting deliverables were novel clinical trial concepts to move into the National Clinical Trials Network. This report provides an overview for the rationale of this meeting and the state of the science related to DDR regulation in cervical cancer.
Intravenous Immunoglobulin-Associated Hemolytic Anemia
Authors: Jacobs Jeremy , Kneib Jessica , Gabbard Amy
Published: March 2020

Intravenous immunoglobulin (IVIG) is an important therapeutic tool for the treatment of a variety of conditions, including immune thrombocytopenic purpura (ITP). Although IVIG has many approved indications and is typically well tolerated, a number of adverse effects have been reported. Hemolysis is a documented but under-recognized adverse effect associated with large individual or cumulative doses of IVIG. Hemolytic complications are typically mild and detected incidentally when screening tests, such as a complete blood count (CBC) showing decreased hemoglobin or a complete metabolic panel (CMP) resulting in elevated bilirubin, are performed for another reason.

Herein, we report a case of significant hemolytic anemia in a 59 year old Caucasian woman, who required packed red blood cell transfusion after administration of IVIG for the treatment of ITP. Increased awareness of the potential for clinically significant hemolysis after the use of moderate cumulative doses of IVIG is needed, particularly in patients with risk factors for hemolysis.
In vitro algicidal effect of polypyrrole on Prototheca species isolates from bovine mastitisAlgicidal activity of polypyrrole on Prototheca spp.
Authors: Ely Valessa Lunkes , Costa Mateus Matiuzzi da , Oliveira Helinando Pequeno de , Silva Júnior Fernando Antonio Gomes da , Pereira Daniela Isabel Brayer , Soares Mauro Pereira , Vargas Agueda Castagna de , Sangioni Luís Antônio , Cargnelutti Juliana Felipetto , Ribeiro Márcio Garcia , Botton Sônia de Avila
Published: March 2020

Algae of the genus Prototheca are microorganisms involved in the occurrence of diseases in humans and animals. In bovine species, Prototheca spp. cause environmental mastitis, productive losses in dairy herds, mainly leading to the discard of infected cows. Currently, there are no effective anti-Prototheca spp. drugs to combat this infection. Thus, the search for an efficacious therapy for Prototheca spp. infections have become essential. Highly soluble polypyrrole (Ppy) is a molecule with known antimicrobial activity. This study aimed to characterize Prototheca spp. isolates from bovine mastitis as well as to evaluate the susceptibility profile and to verify the morphological alterations on Prototheca spp. isolates treated with Ppy. In this research, 36 Brazilian isolates of Prototheca spp. were characterized by restriction fragment length polymorphism polymerase chain reaction (RFLP-PCR) assay for the mitochondrial cytB gene. Additionally, Ppy algicidal activity against these isolates of Prototheca spp. was assessed by minimal microbicidal concentration method in microplates. Further, scanning electron microscopy (SEM) was performed in order to verify the morphological alterations on Prototheca spp. isolates in response to Ppy. The isolates were characterized as belonging to Prototheca zopfii genotype 2 (35/36) and Prototheca blaschkeae (1/36). Ppy had an algicidal effect on all isolates tested at concentrations ranging from 15.625 μg ml−1 to 62.5 μg ml−1. SEM showed changes on planktonic and sessile P. zopfii, including a decrease of the number of cells with the presence of an amorphous substance involving the cells. The algicidal activity of Ppy suggests the therapeutic potential of this molecule in the prevention and treatment of Prototheca spp. in bovine mastitis.
Expectations for the confirmation of Proxima c from a long-term radial velocity follow-up
Authors: Damasso M , Del Sordo F
Published: March 2020

Proxima c, a candidate second planet orbiting Proxima Centauri, was detected with the radial velocity method. The announced long orbital period (5.21$^{+0.26}_{-0.22}$ yr), and small semi-amplitude of the induced Doppler signal (1.2 ± 0.4 $\rm{\,m\,s^{-1}}$), make this detection challenging and a target worthy of a follow-up in the years to come. We intend to evaluate the impact of future data on the statistical significance of the detection through realistic simulated radial velocities to be added to the published data set, spanning up to one orbital period of Proxima c in the time range 2019–2023. We find that the detection significance of Proxima c increases depending not only on the amount of data collected, but also on the number of instruments used, and especially on the time-span covered by the observational campaign. However, on average, we do not get strong statistical evidence, and we predict that, in the best-case scenario, in the next five years the detection of Proxima c can become significant at the 4-σ level. If instead Proxima c does not exist, the detected signal may lower its significance down to 2 σ.
Analysis of absorption lines in the high-resolution spectra of five hot post-AGB candidates
Authors: Herrero A , Parthasarathy M , Simón-Díaz S , Hubrig S , Sarkar G , Muneer S
Published: March 2020

From an analysis of absorption lines in the high-resolution spectra, we have derived the radial velocities, stellar parameters (Teff, log g, wind-strength parameter log Q, and projected rotational velocity), and abundances (C, N, O, and Si) of IRAS 17460-3114, IRAS 18131-3008, IRAS 19336-0400, LSE 45, and LSE 163. Abundances are found to be solar, except for a low Si abundance in IRAS 19336-0400 and a mild CNO pattern in LSE 163, which rotates at an unusual large rotational velocity for its spectral classification. Combining the stellar parameters information with the Gaia DR2 data, we are able to derive absolute magnitudes, radii, and luminosities and clarify the possible post-asymptotic giant branch (AGB) nature of the objects. IRAS 17460-3114 and IRAS 18131-3008 are found to be massive OB stars, whereas IRAS 19336-0400 is found to be a post-AGB star, already showing nebular lines in the spectrum. However, we could not confirm the nature of LSE 45 and LSE 163 as post-AGB stars, although their parameters are much more inconsistent with those of massive stars. In both cases, we find a discrepancy between the spectroscopic mass and that derived from the predictions of post-AGB evolutionary tracks. In addition, LSE 45 lacks nebular lines, which are present in IRAS 19336-0400 at a similar temperature. In the case of LSE 163, the rotational velocity (259 ± 15 $\rm km\, s^{-1}$) would be extremely large for a star evolving to central stars of planetary nebulae. The combination of this rotational velocity, the high Galactic latitude, slightly large radial velocity, and mild CNO enhancement suggests a history of binary interaction.
Probing the theory of gravity with gravitational lensing of gravitational waves and galaxy surveys
Authors: Mukherjee Suvodip , Wandelt Benjamin D , Silk Joseph
Published: March 2020

The cross-correlation of gravitational wave strain with upcoming galaxy surveys probes theories of gravity in a new way. This method enables testing the theory of gravity by combining the effects from both gravitational lensing of gravitational waves and the propagation of gravitational waves in space–time. We find that within 10 yr the combination of the Advanced LIGO (Laser Interferometer Gravitational-Wave Observatory) and VIRGO (Virgo interferometer) detector networks with planned galaxy surveys should detect weak gravitational lensing of gravitational waves in the low-redshift Universe (z < 0.5). With the next-generation gravitational wave experiments such as Voyager, LISA (Laser Interferometer Space Antenna), Cosmic Explorer, and the Einstein Telescope, we can extend this test of the theory of gravity to larger redshifts by exploiting the synergies between electromagnetic wave and gravitational wave probes.
Contribution of uremic dysbiosis to insulin resistance and sarcopenia
Authors: Uchiyama Kiyotaka , Wakino Shu , Irie Junichiro , Miyamoto Junki , Matsui Ayumi , Tajima Takaya , Itoh Tomoaki , Oshima Yoichi , Yoshifuji Ayumi , Kimura Ikuo , Itoh Hiroshi
Published: March 2020

Background

Chronic kidney disease (CKD) leads to insulin resistance (IR) and sarcopenia, which are associated with a high mortality risk in CKD patients; however, their pathophysiologies remain unclear. Recently, alterations in gut microbiota have been reported to be associated with CKD. We aimed to determine whether uremic dysbiosis contributes to CKD-associated IR and sarcopenia.

Methods

CKD was induced in specific pathogen-free mice via an adenine-containing diet; control animals were fed a normal diet. Fecal microbiota transplantation (FMT) was performed by oral gavage in healthy germ-free mice using cecal bacterial samples obtained from either control mice (control-FMT) or CKD mice (CKD-FMT). Vehicle mice were gavaged with sterile phosphate-buffered saline. Two weeks after inoculation, mice phenotypes, including IR and sarcopenia, were evaluated.

Results

IR and sarcopenia were evident in CKD mice compared with control mice. These features were reproduced in CKD-FMT mice compared with control-FMT and vehicle mice with attenuated insulin-induced signal transduction and mitochondrial dysfunction in skeletal muscles. Intestinal tight junction protein expression and adipocyte sizes were lower in CKD-FMT mice than in control-FMT mice. Furthermore, CKD-FMT mice showed systemic microinflammation, increased concentrations of serum uremic solutes, fecal bacterial fermentation products and elevated lipid content in skeletal muscle. The differences in gut microbiota between CKD and control mice were mostly consistent between CKD-FMT and control-FMT mice.

Conclusions

Uremic dysbiosis induces IR and sarcopenia, leaky gut and lipodystrophy.
The nonhuman primate hypothalamo-pituitary-adrenal axis is an orchestrator of programming-aging interactions: role of nutrition
Authors: Nathanielsz Peter W , Huber Hillary F , Li Cun , Clarke Geoffrey D , Kuo Anderson H , Zambrano Elena
Published: March 2020

Developmental programming alters life-course multi-organ function and significantly affects life-course health. Recently, interest has developed in how programming may influence the rate of aging. This review describes interactions of nutrition and programming-aging interactions in hypothalamo-pituitary-adrenal (HPA) development and function from fetal development to old age. A full picture of these interactions requires data on levels of HPA activity relating to the hypothalamic, adrenal cortical, circulating blood, and peripheral cortisol metabolism. Data are provided from studies on our baboon, nonhuman primate model both across the normal life course and in offspring of maternal baboons who were moderately undernourished by a global 30% diet reduction during pregnancy and lactation. Sex differences in offspring outcomes in response to similar challenges are described. The data clearly show programming of increased HPA axis activity by moderate maternal undernutrition. Increased postnatal circulating cortisol concentrations are related to accelerated aging of the brain and cardiovascular systems. Future studies should address peripheral cortisol production and the influence of aging advantage in females. These data support the view that the HPA is an orchestrator of interactions of programming-aging mechanisms.
A review of the uses and reliability of food balance sheets in health research
Authors: Thar Chan-Myae , Jackson Rod , Swinburn Boyd , Mhurchu Cliona Ni
Published: March 2020

Context

Food Balance Sheets (FBSs) are constructed by the Food and Agricultural Organization (FAO) and portray the food supply and utilization pattern of a country over time.

Objective

To examine and analyse the uses of FAO-FBS data in international studies of health and nutrition, and to identify the reported strengths, limitations and reliability of FBS.

Data Sources

PubMed, SCOPUS, EMBASE, Food Science and Technology Abstracts (FSTA) and Google Scholar.

Data Extraction

Data extracted were author, year of publication, country/countries of the study, aim, study design, analysis, data collected, data sources and outcomes. Additional relevant information (e.g. strengths and limitations of the FBS), were also included. The bibliographies of all included studies were further searched, and any potentially relevant studies retrieved and assessed.

Data Analysis

119 eligible studies (all study designs) published from the earliest available to the end of April, 2016 were collated into five categories of use: within-country analysis of food availability, nutrient availability and/or dietary trends (n = 17); inter-country, regional or global comparison of food groups, nutrient availability and/or dietary trends (n = 45); comparison of FBS with other national sources of dietary data (n = 7); association between FBS dietary factors and mortality or health outcomes (n = 45); and modelling studies (n = 5).

Conclusion

Studies indicate that FBS are useful for international comparison and analysis of trends over time, as they are standardized and updated regularly. FBS data are more reliable when averaged over several years; when results are reported as nutrient densities, trends, and percentage of energy or ratios, rather than absolute values. Also, users should be aware that the quality of FBS data depends on the reliability of national input data. The FBS is a vital source of global food composition data and is valuable for epidemiological studies when reported and analysed appropriately.
Early Establishment of Photosynthesis and Auxin Biosynthesis Plays a Key Role in Early Biomass Heterosis in Brassica napus (Canola) Hybrids
Authors: Zhu Anyu , Wang Aihua , Zhang You , Dennis Elizabeth S , Peacock W James , Greaves and Ian K
Published: March 2020

Heterosis or hybrid vigor has been used widely for more than a decade in Canola (Brassica napus) production. Canola hybrids show heterosis in a variety of traits compared to parents, including increased biomass at the early stages of seedling establishment, which is a critical developmental step that impacts future plant growth and seed yield. In this study, we examined transcriptomes of two parental lines, Garnet (Gar) and NX0052 (0052), and their reciprocal hybrids, Gar/0052, at 4 and 8 days after sowing (DAS). In hybrids, early seedling biomass heterosis is correlated with earlier expression of genes in photosynthesis pathways relative to parents. The hybrids also showed early expression of genes in the auxin biosynthesis pathway, consistent with the higher auxin concentrations detected in hybrid seedlings at 4 DAS. Auxin is a key phytohormone that regulates plant development promoting cell expansion and cell proliferation. Consistent with the increased levels of auxin, hybrids have larger and more palisade cells than the parents at the same time point. We propose a possible mechanism of early biomass heterosis through the early establishment of photosynthesis and auxin biosynthesis, providing insights into how transcriptional changes in hybrids are translated into phenotypical heterosis. This finding could be utilized in future Canola breeding to identify hybrid combinations with the superior early seedling establishment and strong levels of hybrid vigor in later plant development.
The iCanCope pain self-management application for adolescents with juvenile idiopathic arthritis: a pilot randomized controlled trial
Authors: Lalloo Chitra , Harris Lauren R , Hundert Amos S , Berard Roberta , Cafazzo Joseph , Connelly Mark , Feldman Brian M , Houghton Kristin , Huber Adam , Laxer Ronald M , Luca Nadia , Schmeling Heinrike , Spiegel Lynn , Tucker Lori B , Pham Quynh , Davies-Chalmers Cleo C , Stinson Jennifer N
Published: March 2020

Objectives

To evaluate the feasibility and preliminary effectiveness of iCanCope with Pain (iCanCope), a smartphone-based pain self-management program, in adolescents with JIA. iCanCope featured symptom tracking, goal-setting, pain coping skills and social support.

Methods

A two-arm pilot randomized controlled trial was used to evaluate the iCanCope app compared with a version with symptom tracking only. Primary (feasibility) outcomes were: participant accrual/attrition rates, success of app deployment, acceptability and adherence. Secondary (preliminary effectiveness) outcomes were: pain intensity, pain-related activity limitations and health-related quality of life. Outcomes were assessed at baseline and 8 weeks. Adherence was defined as the proportion of completed symptom reports: ‘low’ (≤24%); ‘low-moderate’ (25–49%); ‘high-moderate’ (50–75%); or ‘high’ (76–100%). Linear mixed models were applied for preliminary effectiveness analyses as per intention-to-treat.

Results

Adolescents (N = 60) were recruited from three paediatric rheumatology centres. Rates of accrual and attrition were 82 and 13%, respectively. Both apps were deployed with high success (over 85%) and were rated as highly acceptable. Adherence was similar for both groups, with most participants demonstrating moderate-to-high adherence. Both groups exhibited a clinically meaningful reduction in pain intensity (≥1 point) that did not statistically differ between groups. There were no significant changes in activity limitations or health-related quality of life.

Conclusion

The iCanCope pilot randomized controlled trial was feasible to implement in a paediatric rheumatology setting. Both apps were deployed successfully, with high acceptability, and were associated with moderate-to-high adherence. Preliminary reductions in pain intensity warrant a future trial to evaluate effectiveness of iCanCope in improving health outcomes in adolescents with JIA.

Trial registration

ClinicalTrials.gov identifier: NCT02764346.
Ambiguous Encounters: Revisiting Foucault and Goffman at an Activation Programme for Asylum-seekers
Authors: Kohl Katrine Syppli
Published: March 2020

This qualitative study combined the approaches of Foucault and Goffman to investigate the consequences of a “roll-out” neoliberal “activation” programme on Denmark’s reception of asylum-seekers. The analysis found that the activation programme is an ambiguous technology of power intended to shape asylum-seekers into productive citizens by simultaneously disciplining them and improving their health and well-being, while using their labour to reduce costs. The strategic interactions in the job centre reflected the ambiguities created by these oft-incongruent aims, and activation caused conflicts as it amplified activities experienced as meaningless and humiliating. I argue that these consequences stem from the ambiguity, uncertainty, and trouble produced at the intersection of competing projects of rule in a “sensitive space”, and that the individualisation of responsibility for their own marginalisation, simultaneously serve to exclude asylum-seekers and to confine them to categories that license continued institutional discipline. Thereby, the intervention feeds cyclical process of failed integration and ill-fated interventions. Indeed, by individualising the responsibility for integration, such interventions depoliticise the marginalisation of citizens of immigrant decent and legitimise efforts to reduce immigration by fuelling problematisations of immigrants as expensive, deviant, and less employable.
Phylogenetic conservation of soil bacterial responses to simulated global changes
Authors: Isobe Kazuo , Bouskill Nicholas J. , Brodie Eoin L. , Sudderth Erika A. , Martiny Jennifer B. H.
Published: March 2020

Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO
2
concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes.

This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
Interaction-dependent effects of surface structure on microbial spatial self-organization
Authors: Ciccarese Davide , Zuidema Anita , Merlo Valeria , Johnson David R.
Published: March 2020

Surface-attached microbial communities consist of different cell types that, at least to some degree, organize themselves non-randomly across space (referred to as spatial self-organization). While spatial self-organization can have important effects on the functioning, ecology and evolution of communities, the underlying determinants of spatial self-organization remain unclear. Here, we hypothesize that the presence of physical objects across a surface can have important effects on spatial self-organization. Using pairs of isogenic strains of
Pseudomonas stutzeri
, we performed range expansion experiments in the absence or presence of physical objects and quantified the effects on spatial self-organization. We demonstrate that physical objects create local deformities along the expansion frontier, and these deformities increase in magnitude during range expansion. The deformities affect the densities of interspecific boundaries and diversity along the expansion frontier, and thus affect spatial self-organization, but the effects are interaction-dependent. For competitive interactions that promote sectorized patterns of spatial self-organization, physical objects increase the density of interspecific boundaries and diversity. By contrast, for cross-feeding interactions that promote dendritic patterns, they decrease the density of interspecific boundaries and diversity. These qualitatively different outcomes are probably caused by fundamental differences in the orientations of the interspecific boundaries. Thus, in order to predict the effects of physical objects on spatial self-organization, information is needed regarding the interactions present within a community and the general geometric shapes of spatial self-organization that emerge from those interactions.

This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
The evolution of competitive ability for essential resources
Authors: Bernhardt Joey R. , Kratina Pavel , Pereira Aaron Louis , Tamminen Manu , Thomas Mridul K. , Narwani Anita
Published: March 2020

Competition for limiting resources is among the most fundamental ecological interactions and has long been considered a key driver of species coexistence and biodiversity. Species' minimum resource requirements, theirR*s, are key traits that link individual physiological demands to the outcome of competition. However, a major question remains unanswered—to what extent are species’ competitive traits able to evolve in response to resource limitation? To address this knowledge gap, we performed an evolution experiment in which we exposedChlamydomonas reinhardtiifor approximately 285 generations to seven environments in chemostats that differed in resource supply ratios (including nitrogen, phosphorus and light limitation) and salt stress. We then grew the ancestors and descendants in a common garden and quantified their competitive abilities for essential resources. We investigated constraints on trait evolution by testing whether changes in resource requirements for different resources were correlated. Competitive abilities for phosphorus improved in all populations, while competitive abilities for nitrogen and light increased in some populations and decreased in others. In contrast to the common assumption that there are trade-offs between competitive abilities for different resources, we found that improvements in competitive ability for a resource came at no detectable cost. Instead, improvements in competitive ability for multiple resources were either positively correlated or not significantly correlated. Using resource competition theory, we then demonstrated that rapid adaptation in competitive traits altered the predicted outcomes of competition. These results highlight the need to incorporate contemporary evolutionary change into predictions of competitive community dynamics over environmental gradients.

This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
Dormancy dynamics and dispersal contribute to soil microbiome resilience
Authors: Sorensen Jackson W. , Shade Ashley
Published: March 2020

In disturbance ecology, stability is composed of resistance to change and resilience towards recovery after the disturbance subsides. Two key microbial mechanisms that can support microbiome stability include dormancy and dispersal. Specifically, microbial populations that are sensitive to disturbance can be re-seeded by local dormant pools of viable and reactivated cells, or by immigrants dispersed from regional metacommunities. However, it is difficult to quantify the contributions of these mechanisms to stability without, first, distinguishing the active from inactive membership, and, second, distinguishing the populations recovered by local resuscitation from those recovered by dispersed immigrants. Here, we investigate the contributions of dormancy dynamics (activation and inactivation), and dispersal to soil microbial community resistance and resilience. We designed a replicated, 45-week time-series experiment to quantify the responses of the active soil microbial community to a thermal press disturbance, including unwarmed control mesocosms, disturbed mesocosms without dispersal, and disturbed mesocosms with dispersal after the release of the stressor. Communities changed in structure within one week of warming. Though the disturbed mesocosms did not fully recover within 29 weeks, resuscitation of thermotolerant taxa was key for community transition during the press, and both resuscitation of opportunistic taxa and immigration contributed to community resilience. Also, mesocosms with dispersal were more resilient than mesocosms without. This work advances the mechanistic understanding of how microbiomes respond to disturbances in their environment.

This article is part of the theme issue ‘Conceptual challenges in microbial community ecology’.
Accelerating the sustainable development goals through microbiology: some efforts and opportunities
Authors: Fagunwa Omololu E. , Olanbiwoninu Afolake A.
Published: March 2020

Modernization has thrown humanity and other forms of life on our planet into a ditch of problems. Poverty, climate change, injustice and environmental degradation are a few of the shared global problems. The United Nations Sustainable Development Goals (SDGs) are the blueprint to achieve a better and more sustainable future for all. The SDGs are well structured to address the global challenges we face including poverty, inequalities, hunger, climate change, environmental degradation, peace and justice. Five years into the implementation, the SDGs have been driven mainly by international donors and ‘professional’ international development organizations. The world is left with 10 years to achieve these ambitious goals and targets. Various reviews show that little has been achieved overall, and the SDGs will not be a reality if a new strategy is not in place to bring inclusion. Microbiology, the scientific discipline of microbes, their effects and practical uses has insightful influence on our day-to-day living. We present how microbiology and microbiologists could increase the scorecard and accelerate these global goals. Microbiology has a direct link to achieving SDGs addressing food security, health and wellbeing, clean energy, environmental degradation and climate change. A non-classical growing relationship exists between microbiology and other SDGs such as peace, justice, gender equality, decent work and economic growth. The pledge of ‘Leave No One Behind’ will fast track progress and microbiology is in a better position to make this work.