But I’m not ready! Common barriers to writing and how to overcome them

Writing a thesis can feel overwhelming. In this post, Hugh Kearns and Maria Gardiner are here to help. They detail the common reasons why PhD students tend to avoid writing and counter them with strategies to counter procrastination and perfectionism

Effects of Feeding Bt Maize to Sows during Gestation and Lactation on Maternal and Offspring Immunity and Fate of Transgenic Material

peer-reviewedBackground: We aimed to determine the effect of feeding transgenic maize to sows during gestation and lactation on maternal and offspring immunity and to assess the fate of transgenic material. Methodology/Principal Findings: On the day of insemination, sows were assigned to one of two treatments (n = 12/treatment); 1) non-Bt control maize diet or 2) Bt-MON810 maize diet, which were fed for ~143 days throughout gestation and lactation. Immune function was assessed by leukocyte phenotyping, haematology and Cry1Ab-specific antibody presence in blood on days 0, 28 and 110 of gestation and at the end of lactation. Peripheral-blood mononuclear cell cytokine production was investigated on days 28 and 110 of gestation. Haematological analysis was performed on offspring at birth (n = 12/treatment). Presence of the cry1Ab transgene was assessed in sows' blood and faeces on day 110 of gestation and in blood and tissues of offspring at birth. Cry1Ab protein presence was assessed in sows' blood during gestation and lactation and in tissues of offspring at birth. Blood monocyte count and percentage were higher (P<0.05), while granulocyte percentage was lower (P<0.05) in Bt maize-fed sows on day 110 of gestation. Leukocyte count and granulocyte count and percentage were lower (P<0.05), while lymphocyte percentage was higher (P<0.05) in offspring of Bt maize-fed sows. Bt maize-fed sows had a lower percentage of monocytes on day 28 of lactation and of CD4+CD8+ lymphocytes on day 110 of gestation, day 28 of lactation and overall (P<0.05). Cytokine production was similar between treatments. Transgenic material or Cry1Ab-specific antibodies were not detected in sows or offspring. Conclusions/Significance: Treatment differences observed following feeding of Bt maize to sows did not indicate inflammation or allergy and are unlikely to be of major importance. These results provide additional data for Bt maize safety assessment.The research leading to these results has received funding from the European Union's Seventh Framework Programme (FP7/2007–2013) under grant agreement number 211820 and the Teagasc Walsh Fellowship Programme

Coherence resonance in a network of FitzHugh-Nagumo systems: interplay of noise, time-delay and topology

We systematically investigate the phenomena of coherence resonance in time-delay coupled networks of FitzHugh-Nagumo elements in the excitable regime. Using numerical simulations, we examine the interplay of noise, time-delayed coupling and network topology in the generation of coherence resonance. In the deterministic case, we show that the delay-induced dynamics is independent of the number of nearest neighbors and the system size. In the presence of noise, we demonstrate the possibility of controlling coherence resonance by varying the time-delay and the number of nearest neighbors. For a locally coupled ring, we show that the time-delay weakens coherence resonance. For nonlocal coupling with appropriate time-delays, both enhancement and weakening of coherence resonance are possible

Evaluation of the Efficacy and Safety of a Marine-Derived Bacillus Strain for Use as an In-Feed Probiotic for Newly Weaned Pigs

peer-reviewedForty eight individual pigs (8.7±0.26 kg) weaned at 28±1 d of age were used in a 22-d study to evaluate the effect of oral administration of a Bacillus pumilus spore suspension on growth performance and health indicators. Treatments (n = 16) were: (1) non-medicated diet; (2) medicated diet with apramycin (200 mg/kg) and pharmacological levels of zinc oxide (2,500 mg zinc/kg) and (3) B. pumilus diet (non-medicated diet + 1010 spores/day B. pumilus). Final body weight and average daily gain tended to be lower (P = 0.07) and feed conversion ratio was worsened (P<0.05) for the medicated treatment compared to the B. pumilus treatment. Ileal E. coli counts were lower for the B. pumilus and medicated treatments compared to the non-medicated treatment (P<0.05), perhaps as a result of increased ileal propionic acid concentrations (P<0.001). However, the medicated treatment reduced fecal (P<0.001) and cecal (P<0.05) Lactobacillus counts and tended to reduce the total cecal short chain fatty acid (SCFA) concentration (P = 0.10). Liver weights were lighter and concentrations of liver enzymes higher (P<0.05) in pigs on the medicated treatment compared to those on the non-medicated or B. pumilus treatments. Pigs on the B. pumilus treatment had lower overall lymphocyte and higher granulocyte percentages (P<0.001) and higher numbers of jejunal goblet cells (P<0.01) than pigs on either of the other two treatments or the non-medicated treatment, respectively. However, histopathological examination of the small intestine, kidneys and liver revealed no abnormalities. Overall, the B. pumilus treatment decreased ileal E. coli counts in a manner similar to the medicated treatment but without the adverse effects on growth performance, Lactobacillus counts, cecal SCFA concentration and possible liver toxicity experienced with the medicated treatment.The study was funded by the Higher Education Authority/Institutes of Technology Ireland Technological Sector Research Strand III Programme

First Passage and Cooperativity of Queuing Kinetics

We model the kinetics of ligand-receptor systems, where multiple ligands may bind and unbind to the receptor, either randomly or in a specific order. Equilibrium occupation and first occurrence of complete filling of the receptor are determined and compared. At equilibrium, receptors that bind ligands sequentially are more likely to be saturated than those that bind in random order. Surprisingly however, for low cooperativity, the random process first reaches full occupancy faster than the sequential one. This is true {\it except} near a critical binding energy where a 'kinetic trap' arises and the random process dramatically slows down when the number of binding sites $N\geq 8$. These results demonstrate the subtle interplay between cooperativity and sequentiality for a wide class of kinetic phenomena, including chemical binding, nucleation, and assembly line strategies.Comment: 5pp, 5 figure

Threat Models over Space and Time: A Case Study of E2EE Messaging Applications

Threat modelling is foundational to secure systems engineering and should be done in consideration of the context within which systems operate. On the other hand, the continuous evolution of both the technical sophistication of threats and the system attack surface is an inescapable reality. In this work, we explore the extent to which real-world systems engineering reflects the changing threat context. To this end we examine the desktop clients of six widely used end-to-end-encrypted mobile messaging applications to understand the extent to which they adjusted their threat model over space (when enabling clients on new platforms, such as desktop clients) and time (as new threats emerged). We experimented with short-lived adversarial access against these desktop clients and analyzed the results with respect to two popular threat elicitation frameworks, STRIDE and LINDDUN. The results demonstrate that system designers need to both recognise the threats in the evolving context within which systems operate and, more importantly, to mitigate them by rescoping trust boundaries in a manner that those within the administrative boundary cannot violate security and privacy properties. Such a nuanced understanding of trust boundary scopes and their relationship with administrative boundaries allows for better administration of shared components, including securing them with safe defaults

Non-Insertive Acupuncture and Neonatal Abstinence Syndrome: A Case Series from an Inner City Safety Net Hospital

OBJECTIVE: We report on the safety of non-insertive acupuncture (NIA) in 54 newborns diagnosed with Neonatal Abstinence Syndrome (NAS) in a busy inner city hospital. METHODS: For this case series, a retrospective chart review was conducted. Data on participant demographics, number of NIA treatments, provider referrals, and outcomes of interest (sleeping, feeding, and adverse events) were collected. RESULTS: Of the 54 newborns receiving NIA, 86% were non-Hispanic White; 87% were on Medicaid, and gestational age ranged from 33.2 to 42.1 weeks. Out of 54 chart reviews, a total of 92 NIA sessions were documented ranging from 1 to 6 sessions per infant. Of the total number of treatments (n = 92), 73% were requested by a physician. Chart reviews reported restless infants calmed down during NIA, babies slept through or fell asleep immediately following NIA, and better feeding was noted following NIA. There were no adverse events noted in the medical records. CONCLUSIONS: This retrospective chart review shows potential for the use of NIA as an adjunctive treatment in newborns with NAS symptoms during hospitalization. More research is necessary to study whether the incorporation of NIA can result in positive outcomes in newborns withdrawing from narcotics

Effects of feeding Bt MON810 maize to sows during first gestation and lactation on maternal and offspring health indicators

A total of twenty-four sows and their offspring were used in a 20-week study to investigate the effects of feeding GM maize on maternal and offspring health. Sows were fed diets containing GM or non-GM maize from service to the end of lactation. GM maize-fed sows were heavier on day 56 of gestation (P< 0·05). Offspring from sows fed GM maize tended to be lighter at weaning (P= 0·08). Sows fed GM maize tended to have decreased serum total protein (P= 0·08), and increased serum creatinine (P< 0·05) and γ-glutamyltransferase activity (P= 0·07) on day 28 of lactation. Serum urea tended to be decreased on day 110 of gestation in GM maize-fed sows (P= 0·10) and in offspring at birth (P= 0·08). Both platelet count (P= 0·07) and mean cell Hb concentration (MCHC; P= 0·05) were decreased on day 110 of gestation in GM maize-fed sows; however, MCHC tended to be increased in offspring at birth (P= 0·08). There was a minimal effect of feeding GM maize to sows during gestation and lactation on maternal and offspring serum biochemistry and haematology at birth and body weight at weaning

Methyl Selenol as Precursor in Selenite Reduction to Se/S Species by Methane-oxidizing Bacteria.

A wide range of microorganisms have been shown to transform selenium-containing oxyanions to reduced forms of the element, particularly selenium-containing nanoparticles. Such reactions are promising for detoxification of environmental contamination and production of valuable selenium-containing products such as nanoparticles for application in biotechnology. It has previously been shown that aerobic methane-oxidising bacteria, including Methylococcus capsulatus (Bath), are able to perform methane-driven conversion of selenite (SeO32-) to selenium-containing nanoparticles and methylated selenium species. Here, the biotransformation of selenite by Mc. capsulatus (Bath) has been studied in detail via a range of imaging, chromatographic and spectroscopic techniques. The results indicate that the nanoparticles are produced extracellularly and have a composition distinct from nanoparticles previously observed from other organisms. The spectroscopic data from the methanotroph-derived nanoparticles are best accounted for by a bulk structure composed primarily of octameric rings in the form Se8-xSx with an outer coat of cell-derived biomacromolecules. Among a range of volatile methylated selenium and selenium-sulfur species detected, methyl selenol (CH3SeH) was found only when selenite was the starting material, although selenium nanoparticles (both biogenic and chemically produced) could be transformed into other methylated selenium species. This result is consistent with methyl selenol being an intermediate in methanotroph-mediated biotransformation of selenium to all the methylated and particulate products observed.ImportanceAerobic methane-oxidizing bacteria are ubiquitous in the environment. Two well characterised strains, Mc. capsulatus (Bath) and Methylosinus trichosporium OB3b, representing gamma- and alpha-proteobacterial methanotrophs, can convert selenite, an environmental pollutant, to volatile selenium compounds and selenium containing particulates. Both conversions can be harnessed for bioremediation of selenium pollution using biological or fossil methane as the feedstock and these organisms could be used to produce selenium-containing particles for food, and biotechnological applications. Using an extensive suite of techniques we identified precursors of selenium nanoparticle formation, and also that these nanoparticles are made up of eight membered mixed selenium and sulfur rings