An in vitro study into the accuracy of a novel method for recording the mandibular transverse horizontal axis.

OBJECTIVES: To assess the accuracy of a novel, non-invasive method for determining the axis of rotation of articulated dental study casts. METHOD: A 3D structured light scanner was constructed using a projector and two CMOS cameras. Dental stone casts were arbitrarily mounted on an average value articulator. With the teeth together, sets of 10 scans were taken from three different viewpoints. Each scan captured approximately six upper teeth and six lower teeth. The teeth were then propped open, creating 10mm of incisal separation, and the three sets of 10 scans were repeated. From each pair of scans an axis of rotation was calculated using custom software. A total of 900 axes were created this way. The locations of these axes were plotted in sagittal planes located 57.5mm left and right of the midline to represent the position of the temporo-mandibular joints (TMJs). The accuracy of axis location was then assessed. RESULTS: The average radius of error of the individual axes, compared to the real axis, was 2.65 ± 1.01 mm. 61.3% of the axes lay within 3mm of the true axis, and 99.2% of the axes lay within 5mm of the true axis. CONCLUSIONS: The accuracy of this method is clinically acceptable. Further studies are required to confirm the accuracy of the virtual inter-occlusal records at the level of the dentition. Clinical studies are then indicated to determine whether the transverse horizontal axis on a patient can similarly be determined

Thresholds for Abdominal Aortic Aneurysm Repair in England and the United States.

Background Thresholds for repair of abdominal aortic aneurysms vary considerably among countries. Methods We examined differences between England and the United States in the frequency of aneurysm repair, the mean aneurysm diameter at the time of the procedure, and rates of aneurysm rupture and aneurysm-related death. Data on the frequency of repair of intact (nonruptured) abdominal aortic aneurysms, in-hospital mortality among patients who had undergone aneurysm repair, and rates of aneurysm rupture during the period from 2005 through 2012 were extracted from the Hospital Episode Statistics database in England and the U.S. Nationwide Inpatient Sample. Data on the aneurysm diameter at the time of repair were extracted from the U.K. National Vascular Registry (2014 data) and from the U.S. National Surgical Quality Improvement Program (2013 data). Aneurysm-related mortality during the period from 2005 through 2012 was determined from data obtained from the Centers for Disease Control and Prevention and the U.K. Office of National Statistics. Data were adjusted with the use of direct standardization or conditional logistic regression for differences between England and the United States with respect to population age and sex. Results During the period from 2005 through 2012, a total of 29,300 patients in England and 278,921 patients in the United States underwent repair of intact abdominal aortic aneurysms. Aneurysm repair was less common in England than in the United States (odds ratio, 0.49; 95% confidence interval [CI], 0.48 to 0.49; P<0.001), and aneurysm-related death was more common in England than in the United States (odds ratio, 3.60; 95% CI, 3.55 to 3.64; P<0.001). Hospitalization due to an aneurysm rupture occurred more frequently in England than in the United States (odds ratio, 2.23; 95% CI, 2.19 to 2.27; P<0.001), and the mean aneurysm diameter at the time of repair was larger in England (63.7 mm vs. 58.3 mm, P<0.001). Conclusions We found a lower rate of repair of abdominal aortic aneurysms and a larger mean aneurysm diameter at the time of repair in England than in the United States and lower rates of aneurysm rupture and aneurysm-related death in the United States than in England. (Funded by the Circulation Foundation and others.)

Transplacental innate immune training via maternal microbial exposure: role of XBP1-ERN1 axis in dendritic cell precursor programming

We recently reported that offspring of mice treated during pregnancy with the microbial-derived immunomodulator OM-85 manifest striking resistance to allergic airways inflammation, and localized the potential treatment target to fetal conventional dendritic cell (cDC) progenitors. Here, we profile maternal OM-85 treatment-associated transcriptomic signatures in fetal bone marrow, and identify a series of immunometabolic pathways which provide essential metabolites for accelerated myelopoiesis. Additionally, the cDC progenitor compartment displayed treatment-associated activation of the XBP1-ERN1 signalling axis which has been shown to be crucial for tissue survival of cDC, particularly within the lungs. Our forerunner studies indicate uniquely rapid turnover of airway mucosal cDCs at baseline, with further large-scale upregulation of population dynamics during aeroallergen and/or pathogen challenge. We suggest that enhanced capacity for XBP1-ERN1-dependent cDC survival within the airway mucosal tissue microenvironment may be a crucial element of OM-85-mediated transplacental innate immune training which results in postnatal resistance to airway inflammatory disease

Case report 220

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/46818/1/256_2004_Article_BF00352557.pd

Space-efficient merging of succinct de Bruijn graphs

We propose a new algorithm for merging succinct representations of de Bruijn graphs introduced in [Bowe et al. WABI 2012]. Our algorithm is based on the lightweight BWT merging approach by Holt and McMillan [Bionformatics 2014, ACM-BCB 2014]. Our algorithm has the same asymptotic cost of the state of the art tool for the same problem presented by Muggli et al. [bioRxiv 2017, Bioinformatics 2019], but it uses less than half of its working space. A novel important feature of our algorithm, not found in any of the existing tools, is that it can compute the Variable Order succinct representation of the union graph within the same asymptotic time/space bounds.Comment: Accepted to SPIRE'1

A satellite DNA array barcodes chromosome 7 and regulates totipotency via ZFP819.

Mammalian genomes are a battleground for genetic conflict between repetitive elements and KRAB-zinc finger proteins (KZFPs). We asked whether KZFPs can regulate cell fate by using ZFP819, which targets a satellite DNA array, ZP3AR. ZP3AR coats megabase regions of chromosome 7 encompassing genes encoding ZSCAN4, a master transcription factor of totipotency. Depleting ZFP819 in mouse embryonic stem cells (mESCs) causes them to transition to a 2-cell (2C)-like state, whereby the ZP3AR array switches from a poised to an active enhancer state. This is accompanied by a global erosion of heterochromatin roadblocks, which we link to decreased SETDB1 stability. These events result in transcription of active LINE-1 elements and impaired differentiation. In summary, ZFP819 and TRIM28 partner up to close chromatin across Zscan4, to promote exit from totipotency. We propose that satellite DNAs may control developmental fate transitions by barcoding and switching off master transcription factor genes

Who bullies whom at a garden feeder? Interspecific agonistic interactions of small passerines during a cold winter

Interspecific agonistic interactions are important selective factors for maintaining ecological niches of different species, but their outcome is difficult to predict a priori. Here, we examined the direction and intensity of interspecific interactions in an assemblage of small passerines at a garden feeder, focussing on three finch species of various body sizes. We found that large and mediumsized birds usually initiated and won agonistic interactions with smaller species. Also, the frequency of fights increased with decreasing differences in body size between the participants. Finally, the probability of engaging in a fight increased with the number of birds at the feeder

The HUSH complex is a gatekeeper of type I interferon through epigenetic regulation of LINE-1s

The Human Silencing Hub (HUSH) complex is necessary for epigenetic repression of LINE-1 elements. We show that HUSH-depletion in human cell lines and primary fibroblasts leads to induction of interferon-stimulated genes (ISGs) through JAK/STAT signaling. This effect is mainly attributed to MDA5 and RIG-I sensing of double-stranded RNAs (dsRNAs). This coincides with upregulation of primate-conserved LINE-1s, as well as increased expression of full-length hominid-specific LINE-1s that produce bidirectional RNAs, which may form dsRNA. Notably, LTRs nearby ISGs are derepressed likely rendering these genes more responsive to interferon. LINE-1 shRNAs can abrogate the HUSH-dependent response, while overexpression of an engineered LINE-1 construct activates interferon signaling. Finally, we show that the HUSH component, MPP8 is frequently downregulated in diverse cancers and that its depletion leads to DNA damage. These results suggest that LINE-1s may drive physiological or autoinflammatory responses through dsRNA sensing and gene-regulatory roles and are controlled by the HUSH complex

Efficient assembly of very short oligonucleotides using T4 DNA Ligase

<p>Abstract</p> <p>Background</p> <p>In principle, a pre-constructed library of all possible short oligonucleotides could be used to construct many distinct gene sequences. In order to assess the feasibility of such an approach, we characterized T4 DNA Ligase activity on short oligonucleotide substrates and defined conditions suitable for assembly of a plurality of oligonucleotides.</p> <p>Findings</p> <p>Ligation by T4 DNA Ligase was found to be dependent on the formation of a double stranded DNA duplex of at least five base pairs surrounding the site of ligation. However, ligations could be performed effectively with overhangs smaller than five base pairs and oligonucleotides as small as octamers, in the presence of a second, complementary oligonucleotide. We demonstrate the feasibility of simultaneous oligonucleotide phosphorylation and ligation and, as a proof of principle for DNA synthesis through the assembly of short oligonucleotides, we performed a hierarchical ligation procedure whereby octamers were combined to construct a target 128-bp segment of the beta-actin gene.</p> <p>Conclusions</p> <p>Oligonucleotides as short as 8 nucleotides can be efficiently assembled using T4 DNA Ligase. Thus, the construction of synthetic genes, without the need for custom oligonucleotide synthesis, appears feasible.</p