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Background: It is unknown what effect the menstrual cycle can have on the susceptibility to trauma following sexual assault. Objectives: To compare the incidence of genital injuries following sexual assault in women with relationship to the three phases of the menstrual cycle Methods: The design was a retrospective, cohort analysis set in a community-based nurse examiner program over a five-year study period. Sexual assault victims were between the ages of 13 - 40 years and agreed to a forensic examination. The menstrual cycle was divided into three phases: follicular, luteal and menses phase. The primary outcomes were the frequency and type of genital injuries documented in relation to the different phases of the menstrual cycle. Results: Case files of 1376 cases of sexual assault were reviewed; 682 (49.6%) met the inclusion criteria. A total of 220 victims (32.3%) were in the follicular phase, 361 (52.9%) were in the luteal phase and 101 (14.8%) were in the menses phase. The three groups were comparable in terms of demographics, assault characteristics, and overall frequency of non-genital injuries. Assault victims in the follicular phase of the menstrual cycle had significantly more documented genital injuries (72.3%; 95% CI 66.4 - 78.2) compared to the luteal phase (64.0%; 95% CI 59.0 - 68.9) and the menses phase (58.4%; 95% CI 48.8 - 68.0). Conclusion: Forensic examiners documented more genital injuries in the follicular phase of the menstrual cycle. Sex hormones may have confounding effects through influences on vaginal epithelial and mucosal integrity.

Supplemental Material for Signaling through the IL-6-STAT3 Pathway Promotes Proteolytically-Active Macrophage Accumulation Necessary for Development of Small AAA by Raj Patel, SarahRose Hall, Hayes Lanford, Nicholas Ward, R. Tyler Grespin, Mario Figueroa, Victoria Mattia, Ying Xiong, Rupak Mukherjee, Jeffrey Jones, and Jean Marie Ruddy in Vascular and Endovascular Surgery

We present measurements and simulations of semiconductor-superconductor heterostructure devices that are consistent with the observation of topological superconductivity and Majorana zero modes. The devices are fabricated from high-mobility two-dimensional electron gases in which quasi-one-dimensional wires are defined by electrostatic gates. These devices enable measurements of local and non-local transport properties and have been optimized via extensive simulations to ensure robustness against non-uniformity and disorder. Our main result is that several devices, fabricated according to the design's engineering specifications, have passed the topological gap protocol defined in Pikulin \textit{et al.} [arXiv:2103.12217]. This protocol is a stringent test composed of a sequence of three-terminal local and non-local transport measurements performed while varying the magnetic field, semiconductor electron density, and junction transparencies. Passing the protocol indicates a high probability of detection of a topological phase hosting Majorana zero modes as determined by large-scale disorder simulations. Our experimental results are consistent with a quantum phase transition into a topological superconducting phase that extends over several hundred millitesla in magnetic field and several millivolts in gate voltage, corresponding to approximately one hundred micro-electron-volts in Zeeman energy and chemical potential in the semiconducting wire. These regions feature a closing and re-opening of the bulk gap, with simultaneous zero-bias conductance peaks at \textit{both} ends of the devices that withstand changes in the junction transparencies. The extracted maximum topological gaps in our devices are 20-$60\,\mu$eV. This demonstration is a prerequisite for experiments involving fusion and braiding of Majorana zero modes., Comment: Added: a second device design; data from an additional device with larger topological gap; further testing of the TGP via simulations; links to a repo containing the raw data and analysis scripts necessary to reproduce all figures containing experimental or simulated data

Copper (Cu) is the most extensively used bactericide worldwide in many agricultural production systems. However, intensive application of Cu bactericide have increased the selection pressure toward Cu-tolerant pathogens, including Xanthomonas perforans, the causal agent of tomato bacterial spot. However, alternatives for Cu bactericides are limited and have many drawbacks including plant damage and inconsistent effectiveness under field conditions. Also, potential ecological risk on nontarget organisms exposed to field runoff containing Cu is high. However, due to lack of alternatives for Cu, it is still widely used in tomato and other crops around the world in both conventional and organic production systems. In this study, a Cu-tolerant X. perforans strain GEV485, which can tolerate eight tested commercial Cu bactericides, was used in all the field trials to evaluate the efficacy of MgO nanomaterial. Four field experiments were conducted to evaluate the impact of intensive application of MgO nanomaterial on tomato bacterial spot disease severity, and one field experiment was conducted to study the impact of soil accumulation of total and bioavailable Cu, Mg, Mn, and Zn. In the first two field experiments, twice-weekly applications of 200 μg/mL MgO significantly reduced disease severity by 29-38% less in comparison to a conventional Cu bactericide Kocide 3000 and 19-30% less in comparison to the water control applied at the same frequency (p = 0.05). The disease severity on MgO twice-weekly was 12-32% less than Kocide 3000 + Mancozeb treatment. Single weekly applications of MgO had 13-19% higher disease severity than twice weekly application of MgO. In the second set of two field trials, twice-weekly applications of MgO at 1000 μg/mL significantly reduced disease severity by 32-40% in comparison to water control applied at the same frequency (p = 0.05). There was no negative yield impact in any of the trials. The third field experiment demonstrated that application of MgO did not result in significant accumulation of total and bioavailable Mg, Mn, Cu, or Zn in the root-associated soil and in soil farther away from the production bed compared to the water control. However, Cu bactericide contributed to significantly higher Mn, Cu, and Zn accumulation in the soil compared to water control (p = 0.05). This study demonstrates that MgO nanomaterial could be an alternative for Cu bactericide and have potential in reducing risks associated with development of tolerant strains and for reducing Cu load in the environment.

A shortcut review was carried out to establish whether topical lidocaine was effective at reducing pain and improving oral intake in children with painful oral lesions. 34 papers were found using the reported searches, of which two presented the best available evidence to answer the clinical question. The author, date and country of publication, patient group studied, study type, relevant outcomes, results and study weaknesses of these two papers are tabulated. It is concluded that in otherwise healthy paediatric patients with painful oral ulcers, treatment with viscous lidocaine does not improve oral intake, although it may provide some pain relief.

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Additional file 6:Table S6: Genes/contigs representing T6SS in draft genomes as compared to Xcv. (DOC 44 KB)

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Additional file 7:Table S7: Domain architecture and distribution of proteins with HD-GYP, GGDEF and/or EAL domains encoded by genomes of different Xanthomonas strains. (PDF 348 KB)

Additional file 2:Figure S2: 1a) Phylogenetic tree based on MUMi indices; 1b) Distance matrix based on MUMi indices. MUMi program was used to calculate pairwise distances between draft genomes and reference Xanthomonas genomes. (PDF 93 KB)

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Additional file 8:Table S8: Genes unique to Xp, grouped in clusters. (DOC 104 KB)

Additional file 3:Table S3: Whole genome comparisons using MUMmer dnadiff program. % coverage of the aligned contigs and % identities of the respective contigs against reference genomes has been shown for each draft genome. (DOC 36 KB)

Additional file 3:Table S3: Whole genome comparisons using MUMmer dnadiff program. % coverage of the aligned contigs and % identities of the respective contigs against reference genomes has been shown for each draft genome. (DOC 36 KB)

Additional file 5:Table S5: Evidence of the horizontal gene transfer using Alien_hunter analysis. (DOC 33 KB)

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Authors’ original file for figure 8

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Additional file 9:Table S9: Genes common to all pepper pathogens but absent from Xp. (DOC 77 KB)

Additional file 7:Table S7: Domain architecture and distribution of proteins with HD-GYP, GGDEF and/or EAL domains encoded by genomes of different Xanthomonas strains. (PDF 348 KB)

Additional file 6:Table S6: Genes/contigs representing T6SS in draft genomes as compared to Xcv. (DOC 44 KB)

Authors’ original file for figure 7

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Additional file 9:Table S9: Genes common to all pepper pathogens but absent from Xp. (DOC 77 KB)

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Additional file 1:Table S1: General features of the sequencing data and of the de novo assemblies of draft genomes of Xv, Xp and Xg using individual sequencing methods. (DOC 48 KB)

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Authors’ original file for figure 1

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

Additional file 8:Table S8: Genes unique to Xp, grouped in clusters. (DOC 104 KB)

Additional file of Comparative genomics reveals diversity among xanthomonads infecting tomato and pepper

This thesis will defend a new variety of panprotopsychism which does not have a class of so-called combination problems that some popular varieties of panprotopsychism have. Panprotopsychism is the view that conscious entities depend on protophenomenal constituents and that these constituents are fundamental, ubiquitous and neutral. One very popular variety, Constitutive Russellian Panprotopsychism (CRP) has three additional distinctive doctrines. (1) Russellian Monism: protoconsciousness is located in a fundamental constituent’s intrinsic nature. (2) Neutral Monism: protophenomenal properties are neither physical nor phenomenal. (3) Constitution: the right combination of protophenomenal constituents alone is meant to produce consciousness. There are at least three combination problems for CRP. The first is that the conditions for the combination of protoconscious entities, and the nature of these bonds, is a mystery. Consequently, we can conceive of a structurally and protophenomenally duplicate world without any phenomenal properties. This is the Conceivability Problem. Secondly, consciousness seems unified and monadic, which is incompatible with the idea that consciousness has parts. However, if consciousness cannot have parts strong emergence seems necessary, which is undesirable. This is the Composition Problem. Finally, even though microphysical and protophenomenal properties are meant to be isomorphic, the structure of our brains and visual fields are not. This is the Structural Mismatch Problem. I defend Structural Transformational Identity Theory Panprotopsychism (STIP) as a superior alternative. STIP has three distinctive doctrines. (1) Identity Theory Panprotopsychism: fundamental constituents are both simultaneously physical and protophenomenal. (2) Transformational Fusion: multiple fundamental constituents go through intrinsic change to generate a singular simple. (3) Modified Ontic Structural Realism: fundamental constituents, including protophenomenal constituents, are not relata, but relations. Some of these relations are microphysical while others are protophenomenal. My conclusion is that the three combination problems for CRP do not exist for my STIP even though the latter view preserves all of the original intuitions of the former view.

Patients with chronic lymphocytic leukaemia/small lymphocytic lymphoma (CLL/SLL) with deletion 17p [del(17p)] have poor outcomes with chemoimmunotherapy. Ibrutinib is indicated for the treatment of CLL/SLL, including del(17p) CLL/SLL, and allows for treatment without chemotherapy. This integrated analysis was performed to evaluate outcomes in 230 patients with relapsed/refractory del(17p) CLL/SLL from three ibrutinib studies. With a median of 2 prior therapies (range, 1-12), 18% and 79% of evaluable patients had del(11q) or unmutated IGHV, respectively. With a median follow-up of 28months, overall response rate was 85% and estimated 30-month progression-free and overall survival rates were 57% [95% confidence interval (CI) 50-64] and 69% (95% CI 61-75), respectively. Patients with normal lactate dehydrogenase or no bulky disease had the most favourable survival outcomes. Sustained haematological improvements in haemoglobin, platelet count and absolute neutrophil count occurred in 61%, 67% and 70% of patients with baseline cytopenias, respectively. New onset severe cytopenias and infections decreased in frequency over time. Progression-free and overall survival with ibrutinib surpass those of other therapies for patients with del(17p) CLL/SLL. These results provide further evidence of the robust clinical activity of ibrutinib in difficult-to-treat CLL/SLL populations.

When Frank Zappa died in 1993, he left Civilization Phaze III as a last testament to both his musical and thematic purpose. The work received a handful of reviews in the popular music press, and has subsequently been ignored by both the popular press and, with few exceptions, academia. Many are the composers whose careers have been thought describe a mid-period mastery, followed by later decline. This presumption seems to have fallen upon Frank Zappa, apparently due to his retirement from the concert stage, and final years writing music on the Synclavier. This thesis seeks to demonstrate that Zappa's compositional abilities were in no way diminished at the end of his life, but had instead reached a peak level of mastery in composition of his last work. This thesis shall provide an analysis and musical/extra-musical description of this piece, with the intention of situating it in relation to Zappa's compositional legacy, and to establish Civilization Phaze III as the crowning compositional achievement of his career.

Tandem mass spectrometry (MS/MS) based proteomic workflows with a bottom-up approach require enzymatic digestion of proteins to peptide analytes, usually by trypsin. On-line coupling of trypsin digestion of proteins, using an immobilized enzyme reactor (IMER), with liquid chromatography (LC) and MS/MS is becoming a frequently used approach. However, finding IMER digestion conditions that allow quantitative analysis of multiple proteins with wide range of endogenous concentration requires optimization of multiple interactive parameters; digestion buffer flow rate, injection volume, sample dilution, and surfactant type/concentration. In this report, we present a design of experiment (DoE) approach for the optimization of an integrated IMER-LC-MS/MS platform. With bovine serum albumin as a model protein, the digestion efficacy and digestion rate were monitored based on LC-MS/MS peak area count versus protein concentration regression. The optimal parameters were determined through multivariate surface response modelling and consideration of diffusion controlled immobilized enzyme kinetics. The results may provide guidance to other users for the development of quantitative IMER-LC-MS/MS methods for other proteins.

Induction of Ta.14164.1.S1_s_at and Ta.7291.1.S1_s_at is strain specific. XT8 is X. translucens pv. translucens, XT123 is X. translucens pv. cerealis, XT130, XT5523, XT5770 and XT5791 are strains of X. translucens pv. undulosa. M2 is the mutant of XT4699 lack of tal6. The relative expression level is calculated relative to M2 treatment by with 2-∆∆Ct method. A, the relative expression of Ta.14164.1.S1_s_at, corresponding to bHLH gene, was calculated; B, the relative expression of Ta.7291.1.S1_s_at, corresponding to succinate dehydrogenase gene, was calculated. The lowercase letters indicate significantly different groups with P-value

Bacterial population assay. Equal amount of 4x104 dilution of bacterial inoculum of different tal mutants, hrcC mutant and WT were inoculated on 3-week-old Chinese Spring wheat by needleless syringe. At 6DPI, three inoculated leaves (3 cm) were pooled and ground together in each treatment. Samples were serially diluted and 100 μl of diluted samples were added to TSA plates. Plates were incubated at 28 °C for colony formation. Data represents the mean of Log10 CFU/cm leaf ± standard deviation. The * indicates the significant difference of bacterial population of hrcC − mutant compared to other tal mutants or WT at 6DPI under p-value

Validation of all eight TAL mutants in XT4699 by PCR. The sequence of specific primers for each TAL gene and the primer from the vector are provided in Table S6. The desired PCR product size is around 1.5Â kb. The corresponding names of TAL genes are shown for all 8 mutants. A, M1 (tal2 mutant), M2 (tal6 mutant); B, M3 (tal7 mutant), M4 (tal1 mutant); C, M5 (tal5 mutant), M6 (tal8 mutant); D, M7 (tal3 mutant), M8 (tal4 mutant). (PDF 351 kb)

Induction of host genes is impaired by mutation of specific TAL genes. M2 is lack of tal6, M3 is lack of tal7 and M4 is the mutant of tal1. A, relative expression level of Ta.7291.1.S1_at, corresponding to succinate dehydrogenase subunit gene, was calculated compared to M2 treatment; B, relative expression level of Ta.14824.1.S1_at, corresponding to choline transporter related gene, was calculated compared to M3 treatment; C, relative expression level of Ta.9765.1.S1_at, corresponding to cell wall invertase gene, was calculated compared to M4 treatment. 2-∆∆Ct method was applied in calculation. The * indicates significant difference compared to other TAL mutants treated samples with P-value

XT4699-tal7 is a conserved TAL effector gene. Primer pair used for cloning tal7 gene in XT4699 was applied in PCR with template DNA of other strains from North Dakota and Kansas. PCR bands with similar size as XT4699-tal7 were shown in the blue box. (PDF 118 kb)

Phylogenetic tree based on CRISPR Cas loci of X. translucens strains. The sequence of CRISPR Cas genes is annotated in RAST website http://rast.nmpdr.org . The phylogenetic tree was generated using Geneious software Version 6 with the Tamura-Nei genetic distance model and the Neighbor-joining method, with PXO99 CRISPR Cas genes as outgroup. The scale bar indicates number of nucleotide substitutions per site. (PDF 149 kb)

Southern blot analysis of two X. translucens pv. undulosa strains from Kansas. Genomic DNA digested by BamHI and hybridized by sphI fragment of TAL effector gene in X. oryzae pv. oryzae strain AXO1947. The size of blotted bands is consistent with assembly genome of XT4699. (PDF 182 kb)

Data coverage of XT4699 PacBio and Illumina sequences. A) Coverage of PacBio sequences (light blue) and Illumina sequences (orange) across the genome. B) The relationship between Illumina sequencing coverage and GC% of non-overlapping 200Â bp windows. C) Visualization of the alignment of Illumina assembled contigs on the XT4699 reference genome. D) The relationship between PacBio sequencing coverage and GC% of non-overlapping 200Â bp windows. (PDF 487 kb)

Syntenic gene clusters of type III secretion system among X. translucens strains. XT-Rocky and XT4699 are X. translucens pv. undulosa while ART-Xtg29 is X. translucens pv. gramins. White arrows (drawn to scale) represent orientation and position of Hrp genes. Black arrows indicate the two predicted IS elements in ART-Xtg29 strain. The names of Hrp genes are shown above or under the white arrows. The identity of homologous proteins of compared strains is shown between them. (PDF 155 kb)

Syntenic gene clusters of type III secretion system among X. translucens strains. XT-Rocky and XT4699 are X. translucens pv. undulosa while ART-Xtg29 is X. translucens pv. gramins. White arrows (drawn to scale) represent orientation and position of Hrp genes. Black arrows indicate the two predicted IS elements in ART-Xtg29 strain. The names of Hrp genes are shown above or under the white arrows. The identity of homologous proteins of compared strains is shown between them. (PDF 155 kb)