Hybrid Improper Ferroelectricity in Columnar (NaY)MnMnTi4 O12.

We show that cation ordering on A site columns, oppositely displaced via coupling to B site octahedral tilts, results in a polar phase of the columnar perovskite (NaY)MnMnTi4 O12 . This scheme is similar to hybrid improper ferroelectricity found in layered perovskites, and can be considered a realisation of hybrid improper ferroelectricity in columnar perovskites. The cation ordering is controlled by annealing temperature and when present it also polarises the local dipoles associated with pseudo-Jahn-Teller active Mn2+ ions to establish an additional ferroelectric order out of an otherwise disordered dipolar glass. Below TN ≈12 K, Mn2+ spins order, making the columnar perovskites rare systems in which ordered electric and magnetic dipoles may reside on the same transition metal sublattice.

Targeting protein tyrosine phosphatases for CDK6-induced immunotherapy resistance.

Elucidating the mechanisms of resistance to immunotherapy and developing strategies to improve its efficacy are challenging goals. Bioinformatics analysis demonstrates that high CDK6 expression in melanoma is associated with poor progression-free survival of patients receiving single-agent immunotherapy. Depletion of CDK6 or cyclin D3 (but not of CDK4, cyclin D1, or D2) in cells of the tumor microenvironment inhibits tumor growth. CDK6 depletion reshapes the tumor immune microenvironment, and the host anti-tumor effect depends on cyclin D3/CDK6-expressing CD8+ and CD4+ T cells. This occurs by CDK6 phosphorylating and increasing the activities of PTP1B and T cell protein tyrosine phosphatase (TCPTP), which, in turn, decreases tyrosine phosphorylation of CD3ζ, reducing the signal transduction for T cell activation. Administration of a PTP1B and TCPTP inhibitor prove more efficacious than using a CDK6 degrader in enhancing T cell-mediated immunotherapy. Targeting protein tyrosine phosphatases (PTPs) might be an effective strategy for cancer patients who resist immunotherapy treatment.

Team principles for successful interdisciplinary research teams.

Interdisciplinary research teams can be extremely beneficial when addressing difficult clinical problems. The incorporation of conceptual and methodological strategies from a variety of research disciplines and health professions yields transformative results. In this setting, the long-term goal of team science is to improve patient care, with emphasis on population health outcomes. However, team principles necessary for effective research teams are rarely taught in health professional schools. To form successful interdisciplinary research teams in cardio-oncology and beyond, guiding principles and organizational recommendations are necessary. Cardiovascular disease results in annual direct costs of $220 billion (about $680 per person in the US) and is the leading cause of death for cancer survivors, including adult survivors of childhood cancers. Optimizing cardio-oncology research in interdisciplinary research teams has the potential to aid in the investigation of strategies for saving hundreds of thousands of lives each year in the United States and mitigating the annual cost of cardiovascular disease. Despite published reports on experiences developing research teams across organizations, specialties and settings, there is no single journal article that compiles principles for cardiology or cardio-oncology research teams. In this review, recurring threads linked to working as a team, as well as optimal methods, advantages, and problems that arise when managing teams are described in the context of career development and research. The worth and hurdles of a team approach, based on practical lessons learned from establishing our multidisciplinary research team and information gleaned from relevant specialties in the development of a successful team are presented.

Establishing an interdisciplinary research team for cardio-oncology artificial intelligence informatics precision and health equity.

Study objective: A multi-institutional interdisciplinary team was created to develop a research group focused on leveraging artificial intelligence and informatics for cardio-oncology patients. Cardio-oncology is an emerging medical field dedicated to prevention, screening, and management of adverse cardiovascular effects of cancer/ cancer therapies. Cardiovascular disease is a leading cause of death in cancer survivors. Cardiovascular risk in these patients is higher than in the general population. However, prediction and prevention of adverse cardiovascular events in individuals with a history of cancer/cancer treatment is challenging. Thus, establishing an interdisciplinary team to create cardiovascular risk stratification clinical decision aids for integration into electronic health records for oncology patients was considered crucial. Design/setting/participants: Core team members from the Medical College of Wisconsin (MCW), University of Wisconsin-Milwaukee (UWM), and Milwaukee School of Engineering (MSOE), and additional members from Cleveland Clinic, Mayo Clinic, and other institutions have joined forces to apply high-performance computing in cardio-oncology. Results: The team is comprised of clinicians and researchers from relevant complementary and synergistic fields relevant to this work. The team has built an epidemiological cohort of ~5000 cancer survivors that will serve as a database for interdisciplinary multi-institutional artificial intelligence projects. Conclusion: Lessons learned from establishing this team, as well as initial findings from the epidemiology cohort, are presented. Barriers have been broken down to form a multi-institutional interdisciplinary team for health informatics research in cardio-oncology. A database of cancer survivors has been created collaboratively by the team and provides initial insight into cardiovascular outcomes and comorbidities in this population.

Deep learning tools and modeling to estimate the temporal expression of cell cycle proteins from 2D still images.

Automatic characterization of fluorescent labeling in intact mammalian tissues remains a challenge due to the lack of quantifying techniques capable of segregating densely packed nuclei and intricate tissue patterns. Here, we describe a powerful deep learning-based approach that couples remarkably precise nuclear segmentation with quantitation of fluorescent labeling intensity within segmented nuclei, and then apply it to the analysis of cell cycle dependent protein concentration in mouse tissues using 2D fluorescent still images. First, several existing deep learning-based methods were evaluated to accurately segment nuclei using different imaging modalities with a small training dataset. Next, we developed a deep learning-based approach to identify and measure fluorescent labels within segmented nuclei, and created an ImageJ plugin to allow for efficient manual correction of nuclear segmentation and label identification. Lastly, using fluorescence intensity as a readout for protein concentration, a three-step global estimation method was applied to the characterization of the cell cycle dependent expression of E2F proteins in the developing mouse intestine.

The rich physics of A-site-ordered quadruple perovskite manganites AMn7O12.

Perovskite-structure AMnO3 manganites played an important role in the development of numerous physical concepts such as double exchange, small polarons, electron-phonon coupling, and Jahn-Teller effects, and they host a variety of important properties such as colossal magnetoresistance and spin-induced ferroelectric polarization (multiferroicity). A-site-ordered quadruple perovskite manganites AMn7O12 were discovered shortly after, but at that time their exploration was quite limited. Significant progress in their understanding has been reached in recent years after the wider use of high-pressure synthesis techniques needed to prepare such materials. Here we review this progress, and show that the AMn7O12 compounds host rich physics beyond the canonical AMnO3 materials.

Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel.

Hierarchical genotyping approaches can provide insights into the source, geography and temporal distribution of bacterial pathogens. Multiple hierarchical SNP genotyping schemes have previously been developed so that new isolates can rapidly be placed within pre-computed population structures, without the need to rebuild phylogenetic trees for the entire dataset. This classification approach has, however, seen limited uptake in routine public health settings due to analytical complexity and the lack of standardized tools that provide clear and easy ways to interpret results. The BioHansel tool was developed to provide an organism-agnostic tool for hierarchical SNP-based genotyping. The tool identifies split k-mers that distinguish predefined lineages in whole genome sequencing (WGS) data using SNP-based genotyping schemes. BioHansel uses the Aho-Corasick algorithm to type isolates from assembled genomes or raw read sequence data in a matter of seconds, with limited computational resources. This makes BioHansel ideal for use by public health agencies that rely on WGS methods for surveillance of bacterial pathogens. Genotyping results are evaluated using a quality assurance module which identifies problematic samples, such as low-quality or contaminated datasets. Using existing hierarchical SNP schemes for Mycobacterium tuberculosis and Salmonella Typhi, we compare the genotyping results obtained with the k-mer-based tools BioHansel and SKA, with those of the organism-specific tools TBProfiler and genotyphi, which use gold-standard reference-mapping approaches. We show that the genotyping results are fully concordant across these different methods, and that the k-mer-based tools are significantly faster. We also test the ability of the BioHansel quality assurance module to detect intra-lineage contamination and demonstrate that it is effective, even in populations with low genetic diversity. We demonstrate the scalability of the tool using a dataset of ~8100 S. Typhi public genomes and provide the aggregated results of geographical distributions as part of the tool's output. BioHansel is an open source Python 3 application available on PyPI and Conda repositories and as a Galaxy tool from the public Galaxy Toolshed. In a public health context, BioHansel enables rapid and high-resolution classification of bacterial pathogens with low genetic diversity.

Pressure-induced Jahn-Teller switch in the homoleptic hybrid perovskite [(CH3)2NH2]Cu(HCOO)3: orbital reordering by unconventional degrees of freedom.

Through in situ, high-pressure X-ray diffraction experiments we have shown that the homoleptic perovskite-like coordination polymer [(CH3)2NH2]Cu(HCOO)3 undergoes a pressure-induced orbital reordering phase transition above 5.20 GPa. This transition is distinct from previously reported Jahn-Teller switching in coordination polymers, which required at least two different ligands that crystallize in a reverse spectrochemical series. We show that the orbital reordering phase transition in [(CH3)2NH2]Cu(HCOO)3 is instead primarily driven by unconventional octahedral tilts and shifts in the framework, and/or a reconfiguration of A-site cation ordering. These structural instabilities are unique to the coordination polymer perovskites, and may form the basis for undiscovered orbital reorientation phenomena in this broad family of materials.

Nuclear PFKP promotes CXCR4-dependent infiltration by T cell acute lymphoblastic leukemia.

PFKP (phosphofructokinase, platelet), the major isoform of PFK1 expressed in T cell acute lymphoblastic leukemia (T-ALL), is predominantly expressed in the cytoplasm to carry out its glycolytic function. Our study showed that PFKP is a nucleocytoplasmic shuttling protein with functional nuclear export and nuclear localization sequences (NLSs). Cyclin D3/CDK6 facilitated PFKP nuclear translocation by dimerization and by exposing the NLS of PFKP to induce the interaction between PFKP and importin 9. Nuclear PFKP stimulated the expression of C-X-C chemokine receptor type 4 (CXCR4), a chemokine receptor regulating leukemia homing/infiltration, to promote T-ALL cell invasion, which depended on the activity of c-Myc. In vivo experiments showed that nuclear PFKP promoted leukemia homing/infiltration into the bone marrow, spleen, and liver, which could be blocked with CXCR4 antagonists. Immunohistochemical staining of tissues from a clinically well-annotated cohort of T cell lymphoma/leukemia patients showed nuclear PFKP localization in invasive cancers, but not in nonmalignant T lymph node or reactive hyperplasia. The presence of nuclear PFKP in these specimens correlated with poor survival in patients with T cell malignancy, suggesting the potential utility of nuclear PFKP as a diagnostic marker.

Population structure, case clusters, and genetic lesions associated with Canadian Salmonella 4,[5],12:i:- isolates.

Monophasic Salmonella 4,[5]:12:i:- are a major public health problem because they are one of the top five Salmonella serotypes isolated from clinical cases globally and because they can carry resistance to multiple antibiotics. A total of 811 Salmonella 4,[5]:12:i:- and S. Typhimurium whole genome sequences (WGS) were generated. The various genetic lesions causing the Salmonella 4,[5]:12:i:- genotype were identified and assessed with regards to their distribution in the population of 811 Salmonella 4,[5]:12:i:- and S. Typhimurium isolates, their geographical and temporal distribution, and their association with non-human sources. Several clades were identified in the population structure, and the largest two were associated almost exclusively with a short prophage insertion and insertion of a mobile element carrying loci encoding antibiotic and mercury resistance. IS26-mediated deletions and fljB point mutants appeared to spread clonally. 'Inconsistent' Salmonella 4,[5]:12:i:- isolates associated with specific, single amino acid changes in fljA and hin were found in a single clade composed of water, shellfish, and avian isolates. Inclusion of isolates from different case clusters identified previously by PFGE validated some of the clusters and invalidated others. Some wgMLST clusters of clinical isolates composed of very closely related isolates contained an isolate(s) with a different genetic lesion, suggesting continuing mobility of the implicated element responsible. Such cases may need to be left out of epidemiological investigations until sufficient numbers of isolates are included that statistical significance of association with sources is not impaired. Non-human sources were frequently found in or near clinical case clusters. Prospective surveillance and WGS of non-human sources and retrospective analysis by WGS of isolates from existing culture collections provides data critical for epidemiological investigations of food- and waterborne outbreaks.

Controlling Magnetic Anisotropy in a Zero-Dimensional S = 1 Magnet Using Isotropic Cation Substitution.

The [Zn1-xNix(HF2)(pyz)2]SbF6 (x = 0.2; pyz = pyrazine) solid solution exhibits a zero-field splitting (D) that is 22% larger [D = 16.2(2) K (11.3(2) cm-1)] than that observed in the x = 1 material [D = 13.3(1) K (9.2(1) cm-1)]. The substantial change in D is accomplished by an anisotropic lattice expansion in the MN4 (M = Zn or Ni) plane, wherein the increased concentration of isotropic Zn(II) ions induces a nonlinear variation in M-F and M-N bond lengths. In this, we exploit the relative donor atom hardness, where M-F and M-N form strong ionic and weak coordinate covalent bonds, respectively, the latter being more sensitive to substitution of Ni by the slightly larger Zn(II) ion. In this way, we are able to tune the single-ion anisotropy of a magnetic lattice site by Zn-substitution on nearby sites. This effect has possible applications in the field of single-ion magnets and the design of other molecule-based magnetic systems.

Complete Genome Sequences for 36 Canadian Salmonella enterica Serovar Typhimurium and I 1,4,[5],12:i:- Isolates from Clinical and Animal Sources.

Here, we report the complete genome sequences for 36 Canadian isolates of Salmonella enterica subsp. enterica serovar Typhimurium and its monophasic variant I 1,4,[5]:12:i:- from both clinical and animal sources. These genome sequences will provide useful references for understanding the genetic variation within this prominent serotype.

Fragile X-related protein family: a double-edged sword in neurodevelopmental disorders and cancer.

The fragile X-related (FXR) family proteins FMRP, FXR1, and FXR2 are RNA binding proteins that play a critical role in RNA metabolism, neuronal plasticity, and muscle development. These proteins share significant homology in their protein domains, which are functionally and structurally similar to each other. FXR family members are known to play an essential role in causing fragile X mental retardation syndrome (FXS), the most common genetic form of autism spectrum disorder. Recent advances in our understanding of this family of proteins have occurred in tandem with discoveries of great importance to neurological disorders and cancer biology via the identification of their novel RNA and protein targets. Herein, we review the FXR family of proteins as they pertain to FXS, other mental illnesses, and cancer. We emphasize recent findings and analyses that suggest contrasting functions of this protein family in FXS and tumorigenesis based on their expression patterns in human tissues. Finally, we discuss current gaps in our knowledge regarding the FXR protein family and their role in FXS and cancer and suggest future studies to facilitate bench to bedside translation of the findings.

Emergent helical texture of electric dipoles.

Long-range ordering of magnetic dipoles in bulk materials gives rise to a broad range of magnetic structures, from simple collinear ferromagnets and antiferromagnets, to complex magnetic helicoidal textures stabilized by competing exchange interactions. In contrast, dipolar order in dielectric crystals is typically limited to parallel (ferroelectric) and antiparallel (antiferroelectric) collinear alignments of electric dipoles. Here, we report an observation of incommensurate helical ordering of electric dipoles by light hole doping of the quadruple perovskite BiMn7O12 In analogy with magnetism, the electric dipole helicoidal texture is stabilized by competing instabilities. Specifically, orbital ordering and lone electron pair stereochemical activity compete, giving rise to phase transitions from a nonchiral cubic structure to an incommensurate electric dipole and orbital helix via an intermediate density wave.

Distribution of heavy metal resistance elements in Canadian Salmonella 4,[5],12:i:- populations and association with the monophasic genotypes and phenotype.

Salmonella 4,[5],12:i:- are monophasic S. Typhimurium variants incapable of producing the second-phase flagellar antigen. They have emerged since the mid-1990s to become one of the most prevalent Salmonella serotypes causing human disease world-wide. Multiple genetic events associated with different genetic elements can result in the monophasic phenotype. Several jurisdictions have reported the emergence of a Salmonella 4,[5],12:i:- clone with SGI-4 and a genetic element (MREL) encoding a mercury resistance operon and antibiotic resistance loci that disrupts the second phase antigen region near the iroB locus in the Salmonella genome. We have sequenced 810 human and animal Canadian Salmonella 4,[5],12:i:- isolates and determined that isolates with SGI-4 and the mercury resistance element (MREL; also known as RR1&RR2) constitute several global clades containing various proportions of Canadian, US, and European isolates. Detailed analysis of the data provides a clearer picture of how these heavy metal elements interact with bacteria within the Salmonella population to produce the monophasic phenotype. Insertion of the MREL near iroB is associated with several deletions and rearrangements of the adjacent flaAB hin region, which may be useful for defining human case clusters that could represent outbreaks. Plasmids carrying genes encoding silver, copper, mercury, and antimicrobial resistance appear to be derived from IS26 mediated acquisition of these genes from genomes carrying SGI-4 and the MREL. Animal isolates with the mercury and As/Cu/Ag resistance elements are strongly associated with porcine sources in Canada as has been shown previously for other jurisdictions. The data acquired in these investigations, as well as from the extensive literature on the subject, may aid source attribution in outbreaks of the organism and interventions to decrease the prevalence of this clone and reduce its impact on human disease.

High-Pressure Synthesis, Crystal Structures, and Properties of A-Site Columnar-Ordered Quadruple Perovskites NaRMn2Ti4O12 with R = Sm, Eu, Gd, Dy, Ho, Y.

The formation of NaRMn2Ti4O12 compounds (R = rare earth) under high pressure (about 6 GPa) and high temperature (about 1750 K) conditions was studied. Such compounds with R = Sm, Eu, Gd, Dy, Ho, Y adopt an A-site columnar-ordered quadruple-perovskite structure with the generic chemical formula A2A'A″B4O12. Their crystal structures were studied by powder synchrotron X-ray and neutron diffraction between 1.5 and 300 K. They maintain a paraelectric structure with centrosymmetric space group P42/nmc (No. 137) at all temperatures, in comparison with the related CaMnTi2O6 perovskite, in which a ferroelectric transition occurs at 630 K. The centrosymmetric structure was also confirmed by second-harmonic generation. It has a cation distribution of [Na+R3+]A[Mn2+]A'[Mn2+]A″[Ti4+4]BO12 (to match with the generic chemical formula) with statistical distributions of Na+ and R3+ at the large A site and a strongly split position of Mn2+ at the square-planar A' site. We found a C-type long-range antiferromagnetic structure of Mn2+ ions at the A' and A″ sites below TN = 12 K for R = Dy and found that the presence of Dy3+ disturbs the long-range ordering of Mn2+ below a second transition at lower temperatures. The first magnetic transition occurs below 8-13 K in all compounds, but the second magnetic transition occurs only for R = Dy, Sm, Eu. All compounds show large dielectric constants of a possible extrinsic origin similar to that of CaCu3Ti4O12. NaRMn2Ti4O12 with R = Er-Lu crystallized in the GdFeO3-type Pnma perovskite structure, and NaRMn2Ti4O12 with R = La, Nd contained two perovskite phases: an AA'3B4O12-type Im3̅ phase and a GdFeO3-type Pnma phase.

Assessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada.

Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher's exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E. coli; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.

Effect of a bacteriophage T5virus on growth of Shiga toxigenic Escherichia coli and Salmonella strains in individual and mixed cultures.

A previously isolated a bacteriophage, vB_EcoS_AKFV33 of T5virus, demonstrated great potential in biocontrol of Shiga toxigenic Escherichia coli (STEC) O157. This study further evaluated its potential as a biocontrol agent in broth culture against other important non-O157 serogroups of STEC and Salmonella. AKFV33 was capable of lysing isolates of STEC serogroups O26 (n = 1), O145 (n = 1) and Salmonella enterica serovars (n = 6). In a broth culture microplate system, efficacy of AKFV33 for killing STEC O26:H11, O145:NM and Salmonella was improved (P < 0.05) at a lower multiplicity of infection and sampling time (6-10 h), when STEC O157:H7 was also included in the culture. This phage was able to simultaneously reduce numbers of STEC and Salmonella in mixtures with enhanced activity (P < 0.05) against O157:H7 and O26:H11, offering great promise for control of multiple zoonotic pathogens at both pre and post-harvest.

Salmonella serovars associated with Grenadian tree boa (Corallus grenadensis) and their antimicrobial susceptibility.

Cloacal swabs from 45 Grenada bank tree boas (Corallus grenadensis) were sampled during a 12-month period (2011-2012) from the rain forests and scrublands of Grenada. Cloacal swabs were examined by enrichment and selective culture for the presence of Salmonella spp. In all, 16 (35.6%) of the snakes were positive for Salmonella, and six serovars of Salmonella were isolated. The most common serovar was Rubislaw (31.3%), the most frequent serovar recently isolated from green iguanas in Grenada, followed by serovar Braenderup (18.8%), and serovar IV:48:g,z51:- (formerly, S. Marina) (18.8%), also found in green iguanas in this country. The remaining three less frequent serovars were, IV:53:g,z51:-, I:6,7:e,h:- and IIIb:38:i:z. Antimicrobial susceptibility tests conducted by a disc diffusion method against amoxicillin-clavulanic acid, ampicillin, cefotaxime, ciprofloxacin, enrofloxacin, gentamicin, imipenem, nalidixic acid, streptomycin, tetracycline and trimethoprim-sulfamethoxazole showed that drug resistance is minimal, with intermediate susceptibility, only to streptomycin. This is the first report of isolation and antimicrobial susceptibilities of Salmonella serovars from wild Grenadian tree boas.

Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada.

We report high-quality closed reference genomes for 1 bovine strain and 10 human Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from serogroups O26, O45, O91, O103, O104, O111, O113, O121, O145, and O157. We also report draft assemblies, with standardized metadata, for 360 STEC strains isolated from watersheds, animals, farms, food, and human infections.