Modeling molecular development of breast cancer in canine mammary tumors.

Understanding the changes in diverse molecular pathways underlying the development of breast tumors is critical for improving diagnosis, treatment, and drug development. Here, we used RNA-profiling of canine mammary tumors (CMTs) coupled with a robust analysis framework to model molecular changes in human breast cancer. Our study leveraged a key advantage of the canine model, the frequent presence of multiple naturally occurring tumors at diagnosis, thus providing samples spanning normal tissue and benign and malignant tumors from each patient. We showed human breast cancer signals, at both expression and mutation level, are evident in CMTs. Profiling multiple tumors per patient enabled by the CMT model allowed us to resolve statistically robust transcription patterns and biological pathways specific to malignant tumors versus those arising in benign tumors or shared with normal tissues. We showed that multiple histological samples per patient is necessary to effectively capture these progression-related signatures, and that carcinoma-specific signatures are predictive of survival for human breast cancer patients. To catalyze and support similar analyses and use of the CMT model by other biomedical researchers, we provide FREYA, a robust data processing pipeline and statistical analyses framework.

Liquid Crystal Dimers and the Twist-Bend Phases: Non-Symmetric Dimers Consisting of Mesogenic Units of Differing Lengths.

The syntheses and characterisation of the 4-[{[4-({n-[4-(4-cyanophenyl)phenyl]-n-yl}oxy)phenyl]-methylidene}amino]phenyl-4-alkoxybenzoates (CBnOIBeOm) are reported with n=8 and 10 and m=1-10. The two series display fascinating liquid crystal polymorphism. All twenty reported homologues display an enantiotropic nematic (N) phase at high temperature. When the length of the spacer (n) is greater than that of the terminal chain (m), the twist-bend nematic (NTB) phase is observed at temperatures below the N phase. As the length of the terminal chain is increased and extends beyond the length of the spacer up to three smectic phases are observed on cooling the N phase. One of these smectic phases has been assigned as the rare twist-bend smectic C subphase, the SmCTB-α phase. In all the smectic phases, a monolayer packing arrangement is seen, and this is attributed to the anti-parallel associations of the like mesogenic units.

Estimating FST and kinship for arbitrary population structures.

FST and kinship are key parameters often estimated in modern population genetics studies in order to quantitatively characterize structure and relatedness. Kinship matrices have also become a fundamental quantity used in genome-wide association studies and heritability estimation. The most frequently-used estimators of FST and kinship are method-of-moments estimators whose accuracies depend strongly on the existence of simple underlying forms of structure, such as the independent subpopulations model of non-overlapping, independently evolving subpopulations. However, modern data sets have revealed that these simple models of structure likely do not hold in many populations, including humans. In this work, we analyze the behavior of these estimators in the presence of arbitrarily-complex population structures, which results in an improved estimation framework specifically designed for arbitrary population structures. After generalizing the definition of FST to arbitrary population structures and establishing a framework for assessing bias and consistency of genome-wide estimators, we calculate the accuracy of existing FST and kinship estimators under arbitrary population structures, characterizing biases and estimation challenges unobserved under their originally-assumed models of structure. We then present our new approach, which consistently estimates kinship and FST when the minimum kinship value in the dataset is estimated consistently. We illustrate our results using simulated genotypes from an admixture model, constructing a one-dimensional geographic scenario that departs nontrivially from the independent subpopulations model. Our simulations reveal the potential for severe biases in estimates of existing approaches that are overcome by our new framework. This work may significantly improve future analyses that rely on accurate kinship and FST estimates.

Ferroelectric Nematic-Isotropic Liquid Critical End Point.

A critical end point above which an isotropic phase continuously evolves into a polar (ferroelectric) nematic phase with an increasing electric field is found in a ferroelectric nematic liquid crystalline material. The critical end point is approximately 30 K above the zero-field transition temperature from the isotropic to nematic phase and at an electric field of the order of 10 V/µm. Such systems are interesting from the application point of view because a strong birefringence can be induced in a broad temperature range in an optically isotropic phase.

Molecular Shape, Electronic Factors, and the Ferroelectric Nematic Phase: Investigating the Impact of Structural Modifications.

The synthesis and characterisation of two series of low molar mass mesogens, the (4-nitrophenyl) 2-alkoxy-4-(4-methoxybenzoyl)oxybenzoates (NT3.m) and the (3-fluoro-4-nitrophenyl) 2-alkoxy-4-(4-methoxybenzoyl)oxybenzoates (NT3F.m), are reported in order to investigate the effect of changing the position of a lateral alkoxy chain from the methoxy-substituted terminal ring to the central phenyl ring in these two series of materials based on RM734. All members of the NT3.m series exhibited a conventional nematic phase, N, which preceded the ferroelectric nematic phase, NF , whereas all the members of the NT3F.m series exhibited direct NF -I transitions except for NT3F.1 which also exhibited an N phase. These materials cannot be described as wedge-shaped, yet their values of the ferroelectric nematic-nematic transition temperature, T N F N ${{_{{\rm N}{_{{\rm F}}}{\rm N}}}}$ , exceed those of the corresponding materials with the lateral alkoxy chain located on the methoxy-substituted terminal ring. In part, this may be attributed to the effect that changing the position of the lateral alkoxy chain has on the electronic properties of these materials, specifically on the electron density associated with the methoxy-substituted terminal aromatic ring. The value of TNI decreased with the addition of a fluorine atom ortho to the nitro group in NT3F.1, however, the opposite behaviour was found when the transition temperatures of the NF phase were compared which are higher for the NT3F.m series. This may reflect a change in the polarity and polarizability of the NT3F.m series compared to the NT3.m series. Therefore, it is suggested that, rather than simply promoting a tapered shape, the role of the lateral chain in inhibiting anti-parallel associations and its effect on the electronic properties of the molecules are the key factors in driving the formation of the NF phase.

Using Lateral Substitution to Control Conformational Preference and Phase Behaviour of Benzanilide-based Liquid Crystal Dimers.

The inclusion of secondary and tertiary benzanilide-based mesogenic groups into liquid crystal dimers is reported as a means to develop new materials. Furthermore, substitution at the nitrogen atom is shown to introduce an additional synthetic 'handle' to modify the molecular structure of the tertiary materials. The design of these materials has proved challenging due to the strong preferences of 3° benzanilides for the E amide conformation. In this work, lateral substitution is used to modify the conformational preferences of the amide linkage and promote liquid crystallinity for a series of N-methyl benzanilide dimers. As the proportion of the E conformer decreases, the nematic-isotropic transition temperatures increase, and enantiotropic nematic behaviour is observed. We also report the synthesis and characterisation of the analogous 2° benzanilide-based materials, which show nematic and twist-bend nematic behaviour. This approach highlights the effects that seemingly small structural modifications, such as the inclusion and position of a methyl group, can have on molecular shape and hence, liquid crystalline behaviour.

Intrinsically Chiral Twist-Bend Nematogens: Interplay of Molecular and Structural Chirality in the NTB Phase.

Non-symmetric lactate-based chiral liquid crystal dimers containing an odd-membered spacer are shown to exhibit a chiral twist-bend nematic phase which is stable on cooling to room temperature. A comparison of racemic and optically pure materials reveals that the pitch length in the N*TB phase is not influenced by molecular chirality, whereas the nematic-twist-bend nematic transition temperature is increased.

Intrinsically Chiral Twist-Bend Nematogens: Interplay of Molecular and Structural Chirality in the NTB Phase.

The front cover artwork is provided by Dr Rebecca Walker of the Liquid Crystals Group at the University of Aberdeen. The image is a cartoon depiction of the formation of the heliconical chiral twist-bend nematic phase (N*TB ) from its constituent bent molecules. The presence of a single enantiomer of the chiral, lactate-based liquid crystal dimers biases the formation of helices with only one handedness, unlike in the conventional NTB phase, observed for achiral molecules, for which the left- and right-handed helices are doubly degenerate. Read the full text of the Research Article at 10.1002/cphc.202200807.

Exploring the Anti-Hypoxaemia Effect of Hydromethylthionine: A Prospective Study of Phase 3 Clinical Trial Participants.

Methylthioninium chloride (MTC) is a standard treatment for methaemoglobinaemia. A preparation of reduced MTC has been reported to increase blood oxygen saturation (SpO2) and lower respiratory rates in patients with severe COVID-19. We have developed a stable form of reduced methylthionine (hydromethylthionine-mesylate, HMTM) having a benign safety profile in two Phase 3 trials in Alzheimer's disease. The aim of this prospective study was to determine the effects of oral HMTM on SpO2 and methaemoglobin (metHb) levels in a cohort of patients with mild hypoxaemia not due to COVID-19. Eighteen participants randomised to a single dose of 4, 75, 100 or 125 mg doses of HMTM had SpO2 levels below 94% at baseline. Patients were routinely monitored by pulse oximetry after 4 h, and after 2 and 6 weeks of twice daily dosing. Significant ~3% increases in SpO2 occurred within 4 h and were sustained over 2 and 6 weeks with no dose differences. There were small dose-dependent increases (0.060-0.162%) in metHb levels over 2 to 6 weeks. Minimum-energy computational chemistry revealed that HMT can bind within 2.10 Å of heme iron by donating a pair of electrons from the central nitrogen of HMT to d orbitals of heme iron, but with lower affinity than oxygen. In conclusion, HMTM can increase SpO2 without reducing metHb by acting as a strong displaceable field ligand for heme iron. We hypothesise that this facilitates a transition from the low oxygen affinity T-state of heme to the higher affinity R-state. HMTM has potential as an adjunctive treatment for hypoxaemia.

The functional false discovery rate with applications to genomics.

The false discovery rate (FDR) measures the proportion of false discoveries among a set of hypothesis tests called significant. This quantity is typically estimated based on p-values or test statistics. In some scenarios, there is additional information available that may be used to more accurately estimate the FDR. We develop a new framework for formulating and estimating FDRs and q-values when an additional piece of information, which we call an "informative variable", is available. For a given test, the informative variable provides information about the prior probability a null hypothesis is true or the power of that particular test. The FDR is then treated as a function of this informative variable. We consider two applications in genomics. Our first application is a genetics of gene expression (eQTL) experiment in yeast where every genetic marker and gene expression trait pair are tested for associations. The informative variable in this case is the distance between each genetic marker and gene. Our second application is to detect differentially expressed genes in an RNA-seq study carried out in mice. The informative variable in this study is the per-gene read depth. The framework we develop is quite general, and it should be useful in a broad range of scientific applications.

The optimal discovery procedure for significance analysis of general gene expression studies.

MOTIVATION: Analysis of biological data often involves the simultaneous testing of thousands of genes. This requires two key steps: the ranking of genes and the selection of important genes based on a significance threshold. One such testing procedure, called the optimal discovery procedure (ODP), leverages information across different tests to provide an optimal ranking of genes. This approach can lead to substantial improvements in statistical power compared to other methods. However, current applications of the ODP have only been established for simple study designs using microarray technology. Here, we extend this work to the analysis of complex study designs and RNA-sequencing studies. RESULTS: We apply our extended framework to a static RNA-sequencing study, a longitudinal study, an independent sampling time-series study,and an independent sampling dose-response study. Our method shows improved performance compared to other testing procedures, finding more differentially expressed genes and increasing power for enrichment analysis. Thus, the extended ODP enables a favorable significance analysis of genome-wide gene expression studies. AVAILABILITY AND IMPLEMENTATION: The algorithm is implemented in our freely available R package called edge and can be downloaded at https://www.bioconductor.org/packages/release/bioc/html/edge.html. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

New patterns of twist-bend liquid crystal phase behaviour: the synthesis and characterisation of the 1-(4-cyanobiphenyl-4'-yl)-10-(4-alkylaniline-benzylidene-4'-oxy)decanes (CB10O·m).

The synthesis and characterisation of the 1-(4-cyanobiphenyl-4'-yl)-10-(4-alkylanilinebenzylidene-4'-oxy)decanes (CB10O·m) are reported. This series shows a rich liquid crystal polymorphism including twist-bend nematic and smectic phases. All the homologues reported exhibit an enantiotropic conventional nematic phase. For the homologues with m ≤ 10, the local packing in the nematic phases and the layer spacing in the smectic phases indicates an intercalated arrangement of the molecules. An intercalated smectic CA phase is observed if m/11 ≈ 0.5. Either side of this condition, the twist-bend nematic phase is observed, a novel pattern of behaviour for a series on increasing a terminal chain length. For longer chain lengths, m = 12, 14, 16 and 18, two twist-bend smectic C (SmCTB) phases are observed, and the packing of the molecules is now of a bilayer-type. The higher temperature variant is termed SmCTB-SH in which SH (single helix) refers to the presence of a short, distorted clock-type helix. In the lower temperature SmCTB-DH phase, an additional longer helix is superimposed on the short one, and DH denotes double helix.

Distinct differences in the nanoscale behaviors of the twist-bend liquid crystal phase of a flexible linear trimer and homologous dimer.

We synthesized the liquid crystal dimer and trimer members of a series of flexible linear oligomers and characterized their microscopic and nanoscopic properties using resonant soft X-ray scattering and a number of other experimental techniques. On the microscopic scale, the twist-bend phases of the dimer and trimer appear essentially identical. However, while the liquid crystal dimer exhibits a temperature-dependent variation of its twist-bend helical pitch varying from 100 to 170 Å on heating, the trimer exhibits an essentially temperature-independent pitch of 66 Å, significantly shorter than those reported for other twist-bend forming materials in the literature. We attribute this to a specific combination of intrinsic conformational bend of the trimer molecules and a sterically favorable intercalation of the trimers over a commensurate fraction (two-thirds) of the molecular length. We develop a geometric model of the twist-bend phase for these materials with the molecules arranging into helical chain structures, and we fully determine their respective geometric parameters.

Twist-Bend Nematic Glasses: The Synthesis and Characterisation of Pyrene-based Nonsymmetric Dimers.

A selection of pyrene-based liquid crystal dimers have been prepared, containing either methylene-ether or diether linked spacers of varying length and parity. All the diether linked materials, CBOnO.Py (n=5, 6, 11, 12), exhibit conventional nematic and smectic A phases, with the exception of CBO11O.Py which is exclusively nematic. The methylene-ether linked dimer, CBnO.Py, with an even-membered spacer (n=5) was solely nematogenic, but odd-members (n=6, 8, 10) exhibited both nematic and twist-bend nematic phases. Replacement of the cyanobiphenyl fragment by cyanoterphenyl giving CT6O.Py, gave elevated melting and nematic-isotropic transition temperatures, and SmA and SmCA phases were observed on cooling the nematic phase. Intermolecular face-to-face associations of the pyrene moieties drive glass formation, and all these materials have a glass transition temperature at or above room temperature. The stability of the glassy twist-bend nematic phase allowed for its study using AFM, and the helical pitch length, PTB , was measured as 6.3 and 6.7 nm for CB6O.Py and CB8O.Py, respectively. These values are comparable to the shortest pitch of a twist-bend nematic phase measured to date.

Multiple Polar and Non-polar Nematic Phases.

Liquid-crystal materials exhibiting up to three nematic phases are reported. Dielectric response measurements show that while the lower temperature nematic phase has ferroelectric order and the highest temperature nematic phase is apolar, the intermediate phase has local antiferroelectric order. The modification of the molecular structure by increasing the number of lateral fluorine substituents leads to one of the materials showing a direct isotropic-ferronematic phase transition.

Understanding the remarkable difference in liquid crystal behaviour between secondary and tertiary amides: the synthesis and characterisation of new benzanilide-based liquid crystal dimers.

A number of liquid crystal dimers have been synthesised and characterised containing secondary or tertiary (N-methyl) benzanilide-based mesogenic groups. The secondary amides all form nematic phases, and we present the first example of an amide to show the twist-bend nematic (NTB) phase. Only two of the corresponding N-methylated dimers formed a nematic phase and with greatly reduced nematic-isotropic transition temperatures. Characterisation using 2D ROESY NMR experiments, DFT geometry optimisation and X-ray diffraction reveal that there is a change in the preferred conformation of the benzanilide core on methylation, from Z to E. The rotational barrier around the N-C(O) bond has been measured using variable temperature 1H NMR spectroscopy. This dramatic change in shape accounts for the remarkable difference in liquid crystalline behaviour between these secondary and tertiary amide-based materials.

The Chiral Twist-Bend Nematic Phase (N*TB ).

The twist-bend nematic, NTB , phase has been observed for chiral materials in which chirality is introduced through a branched 2-methylbutyl terminal tail. The chiral twist-bend nematic phase, N*TB , is completely miscible with the NTB phase of the standard achiral material, CB6OCB. The N*TB phase exhibits optical textures with lower birefringence than those observed for the achiral NTB phase, suggesting an additional mechanism of averaging molecular orientations. The N*-N*TB transition temperatures for the chiral materials are higher than the NTB -N transition temperatures seen for the corresponding racemic materials. This suggests the double degeneracy of helical twist sense in the N T B * phase is removed by the intrinsic molecular chirality. A square lattice pattern is observed in the N* phase over a temperature range of several degrees above the N*TB -N phase transition, which may be attributed to a non-monotonic dependence of the bend elastic constant.

Molecular curvature, specific intermolecular interactions and the twist-bend nematic phase: the synthesis and characterisation of the 1-(4-cyanobiphenyl-4'-yl)-6-(4-alkylanilinebenzylidene-4'-oxy)hexanes (CB6O.m).

The syntheses and characterisation of the first ten homologues of the 1-(4-cyanobiphenyl-4'-yl)-6-(4-alkylanilinebenzylidene-4'-oxy)hexanes (CB6O.m) are reported. All ten members of the series exhibit an enantiotropic nematic, N, phase, and a monotropic twist-bend nematic, NTB, phase. Only CB6O.10 shows a smectic phase. The assignment of both nematic phases was confirmed using X-ray diffraction. For short chain lengths (m = 1-6) the local packing in both nematic phases is an intercalated arrangement, for intermediate chain lengths a frustrated local structure is seen and for the longest chain length, a bilayer arrangement is observed. This change in the local structure on increasing m has no apparent effect on the stability of either nematic phase, and TNTBN and TNI show a regular dependence on m. Specifically, TNTBN and TNI decrease on increasing m and superimposed upon this is a weak odd-even effect in which the odd members show the higher values. TNI decreases more rapidly than TNTBN on increasing m such that the ratio TNTBN/TNI increases. The lower temperature liquid crystal phase shown by 1-(4-cyanobiphenyl-4'-yloxy)-5-(4-butylanilinebenzylidene-4'-oxy)pentane (CBO5O.4) is reassigned as a twist-bend nematic phase. The transitional properties of the CB6O.m, CB6O.Om and CBO5O.m series are compared.

Spherical-cap droplets of a photo-responsive bent liquid crystal dimer.

Using a photo-responsive dimer exhibiting the transition between nematic (N) and twist-bend nematic (NTB) phases, we prepared spherical cap-shaped droplets on solid substrates exposed to air. The internal director structures of these droplets vary depending on the phase and on the imposed boundary conditions. The structural switching between the N and NTB phases was successfully performed either by temperature control or by UV light-irradiation. The N phase is characterized by an extremely small bend elastic constant K3, and surprisingly, we found that the droplet-air interface induces a planar alignment, in contrast to that seen for typical calamitic liquid crystals. As a consequence, the director configuration was stabilized in a structure substantially different from that normally found in conventional nematic liquid crystalline droplets. In the twist-bend nematic droplets characteristic structures with macroscopic length scales were formed, and they were well controlled by the droplet size. These results indicated that a continuum theory is effective in describing the stabilization mechanism of the macroscopic structure even in the twist-bend nematic liquid crystal droplets exhibiting director modulations on a scale of several molecular lengths.

Co-optimization of Heavy-Duty Fuels and Engines: Cost Benefit Analysis and Implications.

Heavy-duty vehicles require expensive aftertreatment systems for control of emissions such as particulate matter (PM) and nitrogen oxides (NOx) to comply with stringent emission standards. Reduced engine-out emissions could potentially alleviate the emission control burden, and thus bring about reductions in the cost associated with aftertreatment systems, which translates into savings in vehicle ownership. This study evaluates potential reductions in manufacturing and operating costs of redesigned emission aftertreatment systems of line-haul heavy-duty diesel vehicles (HDDVs) with reduced engine-out emissions brought about by co-optimized fuel and engine technologies. Three emissions reduction cases representing conservative, medium, and optimistic engine-out emission reduction benefits are analyzed, compared to a reference case: the total costs of aftertreatment systems (TCA) of the three cases are reduced to $11,400(1.63 ¢/km), $9,100 (1.30 ¢/km), and $8,800 (1.26 ¢/km), respectively, compared to $12,000 (1.71 ¢/km) for the reference case. The largest potential reductions result from reduced diesel exhaust fluid (DEF) usage due to lower NOx emissions. Downsizing aftertreatment devices is not likely, because the sizes of devices are dependent on not only engine-out emissions, but also other factors such as engine displacement. Sensitivity analysis indicates that the price and usage of DEF have the largest impacts on TCA reduction.