Multimodal cell-free DNA whole-genome TAPS is sensitive and reveals specific cancer signals.

The analysis of circulating tumour DNA (ctDNA) through minimally invasive liquid biopsies is promising for early multi-cancer detection and monitoring minimal residual disease. Most existing methods focus on targeted deep sequencing, but few integrate multiple data modalities. Here, we develop a methodology for ctDNA detection using deep (80x) whole-genome TET-Assisted Pyridine Borane Sequencing (TAPS), a less destructive approach than bisulphite sequencing, which permits the simultaneous analysis of genomic and methylomic data.

The influence of unconventional ultrasonic pasteurization on the characteristics of curds obtained from goat milk with the low cholesterol content.

This study aimed to evaluate the influence of different power-time ultrasound regimes of pasteurization on the physical, chemical, organoleptic properties, and lipid quality indices of goat curds characterized by a low cholesterol level. Cholesterol was eliminated by a percentage of 92.1 % by treating the raw goat milk with beta-cyclodextrin in the proportion of 0.

Strong-Isospin-Breaking Correction to the Muon Anomalous Magnetic Moment from Lattice QCD at the Physical Point.

All lattice-QCD calculations of the hadronic-vacuum-polarization contribution to the muon's anomalous magnetic moment to date have been performed with degenerate up- and down-quark masses. Here we calculate directly the strong-isospin-breaking correction to a_{μ}^{HVP} for the first time with physical values of m_{u} and m_{d} and dynamical u, d, s, and c quarks, thereby removing this important source of systematic uncertainty. We obtain a relative shift to be applied to lattice-QCD results obtained with degenerate light-quark masses of δa_{μ}^{HVP,m_{u}≠m_{d}}=+1.

GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data.

Hi-C is one of the main methods for investigating spatial co-localisation of DNA in the nucleus. However, the raw sequencing data obtained from Hi-C experiments suffer from large biases and spurious contacts, making it difficult to identify true interactions. Existing methods use complex models to account for biases and do not provide a significance threshold for detecting interactions.

B→πll Form Factors for New Physics Searches from Lattice QCD.

The rare decay B→πℓ^{+}ℓ^{-} arises from b→d flavor-changing neutral currents and could be sensitive to physics beyond the standard model. Here, we present the first ab initio QCD calculation of the B→π tensor form factor f_{T}. Together with the vector and scalar form factors f_{+} and f_{0} from our companion work [J.

Polycomb repressive complex PRC1 spatially constrains the mouse embryonic stem cell genome.

The Polycomb repressive complexes PRC1 and PRC2 maintain embryonic stem cell (ESC) pluripotency by silencing lineage-specifying developmental regulator genes. Emerging evidence suggests that Polycomb complexes act through controlling spatial genome organization. We show that PRC1 functions as a master regulator of mouse ESC genome architecture by organizing genes in three-dimensional interaction networks.

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C.

Transcriptional control in large genomes often requires looping interactions between distal DNA elements, such as enhancers and target promoters. Current chromosome conformation capture techniques do not offer sufficiently high resolution to interrogate these regulatory interactions on a genomic scale. Here we use Capture Hi-C (CHi-C), an adapted genome conformation assay, to examine the long-range interactions of almost 22,000 promoters in 2 human blood cell types.

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements.

The mammalian genome harbors up to one million regulatory elements often located at great distances from their target genes. Long-range elements control genes through physical contact with promoters and can be recognized by the presence of specific histone modifications and transcription factor binding. Linking regulatory elements to specific promoters genome-wide is currently impeded by the limited resolution of high-throughput chromatin interaction assays.

NVP-QBE170: an inhaled blocker of the epithelial sodium channel with a reduced potential to induce hyperkalaemia.

Background And Purpose: Inhaled amiloride, a blocker of the epithelial sodium channel (ENaC), enhances mucociliary clearance (MCC) in cystic fibrosis (CF) patients. However, the dose of amiloride is limited by the mechanism-based side effect of hyperkalaemia resulting from renal ENaC blockade. Inhaled ENaC blockers with a reduced potential to induce hyperkalaemia provide a therapeutic strategy to improve mucosal hydration and MCC in the lungs of CF patients.

Determination of |V(us)|| from a lattice QCD calculation of the K → πℓν semileptonic form factor with physical quark masses.

We calculate the kaon semileptonic form factor f+(0) from lattice QCD, working, for the first time, at the physical light-quark masses. We use gauge configurations generated by the MILC Collaboration with Nf = 2 + 1 + 1 flavors of sea quarks, which incorporate the effects of dynamical charm quarks as well as those of up, down, and strange. We employ data at three lattice spacings to extrapolate to the continuum limit.

Leptonic-decay-constant ratio f(K+)/f(π+) from lattice QCD with physical light quarks.

A calculation of the ratio of leptonic decay constants f(K+)/f(π+) makes possible a precise determination of the ratio of Cabibbo-Kobayashi-Maskawa (CKM) matrix elements |V(us)|/|V(ud)| in the standard model, and places a stringent constraint on the scale of new physics that would lead to deviations from unitarity in the first row of the CKM matrix. We compute f(K+)/f(π+) numerically in unquenched lattice QCD using gauge-field ensembles recently generated that include four flavors of dynamical quarks: up, down, strange, and charm. We analyze data at four lattice spacings a ≈ 0.

Refining new-physics searches in B→Dτν with lattice QCD.

The semileptonic decay channel B→Dτν is sensitive to the presence of a scalar current, such as that mediated by a charged-Higgs boson. Recently, the BABAR experiment reported the first observation of the exclusive semileptonic decay B→Dτ(-)ν, finding an approximately 2σ disagreement with the standard-model prediction for the ratio R(D)=BR(B→Dτν)/BR(B→Dℓν), where ℓ = e,μ. We compute this ratio of branching fractions using hadronic form factors computed in unquenched lattice QCD and obtain R(D)=0.

Adaptation of the plasma inhibitory activity assay to detect Aurora, ABL and FLT3 kinase inhibition by AT9283 in pediatric leukemia.

Non-invasive assessment of biomarker modulation is important for evaluating targeted therapeutics, particularly in pediatrics. The plasma inhibitory activity (PIA) assay is used clinically to assess FLT3 inhibition ex vivo and guide dosing. AT9283 is a novel Aurora kinase inhibitor with secondary activity against FLT3 and ABL.

Fit-for-purpose biomarker method validation for application in clinical trials of anticancer drugs.

Clinical development of new anticancer drugs can be compromised by a lack of qualified biomarkers. An indispensable component to successful biomarker qualification is assay validation, which is also a regulatory requirement. In order to foster flexible yet rigorous biomarker method validation, the fit-for-purpose approach has recently been developed.

A cancer research UK pharmacokinetic study of BPA-mannitol in patients with high grade glioma to optimise uptake parameters for clinical trials of BNCT.

This paper describes results to-date from a human pharmacokinetic study which began recruitment in December 2007. Results are presented for a single patient recruited in December 2007. A second patient was recruited in July 2008 but detailed data are not available at the time of writing.

Camostat attenuates airway epithelial sodium channel function in vivo through the inhibition of a channel-activating protease.

Inhibition of airway epithelial sodium channel (ENaC) function enhances mucociliary clearance (MCC). ENaC is positively regulated by channel-activating proteases (CAPs), and CAP inhibitors are therefore predicted to be beneficial in diseases associated with impaired MCC. The aims of the present study were to 1) identify low-molecular-weight inhibitors of airway CAPs and 2) to establish whether such CAP inhibitors would translate into a negative regulation of ENaC function in vivo, with a consequent enhancement of MCC.

The guinea-pig tracheal potential difference as an in vivo model for the study of epithelial sodium channel function in the airways.

Background And Purpose: The epithelial sodium channel (ENaC) is a key regulator of airway mucosal hydration and mucus clearance. Negative regulation of airway ENaC function is predicted to be of clinical benefit in the cystic fibrosis lung. The aim of this study was to develop a small animal model to enable the direct assessment of airway ENaC function in vivo.

Capsaicin-induced mucus secretion in rat airways assessed in vivo and non-invasively by magnetic resonance imaging.

Background And Purpose: An up-regulation of the sensory neural pathways in the lung has been implicated in asthma and chronic obstructive pulmonary disease (COPD) and is thought to contribute to mucus hypersecretion, an essential feature of both diseases. The aim of this study was to assess non-invasively the acute effects (up to 60 min) of sensory nerve stimulation by capsaicin in the lung, using magnetic resonance imaging (MRI).

Experimental Approach: Male Brown Norway rats were imaged prior to and 10, 30 and 60 min after intra-tracheal challenge with capsaicin (30 microg kg(-1)) or vehicle (0.

Electrical stimulation induced lumbar medial branch referral patterns.

Study Design: Fluoroscopically guided, minimum threshold electrical stimulation of the right first, second, third, and fourth lumbar medial branches and the fifth lumbar dorsal ramus in each of eight healthy test subjects was performed. The stimulation thresholds and referral patterns were recorded. A composite drawing of the referral patterns was created.

Prevention and management of complications resulting from common spinal injections.

When spinal injections are performed, a needle is placed in or around the spine making the risk of complications unavoidable. Spinal structures or adjacent organs are at risk for direct needle trauma, infection, hematoma, hemorrhage, nerve damage, stroke, allergic reaction, or spinal anesthesia with cardiorespiratory arrest. As a result, physician knowledge and patient preparation and monitoring are critical in maximizing patient safety during the procedure being performed.

Cervical transforaminal injection: review of the literature, complications, and a suggested technique.

Objective: The objective of this paper is to review the literature of cervical transforaminal injections, resulting complications, and to suggest a safe technique.

Methods: A systematic review of the literature was performed. Both the MEDLINE and EMBASE databases were searched for any article relating to cervical epidural injections, cervical transforaminal injections, and complications relating to cervical epidural or cervical transforaminal injections.

Identification with MRI of the pleura as a major site of the acute inflammatory effects induced by ovalbumin and endotoxin challenge in the airways of the rat.

Inflammatory effects in the rat lung have been investigated, non-invasively by MRI, at early time points (3 and 6 h) after ovalbumin (OA) or endotoxin (LPS) challenges. Six hours after challenge with OA, a strong, even inflammatory signal was present around the periphery of the lung in a region corresponding to the pleura. Histological analysis confirmed the presence of marked edema associated with the pleural cavity of OA-treated animals.

Charmed-meson decay constants in three-flavor lattice QCD.

We present the first lattice QCD calculation with realistic sea quark content of the D+-meson decay constant f(D+). We use the MILC Collaboration's publicly available ensembles of lattice gauge fields, which have a quark sea with two flavors (up and down) much lighter than a third (strange). We obtain f(D+)=201+/-3+/-17 MeV, where the errors are statistical and a combination of systematic errors.