Unveiling Bladder Cancer Prognostic Insights by Integrating Patient-Matched Sample and CpG Methylation Analysis.

Bladder cancer prognosis remains a pressing clinical challenge, necessitating the identification of novel biomarkers for precise survival prediction and improved quality of life outcomes. This study proposes a comprehensive strategy to uncover key prognostic biomarkers in bladder cancer using DNA methylation analysis and extreme survival pattern observations in matched pairs of cancer and adjacent normal cells. Unlike traditional approaches that overlook cancer heterogeneity by analyzing entire samples, our methodology leverages patient-matched samples to account for this variability. Specifically, DNA methylation profiles from adjacent normal bladder tissue and bladder cancer tissue collected from the same individuals were analyzed to pinpoint critical methylation changes specific to cancer cells while mitigating confounding effects from individual genetic differences. Utilizing differential threshold settings for methylation levels within cancer-associated pathways enabled the identification of biomarkers that significantly impact patient survival. Our analysis identified distinct survival patterns associated with specific CpG sites, underscoring these sites' pivotal roles in bladder cancer outcomes. By hypothesizing and testing the influence of methylation levels on survival, we pinpointed CpG biomarkers that profoundly affect the prognosis. Notably, CpG markers, such as cg16269144 (PRKCZ), cg16624272 (PTK2), cg11304234, and cg26534425 (IL18), exhibited critical methylation thresholds that correlate with patient mortality. This study emphasizes the importance of tailored approaches to enhancing prognostic accuracy and refining therapeutic strategies for bladder cancer patients. The identified biomarkers pave the way for personalized prognostication and targeted interventions, promising advancements in bladder cancer management and patient care.

Chemical Analysis of an Isotopically Labeled Molecule Using Two-Dimensional NMR Spectroscopy at 34 µT.

Low-field nuclear magnetic resonance (NMR) spectroscopy, conducted at or below a few millitesla, provides only limited spectral information due to its inability to resolve chemical shifts. Thus, chemical analysis based on this technique remains challenging. One potential solution to overcome this limitation is the use of isotopically labeled molecules. However, such compounds, particularly their use in two-dimensional (2D) NMR techniques, have rarely been studied. This study presents the results of both experimental and simulated correlation spectroscopy (COSY) on 1-13C-ethanol at 34.38 µT. The strong heteronuclear coupling in this molecule breaks the magnetic equivalence, causing all J-couplings, including homonuclear coupling, to split the 1H spectrum. The obtained COSY spectrum clearly shows the spectral details. Furthermore, we observed that homonuclear coupling between 1H spins generated cross-peaks only when the associated 1H spins were coupled to identical 13C spin states. Our findings demonstrate that a low-field 2D spectrum, even with a moderate spectral line width, can reveal the J-coupling networks of isotopically labeled molecules.

Frequency Limits of Sequential Readout for Sensing AC Magnetic Fields Using Nitrogen-Vacancy Centers in Diamond.

The nitrogen-vacancy (NV) centers in diamond have the ability to sense alternating-current (AC) magnetic fields with high spatial resolution. However, the frequency range of AC sensing protocols based on dynamical decoupling (DD) sequences has not been thoroughly explored experimentally. In this work, we aimed to determine the sensitivity of the ac magnetic field as a function of frequency using the sequential readout method. The upper limit at high frequency is clearly determined by Rabi frequency, in line with the expected effect of finite DD-pulse width. In contrast, the lower frequency limit is primarily governed by the duration of optical repolarization rather than the decoherence time (T2) of NV spins. This becomes particularly crucial when the repetition (dwell) time of the sequential readout is fixed to maintain the acquisition bandwidth. The equation we provide successfully describes the tendency in the frequency dependence. In addition, at the near-optimal frequency of 1 MHz, we reached a maximum sensitivity of 229 pT/Hz by employing the XY4-(4) DD sequence.

Optical Dynamic Nuclear Polarization of 13C Spins in Diamond at a Low Field with Multi-Tone Microwave Irradiation.

Majority of dynamic nuclear polarization (DNP) experiments have been requiring helium cryogenics and strong magnetic fields for a high degree of nuclear polarization. In this work, we instead demonstrate an optical hyperpolarization of naturally abundant 13C nuclei in a diamond crystal at a low magnetic field and the room temperature. It exploits continuous laser irradiation for polarizing electronic spins of nitrogen vacancy centers and microwave irradiation for transferring the electronic polarization to 13C nuclear spins. We have studied the dependence of 13C polarization on laser and microwave powers. For the first time, a triplet structure corresponding to the 14N hyperfine splitting has been observed in the 13C polarization spectrum. By simultaneously exciting three microwave frequencies at the peaks of the triplet, we have achieved 13C bulk polarization of 0.113 %, leading to an enhancement of 90,000 over the thermal polarization at 17.6 mT. We believe that the multi-tone irradiation can be extended to further enhance the 13C polarization at a low magnetic field.

Hyperpolarization of Nitrile Compounds Using Signal Amplification by Reversible Exchange.

Signal Amplification by Reversible Exchange (SABRE), a hyperpolarization technique, has been harnessed as a powerful tool to achieve useful hyperpolarized materials by polarization transfer from parahydrogen. In this study, we systemically applied SABRE to a series of nitrile compounds, which have been rarely investigated. By performing SABRE in various magnetic fields and concentrations on nitrile compounds, we unveiled its hyperpolarization properties to maximize the spin polarization and its transfer to the next spins. Through this sequential study, we obtained a ~130-fold enhancement for several nitrile compounds, which is the highest number ever reported for the nitrile compounds. Our study revealed that the spin polarization on hydrogens decreases with longer distances from the nitrile group, and its maximum polarization is found to be approximately 70 G with 5 µL of substrates in all structures. Interestingly, more branched structures in the ligand showed less effective polarization transfer mechanisms than the structural isomers of butyronitrile and isobutyronitrile. These first systematic SABRE studies on a series of nitrile compounds will provide new opportunities for further research on the hyperpolarization of various useful nitrile materials.

Organic Reaction Monitoring of a Glycine Derivative Using Signal Amplification by Reversible Exchange-Hyperpolarized Benchtop Nuclear Magnetic Resonance Spectroscopy.

Currently, signal amplification by reversible exchange (SABRE) using para-hydrogen is an attractive method of hyperpolarization for overcoming the sensitivity problems of nuclear magnetic resonance (NMR) spectroscopy. Additionally, SABRE, using the spin order of para-hydrogen, can be applied in reaction monitoring processes for organic chemistry reactions where a small amount of reactant exists. The organic reaction monitoring system created by integrating SABRE and benchtop NMR is the ideal combination for monitoring a reaction and identifying the small amounts of materials in the middle of the reaction. We used a laboratory-built setup, prepared materials by synthesis, and showed that the products obtained by esterification of glycine were also active in SABRE. The products, which were synthesized esterified glycine with nicotinoyl chloride hydrochloride, were observed with a reaction monitoring system. The maximum SABRE enhancement among them (approximately 147-fold) validated the use of this method. This study is the first example of the monitoring of this organic reaction by SABRE and benchtop NMR. It will open new possibilities for applying this system to many other organic reactions and also provide more fruitful future applications such as drug discovery and mechanism study.

Dynamic nuclear polarisation of liquids at one microtesla using circularly polarised RF with application to millimetre resolution MRI.

Magnetic resonance imaging in ultra-low fields is often limited by mediocre signal-to-noise ratio hindering a higher resolution. Overhauser dynamic nuclear polarisation (O-DNP) using nitroxide radicals has been an efficient solution for enhancing the thermal nuclear polarisation. However, the concurrence of positive and negative polarisation enhancements arises in ultra-low fields resulting in a significantly reduced net enhancement, making O-DNP far less attractive. Here, we address this issue by applying circularly polarised RF. O-DNP with circularly polarised RF renders a considerably improved enhancement factor of around 150,000 at 1.2 µT. A birdcage coil was adopted into an ultra-low field MRI system to generate the circularly polarised RF field homogeneously over a large volume. We acquired an MR image of a nitroxide radical solution with an average in-plane resolution of 1 mm. De-noising through compressive sensing further improved the image quality.

Absolute phase effects on CPMG-type pulse sequences.

We describe and analyze the effects of transients within radio-frequency (RF) pulses on multiple-pulse NMR measurements such as the well-known Carr-Purcell-Meiboom-Gill (CPMG) sequence. These transients are functions of the absolute RF phases at the beginning and end of the pulse, and are thus affected by the timing of the pulse sequence with respect to the period of the RF waveform. Changes in transients between refocusing pulses in CPMG-type sequences can result in signal decay, persistent oscillations, changes in echo shape, and other effects. We have explored such effects by performing experiments in two different low-frequency NMR systems. The first uses a conventional tuned-and-matched probe circuit, while the second uses an ultra-broadband un-tuned or non-resonant probe circuit. We show that there are distinct differences between the absolute phase effects in these two systems, and present simple models that explain these differences.

Pressure-driven suspension flow near jamming.

We report here magnetic resonance imaging measurements performed on suspensions with a bulk solid volume fraction (ϕ_{0}) up to 0.55 flowing in a pipe. We visualize and quantify spatial distributions of ϕ and velocity across the pipe at different axial positions. For dense suspensions (ϕ_{0}>0.5), we found a different behavior compared to the known cases of lower ϕ_{0}. Our experimental results demonstrate compaction within the jammed region (characterized by a zero macroscopic shear rate) from the jamming limit ϕ_{m}≈0.58 at its outer boundary to the random close packing limit ϕ_{rcp}≈0.64 at the center. Additionally, we show that ϕ and velocity profiles can be fairly well captured by a frictional rheology accounting for both further compaction of jammed regions as well as normal stress differences.

Absence of static loop-current magnetism at the apical oxygen site in HgBa2CuO4+δ from NMR.

The simple structure of HgBa(2)CuO(4+δ) (Hg1201) is ideal among cuprates for study of the pseudogap phase as a broken symmetry state. We have performed (17)O nuclear magnetic resonance on an underdoped Hg1201 crystal with a transition temperature of 74 K to look for circulating loop currents proposed theoretically and inferred from neutron scattering. The narrow spectra preclude static local fields in the pseudogap phase at the apical site, suggesting that the moments observed with neutrons are fluctuating. The nuclear magnetic resonance frequency shifts are consistent with a dipolar field from the Cu(2+) site.