Modular Pulse Program Generation for NMR Supersequences.

NMR supersequences allow multiple 2D NMR data sets to be acquired in greatly reduced experiment durations through tailored detection of NMR responses within concatenated modules. In NOAH (NMR by Ordered Acquisition using 1H detection) experiments, up to five modules can be combined (or even more when parallel modules are employed), which in theory leads to thousands of plausible supersequences. However, constructing a pulse program for a supersequence is highly time-consuming, requires specialized knowledge, and is error-prone due to its complexity; this has prevented the true potential of the NOAH concept from being fully realized. We introduce here an online tool named GENESIS (GENEration of Supersequences In Silico), available via https://nmr-genesis.co.uk, which systematically generates pulse programs for arbitrary NOAH supersequences compatible with Bruker spectrometers. The GENESIS website provides a unified "one-stop" interface where users may obtain customized supersequences for specific applications, together with all associated acquisition and processing scripts, as well as detailed instructions for running NOAH experiments. Furthermore, it enables the rapid dissemination of new developments in NOAH sequences, such as new modules or improvements to existing modules. Here, we present several such enhancements, including options for solvent suppression, new modules based on pure shift NMR, and improved artifact reduction in HMBC and HMQC modules.

On-the-Fly, Sample-Tailored Optimization of NMR Experiments.

NMR experiments, indispensable to chemists in many areas of research, are often run with generic, unoptimized experimental parameters. This approach makes robust and automated acquisition on different samples and instruments extremely challenging. Here, we present NMR-POISE (Parameter Optimization by Iterative Spectral Evaluation), the first demonstration of on-the-fly, sample-tailored, and fully automated optimization of a wide range of NMR experiments. We illustrate how POISE maximizes spectral sensitivity and quality with a diverse set of 1D and 2D examples, ranging from HSQC and NOESY experiments to ultrafast and pure shift techniques. Our Python implementation of POISE has an interface integrated into Bruker's TopSpin software, one of the most widely used platforms for NMR acquisition and automation, allowing NMR optimizations to be run without direct user supervision. We predict that POISE will find widespread usage in academia and industry, where sample-specific and automated experiment optimization is mandatory.

Bradycardia as an early warning sign for cardiac arrest during routine laparoscopic surgery.

OBJECTIVES: The aim of this study was to identify clinical patterns of occurrence, management and outcomes surrounding cardiac arrest during laparoscopic surgery using the Australian Incident Monitoring Study (AIMS) database to guide possible prevention and treatment. SETTING: The AIMS database includes incident reports from participating clinicians from secondary and tertiary healthcare centres across Australia and New Zealand. PARTICIPANTS: The AIMS database holds over 11 000 peri- and intraoperative incidents. PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcome was to characterize the pattern of events surrounding cardiac arrest. The secondary outcome was to identify successful management strategies in the possible prevention and treatment of cardiac arrest during laparoscopic surgery. RESULTS: Fourteen cases of cardiac arrest during laparoscopic surgery were identified. The majority of cases occurred in 'fit and healthy' patients during elective gynaecological and general surgical procedures. Twelve cases of cardiac arrest were directly associated with pneumoperitoneum with bradycardia preceding cardiac arrest in 75% of these. Management included deflation of pneumoperitoneum, atropine administration and cardiopulmonary resuscitation with circulatory restoration in all cases. The results imply vagal mechanisms associated with peritoneal distension as the predominant contributor to bradycardia and subsequent cardiac arrest during laparoscopy. CONCLUSIONS: Bradycardia during gas insufflation is not necessarily a benign event and appears to be a critical early warning sign for possible impending and unexpected cardiac arrest. Immediate deflation of pneumoperitoneum and atropine administration are effective measures that may alleviate bradycardia and possibly avert progression to cardiac arrest.

The NOAH HSQC-COSY module revisited: A theoretical and practical comparison of pulse sequences.

NMR supersequences, as exemplified by the NOAH (NMR by Ordered Acquisition using 1H detection) technique, are a powerful way of acquiring multiple 2D data sets in much shorter durations. This is accomplished through targeted excitation and detection of the magnetisation belonging to specific isotopologues ('magnetisation pools'). Separately, the HSQC-COSY experiment has recently seen an increase in popularity due to the high signal dispersion in the indirect dimension and the removal of ambiguity traditionally associated with HSQC-TOCSY experiments. Here, we describe how the HSQC-COSY experiment can be integrated as a 'module' within NOAH supersequences. The benefits and drawbacks of several different pulse sequence implementations are discussed, with a particular focus on how sensitivities of other modules in the same supersequence are affected.

Spatially encoded pure-shift diffusion-ordered NMR spectroscopy yielded by chirp excitation.

Spatially-encoded diffusion-ordered NMR spectroscopy (SPEN-DOSY) has emerged as a new time-efficient tool for the analysis of mixtures of small molecules in solution. Time efficiency is achieved using the concept of spatial parallelization of the effective gradient area, instead of the sequential incrementation used in conventional diffusion experiments. The data acquired with such sequences are then usually processed to extract diffusion coefficients, but cases when peak overlap in the 1H spectrum are difficult to address. Such limitation in conventional diffusion experiments is addressed via using the Pure Shift Yielded by CHirp Excitation (PSYCHE)-iDOSY sequence. Here we have adapted the PSYCHE-iDOSY sequence by using echo planar spectroscopic imaging (EPSI) to acquire SPEN-DOSY data. The pure shift mode of PSYCHE separates the overlapped components and a modified Stejskal-Tanner equation is used to extract the corresponding diffusion coefficient. The primary results obtained with the above-mentioned mixtures seem to open the possibility of separating complex mixtures in less time than PSYCHE-iDOSY.

A general scheme for generating NMR supersequences combining high- and low-sensitivity experiments.

NOAH supersequences are a way of collecting multiple 2D NMR experiments in a single measurement. So far, this approach has been limited to experiments with comparable sensitivity. Here, we propose a scheme which overcomes this limitation, combining experiments with very different sensitivities such as 1,1-ADEQUATE, 15N HMBC, and 13C HSQC.

Towards fully optimised and automated ESR spectroscopy.

To address the problems of instrumental imperfection and time-consuming experimental setup in electron spin resonance (ESR), we present ESR-POISE, a user-friendly software package for fully automated and fast on-the-fly optimisation and acquisition of ESR experiments. This open-source package interfaces with Bruker's Xepr software and allows scientists to run user-defined optimisations.

Increasing sensitivity and versatility in NMR supersequences with new HSQC-based modules.

The sensitivity-enhanced HSQC, as well as HSQC-TOCSY, experiments have been modified for incorporation into NOAH (NMR by Ordered Acquisition using 1H detection) supersequences, adding diversity for 13C and 15N modules. Importantly, these heteronuclear modules have been specifically tailored to preserve the magnetisation required for subsequent acquisition of other heteronuclear or homonuclear modules in a supersequence. In addition, we present protocols for optimally combining HSQC and HSQC-TOCSY elements within the same supersequences, yielding high-quality 2D spectra suitable for structure characterisation but with greatly reduced experiment durations. We further demonstrate that these time savings can translate to increased detection sensitivity per unit time.

Parallel NMR Supersequences: Ten Spectra in a Single Measurement.

The principles employed in parallel NMR and MRI are applied to NMR supersequences yielding as many as ten 2D NMR spectra in one measurement. We present a number of examples where two NOAH (NMR by Ordered Acquisition using 1H-detection) supersequences are recorded in parallel, thus dramatically increasing the information content obtained in a single NMR experiment. The two parallel supersequences entangled by time-sharing schemes (IPAP-seHSQC, HSQC-COSY, and HSQC-TOCSY) incorporate also modified (sequential and/or interleaved) conventional pulse schemes (modules), including HMBC, TOCSY, COSY, CLIP-COSY, NOESY, and ROESY. Such parallel supersequences can be tailored for specific applications, for instance, the analysis and characterization of molecular structure of complex organic molecules from a single measurement. In particular, the CASPER software was used to establish the structure of a tetrasaccharide, ß-LNnTOMe, with a high degree of confidence from a single measurement involving a parallel NOAH-5 supersequence.

Young-onset colorectal cancer is associated with a personal history of type 2 diabetes.

BACKGROUND: Colorectal cancer (CRC) is rising in incidence in young adults, and this observation is currently unexplained. We investigated whether having a personal history of type 2 diabetes mellitus (T2D) was a potential risk factor for young-onset colorectal cancer (YOCRC). METHODS: The South Australian Young Onset (SAYO) CRC study is a series of young adults with CRC below age 55. Ninety unrelated YOCRC cases were recruited to the study. Personal history and detailed family history of T2D were obtained at face-to-face interview and confirmed from medical records. Whole exome sequencing was conducted on germline DNA from each CRC case. Controls for personal history studies of T2D were 240 patients with proven clear colonoscopies and no known CRC predispositions. RESULTS: The median age of YOCRC cases was 44 years (18-54) and of controls was 45 years (18-54), and 53% of both cases and controls were females (P = 0.99). Left-sided (distal) CRC was seen in 67/89 (75%) of cases. A personal history of T2D was confirmed in 17/90 (19%) YOCRC patients compared with controls (12/240, 5%; P < 0.001; odds ratio = 4.4; 95% confidence interval, 2.0-9.7). YOCRC patients frequently reported at least one first-degree relative with T2D (32/85, 38%). Ten of 87 (12%) of YOCRC cases had CRC-related pathogenic germline variants, however, no pathogenic variants in familial diabetes-associated genes were seen. CONCLUSIONS: Though the mechanism remains unclear, our observations suggest that there is enrichment for personal history of T2D in YOCRC patients. IMPACT: A diagnosis of T2D could therefore potentially identify a subset of young adults at increased risk for CRC and in whom early screening might be appropriate.

Implementing a Global Expanded Access Program (EAP) for Infantile-Onset Spinal Muscular Atrophy (Type I): Understanding the Imperative, Impact and Challenges.

Nusinersen is the first disease-modifying therapy approved for the treatment of spinal muscular atrophy (SMA), a rare genetic disorder characterized by severe progressive muscular atrophy and weakness. An expanded access program (EAP) provides investigational treatment to patients without other treatment options. An EAP providing nusinersen treatment to individuals with the most severe form of SMA, infantile-onset SMA (consistent with SMA Type I), has enrolled over 800 participants as of September 2018, making it one of the largest in rare disease history. The successes, challenges experienced and opportunities for future consideration during the implementation of the nusinersen EAP are discussed.

A General Copper-Catalyzed Synthesis of Ynamides from 1,2-Dichloroenamides.

Ynamides are accessed via copper-catalyzed coupling of Grignard or organozinc nucleophiles with chloroynamides, formed in situ from 1,2-dichloroenamides. The reaction exhibits a broad substrate scope, is readily scaled, and overcomes typical limitations in ynamide synthesis such as the use of ureas, carbamates, and bulky or aromatic amide derivatives. This modular approach contrasts with previous routes by installing both the N- and C-substituents of the ynamide as nucleophilic components.