High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging.

Resolving the spatial distribution of RNA and protein in tissues at subcellular resolution is a challenge in the field of spatial biology. We describe spatial molecular imaging, a system that measures RNAs and proteins in intact biological samples at subcellular resolution by performing multiple cycles of nucleic acid hybridization of fluorescent molecular barcodes. We demonstrate that spatial molecular imaging has high sensitivity (one or two copies per cell) and very low error rate (0.0092 false calls per cell) and background (~0.04 counts per cell). The imaging system generates three-dimensional, super-resolution localization of analytes at ~2 million cells per sample. Cell segmentation is morphology based using antibodies, compatible with formalin-fixed, paraffin-embedded samples. We measured multiomic data (980 RNAs and 108 proteins) at subcellular resolution in formalin-fixed, paraffin-embedded tissues (nonsmall cell lung and breast cancer) and identified >18 distinct cell types, ten unique tumor microenvironments and 100 pairwise ligand-receptor interactions. Data on >800,000 single cells and ~260 million transcripts can be accessed at http://nanostring.com/CosMx-dataset .

Home-based newborn care voucher initiative in Assam: An evaluation.

BACKGROUND: An innovative home-based newborn care (HBNC) voucher system has been introduced in Assam to improve home visits of accredited social health activists (ASHAs), make them more accountable, and empower the community. OBJECTIVE: This study aimed to evaluate the effectiveness of HBNC voucher initiative in Assam. METHODS: A mixed methodology study was conducted in 2018 including 4 districts of Assam. A quantitative study was done among a sample of 836 lactating mothers by interviewing them through house-to-house visits. A qualitative study was done by in-depth interview of various health-care service providers. RESULTS: Of 836 lactating mothers, 65% received HBNC voucher; 45.6% received at the time of discharge, and 5.3% during antenatal care. The purpose of HBNC vouchers as a tool of validating ASHAs' home visits was explained to only 14.5% of lactating mothers. Examination of newborn (44.6%), counseling on breastfeeding (57.1%), counseling on care of baby (39.2%), and counseling on immunization (49.2%) were the services commonly provided by ASHA during HBNC visits. Voucher system improved incentive payment system, but uninterrupted supply was a problem area as stated by ASHAs. Auxiliary nurse midwives and ASHA supervisors told that voucher system had improved ASHA home visits, payment system, and increased identification of danger signs of newborns. CONCLUSIONS: HBNC voucher system as an innovative approach was found to be effective. Coverage of services varied among different districts. Uninterrupted supply of the vouchers, periodic resensitization of health workers on its use, and increasing awareness among the community is needed to be sustained.

Two-Photon Microscopy Analysis of Gold Nanoparticle Uptake in 3D Cell Spheroids.

Nanomaterials can be synthesized from a wide range of material systems in numerous morphologies, creating an extremely diverse portfolio. As result of this tunability, these materials are emerging as a new class of nanotherapeutics and imaging agents. One particularly interesting nanomaterial is the gold nanoparticle. Due to its inherent biocompatibility and tunable photothermal behavior, it has made a rapid transition from the lab setting to in vivo testing. In most nanotherapeutic applications, the efficacy of the agent is directly related to the target of interest. However, the optimization of the AuNP size and shape for efficacy in vitro, prior to testing in in vivo models of a disease, has been largely limited to two dimensional monolayers of cells. Two dimensional cell cultures are unable to reproduce conditions experienced by AuNP in the body. In this article, we systematically investigate the effect of different properties of AuNP on the penetration depth into 3D cell spheroids using two-photon microscopy. The 3D spheroids are formed from the HCT116 cell line, a colorectal carcinoma cell line. In addition to studying different sizes and shapes of AuNPs, we also study the effect of an oligo surface chemistry. There is a significant difference between AuNP uptake profiles in the 2D monolayers of cells as compared to the 3D cell spheroids. Additionally, the range of sizes and shapes studied here also exhibit marked differences in uptake penetration depth and efficacy. Finally, our results demonstrate that two-photon microscopy enables quantitative AuNP localization and concentration data to be obtained at the single spheroid level without fluorescent labeling of the AuNP, thus, providing a viable technique for large scale screening of AuNP properties in 3D cell spheroids as compared to tedious and time consuming techniques like electron microscopy.

Use of technology in follow-up of HIV positive pregnant women and their babies till 18 months of age- an innovation by Maharashtra State AIDS Control Society (MSACS), India.

OBJECTIVE: The purpose of this study is to assess the utility of web-based mobile technology monitoring tool, for ensuring linkages, and tracking of HIV-exposed child until 18 months of age. METHODS: The 'early infant diagnosis (EID) Follow-up System' was designed as a tool for reminding the field level staff for follow-up of HIV-exposed babies. Using Java Swing Framework, software was developed which generates automatic advance SMS alerts regarding patient information to the Counsellor of the respective Integrated Counselling and Testing Center and district supervisor, 7 days prior to due dates. Simultaneously, system generated e-mail is sent to district program officer for monitoring and updating the line-list. RESULTS: Before the introduction of 'EID Follow-up System' in June 2013, only 55.9% (637/1139) of the HIV-exposed babies born were tested at 6 weeks for DNA-Polymerase Chain Reaction during April 2011-March 2012. However, after its introduction, 68.4% (1117/1631) of them were tested during April 2012-March 2013. Correspondingly, the 18 months confirmatory HIV testing in eligible babies increased from 45.6% (934/2044) to 54.7%(1118/2044) during the same period. CONCLUSION: The replicable technology driven initiative would help in strengthening the follow-up mechanisms and reach every HIV-exposed child for EID.

Droplet Digital Enzyme-Linked Oligonucleotide Hybridization Assay for Absolute RNA Quantification.

We present a continuous-flow droplet-based digital Enzyme-Linked Oligonucleotide Hybridization Assay (droplet digital ELOHA) for sensitive detection and absolute quantification of RNA molecules. Droplet digital ELOHA incorporates direct hybridization and single enzyme reaction via the formation of single probe-RNA-probe (enzyme) complex on magnetic beads. It enables RNA detection without reverse transcription and PCR amplification processes. The magnetic beads are subsequently encapsulated into a large number of picoliter-sized droplets with enzyme substrates in a continuous-flow device. This device is capable of generating droplets at high-throughput. It also integrates in-line enzymatic incubation and detection of fluorescent products. Our droplet digital ELOHA is able to accurately quantify (differentiate 40% difference) as few as ~600 RNA molecules in a 1 mL sample (equivalent to 1 aM or lower) without molecular replication. The absolute quantification ability of droplet digital ELOHA is demonstrated with the analysis of clinical Neisseria gonorrhoeae 16S rRNA to show its potential value in real complex samples.

Microfluidic continuous flow digital loop-mediated isothermal amplification (LAMP).

Digital nucleic acid detection is rapidly becoming a popular technique for ultra-sensitive and quantitative detection of nucleic acid molecules in a wide range of biomedical studies. Digital polymerase chain reaction (PCR) remains the most popular way of conducting digital nucleic acid detection. However, due to the need for thermocycling, digital PCR is difficult to implement in a streamlined manner on a single microfluidic device, leading to complex fragmented workflows and multiple separate devices and instruments. Loop-mediated isothermal amplification (LAMP) is an excellent isothermal alternative to PCR with potentially better specificity than PCR because of the use of multiple primer sets for a nucleic acid target. Here we report a microfluidic droplet device implementing all the steps required for digital nucleic acid detection including droplet generation, incubation and in-line detection for digital LAMP. As compared to microchamber or droplet array-based digital assays, the continuous flow operation of this device eliminates the constraints on the number of total reactions imposed by the footprint of the device and the analysis throughput caused by the time for lengthy incubation and transfer of materials between instruments.

A barcode-free combinatorial screening platform for matrix metalloproteinase screening.

Application of droplet microfluidics to combinatorial screening applications remains elusive because of the need for composition-identifying unique barcodes. Here we propose a barcode-free continuous flow droplet microfluidic platform to suit the requirements of combinatorial screening applications. We demonstrate robust and repeatable functioning of this platform with matrix metalloproteinase activity screening as a sample application.

A serial sample loading system: interfacing multiwell plates with microfluidic devices.

There is an increasing demand for novel high-throughput screening (HTS) technologies in the pharmaceutical and biotechnological industries. The robotic sample-handling techniques currently used in these industries, although fast, are still limited to operating in multiwell plates with the sample volumes per reaction in the microliter regime. Digital microfluidics offers an alternative for reduction in sample volume consumption for HTS but lacks a reliable technique for transporting a large number of samples to the microfluidic device. In this report, we develop a technique for serial delivery of sample arrays to a microfluidic device from multiwell plates, through a single sample inlet. Under this approach, a serial array of sample plugs, separated by an immiscible carrier fluid, is loaded into a capillary and delivered to a microfluidic device. Similar approaches have been attempted in the past, however, either with a slower sample loading device such as a syringe pump or vacuum-based sample loading with limited driving pressure. We demonstrated the application of our positive-pressure-based serial sample loading (SSL) system to load a series of sample plugs into a capillary. The adaptability of the SSL system to generate sample plugs with a variety of volumes in a predictable manner was also demonstrated.

Droplet microfluidics for amplification-free genetic detection of single cells.

In this article we present a novel droplet microfluidic chip enabling amplification-free detection of single pathogenic cells. The device streamlines multiple functionalities to carry out sample digitization, cell lysis, probe-target hybridization for subsequent fluorescent detection. A peptide nucleic acid fluorescence resonance energy transfer probe (PNA beacon) is used to detect 16S rRNA present in pathogenic cells. Initially the sensitivity and quantification abilities of the platform are tested using a synthetic target mimicking the actual expression level of 16S rRNA in single cells. The capability of the device to perform "sample-to-answer" pathogen detection of single cells is demonstrated using E. coli as a model pathogen.

Microfluidic platform for on-demand generation of spatially indexed combinatorial droplets.

We propose a highly versatile and programmable nanolitre droplet-based platform that accepts an unlimited number of sample plugs from a multi-well plate, performs digitization of these sample plugs into smaller daughter droplets and subsequent synchronization-free, robust injection of multiple reagents into the sample daughter droplets on-demand. This platform combines excellent control of valve-based microfluidics with the high-throughput capability of droplet microfluidics. We demonstrate the functioning of a proof-of-concept device which generates combinatorial mixture droplets from a linear array of sample plugs and four different reagents, using food dyes to mimic samples and reagents. Generation of a one dimensional array of the combinatorial mixture droplets on the device leads to automatic spatial indexing of these droplets, precluding the need to include a barcode in each droplet to identify its contents. We expect this platform to further expand the range of applications of droplet microfluidics to include applications requiring a high degree of multiplexing as well as high throughput analysis of multiple samples.

Single-molecule analysis enables free solution hydrodynamic separation using yoctomole levels of DNA.

Single-molecule free solution hydrodynamic separation (SML-FSHS) cohesively integrates cylindrical illumination confocal spectroscopy with free solution hydrodynamic separation. This technique enables single-molecule analysis of size separated DNA with 100% mass detection efficiency, high sizing resolution and wide dynamic range, surpassing the performance of single molecule capillary electrophoresis. Furthermore, SML-FSHS required only a bare fused silica microcapillary and simple pressure control rather than complex high voltage power supplies, sieving matrices, and wall coatings. The wide dynamic range and high sizing resolution of SML-FSHS was demonstrated by separating both large DNA (23 vs 27 kbp) and small DNA (100 vs 200 bp) under identical conditions. Separations were successfully performed with near zero sample consumption using as little as 5 pL of sample and 240 yoctomoles (∼150 molecules) of DNA. Quantitative accuracy was predominantly limited by molecular shot noise. Furthermore, the ability of this method to analyze of single molecule nanosensors was investigated. SML-FSHS was used to examine the thermodynamic equilibrium between stochastically open molecular beacon and target-bound molecular beacon in the detection of E. coli 16s rRNA targets.

Motor adaptation as a process of reoptimization.

Adaptation is sometimes viewed as a process in which the nervous system learns to predict and cancel effects of a novel environment, returning movements to near baseline (unperturbed) conditions. An alternate view is that cancellation is not the goal of adaptation. Rather, the goal is to maximize performance in that environment. If performance criteria are well defined, theory allows one to predict the reoptimized trajectory. For example, if velocity-dependent forces perturb the hand perpendicular to the direction of a reaching movement, the best reach plan is not a straight line but a curved path that appears to overcompensate for the forces. If this environment is stochastic (changing from trial to trial), the reoptimized plan should take into account this uncertainty, removing the overcompensation. If the stochastic environment is zero-mean, peak velocities should increase to allow for more time to approach the target. Finally, if one is reaching through a via-point, the optimum plan in a zero-mean deterministic environment is a smooth movement but in a zero-mean stochastic environment is a segmented movement. We observed all of these tendencies in how people adapt to novel environments. Therefore, motor control in a novel environment is not a process of perturbation cancellation. Rather, the process resembles reoptimization: through practice in the novel environment, we learn internal models that predict sensory consequences of motor commands. Through reward-based optimization, we use the internal model to search for a better movement plan to minimize implicit motor costs and maximize rewards.

Neural correlates of reach errors.

Reach errors may be broadly classified into errors arising from unpredictable changes in target location, called target errors, and errors arising from miscalibration of internal models (e.g., when prisms alter visual feedback or a force field alters limb dynamics), called execution errors. Execution errors may be caused by miscalibration of dynamics (e.g., when a force field alters limb dynamics) or by miscalibration of kinematics (e.g., when prisms alter visual feedback). Although all types of errors lead to similar on-line corrections, we found that the motor system showed strong trial-by-trial adaptation in response to random execution errors but not in response to random target errors. We used functional magnetic resonance imaging and a compatible robot to study brain regions involved in processing each kind of error. Both kinematic and dynamic execution errors activated regions along the central and the postcentral sulci and in lobules V, VI, and VIII of the cerebellum, making these areas possible sites of plastic changes in internal models for reaching. Only activity related to kinematic errors extended into parietal area 5. These results are inconsistent with the idea that kinematics and dynamics of reaching are computed in separate neural entities. In contrast, only target errors caused increased activity in the striatum and the posterior superior parietal lobule. The cerebellum and motor cortex were as strongly activated as with execution errors. These findings indicate a neural and behavioral dissociation between errors that lead to switching of behavioral goals and errors that lead to adaptation of internal models of limb dynamics and kinematics.