Reconstructing Prehistoric African Population Structure.

We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP.

Ancient DNA and deep population structure in sub-Saharan African foragers.

Multiple lines of genetic and archaeological evidence suggest that there were major demographic changes in the terminal Late Pleistocene epoch and early Holocene epoch of sub-Saharan Africa1-4. Inferences about this period are challenging to make because demographic shifts in the past 5,000 years have obscured the structures of more ancient populations3,5. Here we present genome-wide ancient DNA data for six individuals from eastern and south-central Africa spanning the past approximately 18,000 years (doubling the time depth of sub-Saharan African ancient DNA), increase the data quality for 15 previously published ancient individuals and analyse these alongside data from 13 other published ancient individuals. The ancestry of the individuals in our study area can be modelled as a geographically structured mixture of three highly divergent source populations, probably reflecting Pleistocene interactions around 80-20 thousand years ago, including deeply diverged eastern and southern African lineages, plus a previously unappreciated ubiquitous distribution of ancestry that occurs in highest proportion today in central African rainforest hunter-gatherers. Once established, this structure remained highly stable, with limited long-range gene flow. These results provide a new line of genetic evidence in support of hypotheses that have emerged from archaeological analyses but remain contested, suggesting increasing regionalization at the end of the Pleistocene epoch.

Time-efficient filtering of imaging polarimetric data by checking physical realizability of experimental mueller matrices.

MOTIVATION: Imaging Mueller polarimetry has already proved its potential for biomedicine, remote sensing and metrology. The real-time applications of this modality require both video rate image acquisition and fast data post-processing algorithms. First, one must check the physical realizability of the experimental Mueller matrices in order to filter out non-physical data, ie to test the positive semi-definiteness of the 4 × 4 Hermitian coherency matrix calculated from the elements of corresponding Mueller matrix pixel-wise. For this purpose, we compared the execution time for the calculations of i) eigenvalues, ii) Cholesky decomposition, iii) Sylvester's criterion, and iv) coefficients of the characteristic polynomial (two different approaches) of the Hermitian coherency matrix, all calculated for the experimental Mueller matrix images (600 pixels × 700 pixels) of mouse uterine cervix. The calculations were performed using C ++ and Julia programming languages. RESULTS: Our results showed the superiority of the algorithm iv) based on the simplification via Pauli matrices over other algorithms for our dataset. The sequential implementation of latter algorithm on a single core already satisfies the requirements of real-time polarimetric imaging. This can be further amplified by the proposed parallelization (e.g., we achieve a 5-fold speed up on 6 cores). AVAILABILITY AND IMPLEMENTATION: The source codes of the algorithms and experimental data are available at https://github.com/pogudingleb/mueller_matrices.

Identification of the functional PD-L1 interface region responsible for PD-1 binding and initiation of PD-1 signaling.

The PD-1/PD-L1 checkpoint pathway is important for regulating immune responses and can be targeted by immunomodulatory drugs to treat a variety of immune disorders. However, the precise protein-protein interactions required for the initiation of PD-1/PD-L1 signaling are currently unknown. Previously, we designed a series of first-generation PD-1 targeting peptides based on the native interface region of programmed death ligand 1 (PD-L1) that effectively reduced PD-1/PD-L1 binding. In this work, we further characterized the previously identified lead peptide, MN1.1, to identify key PD-1 binding residues and design an optimized peptide, MN1.4. We show MN1.4 is significantly more stable than MN1.1 in serum and retains the ability to block PD-1/PD-L1 complex formation. We further characterized the immunomodulatory effects of MN1.4 treatment by measuring markers of T cell activation in a co-culture model with ovarian cancer cells and peripheral blood mononuclear cells. We found MN1.4 treatment reduced cytokine secretion and suppressed T cell responses in a similar manner as recombinant PD-L1. Therefore, the PD-L1 interface region used to design MN1.4 appeared sufficient to initiate PD-1 signaling and likely represents the minimum necessary region of PD-L1 required for PD-1 recognition. We propose a peptide agonist for PD-1, such as MN1.4, could have several applications for treating autoimmune disorders caused by PD-1 deficiencies such as type 1 diabetes, inflammatory arthritis, or autoimmune side effects arising from monoclonal antibody-based cancer immunotherapies.

Is a complete Mueller matrix necessary in biomedical imaging?

The advent of imagers with integrated linear polarization selectivity opens new opportunities for researchers interested in the polarization properties of biological tissues. In this Letter, we explore the mathematical framework necessary to obtain common parameters of interest: azimuth; retardance; and depolarization with reduced Mueller matrices that can be measured with the new instrumentation. We show that in the case of acquisition close to the tissue normal, simple algebraic analysis of the reduced form of the Mueller matrix yields results very close to those obtained with more complex decomposition algorithms applied to a complete Mueller matrix.

Self validating Mueller matrix Micro-Mesoscope (SAMMM) for the characterization of biological media.

Reflectance Mueller matrix (MM) polarimetry is being used to characterize biological media in multiple clinical applications. The origin of the reflectance polarimetric data is often unclear due to the impact of multiple scattering and tissue heterogeneity. We have developed a new, to the best of our knowledge, multimodal imaging technique combining MM reflectance, MM digital confocal imaging, and co-registered nonlinear microscopy techniques. The instrument unveils the origin of reflectance polarimetric signature in terms of confocal reflectance data. The reconstructed reflected MM demonstrates the capability of our method to provide depth-resolved 3D polarization response from complex biological media in terms of depolarization, retardance, and orientation parameters.

A Method to Quantify Tensile Biaxial Properties of Mouse Aortic Valve Leaflets.

Understanding aortic valve (AV) mechanics is crucial in elucidating both the mechanisms that drive the manifestation of valvular diseases as well as the development of treatment modalities that target these processes. Genetically modified mouse models have become the gold standard in assessing biological mechanistic influences of AV development and disease. However, very little is known about mouse aortic valve leaflet (MAVL) tensile properties due to their microscopic size (∼500 µm long and 45 µm thick) and the lack of proper mechanical testing modalities to assess uniaxial and biaxial tensile properties of the tissue. We developed a method in which the biaxial tensile properties of MAVL tissues can be assessed by adhering the tissues to a silicone rubber membrane utilizing dopamine as an adhesive. Applying equiaxial tensile loads on the tissue-membrane composite and tracking the engineering strains on the surface of the tissue resulted in the characteristic orthotropic response of AV tissues seen in human and porcine tissues. Our data suggest that the circumferential direction is stiffer than the radial direction (n = 6, P = 0.0006) in MAVL tissues. This method can be implemented in future studies involving longitudinal mechanical stimulation of genetically modified MAVL tissues bridging the gap between cellular biological mechanisms and valve mechanics in popular mouse models of valve disease.

Cooking Chemistry Transforms Proteins into High-Strength Adhesives.

In prior generations, proteins were taken from horses and other animals to make glues. Petroleum-derived polymers including epoxies and cyanoacrylates have since replaced proteins owing to improved performance. These modern materials come at a cost of toxicity as well as being derived from limited resources. Ideally, replacement adhesives will be made from benign, cheap, and renewable feedstocks. Such a transition to biobased materials, however, will not occur until similar or improved performance can be achieved. We have discovered that coupling of proteins and sugars gives rise to strong adhesives. An unexpected connection was made between adhesion and Maillard chemistry, known to be at the heart of cooking foods. Cross-linked proteins bonded metal and wood with high strengths, in some cases showing forces exceeding those withstood by the substrates themselves. Simple cooking chemistry may provide a route to future high-performance materials derived from low-cost, environmentally benign components.

Spatially resolved chemical analysis of cicada wings using laser-ablation electrospray ionization (LAESI) imaging mass spectrometry (IMS).

Laser-ablation electrospray ionization (LAESI) imaging mass spectrometry (IMS) is an emerging bioanalytical tool for direct imaging and analysis of biological tissues. Performing ionization in an ambient environment, this technique requires little sample preparation and no additional matrix, and can be performed on natural, uneven surfaces. When combined with optical microscopy, the investigation of biological samples by LAESI allows for spatially resolved compositional analysis. We demonstrate here the applicability of LAESI-IMS for the chemical analysis of thin, desiccated biological samples, specifically Neotibicen pruinosus cicada wings. Positive-ion LAESI-IMS accurate ion-map data was acquired from several wing cells and superimposed onto optical images allowing for compositional comparisons across areas of the wing. Various putative chemical identifications were made indicating the presence of hydrocarbons, lipids/esters, amines/amides, and sulfonated/phosphorylated compounds. With the spatial resolution capability, surprising chemical distribution patterns were observed across the cicada wing, which may assist in correlating trends in surface properties with chemical distribution. Observed ions were either (1) equally dispersed across the wing, (2) more concentrated closer to the body of the insect (proximal end), or (3) more concentrated toward the tip of the wing (distal end). These findings demonstrate LAESI-IMS as a tool for the acquisition of spatially resolved chemical information from fragile, dried insect wings. This LAESI-IMS technique has important implications for the study of functional biomaterials, where understanding the correlation between chemical composition, physical structure, and biological function is critical. Graphical abstract Positive-ion laser-ablation electrospray ionization mass spectrometry coupled with optical imaging provides a powerful tool for the spatially resolved chemical analysis of cicada wings.

Noninvasive imaging technologies for cutaneous wound assessment: A review.

The ability to phenotype wounds for the purposes of assessing severity, healing potential and treatment is an important function of evidence-based medicine. A variety of optical technologies are currently in development for noninvasive wound assessment. To varying extents, these optical technologies have the potential to supplement traditional clinical wound evaluation and research, by providing detailed information regarding skin components imperceptible to visual inspection. These assessments are achieved through quantitative optical analysis of tissue characteristics including blood flow, collagen remodeling, hemoglobin content, inflammation, temperature, vascular structure, and water content. Technologies that have, to this date, been applied to wound assessment include: near infrared imaging, thermal imaging, optical coherence tomography, orthogonal polarization spectral imaging, fluorescence imaging, laser Doppler imaging, microscopy, spatial frequency domain imaging, photoacoustic detection, and spectral/hyperspectral imaging. We present a review of the technologies in use or development for these purposes with three aims: (1) providing basic explanations of imaging technology concepts, (2) reviewing the wound imaging literature, and (3) providing insight into areas for further application and exploration. Noninvasive imaging is a promising advancement in wound assessment and all technologies require further validation.

Three-dimensional printing of tissue phantoms for biophotonic imaging.

We have investigated the potential of tissue phantoms fabricated with thermosoftening- and photopolymerization-based three-dimensional (3D) printers for use in evaluation of biophotonic imaging systems. The optical properties of printed polymer samples were measured and compared to biological tissues. Phantoms with subsurface channels as small as 0.2 mm in diameter were fabricated and imaged with microscopy, x-ray microtomography, and optical coherence tomography to characterize morphology. These phantoms were then implemented to evaluate the penetration depth of a hyperspectral reflectance imaging system used in conjunction with a near-infrared contrast agent. Results indicated that 3D printing may provide a suitable platform for performance testing in biophotonics, although subsurface imaging is critical to mitigate printer-to-printer variability in matrix homogeneity and feature microstructure.

Vascular contrast in narrow-band and white light imaging.

Narrow-band imaging (NBI) is a spectrally selective reflectance imaging technique that is used clinically for enhancing visualization of superficial vasculature and has shown promise for applications such as early endoscopic detection of gastrointestinal neoplasia. We have studied the effect of vessel geometry and illumination wavelength on vascular contrast using idealized geometries in order to more quantitatively understand NBI and broadband or white light imaging of mucosal tissue. Simulations were performed using a three-dimensional, voxel-based Monte Carlo model incorporating discrete vessels. In all cases, either 415 or 540 nm illumination produced higher contrast than white light, yet white light did not always produce the lowest contrast. White light produced the lowest contrast for small vessels and intermediate contrast for large vessels (diameter≥100 µm) at deep regions (vessel depth≥200 µm). The results show that 415 nm illuminations provided superior contrast for smaller vessels at shallow depths while 540 nm provided superior contrast for larger vessels in deep regions. Besides 540 nm, our studies also indicate the potential of other wavelengths to achieve high contrast of large vessels at deep regions. Simulation results indicate the importance of three key mechanisms in determining spectral variations in contrast: intravascular hemoglobin (Hb) absorption in the vessel of interest, diffuse Hb absorption from collateral vasculature, and bulk tissue scattering. Measurements of NBI contrast in turbid phantoms incorporating 0.1-mm-diameter hemoglobin-filled capillary tubes indicated good agreement with modeling results. These results provide quantitative insights into light-tissue interactions and the effect of device and tissue properties on NBI performance.

In vitro evaluation of fluorescence glucose biosensor response.

Rapid, accurate, and minimally-invasive glucose biosensors based on Förster Resonance Energy Transfer (FRET) for glucose measurement have the potential to enhance diabetes control. However, a standard set of in vitro approaches for evaluating optical glucose biosensor response under controlled conditions would facilitate technological innovation and clinical translation. Towards this end, we have identified key characteristics and response test methods, fabricated FRET-based glucose biosensors, and characterized biosensor performance using these test methods. The biosensors were based on competitive binding between dextran and glucose to concanavalin A and incorporated long-wavelength fluorescence dye pairs. Testing characteristics included spectral response, linearity, sensitivity, limit of detection, kinetic response, reversibility, stability, precision, and accuracy. The biosensor demonstrated a fluorescence change of 45% in the presence of 400 mg/dL glucose, a mean absolute relative difference of less than 11%, a limit of detection of 25 mg/dL, a response time of 15 min, and a decay in fluorescence intensity of 72% over 30 days. The battery of tests presented here for objective, quantitative in vitro evaluation of FRET glucose biosensors performance have the potential to form the basis of future consensus standards. By implementing these test methods for a long-visible-wavelength biosensor, we were able to demonstrate strengths and weaknesses with a new level of thoroughness and rigor.

Selective formation of metastable ferrihydrite in the chiton tooth.

Metastable precursors are thought to play a major role in the ability of organisms to create mineralized tissues. Of particular interest are the hard and abrasion-resistant teeth formed by chitons, a class of rock-grazing mollusks. The formation of chiton teeth relies on the precipitation of metastable ferrihydrite (Fh) in an organic scaffold as a precursor to magnetite. In vitro synthesis of Fh under physiological conditions has been challenging. Using a combination of X-ray absorption and electron paramagnetic resonance spectroscopy, we show that, prior to Fh formation in the chiton tooth, iron ions are complexed by the organic matrix. In vitro experiments demonstrate that such complexes facilitate the formation of Fh under physiological conditions. These results indicate that acidic molecules may be integral to controlling Fh formation in the chiton tooth. This biological approach to polymorph selection is not limited to specialized proteins and can be expropriated using simple chemistry.

Special Section Guest Editorial: Polarimetry in Biomedical Optics.

The editorial introduces the two-issue JBO Special Section on Polarimetry in Biomedical Optics and provides resources for further exploration.

Predictors of Human Papillomavirus Vaccine Intention and Uptake Among US Hispanic Parents: A Cross-Sectional Study.

Introduction: This study explored the influence of the Theory of Planned Behavior constructs on human papillomavirus (HPV) vaccine (HPVV) intentions and uptake among Hispanic parents in South Florida for their children aged 9-21. Method: A descriptive exploratory analysis was conducted using 39 surveys completed by Hispanic parents. These surveys encompassed demographic data and questions about HPVV uptake, intention, attitudes, subjective norms, knowledge, self-efficacy, and awareness. Results: Most participants were uninsured (77%), unemployed (59%), and had low Americanism acculturation (74%). A little over half were aware of the HPVV (54%), yet most had high positive HPVV attitudes (95%) and self-efficacy (85%). HPVV intentions within the year were also high (82%); however, HPVV uptake (45%) and HPVV knowledge (40%) were low at the time of the study. Most parents reported physicians (72%) and nurses/nurse practitioners (59%) as the most influential individuals in their decision-making. A statistically significant relationship between HPVV intention and HPVV attitude (X_Wald^2 (1) = 5.71, p = 0.02., OR = 5.11) and between HPVV uptake and HPVV awareness (X_Wald^2 (1) = 4.63, p = 0.03., OR = 12) were observed. Conclusion: This study recommends further research and targeted interventions to improve HPVV awareness among Hispanic communities. The participants' highly positive attitudes and self-efficacy provide a hopeful outlook for future vaccination efforts within this demographic.

Quantitative Assessment of Collagen Remodeling during a Murine Pregnancy.

Uterine cervical remodeling is a fundamental feature of pregnancy, facilitating the delivery of the fetus through the cervical canal. Yet, we still know very little about this process due to the lack of methodologies that can quantitatively and unequivocally pinpoint the changes the cervix undergoes during pregnancy. We utilize polarization-resolved second harmonic generation to visualize the alterations the cervix extracellular matrix, specifically collagen, undergoes during pregnancy with exquisite resolution. This technique provides images of the collagen orientation at the pixel level (0.4 µm) over the entire murine cervical section. They show tight and ordered packing of collagen fibers around the os at the early stage of pregnancy and their disruption at the later stages. Furthermore, we utilize a straightforward statistical analysis to demonstrate the loss of order in the tissue, consistent with the loss of mechanical properties associated with this process. This work provides a deeper understanding of the parturition process and could support research into the cause of pathological or premature birth.

Tissue mimicking materials and finger phantom design for pulse oximetry.

Pulse oximetry represents a ubiquitous clinical application of optics in modern medicine. Recent studies have raised concerns regarding the potential impact of confounders, such as variable skin pigmentation and perfusion, on blood oxygen saturation measurement accuracy in pulse oximeters. Tissue-mimicking phantom testing offers a low-cost, well-controlled solution for characterizing device performance and studying potential error sources, which may thus reduce the need for costly in vivo trials. The purpose of this study was to develop realistic phantom-based test methods for pulse oximetry. Material optical and mechanical properties were reviewed, selected, and tuned for optimal biological relevance, e.g., oxygenated tissue absorption and scattering, strength, elasticity, hardness, and other parameters representing the human finger's geometry and composition, such as blood vessel size and distribution, and perfusion. Relevant anatomical and physiological properties are summarized and implemented toward the creation of a preliminary finger phantom. To create a preliminary finger phantom, we synthesized a high-compliance silicone matrix with scatterers for embedding flexible tubing and investigated the addition of these scatterers to novel 3D printing resins for optical property control without altering mechanical stability, streamlining the production of phantoms with biologically relevant characteristics. Phantom utility was demonstrated by applying dynamic, pressure waveforms to produce tube volume change and resultant photoplethysmography (PPG) signals. 3D printed phantoms achieved more biologically relevant conditions compared to molded phantoms. These preliminary results indicate that the phantoms show strong potential to be developed into tools for evaluating pulse oximetry performance. Gaps, recommendations, and strategies are presented for continued phantom development.

Speculum-free portable preterm imaging system.

Significance: Preterm birth is defined as a birth before 37 weeks of gestation and is one of the leading contributors to infant mortality rates globally. Premature birth can lead to life-long developmental impairment for the child. Unfortunately, there is a significant lack of tools to diagnose preterm birth risk, which limits patient care and the development of new therapies. Aim: To develop a speculum-free, portable preterm imaging system (PPRIM) for cervical imaging; testing of the PPRIM system to resolve polarization properties of birefringent samples; and testing of the PPRIM under an IRB on healthy, non-pregnant volunteers for visualization and polarization analysis of cervical images. Approach: The PPRIM can perform 4×3 Mueller-matrix imaging to characterize the remodeling of the uterine cervix during pregnancy. The PPRIM is built with a polarized imaging probe and a flexible insertable sheath made with a compatible flexible rubber-like material to maximize comfort and ease of use. Results: The PPRIM device is developed to meet specific design specifications as a speculum-free, portable, and comfortable imaging system with polarized imaging capabilities. This system comprises a main imaging component and a flexible silicone inserter. The inserter is designed to maximize comfort and usability for the patient. The PPRIM shows high-resolution imaging capabilities at the 20 mm working distance and 25 mm circular field of view. The PPRIM demonstrates the ability to resolve birefringent sample orientation and full field capture of a healthy, non-pregnant cervix. Conclusion: The development of the PPRIM aims to improve access to the standard of care for women's reproductive health using polarized Mueller-matrix imaging of the cervix and reduce infant and maternal mortality rates and better quality of life.

Insertable Glucose Sensor Using a Compact and Cost-Effective Phosphorescence Lifetime Imager and Machine Learning.

Optical continuous glucose monitoring (CGM) systems are emerging for personalized glucose management owing to their lower cost and prolonged durability compared to conventional electrochemical CGMs. Here, we report a computational CGM system, which integrates a biocompatible phosphorescence-based insertable biosensor and a custom-designed phosphorescence lifetime imager (PLI). This compact and cost-effective PLI is designed to capture phosphorescence lifetime images of an insertable sensor through the skin, where the lifetime of the emitted phosphorescence signal is modulated by the local concentration of glucose. Because this phosphorescence signal has a very long lifetime compared to tissue autofluorescence or excitation leakage processes, it completely bypasses these noise sources by measuring the sensor emission over several tens of microseconds after the excitation light is turned off. The lifetime images acquired through the skin are processed by neural network-based models for misalignment-tolerant inference of glucose levels, accurately revealing normal, low (hypoglycemia) and high (hyperglycemia) concentration ranges. Using a 1 mm thick skin phantom mimicking the optical properties of human skin, we performed in vitro testing of the PLI using glucose-spiked samples, yielding 88.8% inference accuracy, also showing resilience to random and unknown misalignments within a lateral distance of ∼4.7 mm with respect to the position of the insertable sensor underneath the skin phantom. Furthermore, the PLI accurately identified larger lateral misalignments beyond 5 mm, prompting user intervention for realignment. The misalignment-resilient glucose concentration inference capability of this compact and cost-effective PLI makes it an appealing wearable diagnostics tool for real-time tracking of glucose and other biomarkers.