Bottom-up data integration in polymer models of chromatin organization.

Cellular functions crucially depend on the precise execution of complex biochemical reactions taking place on the chromatin fiber in the tightly packed environment of the cell nucleus. Despite the availability of large datasets probing this process from multiple angles, bottom-up frameworks that allow the incorporation of the sequence-specific nature of biochemistry in a unified model of 3D chromatin structure remain scarce. Here, we propose Sequence-Enhanced Magnetic Polymer (SEMPER), a novel stochastic polymer model that naturally incorporates observational data about sequence-driven biochemical processes, such as binding of transcription factor proteins, in a 3D model of chromatin structure. We introduce a novel approximate Bayesian algorithm to quantify a posteriori the relative importance of various factors, including the polymeric nature of DNA, in determining chromatin epigenetic state, thus providing a transparent way to generate biological hypotheses. Although accurate prediction of contact frequencies (a problem already extensively studied in the literature) is not our main aim, as a by-product of the inference procedure and without additional input from the genome 3D structure, our model can predict with reasonable accuracy some notable and nontrivial conformational features of chromatin folding within the nucleus. Our work highlights the importance of introducing physically realistic statistical models for predicting chromatin states from epigenetic data and opens the way to a new class of more systematic approaches to interpreting epigenomic data.

Predictors of inpatient admission likelihood and prolonged length of stay among cerebrovascular disease patients: A nationwide emergency department sample analysis.

PURPOSE: To examine the hospital- and patient-related factors associated with increased likelihood of inpatient admission and extended hospitalization. METHODS: We applied multivariate logistic regression to a subset of ED hospital and patient characteristics linearly extrapolated from the 2019 National Emergency Department Sample database (n=626,508). Patient characteristics with 10 or fewer ED visits after national extrapolation were not reported in the current study to maintain patient confidentiality, in accordance with the HCUP Data Use Agreement. All selected ED visits represented a primary diagnosis of CVD (ICD-10 codes 160-168). All reported hospital and patient characteristics were subject to adjustment for covariates. P-values < 0.05 were considered statistically significant. MAIN FINDINGS: Medicare beneficiaries report higher inpatient admission rates than uninsured OR 0.81 (0.73-0.91) and privately insured OR 0.86 (0.79-0.94) individuals. Black and Native-American patients were 37% and 55% more likely to be hospitalized long (>75th percentile) (OR 1.37 [1.25-1.50], OR 1.55 [1.14-2.10]). Northeast emergency departments reported an increased odds of admission compared to the Midwest OR (0.40-0.62), South OR 0.79 (0.63-0.98) and West OR 0.52 (0.39-0.69). Patients with multiple comorbidities (mCCI = 3+) were 226% more likely to have a longer stay OR 3.26 (3.09-3.45) than patients presenting with zero or few comorbidities. Level I, II, and III trauma centers report distinctly high odds of inpatient admission (OR 3.54 [2.84-4.42], OR 2.68 [2.14-3.35], OR 1.51 [1.25-1.84]). PRINCIPAL CONCLUSIONS: Likelihoods of inpatient admission and long hospital stays were observably stratified through multiple, independently acting hospital and patient characteristics. Significant associations were stratified by race/ethnicity, location, and clinical presentation, among others. Attention to the factors reported here may serve well to mitigate emergency department crowding and its sobering impact on United States healthcare systems and patients.

Non-Invasive Blood Flow Speed Measurement Using Optics.

Non-invasive measurement of the arterial blood speed gives important health information such as cardio output and blood supplies to vital organs. The magnitude and change in arterial blood speed are key indicators of the health conditions and development and progression of diseases. We demonstrated a simple technique to directly measure the blood flow speed in main arteries based on the diffused light model. The concept is demonstrated with a phantom that uses intralipid hydrogel to model the biological tissue and an embedded glass tube with flowing human blood to model the blood vessel. The correlation function of the measured photocurrent was used to find the electrical field correlation function via the Siegert relation. We have shown that the characteristic decorrelation rate (i.e., the inverse of the decoherent time) is linearly proportional to the blood speed and independent of the tube diameter. This striking property can be explained by an approximate analytic solution for the diffused light equation in the regime where the convective flow is the dominating factor for decorrelation. As a result, we have demonstrated a non-invasive method of measuring arterial blood speed without any prior knowledge or assumption about the geometric or mechanic properties of the blood vessels.

Frequency- and Power-Dependent Photoresponse of a Perovskite Photodetector Down to the Single-Photon Level.

Organometallic halide perovskites attract strong interests for their high photoresponsivity and solar cell efficiency. However, there was no systematic study of their power- and frequency-dependent photoresponsivity. We identified two different power-dependent photoresponse types in methylammonium lead iodide perovskite (MAPbI3) photodetectors. In the first type, the photoresponse remains constant from 5 Hz to 800 MHz. In the second type, absorption of a single photon can generate a persistent photoconductivity of 30 pA under an applied electric field of 2.5 × 104 V/cm. Additional absorbed photons, up to 8, linearly increase the persistent photoconductivity, which saturates with the absorption of more than 10 photons. This is different than single-photon avalanche detectors (SPADs) because the single-photon response is persistent as long as the device is under bias, providing unique opportunities for novel electronic and photonic devices such as analogue memories for neuromorphic computing. We propose an avalanche-like process for iodine ions and estimate that absorption of a single 0.38 aJ photon triggers the motion of 108-9 ions, resulting in accumulations of ions and charged vacancies at the MAPbI3/electrode interfaces to cause the band bending and change of electric material properties. We have made the first observation that single-digit photon absorption can alter the macroscopic electric and optoelectronic properties of a perovskite thin film.

Machine Learning Based Real-Time Image-Guided Cell Sorting and Classification.

Cell classification based on phenotypical, spatial, and genetic information greatly advances our understanding of the physiology and pathology of biological systems. Technologies derived from next generation sequencing and fluorescent activated cell sorting are cornerstones for cell- and genomic-based assays supporting cell classification and mapping. However, there exists a deficiency in technology space to rapidly isolate cells based on high content image information. Fluorescence-activated cell sorting can only resolve cell-to-cell variation in fluorescence and optical scattering. Utilizing microfluidics, photonics, computation microscopy, real-time image processing and machine learning, we demonstrate an image-guided cell sorting and classification system possessing the high throughput of flow cytometer and high information content of microscopy. We demonstrate the utility of this technology in cell sorting based on (1) nuclear localization of glucocorticoid receptors, (2) particle binding to the cell membrane, and (3) DNA damage induced γ-H2AX foci. © 2019 International Society for Advancement of Cytometry.

Room-temperature long-wave infrared detector with thin double layers of amorphous germanium and amorphous silicon.

A longwave-infrared photodetector made of double layers of 100nm amorphous germanium (a-Ge) and 25nm amorphous silicon (a-Si) have been demonstrated. Under room temperature, the device shows the responsivity of 1.7 A/W, detectivity of 6×108 Jones, and noise equivalent power (NEP) of 5pW/√Hz under 5V bias and at 20kHz operation. Studies of frequency dependent characteristics and device modeling indicate that, above 100Hz or beyond the bandwidth of thermal response, the device operates as a quantum detector having the photoelectrons produced by optical excitation from the bandtail states to the mobile states of a-Ge. The superior device performance may be attributed to the combination of two amplification mechanisms: photoconductive gain in a-Ge and cycling excitation process (CEP) in a-Si, with the latter being the dominant factor. Besides its attractive performance, the device has a simple structure and is easy to fabricate at low cost, thus holding promise for night vision, sensing, autonomous driving, and many other applications.

Structures of the Multidrug Transporter P-glycoprotein Reveal Asymmetric ATP Binding and the Mechanism of Polyspecificity.

P-glycoprotein (P-gp) is a polyspecific ATP-dependent transporter linked to multidrug resistance in cancer; it plays important roles in determining the pharmacokinetics of many drugs. Understanding the structural basis of P-gp, substrate polyspecificity has been hampered by its intrinsic flexibility, which is facilitated by a 75-residue linker that connects the two halves of P-gp. Here we constructed a mutant murine P-gp with a shortened linker to facilitate structural determination. Despite dramatic reduction in rhodamine 123 and calcein-AM transport, the linker-shortened mutant P-gp possesses basal ATPase activity and binds ATP only in its N-terminal nucleotide-binding domain. Nine independently determined structures of wild type, the linker mutant, and a methylated P-gp at up to 3.3 Å resolution display significant movements of individual transmembrane domain helices, which correlated with the opening and closing motion of the two halves of P-gp. The open-and-close motion alters the surface topology of P-gp within the drug-binding pocket, providing a mechanistic explanation for the polyspecificity of P-gp in substrate interactions.

Computational cell analysis for label-free detection of cell properties in a microfluidic laminar flow.

Although a flow cytometer, being one of the most popular research and clinical tools for biomedicine, can analyze cells based on the cell size, internal structures such as granularity, and molecular markers, it provides little information about the physical properties of cells such as cell stiffness and physical interactions between the cell membrane and fluid. In this paper, we propose a computational cell analysis technique using cells' different equilibrium positions in a laminar flow. This method utilizes a spatial coding technique to acquire the spatial position of the cell in a microfluidic channel and then uses mathematical algorithms to calculate the ratio of cell mixtures. Most uniquely, the invented computational cell analysis technique can unequivocally detect the subpopulation of each cell type without labeling even when the cell type shows a substantial overlap in the distribution plot with other cell types, a scenario limiting the use of conventional flow cytometers and machine learning techniques. To prove this concept, we have applied the computation method to distinguish live and fixed cancer cells without labeling, count neutrophils from human blood, and distinguish drug treated cells from untreated cells. Our work paves the way for using computation algorithms and fluidic dynamic properties for cell classification, a label-free method that can potentially classify over 200 types of human cells. Being a highly cost-effective cell analysis method complementary to flow cytometers, our method can offer orthogonal tests in companion with flow cytometers to provide crucial information for biomedical samples.

Emergence characteristics comparing endotracheal tube to reinforced laryngeal mask airway during endoscopic sinus surgery - A randomised controlled study.

Background and Aims: During endoscopic sinus surgery, anaesthetic conditions significantly impact the intraoperative surgical field and bleeding during emergence. While the endotracheal tube (ETT) has been traditionally used in sinus surgery, a reinforced laryngeal mask airway (RLMA) that produces less upper airway stimulation may result in smoother emergence. Methods: A randomised controlled trial of 72 patients undergoing elective sinus surgery was conducted, with the allocation of airway technique to either ETT with a throat pack or RLMA. The primary outcome measure was emergence time, measured by time to opening eyes on commands at the cessation of anaesthesia, and the secondary outcomes were time to removal of airway device, remifentanil use, procedure times, mean arterial pressure (MAP) and the RLMA grade of blood contamination. The continuous variables were analysed using Student's t-tests and discrete variables, count tables were analysed using Fisher's exact tests. Results: There was no significant difference in the emergence time between the ETT and RLMA groups (P = 0.83). Remifentanil use was significantly higher in the ETT group than in the RLMA group (P = 0.022). The ETT group showed a significantly increased total anaesthetic time (P = 0.01). MAP was not significant during preinduction, maintenance or post-RMLA removal. The highest grade of contamination was grade 2 in RLMA. RLMA had lower rates of postoperative adverse events. Conclusions: RLMA comparable to ETT in terms of emergence time. The RMLA group had lower remifentanil use, anaesthesia duration and fewer postoperative adverse events such as cough and throat pain.

Trends in Volume and Charges of Retinal Tear Patients in the Emergency Department.

PURPOSE: To characterize retinal tears (RTs) and calculate the economic burden of RTs that present to the emergency department (ED) in the US. METHODS: We used a large national ED database to retrospectively analyze RTs that presented to the ED from 2006 to 2019. Using extrapolation methods, national of the RT patient ED volume, demographics, comorbidities, disposition, inpatient (IP) charges, and ED charges were calculated. RESULTS: During the period between 2006 and 2019, 15841 ED encounters had RT listed as the primary diagnosis. The average annual RT ED encounters was 2,640 ± 856 and comprised an average of 6.4 × 10-5% of all ED visits annually. The number and ED percentage of RT encounters did not change during this time period (p = .22, p = .67, respectively). Most patients were males, Caucasian, paid with private insurance, and admitted to EDs in the Northeast. The most common comorbidities were hypertension (19%), a history of cataracts (15%), and diabetes (7.2%). During this time period, RTs charges added up to more than $79 million and $33 million in the ED and IP settings, respectively. Mean per-encounter ED and IP charges increased by 145% (p = .0008) and 86% (p = .0047), respectively. CONCLUSION: Despite the stable number of RT patients presenting to the ED, RTs place a significant economic burden to the healthcare system, which increases yearly. We recommend physicians and policy makers to work together to pass laws that could prevent the increasing healthcare charges.

Virtual Interviewing for Radiology Residency: Pluses, Minuses, and A Review of the Literature.

This article reviews current medical literature to assess the benefits and drawbacks of virtual interviews for radiology residencies as well as the downstream effects of these changes, best practices, and potential future recruitment methods. Topics covered include the effects of remote recruitment in promoting accessibility and applicant diversity and equality as well as fiscal, environmental, and time savings in combination with technical challenges, the complications of over application, challenges in assessment of program culture and location, impact on morale, and hidden financial and emotional costs. Learnings from other medical specialties are highlighted in addition to the process of signaling, guidelines for conducting and participating in virtual interviews, and matters for future consideration.

Enhanced cellular longevity arising from environmental fluctuations.

Cellular longevity is regulated by both genetic and environmental factors. However, the interactions of these factors in the context of aging remain largely unclear. Here, we formulate a mathematical model for dynamic glucose modulation of a core gene circuit in yeast aging, which not only guided the design of pro-longevity interventions, but also revealed the theoretical principles underlying these interventions. We introduce the dynamical systems theory to capture two general means for promoting longevity - the creation of a stable fixed point in the "healthy" state of the cell and the dynamic stabilization of the system around this healthy state through environmental oscillations. Guided by the model, we investigate how both of these can be experimentally realized by dynamically modulating environmental glucose levels. The results establish a paradigm for theoretically analyzing the trajectories and perturbations of aging that can be generalized to aging processes in diverse cell types and organisms.

Structures of Cancer Antigen Mesothelin and Its Complexes with Therapeutic Antibodies.

The tumor-associated antigen mesothelin is expressed at high levels on the cell surface of many human cancers, while its expression in normal tissues is limited. The binding of mesothelin to the tumor-associated cancer antigen 125 (CA-125) can lead to heterotypic cell adhesion and tumor metastasis within the pleural and peritoneal cavities. Immunotherapeutic strategies targeting mesothelin are being intensively investigated. Here, we report the crystal structures of mesothelin that reveal a compact, right-handed solenoid consisting of 24 short helices and connecting loops. These helices form a nine-layered spiral coil that resembles ARM/HEAT family proteins. Glycan attachments have been identified in the structure for all three predicted N-glycosylation sites and confirmed with samples from cell culture and patient ascites. The structures of full-length mesothelin and its complex with the Fab of MORAb-009 reveal the interaction of the antibody with the complete epitope, which has not been reported previously. The N-terminal half of mesothelin is conformationally rigid, suitable for eliciting specific antibodies, whereas its C-terminal portion is more flexible. The structure of the C-terminal shedding-resistant fragment of mesothelin complexed with a mAb 15B6 displays an extended linear epitope and helps explain the protection afforded by the antibody for the shedding sites. Significance: The structures of full-length mesothelin and its complexes with antibodies reported here are the first to be determined experimentally, providing atomic models for structural organization of this protein and its interactions with antibodies. It offers insights into the function of mesothelin and guidance for further development of therapeutic antibodies.

Discovery of a new class of ghrelin receptor antagonists.

A series of benzodiazepine antagonists of the human ghrelin receptor GHSR1a were synthesized and their antagonism and metabolic stability were evaluated. The potency of these analogs was determined using a functional aequorin (Euroscreen) luminescent assay measuring the intracellular Ca(2+) concentration, and their metabolic stability was measured using an in vitro rat and human S9 hepatocyte assay. These efforts led to the discovery of a potent ghrelin antagonist with good rat pharmacokinetic properties.

AMG 837: a potent, orally bioavailable GPR40 agonist.

The discovery that certain long chain fatty acids potentiate glucose stimulated insulin secretion through the previously orphan receptor GPR40 sparked interest in GPR40 agonists as potential antidiabetic agents. Optimization of a series of ß-substituted phenylpropanoic acids led to the identification of (S)-3-(4-((4'-(trifluoromethyl)biphenyl-3-yl)methoxy)phenyl)hex-4-ynoic acid (AMG 837) as a potent GPR40 agonist with a superior pharmacokinetic profile and robust glucose-dependent stimulation of insulin secretion in rodents.

Increased anticoagulant activity of thrombin-binding DNA aptamers by nanoscale organization on DNA nanostructures.

Control over thrombin activity is much desired to regulate blood clotting in surgical and therapeutic situations. Thrombin-binding RNA and DNA aptamers have been used to inhibit thrombin activity and thus the coagulation cascade. Soluble DNA aptamers, as well as two different aptamers tethered by a flexible single-strand linker, have been shown to possess anticoagulant activity. Here, we link multiple aptamers at programmed positions on DNA nanostructures to optimize spacing and orientation of the aptamers and thereby to maximize anticoagulant activity in functional assays. By judicious engineering of the DNA nanostructures, we have created a novel, functional DNA nanostructure, which is a multi-aptamer inhibitor with activity eightfold higher than free aptamer. Reversal of the thrombin inhibition was also achieved by the use of single-stranded DNA antidotes, thus enabling significant control over blood coagulation. FROM THE CLINICAL EDITOR: Thrombin inhibition via DNA aptamers has recently become a possibility. In this study, thrombin-binding DNA aptamers were further optimized by nanoscale organization on DNA nanostructures. The authors have created a novel, functional DNA nanostructure, which is a multi-aptamer inhibitor with activity eightfold higher than that of free aptamer. Reversal of thrombin inhibition was also achieved by single-stranded DNA antidotes, enabling significant control over the coagulation pathway.

Carpal Tunnel Syndrome: Pathophysiology and Comprehensive Guidelines for Clinical Evaluation and Treatment.

In carpal tunnel syndrome (CTS), the median nerve is compressed at the level of the carpal tunnel in the wrist. This entrapment manifests as unpleasant symptoms, such as burning, tingling, or numbness in the palm that extends to the fingers. As the disease progresses, afflicted individuals also report decreased grip strength accompanied by hand weakness and restricted movement. The first half of this review elaborates on CTS pathology by providing readers with a comprehensive understanding of the etiology, relevant anatomy, and disease mechanism. CTS is considered the most common entrapment neuropathy, affecting around 3-6% of the adult population. Further, CTS prevalence has seen a dramatic increase in the last few decades paralleling the growth of everyday technology usage. Despite how common it is to have CTS, it can be quite challenging for physicians to make a definite diagnosis due to differentials that present with overlapping symptoms. Even more difficult can be deciding on a course of treatment that is the most effective and considerate of patient needs. Thus arises the need for clear clinical direction, and hence we end with a discussion around such guidelines that serve as a starting point toward effective diagnoses and patient treatment.

Forty Years Since the Epidemic: Modern Paradigms in HIV Diagnosis and Treatment.

Human immunodeficiency virus (HIV) is a viral infection that, when transmitted through the exchange of certain bodily fluids, destroys various immune cells and contributes to an overall weakened immune system. If left untreated, HIV progresses to acquired immunodeficiency syndrome (AIDS) - a chronic, life-threatening condition that puts patients at risk for opportunistic infections. Since the emergence of HIV nearly a century ago, the world has seen tremendous advances in elucidating its pathology and progression. These advances have been accompanied by an increased understanding of how subsequent effects and symptoms manifest in afflicted individuals. These discoveries, coupled with the ever-improving technologies and methodologies used for detection and treatment, provide the scientific and medical community with a solid grasp of HIV. Despite this significant headway, there is still much progress to be made; medical advances have allowed people with HIV to manage their disease and live a longer, healthier life, but a definite cure is yet to be found. Thus, the following literature review serves as both an extensive compendium of our current understanding of HIV - its pathology, testing/detection, repercussions, and treatment - and an acknowledgement of the areas that still require further research.

Weave tile architecture construction strategy for DNA nanotechnology.

Architectural designs for DNA nanostructures typically fall within one of two broad categories: tile-based designs (assembled from chemically synthesized oligonucleotides) and origami designs (woven structures employing a biological scaffold strand and synthetic staple strands). Both previous designs typically contain many Holliday-type multi-arm junctions. Here we describe the design, implementation, and testing of a unique architectural strategy incorporating some aspects of each of the two previous design categories but without multi-arm junction motifs. Goals for the new design were to use only chemically synthesized DNA, to minimize the number of component strands, and to mimic the back-and-forth, woven strand routing of the origami architectures. The resulting architectural strategy employs "weave tiles" formed from only two oligonucleotides as basic building blocks, thus decreasing the burden of matching multiple strand stoichiometries compared to previous tile-based architectures and resulting in a structurally flexible tile. As an example application, we have shown that the four-helix weave tile can be used to increase the anticoagulant activity of thrombin-binding aptamers in vitro.

Identification of piperazine-bisamide GHSR antagonists for the treatment of obesity.

Piperazine-bisamide analogs were discovered as partial agonists of human growth hormone secretagogue receptor (GHSR) in a high throughput screen. The partial agonists were optimized for potency and converted into antagonists through structure-activity relationship (SAR) studies. The efforts also led to the identification of potent antagonist with favorable PK profile suitable as a tool compound for in vivo studies.