Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data.

We have developed periscope, a tool for the detection and quantification of subgenomic RNA (sgRNA) in SARS-CoV-2 genomic sequence data. The translation of the SARS-CoV-2 RNA genome for most open reading frames (ORFs) occurs via RNA intermediates termed "subgenomic RNAs." sgRNAs are produced through discontinuous transcription, which relies on homology between transcription regulatory sequences (TRS-B) upstream of the ORF start codons and that of the TRS-L, which is located in the 5' UTR. TRS-L is immediately preceded by a leader sequence. This leader sequence is therefore found at the 5' end of all sgRNA. We applied periscope to 1155 SARS-CoV-2 genomes from Sheffield, United Kingdom, and validated our findings using orthogonal data sets and in vitro cell systems. By using a simple local alignment to detect reads that contain the leader sequence, we were able to identify and quantify reads arising from canonical and noncanonical sgRNA. We were able to detect all canonical sgRNAs at the expected abundances, with the exception of ORF10. A number of recurrent noncanonical sgRNAs are detected. We show that the results are reproducible using technical replicates and determine the optimum number of reads for sgRNA analysis. In VeroE6 ACE2+/- cell lines, periscope can detect the changes in the kinetics of sgRNA in orthogonal sequencing data sets. Finally, variants found in genomic RNA are transmitted to sgRNAs with high fidelity in most cases. This tool can be applied to all sequenced COVID-19 samples worldwide to provide comprehensive analysis of SARS-CoV-2 sgRNA.

Dapagliflozin reduces systemic inflammation in patients with type 2 diabetes without known heart failure.

OBJECTIVE: Sodium glucose cotransporter 2 (SGLT2) inhibitors significantly improve cardiovascular outcomes in diabetic patients; however, the mechanism is unclear. We hypothesized that dapagliflozin improves cardiac outcomes via beneficial effects on systemic and cardiac inflammation and cardiac fibrosis. RESEARCH AND DESIGN METHODS: This randomized placebo-controlled clinical trial enrolled 62 adult patients (mean age 62, 17% female) with type 2 diabetes (T2D) without known heart failure. Subjects were randomized to 12 months of daily 10 mg dapagliflozin or placebo. For all patients, blood/plasma samples and cardiac magnetic resonance imaging (CMRI) were obtained at time of randomization and at the end of 12 months. Systemic inflammation was assessed by plasma IL-1B, TNFα, IL-6 and ketone levels and PBMC mitochondrial respiration, an emerging marker of sterile inflammation. Global myocardial strain was assessed by feature tracking; cardiac fibrosis was assessed by T1 mapping to calculate extracellular volume fraction (ECV); and cardiac tissue inflammation was assessed by T2 mapping. RESULTS: Between the baseline and 12-month time point, plasma IL-1B was reduced (- 1.8 pg/mL, P = 0.003) while ketones were increased (0.26 mM, P = 0.0001) in patients randomized to dapagliflozin. PBMC maximal oxygen consumption rate (OCR) decreased over the 12-month period in the placebo group but did not change in patients receiving dapagliflozin (- 158.9 pmole/min/106 cells, P = 0.0497 vs. - 5.2 pmole/min/106 cells, P = 0.41), a finding consistent with an anti-inflammatory effect of SGLT2i. Global myocardial strain, ECV and T2 relaxation time did not change in both study groups. GOV REGISTRATION: NCT03782259.

Measles Outbreak Associated with a Migrant Shelter - Chicago, Illinois, February-May 2024.

Measles, a highly contagious respiratory virus with the potential to cause severe complications, hospitalization, and death, was declared eliminated from the United States in 2000; however, with ongoing global transmission, infections in the United States still occur. On March 7, 2024, the Chicago Department of Public Health (CDPH) confirmed a case of measles in a male aged 1 year residing in a temporary shelter for migrants in Chicago. Given the congregate nature of the setting, high transmissibility of measles, and low measles vaccination coverage among shelter residents, measles virus had the potential to spread rapidly among approximately 2,100 presumed exposed shelter residents. CDPH immediately instituted outbreak investigation and response activities in collaboration with state and local health departments, health care facilities, city agencies, and shelters. On March 8, CDPH implemented active case-finding and coordinated a mass vaccination campaign at the affected shelter (shelter A), including vaccinating 882 residents and verifying previous vaccination for 784 residents over 3 days. These activities resulted in 93% measles vaccination coverage (defined as receipt of ≥1 recorded measles vaccine dose) by March 11. By May 13, a total of 57 confirmed measles cases associated with residing in or having contact with persons from shelter A had been reported. Most cases (41; 72%) were among persons who did not have documentation of measles vaccination and were considered unvaccinated. In addition, 16 cases of measles occurred among persons who had received ≥1 measles vaccine dose ≥21 days before first known exposure. This outbreak underscores the need to ensure high vaccination coverage among communities residing in congregate settings.

Genomic loci susceptible to systematic sequencing bias in clinical whole genomes.

Accurate massively parallel sequencing (MPS) of genetic variants is key to many areas of science and medicine, such as cataloging population genetic variation and diagnosing genetic diseases. Certain genomic positions can be prone to higher rates of systematic sequencing and alignment bias that limit accuracy, resulting in false positive variant calls. Current standard practices to differentiate between loci that can and cannot be sequenced with high confidence utilize consensus between different sequencing methods as a proxy for sequencing confidence. These practices have significant limitations, and alternative methods are required to overcome them. We have developed a novel statistical method based on summarizing sequenced reads from whole-genome clinical samples and cataloging them in "Incremental Databases" that maintain individual confidentiality. Allele statistics were cataloged for each genomic position that consistently showed systematic biases with the corresponding MPS sequencing pipeline. We found systematic biases present at ∼1%-3% of the human autosomal genome across five patient cohorts. We identified which genomic regions were more or less prone to systematic biases, including large homopolymer flanks (odds ratio = 23.29-33.69) and the NIST high confidence genomic regions (odds ratio = 0.154-0.191). We confirmed our predictions on a gold-standard reference genome and showed that these systematic biases can lead to suspect variant calls within clinical panels. Our results recommend increased caution to address systematic biases in whole-genome sequencing and alignment. This study provides the implementation of a simple statistical approach to enhance quality control of clinically sequenced samples by flagging variants at suspect loci for further analysis or exclusion.

Role of mitochondria in the myopathy of juvenile dermatomyositis and implications for skeletal muscle calcinosis.

OBJECTIVES: To elucidate mechanisms contributing to skeletal muscle calcinosis in patients with juvenile dermatomyositis. METHODS: A well-characterized cohorts of JDM (n = 68), disease controls (polymyositis, n = 7; juvenile SLE, n = 10, and RNP + overlap syndrome, n = 12), and age-matched health controls (n = 17) were analyzed for circulating levels of mitochondrial (mt) markers including mtDNA, mt-nd6, and anti-mitochondrial antibodies (AMAs) using standard qPCR, ELISA, and novel-in-house assays, respectively. Mitochondrial calcification of affected tissue biopsies was confirmed using electron microscopy and energy dispersive X-ray analysis. A human skeletal muscle cell line, RH30, was used to generate an in vitro calcification model. Intracellular calcification is measured by flow cytometry and microscopy. Mitochondria were assessed for mtROS production and membrane potential by flow cytometry and real-time oxygen consumption rate by Seahorse bioanalyzer. Inflammation (interferon-stimulated genes) was measured by qPCR. RESULTS: In the current study, patients with JDM exhibited elevated levels of mitochondrial markers associated with muscle damage and calcinosis. Of particular interest are AMAs predictive of calcinosis. Human skeletal muscle cells undergo time- and dose-dependent accumulation of calcium phosphate salts with preferential localization to mitochondria. Calcification renders skeletal muscle cells mitochondria stressed, dysfunctional, destabilized, and interferogenic. Further, we report that inflammation induced by interferon-alpha amplifies mitochondrial calcification of human skeletal muscle cells via the generation of mitochondrial reactive oxygen species (mtROS). CONCLUSIONS: Overall, our study demonstrates the mitochondrial involvement in the skeletal muscle pathology and calcinosis of JDM and mtROS as a central player in the calcification of human skeletal muscle cells. Therapeutic targeting of mtROS and/or upstream inducers, such as inflammation, may alleviate mitochondrial dysfunction, leading to calcinosis. AMAs can potentially identify patients with JDM at risk for developing calcinosis.

Civilian Medical Responder Perspectives to a Federal Military Medical Deployment in New York City during the COVID-19 Pandemic.

OBJECTIVES: This study aims to describe the civilian experience and perceptions of the patient coordination and management at the interface of the New York City (NYC) civilian and the military health systems during a large-scale public health emergency. METHODS: A qualitative study design was implemented with interviews conducted using a basic descriptive approach. Purposive sampling was used to recruit participants with experience working during the first wave of COVID-19 in NYC. Inclusion criteria were civilians who worked at the Javits Center, the USNS Comfort, or NYC hospitals, who interfaced with patient transfer and military personnel during the city-wide medical response to COVID-19. Semi-structured video interviews were conducted between July 20, 2021 and March 11, 2022. RESULTS: Civilian responders working in the clinical and transfer operations of patients to military facilities in NYC during March and April of 2020 described initial confusion, as well as logistical (patient selection, transfer logistics, patient tracking), communication, and leadership challenges. While the military deployment was felt to be necessary to address the surge capacity in hospitals, the lack of clarity about military medical resources and frameworks for response resulted in confusion about what was being offered by the military deployment. This was balanced by the positive impression of working with military members and the resources that they brought to the response more generally. The need for future trainings and exercises were highlighted. CONCLUSIONS: Initial challenges with civilian-military roles and responsibilities, regional needs assessment, patient selection, and logistics were ultimately resolved through adaptation of civilian and military leadership. Improvements in patient tracking, medical records, and standard hospital admission and discharge functions for patients in military alternative care facilities were identified as areas for improvement. Civilian government, health care, and military leaders should consider these ideas when planning for future military deployments in support of a domestic medical response.

Bilateral treatment of the masseter with botulinum toxin: Consequences for mastication, muscle force and the mandibular condyle.

BACKGROUND: Clinical use of botulinum neurotoxins (BoNTs) in masticatory muscles is usually bilateral, but most studies on the functional consequences of BoNT treatment have used unilaterally treated animals. OBJECTIVES: To test the hypothesis that bilateral BoNT treatment of the rabbit masseter hampers mastication and to assess its effects on bone density of the mandibular condyles. METHODS: Ten 5-month-old female rabbits received injections of BoNT into both masseter muscles and nine sham animals received saline. Body weight, incisor bite force during masseter tetany, and surface and fine-wire electromyography (EMG) of the masseter and medial pterygoid muscles were assessed at regular intervals. Half the sample was terminated after 4 weeks and the remainder after 12 weeks. Muscles were weighed and mandibular condyles were scanned with microCT to analyse bone density. RESULTS: BoNT rabbits lost weight and required a soft-food diet. Incisor occlusal force plummeted after BoNT injection and remained lower than the shams. The duration of masticatory cycles was increased in the BoNT rabbits for 5 weeks, with most of the increase due to the adductor burst. Masseteric EMG amplitude began to improve at Week 5, but remained low on the working side throughout the experiment. At the 12-week endpoint, masseter muscles were smaller in the BoNT rabbits. Medial pterygoid muscles did not compensate. Condylar bone density was reduced. CONCLUSION: Bilateral treatment of the rabbit masseter by BoNT severely affected chewing performance. Even after a 3-month recovery period, deficits remained in bite force, muscle size and condylar bone density.

A regularized functional regression model enabling transcriptome-wide dosage-dependent association study of cancer drug response.

Cancer treatments can be highly toxic and frequently only a subset of the patient population will benefit from a given treatment. Tumour genetic makeup plays an important role in cancer drug sensitivity. We suspect that gene expression markers could be used as a decision aid for treatment selection or dosage tuning. Using in vitro cancer cell line dose-response and gene expression data from the Genomics of Drug Sensitivity in Cancer (GDSC) project, we build a dose-varying regression model. Unlike existing approaches, this allows us to estimate dosage-dependent associations with gene expression. We include the transcriptomic profiles as dose-invariant covariates into the regression model and assume that their effect varies smoothly over the dosage levels. A two-stage variable selection algorithm (variable screening followed by penalized regression) is used to identify genetic factors that are associated with drug response over the varying dosages. We evaluate the effectiveness of our method using simulation studies focusing on the choice of tuning parameters and cross-validation for predictive accuracy assessment. We further apply the model to data from five BRAF targeted compounds applied to different cancer cell lines under different dosage levels. We highlight the dosage-dependent dynamics of the associations between the selected genes and drug response, and we perform pathway enrichment analysis to show that the selected genes play an important role in pathways related to tumorigenesis and DNA damage response.

Long-term effects on alveolar bone with bone-anchored and tooth-anchored rapid palatal expansion.

INTRODUCTION: The purpose of this study was to evaluate the long-term effects of bone-anchored and tooth-anchored expansion appliances on alveolar bone in vertical and horizontal dimensions, compared with controls, using cone-beam computed tomography. METHODS: We evaluated 180 cone-beam computed tomography scans for 60 patients at 3-time points: T1 (pretreatment), T2 (postexpansion), and T3 (posttreatment), for 3 groups: bone-anchored expansion appliance (BA), tooth-anchored expansion appliance (TA), and controls (T1-T3: BA, 2 years 8 months; TA, 2 years 9 months; control: 2 years 7 months). The intermolar width, molar angulation, palatal width, vertical buccal bone height, buccal bone thickness at the alveolar crest, and root apex were measured in the 3 groups at different time points. RESULTS: In the short term, both BA and TA led to a statistically significant increase in the intermolar width and vertical buccal bone loss after expansion compared with controls. Vertical buccal bone loss was significantly greater in TA than in BA. In addition, TA led to significantly increased molar angulation (buccal tipping) compared with controls at T2. There were no significant differences in the 3 groups in the long term except vertical buccal bone loss, which was significantly greater in TA than controls. A substantial correlation was found between molar angulation and vertical buccal bone loss, and a moderate negative correlation was found between intermolar width and buccal bone thickness at the alveolar crest at T3. CONCLUSIONS: There was no difference in the treatment outcomes between the 3 groups in the long term except vertical buccal bone loss, which was significantly increased in the TA group compared with controls.

Value of systematic genetic screening of patients with amyotrophic lateral sclerosis.

OBJECTIVE: The clinical utility of routine genetic sequencing in amyotrophic lateral sclerosis (ALS) is uncertain. Our aim was to determine whether routine targeted sequencing of 44 ALS-relevant genes would have a significant impact on disease subclassification and clinical care. METHODS: We performed targeted sequencing of a 44-gene panel in a prospective case series of 100 patients with ALS recruited consecutively from the Sheffield Motor Neuron Disorders Clinic, UK. All participants were diagnosed with ALS by a specialist Consultant Neurologist. 7/100 patients had familial ALS, but the majority were apparently sporadic cases. RESULTS: 21% of patients with ALS carried a confirmed pathogenic or likely pathogenic mutation, of whom 93% had no family history of ALS. 15% met the inclusion criteria for a current ALS genetic-therapy trial. 5/21 patients with a pathogenic mutation had an additional variant of uncertain significance (VUS). An additional 21% of patients with ALS carried a VUS in an ALS-associated gene. Overall, 13% of patients carried more than one genetic variant (pathogenic or VUS). Patients with ALS carrying two variants developed disease at a significantly earlier age compared with patients with a single variant (median age of onset=56 vs 60 years, p=0.0074). CONCLUSIONS: Routine screening for ALS-associated pathogenic mutations in a specialised ALS referral clinic will impact clinical care in 21% of cases. An additional 21% of patients have variants in the ALS gene panel currently of unconfirmed significance after removing non-specific or predicted benign variants. Overall, variants within known ALS-linked genes are of potential clinical importance in 42% of patients.

Whole-Blood RNA Profiles Associated with Pulmonary Arterial Hypertension and Clinical Outcome.

Rationale: Idiopathic and heritable pulmonary arterial hypertension (PAH) are rare but comprise a genetically heterogeneous patient group. RNA sequencing linked to the underlying genetic architecture can be used to better understand the underlying pathology by identifying key signaling pathways and stratify patients more robustly according to clinical risk.Objectives: To use a three-stage design of RNA discovery, RNA validation and model construction, and model validation to define a set of PAH-associated RNAs and a single summarizing RNA model score. To define genes most likely to be involved in disease development, we performed Mendelian randomization (MR) analysis.Methods: RNA sequencing was performed on whole-blood samples from 359 patients with idiopathic, heritable, and drug-induced PAH and 72 age- and sex-matched healthy volunteers. The score was evaluated against disease severity markers including survival analysis using all-cause mortality from diagnosis. MR used known expression quantitative trait loci and summary statistics from a PAH genome-wide association study.Measurements and Main Results: We identified 507 genes with differential RNA expression in patients with PAH compared with control subjects. A model of 25 RNAs distinguished PAH with 87% accuracy (area under the curve 95% confidence interval: 0.791-0.945) in model validation. The RNA model score was associated with disease severity and long-term survival (P = 4.66 × 10-6) in PAH. MR detected an association between SMAD5 levels and PAH disease susceptibility (odds ratio, 0.317; 95% confidence interval, 0.129-0.776; P = 0.012).Conclusions: A whole-blood RNA signature of PAH, which includes RNAs relevant to disease pathogenesis, associates with disease severity and identifies patients with poor clinical outcomes. Genetic variants associated with lower SMAD5 expression may increase susceptibility to PAH.

Aligning SARS-CoV-2 indicators via an epidemic model: application to hospital admissions and RNA detection in sewage sludge.

Ascertaining the state of coronavirus outbreaks is crucial for public health decision-making. Absent repeated representative viral test samples in the population, public health officials and researchers alike have relied on lagging indicators of infection to make inferences about the direction of the outbreak and attendant policy decisions. Recently researchers have shown that SARS-CoV-2 RNA can be detected in municipal sewage sludge with measured RNA concentrations rising and falling suggestively in the shape of an epidemic curve while providing an earlier signal of infection than hospital admissions data. The present paper presents a SARS-CoV-2 epidemic model to serve as a basis for estimating the incidence of infection, and shows mathematically how modeled transmission dynamics translate into infection indicators by incorporating probability distributions for indicator-specific time lags from infection. Hospital admissions and SARS-CoV-2 RNA in municipal sewage sludge are simultaneously modeled via maximum likelihood scaling to the underlying transmission model. The results demonstrate that both data series plausibly follow from the transmission model specified and provide a 95% confidence interval estimate of the reproductive number R0 ≈ 2.4 ± 0.2. Sensitivity analysis accounting for alternative lag distributions from infection until hospitalization and sludge RNA concentration respectively suggests that the detection of viral RNA in sewage sludge leads hospital admissions by 3 to 5 days on average. The analysis suggests that stay-at-home restrictions plausibly removed 89% of the population from the risk of infection with the remaining 11% exposed to an unmitigated outbreak that infected 9.3% of the total population.

Nanotechnology applications for cardiovascular disease treatment: Current and future perspectives.

A large majority of cardiovascular nanomedicine research has focused on fabricating designer nanoparticles for improved targeting as a means to overcome biological barriers. For cardiac related disorders, such as atherosclerosis, hypertension, and myocardial infarction, designer micro or nanoparticles are often administered into the vasculature or targeted vessel with the hope to circumvent problems associated with conventional drug delivery, including negative systemic side effects. Additionally, novel nano-drug carriers that enter circulation can be selectively uptaken by immune cells with the intended purpose that they modulate inflammatory processes and migrate locally to plaque for therapeutic payload delivery. Indeed, innovative design in nanoparticle composition, formulation, and functionalization has advanced the field as a means to achieve therapeutic efficacy for a variety of cardiac disease indications. This perspective aims to discuss these advances and provide new interpretations of how nanotechnology can be best applied to aid in cardiovascular disease treatment. In an effort to spark discussions on where the field of research should go, we share our outlook in new areas of nanotechnological inclusion and integration, such as in vascular, implantable, or wearable device technologies as well as nanocomposites and nanocoatings. Further, as cardiovascular diseases (CVD) increasingly claim a number of lives globally, we propose more attention should be placed by researchers on nanotechnological approaches for risk factor treatment to aid in early prevention and treatment of CVD.

Conversational ontology operator: patient-centric vaccine dialogue management engine for spoken conversational agents.

BACKGROUND: Previously, we introduced our Patient Health Information Dialogue Ontology (PHIDO) that manages the dialogue and contextual information of the session between an agent and a health consumer. In this study, we take the next step and introduce the Conversational Ontology Operator (COO), the software engine harnessing PHIDO. We also developed a question-answering subsystem called Frankenstein Ontology Question-Answering for User-centric Systems (FOQUS) to support the dialogue interaction. METHODS: We tested both the dialogue engine and the question-answering system using application-based competency questions and questions furnished from our previous Wizard of OZ simulation trials. RESULTS: Our results revealed that the dialogue engine is able to perform the core tasks of communicating health information and conversational flow. Inter-rater agreement and accuracy scores among four reviewers indicated perceived, acceptable responses to the questions asked by participants from the simulation studies, yet the composition of the responses was deemed mediocre by our evaluators. CONCLUSIONS: Overall, we present some preliminary evidence of a functioning ontology-based system to manage dialogue and consumer questions. Future plans for this work will involve deploying this system in a speech-enabled agent to assess its usage with potential health consumer users.

SOX2 and PI3K Cooperate to Induce and Stabilize a Squamous-Committed Stem Cell Injury State during Lung Squamous Cell Carcinoma Pathogenesis.

Although cancers are considered stem cell diseases, mechanisms involving stem cell alterations are poorly understood. Squamous cell carcinoma (SQCC) is the second most common lung cancer, and its pathogenesis appears to hinge on changes in the stem cell behavior of basal cells in the bronchial airways. Basal cells are normally quiescent and differentiate into mucociliary epithelia. Smoking triggers a hyperproliferative response resulting in progressive premalignant epithelial changes ranging from squamous metaplasia to dysplasia. These changes can regress naturally, even with chronic smoking. However, for unknown reasons, dysplasias have higher progression rates than earlier stages. We used primary human tracheobronchial basal cells to investigate how copy number gains in SOX2 and PIK3CA at 3q26-28, which co-occur in dysplasia and are observed in 94% of SQCCs, may promote progression. We find that SOX2 cooperates with PI3K signaling, which is activated by smoking, to initiate the squamous injury response in basal cells. This response involves SOX9 repression, and, accordingly, SOX2 and PI3K signaling levels are high during dysplasia, while SOX9 is not expressed. By contrast, during regeneration of mucociliary epithelia, PI3K signaling is low and basal cells transiently enter a SOX2LoSOX9Hi state, with SOX9 promoting proliferation and preventing squamous differentiation. Transient reduction in SOX2 is necessary for ciliogenesis, although SOX2 expression later rises and drives mucinous differentiation, as SOX9 levels decline. Frequent coamplification of SOX2 and PIK3CA in dysplasia may, thus, promote progression by locking basal cells in a SOX2HiSOX9Lo state with active PI3K signaling, which sustains the squamous injury response while precluding normal mucociliary differentiation. Surprisingly, we find that, although later in invasive carcinoma SOX9 is generally expressed at low levels, its expression is higher in a subset of SQCCs with less squamous identity and worse clinical outcome. We propose that early pathogenesis of most SQCCs involves stabilization of the squamous injury state in stem cells through copy number gains at 3q, with the pro-proliferative activity of SOX9 possibly being exploited in a subset of SQCCs in later stages.

Architecture and usability of OntoKeeper, an ontology evaluation tool.

BACKGROUND: The existing community-wide bodies of biomedical ontologies are known to contain quality and content problems. Past research has revealed various errors related to their semantics and logical structure. Automated tools may help to ease the ontology construction, maintenance, assessment and quality assurance processes. However, there are relatively few tools that exist that can provide this support to knowledge engineers. METHOD: We introduce OntoKeeper as a web-based tool that can automate quality scoring for ontology developers. We enlisted 5 experienced ontologists to test the tool and then administered the System Usability Scale to measure their assessment. RESULTS: In this paper, we present usability results from 5 ontologists revealing high system usability of OntoKeeper, and use-cases that demonstrate its capabilities in previous published biomedical ontology research. CONCLUSION: To the best of our knowledge, OntoKeeper is the first of a few ontology evaluation tools that can help provide ontology evaluation functionality for knowledge engineers with good usability.

Developmental validation of GlobalFiler™ PCR amplification kit: a 6-dye multiplex assay designed for amplification of casework samples.

The GlobalFiler™ PCR Amplification Kit is a single multiplex assay that amplifies a set of 24 markers, which encompass the European Standard Set and CODIS (Combined DNA Index System) recommended composite set of loci. In addition to more loci and a 6-dye chemistry format, the Master Mix has been formulated to allow higher sample loading volume for trace DNA samples. The GlobalFiler™ Kit has been optimized to deliver high performance on casework samples, while also delivering fast thermal cycling, with an amplification time of approximately 80 min. Here, we report the results of the developmental validation study which followed the SWGDAM (Scientific Working Group on DNA Analysis Methods) guidelines and includes data for PCR-based studies, sensitivity, species specificity, stability, precision, reproducibility and repeatability, concordance, stutter, DNA mixtures, and performance on mock casework samples. The results validate the multiplex design as well as demonstrate the kit's robustness, reliability, and suitability as an assay for human identification with casework DNA samples.

Structure and control of charge density waves in two-dimensional 1T-TaS2.

The layered transition metal dichalcogenides host a rich collection of charge density wave phases in which both the conduction electrons and the atomic structure display translational symmetry breaking. Manipulating these complex states by purely electronic methods has been a long-sought scientific and technological goal. Here, we show how this can be achieved in 1T-TaS2 in the 2D limit. We first demonstrate that the intrinsic properties of atomically thin flakes are preserved by encapsulation with hexagonal boron nitride in inert atmosphere. We use this facile assembly method together with transmission electron microscopy and transport measurements to probe the nature of the 2D state and show that its conductance is dominated by discommensurations. The discommensuration structure can be precisely tuned in few-layer samples by an in-plane electric current, allowing continuous electrical control over the discommensuration-melting transition in 2D.

Absence of a Band Gap at the Interface of a Metal and Highly Doped Monolayer MoS2.

High quality electrical contact to semiconducting transition metal dichalcogenides (TMDCs) such as MoS2 is key to unlocking their unique electronic and optoelectronic properties for fundamental research and device applications. Despite extensive experimental and theoretical efforts reliable ohmic contact to doped TMDCs remains elusive and would benefit from a better understanding of the underlying physics of the metal-TMDC interface. Here we present measurements of the atomic-scale energy band diagram of junctions between various metals and heavily doped monolayer MoS2 using ultrahigh vacuum scanning tunneling microscopy (UHV-STM). Our measurements reveal that the electronic properties of these junctions are dominated by two-dimensional metal-induced gap states (MIGS). These MIGS are characterized by a spatially growing measured gap in the local density of states (L-DOS) of the MoS2 within 2 nm of the metal-semiconductor interface. Their decay lengths extend from a minimum of ∼0.55 nm near midgap to as long as 2 nm near the band edges and are nearly identical for Au, Pd, and graphite contacts, indicating that it is a universal property of the monolayer semiconductor. Our findings indicate that even in heavily doped semiconductors, the presence of MIGS sets the ultimate limit for electrical contact.

Molecular heterogeneity of non-small cell lung carcinoma patient-derived xenografts closely reflect their primary tumors.

Availability of lung cancer models that closely mimic human tumors remains a significant gap in cancer research, as tumor cell lines and mouse models may not recapitulate the spectrum of lung cancer heterogeneity seen in patients. We aimed to establish a patient-derived tumor xenograft (PDX) resource from surgically resected non-small cell lung cancer (NSCLC). Fresh tumor tissue from surgical resection was implanted and grown in the subcutaneous pocket of non-obese severe combined immune deficient (NOD SCID) gamma mice. Subsequent passages were in NOD SCID mice. A subset of matched patient and PDX tumors and non-neoplastic lung tissues were profiled by whole exome sequencing, single nucleotide polymorphism (SNP) and methylation arrays, and phosphotyrosine (pY)-proteome by mass spectrometry. The data were compared to published NSCLC datasets of NSCLC primary and cell lines. 127 stable PDXs were established from 441 lung carcinomas representing all major histological subtypes: 52 adenocarcinomas, 62 squamous cell carcinomas, one adeno-squamous carcinoma, five sarcomatoid carcinomas, five large cell neuroendocrine carcinomas, and two small cell lung cancers. Somatic mutations, gene copy number and expression profiles, and pY-proteome landscape of 36 PDXs showed greater similarity with patient tumors than with established cell lines. Novel somatic mutations on cancer associated genes were identified but only in PDXs, likely due to selective clonal growth in the PDXs that allows detection of these low allelic frequency mutations. The results provide the strongest evidence yet that PDXs established from lung cancers closely mimic the characteristics of patient primary tumors.