A comparison between full-length 16S rRNA Oxford nanopore sequencing and Illumina V3-V4 16S rRNA sequencing in head and neck cancer tissues.

Describing the microbial community within the tumour has been a key aspect in understanding the pathophysiology of the tumour microenvironment. In head and neck cancer (HNC), most studies on tissue samples have only performed 16S rRNA short-read sequencing (SRS) on V3-V5 region. SRS is mostly limited to genus level identification. In this study, we compared full-length 16S rRNA long-read sequencing (FL-ONT) from Oxford Nanopore Technology (ONT) to V3-V4 Illumina SRS (V3V4-Illumina) in 26 HNC tumour tissues. Further validation was also performed using culture-based methods in 16 bacterial isolates obtained from 4 patients using MALDI-TOF MS. We observed similar alpha diversity indexes between FL-ONT and V3V4-Illumina. However, beta-diversity was significantly different between techniques (PERMANOVA - R2 = 0.131, p < 0.0001). At higher taxonomic levels (Phylum to Family), all metrics were more similar among sequencing techniques, while lower taxonomy displayed more discrepancies. At higher taxonomic levels, correlation in relative abundance from FL-ONT and V3V4-Illumina were higher, while this correlation decreased at lower levels. Finally, FL-ONT was able to identify more isolates at the species level that were identified using MALDI-TOF MS (75% vs. 18.8%). FL-ONT was able to identify lower taxonomic levels at a better resolution as compared to V3V4-Illumina 16S rRNA sequencing.

Customised acoustic therapy delivered through a web-based platform-An innovative approach to tinnitus treatment.

OBJECTIVES: Customised acoustic therapy aims to moderate the neural pathways implicated in the pathophysiology of tinnitus. This study aimed to assess the efficacy of customised acoustic therapy administered via a web-based treatment platform. DESIGN: Clinical trial with prospective recruitment. Fifty-eight participants underwent 6 weeks of customised acoustic therapy. SETTING: Treatment was delivered for 2 h each day using a smartphone, tablet or computer. Treatment was integrated into usual daily activities. PARTICIPANTS: Participants with subjective tinnitus were recruited through public and private otolaryngology clinics and electronic and print media. MAIN OUTCOMES MEASURED: FiveQ, a novel 5 question tinnitus questionnaire, was measured at baseline and each week of treatment. Statistical analyses, including Wilcoxon, Mann-Whitney and mixed linear regression, were used to assess treatment efficacy and identify factors associated with treatment response. RESULTS: 39/58 participants (67.2%) had an improvement in symptom severity scores, 4 had no change (6.9%) and 15 had a decline from baseline (25.9%). Mean FiveQ scores improved by 22.9% from 40.8 (SD = 21.4) at baseline to 31.5 (SD = 21.3) following 6 weeks of treatment (p < 0.001). With the exception of the slight tinnitus group, all other groups (from mild to catastrophic) demonstrated a treatment response. Participants with low frequency tinnitus (<2000 Hz) had a significantly greater treatment response (p < 0.001). CONCLUSION: Customised acoustic therapy administered via a web-based platform demonstrated encouraging efficacy. At least mild symptoms at baseline and low frequency tinnitus were associated with a greater treatment response. Customised acoustic therapy offers accessible and efficacious tinnitus treatment, however longer term clinical studies are required to confirm the observed initial benefit is maintained.

FiveQ: A new easy-to-use validated clinical instrument for tinnitus severity.

OBJECTIVES: Tinnitus is a complex and debilitating phenomenon with potentially significant implications on quality of life. New presentations can be resource and time intensive for clinicians. Validated comprehensive tinnitus questionnaires may lack practical utility in the high-volume clinical setting. Concise, targeted questionnaires may offer an efficient alternative. This study aimed to assess the validity of the FiveQ, a novel five question construct designed to measure tinnitus severity. Convergent validity was assessed through correlating FiveQ against two comprehensive validated questionnaires, the Tinnitus Handicap Questionnaire (THQ) and Tinnitus Handicap Inventory (THI). DESIGN: Cross-sectional study with prospective recruitment. The 117 voluntarily recruited participants completed the FiveQ, THI and THQ questionnaires. Results were comparatively analysed. SETTING: Recruitment was via electronic and print media, audiology clinics and public and private otolaryngology outpatient clinics. Surveys were completed electronically. PARTICIPANTS: Members of the public aged over 18 with subjective tinnitus were invited to participate. MAIN OUTCOME MEASURED: Analyses for establishing the content validity, construct validity, internal consistency, explorary factor analysis, and responsiveness of FiveQ was performed. RESULTS: FiveQ demonstrated a high positive correlation with both the THI (r = 0.773, p < .001) and THQ (r = 0.808, p < .001). Internal consistency for FiveQ reached an acceptable threshold (Cronbach's alpha 0.86). Exploratory factor analysis demonstrated that one latent factor underlies the five items of the FiveQ. FiveQ demonstrated better responsiveness than both the THI and THQ after a 6 week interval repeat measurement. CONCLUSION: FiveQ demonstrated high-positive correlations with existing validated tinnitus questionnaires as well as acceptable internal consistency and factor analysis. The concise construct of FiveQ allows clinicians to efficiently estimate tinnitus severity, target treatment towards dominant symptoms and establish a reliable estimation of treatment response following interventions.

Housing Boston's Chronically Homeless Unsheltered Population: 14 Years Later.

OBJECTIVE: The long-term outcomes of permanent supportive housing for chronically unsheltered individuals, or rough sleepers, are largely unknown. We therefore assessed housing outcomes for a group of unsheltered individuals who were housed directly from the streets after living outside for decades. METHODS: Using an open-cohort design, 73 chronically unsheltered individuals were enrolled and housed in permanent supportive housing directly from the streets of Boston from 2005 to 2019. Through descriptive, regression, and survival analysis, we assessed housing retention, housing stability, and predictors of survival. RESULTS: Housing retention at ≥1 year was 82% yet fell to 36% at ≥5 years; corresponding Kaplan-Meier estimates for retention were 72% at ≥1, 42.5% at ≥5, and 37.5% at ≥10 years. Nearly half of the cohort (45%) died while housed. The co-occurrence of medical, psychiatric, and substance use disorder, or "trimorbidity," was common. Moves to a new apartment were also common; 38% were moved 45 times to avoid an eviction. Each subsequent housing relocation increased the risk of a tenant returning to homelessness. Three or more housing relocations substantially increased the risk of death. CONCLUSIONS: Long-term outcomes for this permanent supportive housing program for chronically unsheltered individuals showed low housing retention and poor survival. Housing stability for this vulnerable population likely requires more robust and flexible and long-term medical and social supports.

ESCRT-III-associated proteins and spastin inhibit protrudin-dependent polarised membrane traffic.

Mutations in the gene encoding the microtubule severing ATPase spastin are the most frequent cause of hereditary spastic paraplegia, a genetic condition characterised by length-dependent axonal degeneration. Here, we show that HeLa cells lacking spastin and embryonic fibroblasts from a spastin knock-in mouse model become highly polarised and develop cellular protrusions. In HeLa cells, this phenotype was rescued by wild-type spastin, but not by forms unable to sever microtubules or interact with endosomal ESCRT-III proteins. Cells lacking the spastin-interacting ESCRT-III-associated proteins IST1 or CHMP1B also developed protrusions. The protrusion phenotype required protrudin, a RAB-interacting protein that interacts with spastin and localises to ER-endosome contact sites, where it promotes KIF5-dependent endosomal motility to protrusions. Consistent with this, the protrusion phenotype in cells lacking spastin also required KIF5. Lack or mutation of spastin resulted in functional consequences for receptor traffic of a pathway implicated in HSP, as Bone Morphogenetic Protein receptor distribution became polarised. Our results, therefore, identify a novel role for ESCRT-III proteins and spastin in regulating polarised membrane traffic.

When did Homo sapiens first reach Southeast Asia and Sahul?

Anatomically modern humans (Homo sapiens, AMH) began spreading across Eurasia from Africa and adjacent Southwest Asia about 50,000-55,000 years ago (ca 50-55 ka). Some have argued that human genetic, fossil, and archaeological data indicate one or more prior dispersals, possibly as early as 120 ka. A recently reported age estimate of 65 ka for Madjedbebe, an archaeological site in northern Sahul (Pleistocene Australia-New Guinea), if correct, offers what might be the strongest support yet presented for a pre-55-ka African AMH exodus. We review evidence for AMH arrival on an arc spanning South China through Sahul and then evaluate data from Madjedbebe. We find that an age estimate of >50 ka for this site is unlikely to be valid. While AMH may have moved far beyond Africa well before 50-55 ka, data from the region of interest offered in support of this idea are not compelling.

' if U equals U what does the second U mean?': sexual minority men's accounts of HIV undetectability and untransmittable scepticism.

The everyday meaning and use of HIV 'undetectability' raises significant questions about the social and sexual significance of this state of viral suppression. We conducted in-depth, semi-structured interviews with 25 sexual minority men living in Vancouver, Canada, including men living with HIV. Interviews were audio-recorded, transcribed verbatim and analysed using grounded theory. Most participants understood being undetectable to signify that someone living with HIV is at a 'low,' 'lower,' or 'slim to no' risk of sexually transmitting HIV, as opposed to meaning 'uninfectious' or 'untransmittable'. Men discussed how undetectability was communicated in-person and online, including via sexual networking apps, and revealed how it is sometimes confused or conflated with another biomedical advance in HIV-prevention, namely pre-exposure prophylaxis (PrEP). HIV-negative men expressed significant scientific scepticism, a reluctance to incorporate a partner's low viral load or undetectable HIV status into their sexual decision-making, and an enduring fear associated with knowingly having sex with someone who is HIV-positive. We describe this as a form of untransmittable scepticism. While international campaigns have worked to communicate the scientific message that 'undetectable equals untransmittable' (U = U), the sexual stigma attached to HIV remains durable among some gay, bisexual, queer and other men who have sex with men.

Substance consumption and intoxication patterns in a medically supervised overdose prevention program for people experiencing homelessness.

Background: Opioid overdose is a leading cause of death among homeless individuals. Combining psychoactive substances with opioids increases overdose risk. This study aimed to describe intoxication patterns at a drop-in space offering medical monitoring and harm reduction services to individuals who arrive intoxicated and at risk of overdose. Methods: We examined data from visits to the Supportive Place for Observation and Treatment at Boston Health Care for the Homeless Program between January 1, 2017 and December 31, 2017. We used k-means cluster analysis to characterize intoxication patterns based on clinically assessed sedation levels and vital sign parameters. Multinomial logistic regression analysis assessed demographic and substance consumption predictors of cluster membership. Linear and logistic regression models examined associations between cluster membership and care outcomes. Results: Across 305 care episodes involving 156 unique patients, cluster analysis revealed 3 distinct intoxication patterns. Cluster A (26.6%) had mild sedation and normal vital signs. Cluster B (44.5%) featured greater sedation with bradycardia and/or hypotension. Cluster C (28.9%) was comparable to cluster B but with the addition of hypoxia. Self-reported consumption of non-opioid sedatives prior to arrival was common (63.3% of episodes) and predicted membership in cluster B (aOR 2.75, 95% CI 1.40, 5.40) and cluster C (aOR 3.38, 95% CI 1.48, 7.70). In comparison to cluster A episodes, cluster C episodes were longer (mean 4.8 vs. 2.3 hours, p < 0.001) and more likely to require supplemental oxygen (27.3% vs. 2.5%, p < 0.001). Few episodes required hospital transfer (4.7%) or naloxone (1.0%). No deaths occurred. Conclusions: In a medically supervised overdose monitoring program, reported use of non-opioid sedatives strongly predicted more complex clinical courses and should be factored into overdose prevention efforts. Low-threshold medical monitoring in an ambulatory setting was sufficient for most episodes, suggesting a role for such programs in reducing harm and averting costly emergency services.

Ultrasound Image Classification of Thyroid Nodules Using Machine Learning Techniques.

Background and Objectives: Thyroid nodules are lumps of solid or liquid-filled tumors that form inside the thyroid gland, which can be malignant or benign. Our aim was to test whether the described features of the Thyroid Imaging Reporting and Data System (TI-RADS) could improve radiologists' decision making when integrated into a computer system. In this study, we developed a computer-aided diagnosis system integrated into multiple-instance learning (MIL) that would focus on benign-malignant classification. Data were available from the Universidad Nacional de Colombia. Materials and Methods: There were 99 cases (33 Benign and 66 malignant). In this study, the median filter and image binarization were used for image pre-processing and segmentation. The grey level co-occurrence matrix (GLCM) was used to extract seven ultrasound image features. These data were divided into 87% training and 13% validation sets. We compared the support vector machine (SVM) and artificial neural network (ANN) classification algorithms based on their accuracy score, sensitivity, and specificity. The outcome measure was whether the thyroid nodule was benign or malignant. We also developed a graphic user interface (GUI) to display the image features that would help radiologists with decision making. Results: ANN and SVM achieved an accuracy of 75% and 96% respectively. SVM outperformed all the other models on all performance metrics, achieving higher accuracy, sensitivity, and specificity score. Conclusions: Our study suggests promising results from MIL in thyroid cancer detection. Further testing with external data is required before our classification model can be employed in practice.

Sexual Health Knowledge, Attitudes, and Perceptions Among Men Who Have Sex With Men During Co-Occurring Sexually Transmitted Infection Epidemics in Toronto, Canada: A Qualitative Study.

BACKGROUND: Our objective was to explore the sexual health knowledge, attitudes, and perceptions of men who have sex with men (MSM). METHODS: In-depth interviews were conducted with 31 MSM who lived, worked, or socialized in Toronto in June and July 2016. Participants were asked about concepts of risky sex and knowledge of, and attitudes toward, sexually transmitted infections (STIs), especially syphilis, and potential interventions. Thematic analysis was used to analyze interview transcripts. RESULTS: The prevention of STI relied on HIV prevention strategies. No one used condoms for oral sex, nor did they intend to. Pre-exposure prophylaxis was perceived as both threatening and liberating. Concepts of risky sex included emotional risk. Conversations with partners about STI testing were easier than STI status. Stigma and concealment of sexual identity were barriers to sexual health care. None of the participants recommended sexual behavior or sexual health interventions. Instead, recommendations centered on social changes to reduce or eliminate shame, embarrassment, stigma, and discrimination around both STIs and sexual orientation. CONCLUSION: Participants were thinking about sexual risk and using a variety of ways to prevent STI transmission, although most relied on HIV prevention strategies, possibly because they knew little about other STIs, and other STIs were perceived as curable, especially syphilis. Interventions promoting conversations about STI testing may be promising and will also reduce stigma as STI testing is normalized. Social and clinic interventions focused on creating psychologically safe spaces to disclose sexual identity and providing sexual orientation affirming health care may reduce STIs and improve sexual health for MSM.

The Social Geography of Partner Selection in Toronto, Canada: A Qualitative Description of "Convection Mixing".

The geographic distribution of sexually transmitted infections reflects the underlying social process of sexual partner selection. This qualitative study explored the social geography of partner selection among sexual minority men and used the results to develop a mid-range theory of STI transmission. In-depth interviews with 31 sexual minority men who lived, worked, or socialized in Toronto, Canada, occurred in June and July 2016. Participants were asked how they found sexual partners and reconstructed their egocentric sexual networks for the previous 3 months. Participants described an iterative process of partner selection involving intention (sex versus dating), connecting with community, and selecting a partner based on intersecting partner characteristics (external, internal, and emergent feelings when interacting with potential partners) and personal preferences. Geography influenced partner selection three ways: (1) participant search patterns maximized the number of potential partners in the shortest distance possible; (2) the density of sexual minority men in a participant's community directly impacted participant's social and sexual isolations; and (3) geosexual isolation influenced sexual mixing patterns. Participants described "convection mixing," where assortative urban mixing nested within disassortative suburban mixing resulted in movement from the suburbs to downtown and back to the suburbs. We theorize that convection mixing may be contributing to the persistence of STI epidemics in core and outbreak areas by creating STI reservoirs outside of, and connected to, core and outbreak areas.

SPIN2: Predicting sequence profiles from protein structures using deep neural networks.

Designing protein sequences that can fold into a given structure is a well-known inverse protein-folding problem. One important characteristic to attain for a protein design program is the ability to recover wild-type sequences given their native backbone structures. The highest average sequence identity accuracy achieved by current protein-design programs in this problem is around 30%, achieved by our previous system, SPIN. SPIN is a program that predicts sequences compatible with a provided structure using a neural network with fragment-based local and energy-based nonlocal profiles. Our new model, SPIN2, uses a deep neural network and additional structural features to improve on SPIN. SPIN2 achieves over 34% in sequence recovery in 10-fold cross-validation and independent tests, a 4% improvement over the previous version. The sequence profiles generated from SPIN2 are expected to be useful for improving existing fold recognition and protein design techniques. SPIN2 is available at http://sparks-lab.org.

Expression characterization of the herbicide tolerance gene Aryloxyalkanoate Dioxygenase (aad-1) controlled by seven combinations of regulatory elements.

BACKGROUND: Availability of well characterized maize regulatory elements for gene expression in a variety of tissues and developmental stages provides effective alternatives for single and multigene transgenic concepts. We studied the expression of the herbicide tolerance gene aryloxyalkanoate dioxygenase (aad-1) driven by seven different regulatory element construct designs including the ubiquitin promoters of maize and rice, the actin promoters of melon and rice, three different versions of the Sugarcane Bacilliform Badnavirus promoters in association with other regulatory elements of gene expression. RESULTS: Gene expression of aad-1 was characterized at the transcript and protein levels in a collection of maize tissues and developmental stages. Protein activity against its target herbicide was characterized by herbicide dosage response. Although differences in transcript and protein accumulation were observed among the different constructs tested, all events were tolerant to commercially relevant rates of quizalafop-P-ethyl compared to non-traited maize under greenhouse conditions. DISCUSSION: The data reported demonstrate how different regulatory elements affect transcript and protein accumulation and how these molecular characteristics translate into the level of herbicide tolerance. The level of transcript detected did not reflect the amount of protein quantified in a particular tissue since protein accumulation may be influenced not only by levels of transcript produced but also by translation rate, post-translational regulation mechanisms and protein stability. The amount of AAD-1 enzyme produced with all constructs tested showed sufficient enzymatic activity to detoxify the herbicide and prevent most herbicidal damage at field-relevant levels without having a negative effect on plant health. CONCLUSIONS: Distinctive profiles of aad-1 transcript and protein accumulation were observed when different regulatory elements were utilized in the constructs under study. The ZmUbi and the SCBV constructs showed the most consistent robust tolerance, while the melon actin construct provided the lowest level of tolerance compared to the other regulatory elements used in this study. These data provide insights into the effects of differing levels of gene expression and how these molecular characteristics translate into the level of herbicide tolerance. Furthermore, these data provide valuable information to optimize future designs of single and multiple gene constructs for maize research and crop improvement.

Conceptualizing Geosexual Archetypes: Mapping the Sexual Travels and Egocentric Sexual Networks of Gay and Bisexual Men in Toronto, Canada.

BACKGROUND: There are complex, synergistic, and persistent sexually transmitted infection (STI) epidemics affecting gay, bisexual and other men who have sex with men (gbMSM) in every major urban centre across North America. We explored the spatial architecture of egocentric sexual networks for gbMSM in Toronto, Canada. METHODS: Our integrative mixed methods study included in-depth interviews with 31 gbMSM between May and July 2016. During interviews, participants mapped their egocentric sexual network for the preceding 3 months geographically. At the end, a self-administered survey was used to collect sociodemographic characteristics, online technology use, and STI testing and history. RESULTS: We identified 6 geosexual archetypes: hosters, house-callers, privates, rovers, travellers, and geoflexibles. Hosters always, or almost always (≥80%), hosted sex at their home. House-callers always, or almost always (≥80%), had sex at their partner's home. Rovers always or almost always (≥80%) had sex at public venues (eg, bath houses, sex clubs) and other public spaces (eg, parks, cruising sites). Privates had sex in private-their own home or their partner's (part hoster, part house-caller). Travellers had sex away from their home, either at a partner's home or some other venue or public space (part house-caller, part rover). Geoflexibles had sex in a variety of locations-their home, their partner's home, or public venues. All hosters and rovers, and to a lesser extent, geoflexibles, reported a history of syphilis and human immunodeficiency virus. CONCLUSIONS: Prioritizing interventions to hosters, rovers, and geoflexibles may have an important impact on reducing STI transmission.

The medical home for children with autism spectrum disorder: an essential element whose time has come.

PURPOSE OF REVIEW: The purpose of this review is to describe the role of the medical home in children with autism spectrum disorder (ASD). A high-quality medical home is essential, given the increase in prevalence of ASD and the array of services, community partners, specialists, therapists, and healthcare team members needed to care for this population. RECENT FINDINGS: Providing care through the medical home model results in fewer unmet needs. Care coordination and integration are the aspects of the medical home currently most lacking. Navigating the healthcare landscape for children with ASD may be enhanced with patient navigators, integration of physical and behavioral health, and telehealth services. SUMMARY: Children with ASD have an increased number of medical and mental health needs. Obtaining care via a medical home has been shown to decrease unmet healthcare needs. However, they are less likely to receive care through the medical home model compared with other children with special healthcare needs. Barriers identified by families include a lack of early identification, limited knowledge on educational plans, and unknown community resources. Barriers identified by providers include lack of time, training, and resources. Providing care coordination and family-centered care in a medical home model are essential for children with ASD.

Hunter-gatherer studies and human evolution: A very selective review.

The century long publication of this journal overlapped major changes in the sciences it covers. We have been eyewitnesses to vast changes during the final third of the last century and beginning of this one, momentous enough to fundamentally alter our work separately and collectively. One (NBJ) from animal ethology, another from western North American archaeology (JOC), and a third (KH) from cultural anthropology came to longtime collaboration as evolutionary ecologists with shared focus on studying modern hunter-gatherers to guide hypotheses about human evolution. Our findings have radically revised hypotheses each of us took for granted when we began. Our (provisional) conclusions are not the consensus among hunter-gatherer specialists; but grateful that personal reflections are invited, we aim to explain how and why we continue to bet on them.