System-wide analysis of RNA and protein subcellular localization dynamics.

Although the subcellular dynamics of RNA and proteins are key determinants of cell homeostasis, their characterization is still challenging. Here we present an integrative framework to simultaneously interrogate the dynamics of the transcriptome and proteome at subcellular resolution by combining two methods: localization of RNA (LoRNA) and a streamlined density-based localization of proteins by isotope tagging (dLOPIT) to map RNA and protein to organelles (nucleus, endoplasmic reticulum and mitochondria) and membraneless compartments (cytosol, nucleolus and cytosolic granules). Interrogating all RNA subcellular locations at once enables system-wide quantification of the proportional distribution of RNA. We obtain a cell-wide overview of localization dynamics for 31,839 transcripts and 5,314 proteins during the unfolded protein response, revealing that endoplasmic reticulum-localized transcripts are more efficiently recruited to cytosolic granules than cytosolic RNAs, and that the translation initiation factor eIF3d is key to sustaining cytoskeletal function. Overall, we provide the most comprehensive overview so far of RNA and protein subcellular localization dynamics.

A worldwide perspective on large carnivore attacks on humans.

Large carnivores have long fascinated human societies and have profound influences on ecosystems. However, their conservation represents one of the greatest challenges of our time, particularly where attacks on humans occur. Where human recreational and/or livelihood activities overlap with large carnivore ranges, conflicts can become particularly serious. Two different scenarios are responsible for such overlap: In some regions of the world, increasing human populations lead to extended encroachment into large carnivore ranges, which are subject to increasing contraction, fragmentation, and degradation. In other regions, human and large carnivore populations are expanding, thus exacerbating conflicts, especially in those areas where these species were extirpated and are now returning. We thus face the problem of learning how to live with species that can pose serious threats to humans. We collected a total of 5,440 large carnivore (Felidae, Canidae, and Ursidae; 12 species) attacks worldwide between 1950 and 2019. The number of reported attacks increased over time, especially in lower-income countries. Most attacks (68%) resulted in human injuries, whereas 32% were fatal. Although attack scenarios varied greatly within and among species, as well as in different areas of the world, factors triggering large carnivore attacks on humans largely depend on the socioeconomic context, with people being at risk mainly during recreational activities in high-income countries and during livelihood activities in low-income countries. The specific combination of local socioeconomic and ecological factors is thus a risky mix triggering large carnivore attacks on humans, whose circumstances and frequencies cannot only be ascribed to the animal species. This also implies that effective measures to reduce large carnivore attacks must also consider the diverse local ecological and social contexts.

AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact.

In recent decades, field and semi-field studies of malaria transmission have gathered geographic-specific information about mosquito ecology, behaviour and their sensitivity to interventions. Mathematical models of malaria transmission can incorporate such data to infer the likely impact of vector control interventions and hence guide malaria control strategies in various geographies. To facilitate this process and make model predictions of intervention impact available for different geographical regions, we developed AnophelesModel. AnophelesModel is an online, open-access R package that quantifies the impact of vector control interventions depending on mosquito species and location-specific characteristics. In addition, it includes a previously published, comprehensive, curated database of field entomological data from over 50 Anopheles species, field data on mosquito and human behaviour, and estimates of vector control effectiveness. Using the input data, the package parameterizes a discrete-time, state transition model of the mosquito oviposition cycle and infers species-specific impacts of various interventions on vectorial capacity. In addition, it offers formatted outputs ready to use in downstream analyses and by other models of malaria transmission for accurate representation of the vector-specific components. Using AnophelesModel, we show how the key implications for intervention impact change for various vectors and locations. The package facilitates quantitative comparisons of likely intervention impacts in different geographical settings varying in vector compositions, and can thus guide towards more robust and efficient malaria control recommendations. The AnophelesModel R package is available under a GPL-3.0 license at https://github.com/SwissTPH/AnophelesModel.

First report of Cryptostroma corticale causing sooty bark disease in California and first worldwide report of silver maple as a host.

In November 2022 and February 2023, CAL FIRE tree health experts examined four maples (Acer spp.) planted decades earlier in a residential setting in Elk Grove, Sacramento Co., California (USA). Three of the trees were silver maples (Acer saccharinum ) and one was a Norway maple (A. platanoides); both species are exotic to California. The trees were in an irreversible state of decline, with the canopy substantially thinned and browning. Extensive bark cankers elongating longitudinally along the stem were visible on all trees (Fig. S1). Cankers were filled by fungal stromata protruding through the bark and producing masses of elliptical dark brown conidia (Fig. S2), approximately 5.5 x 3.7 um in size, giving the cankers a sooty appearance. The cankered bark could be peeled off easily, revealing dark and discrete lesions in the phloem and xylem. Samples from the three trees were shipped to the U.C. Berkeley Forest Pathology and Mycology Laboratory and to the CDFA PPDC in Sacramento, CA. In the laboratories, small wood chips were taken from the margins of the lesions, surface sterilized by dipping them for 30 seconds in 70% Ethanol, rinsed for 30 seconds in sterile water and plated onto 2.5% Malt Extract Agar amended with 0.3g/L Streptomycin or onto one-half strength acidified potato dextrose agar (APDA). Two morphologically identical cultures were obtained, one (T2) from a silver maple and one (T6) from the Norway maple. Cultures were then grown in liquid 2.5% malt extract broth and, after one week, DNA was extracted using the Qiagen Plant DNeasy DNA extraction kit. The ITS sequences are diagnostic for this fungus (Li et al. 2021) and those of the two cultures (GB OR064033 and OR933565) were 100% homologous to GenBank sequences of Cryptostroma corticale ( e.g. GB OP474010-11). The RPB2 sequence of T2 ( GB OR992132) was 100% homologous to that of C. corticale (GB HG934116.1). The isolate obtained from silver maple was inoculated in four potted silver maples by removing a bark disk 50 mm in diameter with a cork borer in three spots staggered at different heights and sides on the stem, placing a colonized agar plug of C. corticale in contact with the phloem, replacing the bark disk and wrapping with parafilm. Two control trees were mock inoculated using sterile agar plugs. Trees were in 57 L pots, had an average stem caliper of 2.7 cm, an average height of 3.5 m and were kept in a lath house at average high temperatures of 18-24 degrees C. After ten weeks, average lesion length was 15.4 cm (SE= 4.6) and 4.3 cm (SE=2.3) in the fungus-inoculated and control trees, respectively. An ANOVA test, nesting lesions sizes within tree, determined lesions lengths were different between inoculated and mock trees (P= 0.04). The fungus was reisolated from all points in all inoculated trees but never from control trees. C. corticale was first described in the UK from sycamore maple (Acer pseudoplatanus) (Gregory et al. 1949) and is an emerging problem in Europe (Muller et al. 2023). In North America, it has been reported from A. negundo, A. campestre, A. macrophyllum and Cornus nuttallii (Worral 2020), and it appears to be present in the Pacific Northwest (Brooks et al. 2023, Goree 1969). Norway maple is included in the European Plant Protection Organization list of hosts for C. corticale (EPPO 2023), however our finding of C. corticale on silver maple is a first report of this host worldwide and of this pathogen in California. This report is noteworthy, given that C. corticale is also a human pathogen infecting the respiratory system (Braun et al. 2021).

Age differences in mental health from May through August 2020 among U.S. adults: trajectories and the role of pandemic, lifestyle, and social factors.

Objectives: Using nationally representative data among U.S. adults, we assess age differences in changes in mental health both from 2018 to May 2020 and during the pandemic. We also examine factors explaining age differences in mental health.Methods: We analyzed 2018 General Social Survey data (N = 2,348; age 18-89) and three waves of COVID Response Tracking Study data (N = 2,279; age 20-94) spanning May-August 2020. Outcomes included happiness, loneliness, stress, positive affect, and negative affect.Results: U.S. adults reported greater loneliness and less happiness in May 2020 versus 2018. Only loneliness and negative affect changed significantly from May to August 2020, showing declines. Mental health trajectories did not differ significantly by age. Overall, older adults reported lower loneliness, stress, and negative affect than younger adults during 2020. Older age was associated with two factors linked with better mental health: less likelihood of COVID-19 exposure and greater satisfaction with social activities and relationships. However, none of the factors examined herein explained age differences in mental health.Conclusion: Although mental health trajectories during the pandemic were similar across ages, older adults tended to report better mental health than younger adults. Future research should identify factors that explain age differences in mental health that persisted into 2020.

Aeroacoustic performance of a seal vibrissa shaped cylinder.

Bio-inspired geometries have many applications in engineering, including in the field of noise control. In this work, the aeroacoustic performance of a seal vibrissa shaped cylinder (SVSC) is investigated and compared to that of a circular cylinder at Re = 37 000. Experiments conducted in an anechoic wind tunnel are compared to results from a hybrid aeroacoustic simulation with excellent agreement observed between the two. The overall sound pressure level is found to be 24.3 dB lower for the SVSC, and no prominent narrowband component is observed in the acoustic spectrum. Analysis of the flow field and surface pressure fluctuations reveals that this is because the usual large-scale alternating vortex shedding realized for bluff body flows is absent for the SVSC. Instead, smaller uncorrelated vortices are shed from the upper and lower sides of the geometry, which, when combined with a lower spanwise correlation, results in a much lower acoustic intensity spread over a broader frequency range.

Developing a novel device, Eggcell, to improve temperature stability during oocyte collection for IVF.

RESEARCH QUESTION: What temperature fluctuations are oocytes exposed to during oocyte retrieval? Can an alternative method of oocyte retrieval be designed to minimize these fluctuations? DESIGN: Mock oocyte retrieval procedures were performed to investigate the change in temperature when the follicular fluid is drained into collection tubes and when the fluid is subsequently poured into dishes to allow identification of the cumulus-oocyte complex (COC). A new device, the Eggcell, has been designed that addresses the problem of these temperature fluctuations. To confirm its safety and demonstrate the clinical applicability of Eggcell, laboratory validation was performed prior to use with human participants (n = 15). RESULTS: Eggcell meets its design specification to provide temperature stability within the physiological range for aspirated follicular fluid. The COC can be successfully retained within the chamber (n = 180) without evidence of loss or damage to the oocytes or compromise of fertilization rate, blastocyst development or clinical outcome. CONCLUSIONS: This study has demonstrated the successful first stages of development of a new medical device. Further studies are needed for comparative evaluation of clinical outcome with standard technology.

Low versus high level of response to alcohol affects amygdala functional connectivity during processing of emotional stimuli.

BACKGROUND: Low levels of response (low LR) to alcohol predict heavy drinking and alcohol problems. Functional magnetic resonance imaging (fMRI) studies of emotion processing have shown that low LR individuals exhibit lower activation in task-related brain regions following both placebo and alcohol administration, but these studies did not examine functional brain networks that might contribute to the phenomena. The current study expands upon the earlier results by evaluating whether functional connectivity differences between the amygdala and other brain regions modulated by emotional face processing are associated with LR. Based on prior findings, we hypothesized that low LR is related to lower functional connectivity in fronto-amygdalar functional circuits, which underlie the processing of emotional stimuli. METHODS: Secondary analyses were conducted on data from a double-blind, placebo-controlled, within-subjects, cross-over study in 108 18-to-25-year-old low and high LR sex-matched pairs without alcohol use disorder at baseline. Participants performed modified emotional faces processing tasks after receiving placebo or approximately 0.7 ml/kg of ethanol. Psychophysiological interaction analyses examined functional connectivity between left and right amygdalae and related brain circuits using LR-by-alcohol general linear models. The data included 54 sex-matched pairs with 216 fMRI scans comprising alcohol and placebo conditions. RESULTS: Compared with individuals with high LR, low LR subjects demonstrated lower functional connectivity between the amygdala and the frontal lobes, insula, and parietal regions, while processing angry and happy faces. Interactions showed lower connectivity following alcohol in low LR and higher connectivity in high LR groups. CONCLUSIONS: Low LR individuals demonstrated lower functional connectivity in response both to placebo and a modest dose of ethanol. Attenuated connectivity among low LR individuals when processing emotional faces may contribute to an impaired ability to recognize alcohol intoxication in social situations and to appraise angry and happy emotions irrespective of whether alcohol is consumed.

The Practice of Pre-trial Detention in England & Wales - Changing Law and Changing Culture.

Pre-trial detention empowers criminal courts to imprison defendants before they have been convicted of an offence. This is a significant power which should be subject to a rigourous decision-making process. A 2016 study of pre-trial detention practice in England and Wales highlighted concerns about such processes, recommending changes to law and practice in that jurisdiction. In 2017, several of these recommendations became law. This article details a follow-up empirical study, conducted in 2020, which sought to examine the impact of these changes on day-to-day pre-trial detention practice in criminal courts. After analysing the data, the article concludes that the changes in fact had minimal impact on practice, and suggests that changing the law does not necessarily translate into a change in the culture of pre-trial detention practice.

Endorsement of specific alcohol use disorder criterion items changes with age in individuals with persistent alcohol use disorders in 2 generations of the San Diego Prospective Study.

BACKGROUND: Diagnostic and Statistical Manual (DSM) alcohol use disorder (AUD) criteria are written in broad enough terms to apply to diverse populations. The current analyses evaluate whether the endorsement of criteria changes with increasing age in individuals with persistent AUDs. METHODS: Data regarding AUDs persisting across 3 timepoints between average ages of 31 and 43 were gathered about every 5 years from 318 interviews for 106 San Diego Prospective Study (SDPS) AUD male probands. Similar data regarding persistent AUDs across 2 timepoints were obtained from 136 interviews with 68 SDPS AUD offspring between average ages of 21 and 27. Changes in the endorsement of each AUD criterion were evaluated using Cochran's Q test. RESULTS: For AUD probands across time, significant decreases were observed in the proportions endorsing 4 criteria (tolerance, withdrawal, failure to fulfill obligations, and using alcohol in hazardous situations). Increased rates of endorsement were documented for 3 criteria (drinking alcohol in higher amounts or for longer periods of time, spending a great deal of time regarding alcohol, and continued use despite social or interpersonal problems). Significant increases in rates of endorsements for offspring were seen for spending a great deal of time regarding alcohol and giving up or reducing important activities in order to drink. CONCLUSIONS: These data indicate that the salience of many DSM AUD criterion items changed significantly with age in both SDPS generations among individuals with persistent AUDs. The current results support the need for additional systematic research to determine whether specific criterion items might need to be weighted differently in evaluating older and younger individuals with persistent AUDs.

Relationship between level of response to alcohol and acute tolerance.

BACKGROUND: A low level of response (low LR) to alcohol correlates with the later development of alcohol-related problems. Although some of the underpinnings of LR are understood, little is known about the potential relationship between LR and acute tolerance. The current analyses tested the hypothesis that a low LR will be explained in part by more intense acute tolerance to alcohol during a drinking session. METHODS: Data were generated through a reanalysis of data from 120 individuals who were 18- to 25-year-old, sex-matched pairs of low and high LR drinkers who at baseline did not meet criteria for an alcohol use disorder. Each subject participated in an oral alcohol challenge in which they consumed about 0.7 ml ethanol per kg and acute tolerance was measured as the differences in alcohol's effects at similar breath alcohol levels (BrACs) during the rising and falling breath alcohol concentration (BrAC) curve. Measures included aspects of the Subjective High Assessment Scale (SHAS) and body sway. RESULTS: Contrary to our hypothesis, but similar to results with other alcohol measures, acute tolerance was significantly attenuated in low LR compared with high LR individuals on most SHAS scores. Neither LR group demonstrated acute tolerance to alcohol for sleepiness or body sway. Men and women did not differ on any of these measures. CONCLUSION: These data do not support a role of acute tolerance in the low LR to alcohol as measured by subjective feelings of intoxication or body sway in these subjects, findings that were similar across males and females. In addition, consistent with the literature, the analyses demonstrated differences across measures such that acute tolerance was observed for most measures of subjective effects but not for body sway. Among the subjective effects, acute tolerance was observed for alcohol's intoxicating effect but not for feeling sleepy.

Cross-sectional and prospective associations of drinking characteristics with scores from the Self-Report of the Effects of Alcohol questionnaire and findings from alcohol challenges.

BACKGROUND: Data from 2 generations of participants in the San Diego Prospective Study (SDPS) were used to compare cross-sectional and prospective relationships of 5 measures of the low level of response (low LR) to alcohol to 2 key alcohol-related outcomes. METHODS: The analyses used data from 373 SDPS male probands and 158 male and female offspring of these individuals to evaluate relationships of 5 LR measures to the prior 5-year maximum drinks per occasion and the number of 11 DSM-IV alcohol use disorder (AUD) criteria experienced. Probands' LR measures included responses to alcohol challenges administered 15 years previously, and ratings for both generations included measures of the number of standard drinks during four periods: the first five times of drinking (SRE-5), the prior three drinking months (SRE-3), the period of heaviest drinking (SRE-H), and a total average across all time frames (SRE-T). Analyses included zero-order correlations, correlations using covariates, and hierarchical multiple regression analyses. RESULTS: All 5 LR measures were correlated with aspects of maximum drinks and the number of AUD criteria, but the most robust results were seen for SRE-3 and maximum drinks. Correlations were less consistent for SRE-5, a measure more closely related to outcomes in the offspring. Hierarchical regression analyses supported most of these conclusions and showed that alcohol challenge-based LRs added significant information regarding maximum drinks even when evaluated with SRE values. The close correlation between SRE-H and SRE-T argues against the need for studies to include both measures. The patterns of results were similar irrespective of whether covariates were included. CONCLUSIONS: There were significant correlations of maximum drinks and the number of AUD criteria with findings from prior alcohol challenges and all SRE scores. Challenges and SRE reports are related but not identical LR measures. All SRE scores, including SRE-5, offered useful information regarding subsequent drinking behavior.

Low Referral Rates for Genetic Assessment of Patients With Multiple Adenomas in United Kingdom Bowel Cancer Screening Programs.

BACKGROUND: Approximately 1 in 20 cases of colorectal cancer are caused by monogenic syndromes. Published guidelines recommend that patients with 10 or more adenomas be referred for genetic testing, based on evidence that colorectal cancer risk is associated with adenoma multiplicity. OBJECTIVE: The aim of this study was to determine adherence to guidelines on referral for genetic screening in patients with 10 or more adenomas. DESIGN: A cross-sectional study was performed of prospectively collected data from the UK Bowel Cancer Screening Programme between May 2007 and June 2018. Only histologically confirmed adenomas were included. Clinicopathological data were recorded from patient records, and referrals to clinical genetics services were ascertained. SETTING: Data were obtained from 3 centers in London, United Kingdom. PATIENTS: A total of 17,450 subjects underwent colonoscopy following an abnormal fecal occult blood test. MAIN OUTCOME MEASURES: We quantified patients with 10 or more adenomas and the proportion referred for genetic screening. RESULTS: The adenoma detection rate was 50.6% among 17,450 patients who underwent colonoscopy (8831 had 1 or more adenomas). Three hundred forty-seven patients (2.0%) had 10 or more adenomas. Patients with 10 or more adenomas were more likely to be male than those with fewer than 10 adenomas (76.9% vs 53.4%; p < 0.0001). A family history was collected in 37.8% of the multiple adenoma population. Of 347 patients with 10 or more adenomas, 28 (8.1%) were referred for genetic assessment. LIMITATIONS: All 3 screening centers were in a single city. No genetic outcome data were available to permit analysis of actual rates of inherited cancer syndromes in this population. CONCLUSIONS: In this study, almost 1 in 50 patients had 10 or more adenomas. Despite guidelines advising genetic testing in this group, referral rates are low. A referral pathway and management strategies should be established to address this patient population. See Video Abstract at http://links.lww.com/DCR/B630. TASAS BAJAS DE DERIVACIN PARA LA EVALUACIN GENTICA DE PACIENTES CON ADENOMAS MLTIPLES EN LOS PROGRAMAS DE DETECCIN DEL CNCER DE INTESTINO DEL REINO UNIDO: ANTECEDENTES:Aproximadamente uno de cada veinte casos de cáncer colorrectal son causados por síndromes monogénicos. Las pautas publicadas recomiendan que los pacientes con diez o más adenomas sean derivados para pruebas genéticas, basándose en la evidencia de que el riesgo de cáncer colorrectal está asociado con la multiplicidad de adenomas.OBJETIVO:El objetivo de este estudio fue determinar la adherencia a las guías de derivación para cribado genético en pacientes con diez o más adenomas.DISEÑO:Se realizó un estudio transversal de datos recolectados prospectivamente del Programa de Detección de Cáncer de Intestino del Reino Unido entre mayo de 2007 y junio de 2018. Solo se incluyeron los adenomas confirmados histológicamente. Los datos clínico-patológicos se registraron a partir de los registros de los pacientes y se determinaron las derivaciones a los servicios de genética clínica.AJUSTE ENTORNO CLINICO:Los datos se obtuvieron de tres centros en Londres, Reino Unido.PACIENTES:Un total de 17.450 17450 sujetos pacientes se sometieron a una colonoscopia después de una prueba de sangre oculta en heces anormal positiva.PRINCIPALES MEDIDAS DE RESULTADO VOLARACION:cuantificamos los pacientes con diez o más adenomas y la proporción remitida para cribado genético.RESULTADOS:La tasa de detección de adenomas fue del 50,6% entre 17.450 17450 pacientes que se sometieron a colonoscopia (8.831 8831 tenían uno o más adenomas). 347 pacientes (2,0%) tenían 10 o más adenomas. Los pacientes con 10 o más adenomas tenían más probabilidades de ser hombres que aquellos con menos de 10 adenomas (76,9% frente versus a 53,4%; p <0,0001). Se recogieron antecedentes familiares en el 37,8% de la población de adenomas múltiples. De 347 pacientes con 10 o más adenomas, 28 (8,1%) fueron remitidos para evaluación genética.LIMITACIONES:Los tres centros de detección se encontraban en una sola ciudad. No se disponía de datos de resultados genéticos que permitieran el análisis de las tasas reales de síndromes de cáncer hereditario en esta población.CONCLUSIONES:En este estudio, casi uno de cada cincuenta pacientes tenía diez o más adenomas. A pesar de las pautas que recomiendan las pruebas genéticas en este grupo, las tasas de derivación son bajas. Se debe establecer una vía de derivación y estrategias de manejo para abordar esta población de pacientes. Consulte Video Resumen en http://links.lww.com/DCR/B630.

Cascade Programming for 10 kHz Spinal Cord Stimulation: A Single Center Case Series of 114 Patients With Neuropathic Back and Leg Pain.

OBJECTIVE: Ten kilohertz spinal cord stimulation (SCS) is usually initiated in a single-bipolar configuration over the radiological reference point T9/T10 intervertebral disc space for neuropathic back and leg pain. Cascade is a duty-cycled, multi-bipolar contact configuration across an entire eight-contact lead. Potential advantages by using a broader area of SCS coverage include mitigation against minor lead migration and a reduction in the need for reprogramming. We report here the results of a retrospective case series of 114 patients using Cascade. MATERIALS AND METHODS: Retrospective data were collected over two years. We selected patients with neuropathic back with or without/leg pain who had a trial of SCS. Pain assessments using Numerical Rating Scales (NRS) and Patient Global Impression of Change (PGIC) scores were collected at baseline, six months, and last follow-up beyond 12 months (mean 15.1 months). Patients were programmed with 10 kHz SCS using Cascade during the trial, which was continued unless reporting inadequate pain relief. Morbidity and deviations from Cascade programming were also obtained. RESULTS: At six months, 87 of 97 (90.6%) patients with active devices were using Cascade and 58 of 72 (81%) patients at the last follow-up >12 months. There was a significant reduction in back NRS (8.3 vs. 3.9 [p < 0.0001], N = 97) and leg pain (7.53 vs. 3.83 [p < 0.0001], N = 77) at 6 months and last follow-up >12 months back (8.3 vs. 3.95 [p < 0.0001] N = 72), leg (7.53 vs. 3.534 [p < 0.0001], N = 58). The PGIC score was 6 of 7 or all of 7 in 72% of patients (70/97) at six months and in 68% (49/72) of patients at the last follow-up beyond 12 months. CONCLUSION: Cascade is an effective programming methodology that may have benefits over a single-bipole configuration for 10 kHz SCS, particularly during a trial of stimulation. Results from this study suggest it is a durable program for patients with neuropathic back and leg pain.

Moving Profiling Spatial Proteomics Beyond Discrete Classification.

The spatial subcellular proteome is a dynamic environment; one that can be perturbed by molecular cues and regulated by post-translational modifications. Compartmentalization of this environment and management of these biomolecular dynamics allows for an array of ancillary protein functions. Profiling spatial proteomics has proved to be a powerful technique in identifying the primary subcellular localization of proteins. The approach has also been refashioned to study multi-localization and localization dynamics. Here, the analytical approaches that have been applied to spatial proteomics thus far are critiqued, and challenges particularly associated with multi-localization and dynamic relocalization is identified. To meet some of the current limitations in analytical processing, it is suggested that Bayesian modeling has clear benefits over the methods applied to date and should be favored whenever possible. Careful consideration of the limitations and challenges, and development of robust statistical frameworks, will ensure that profiling spatial proteomics remains a valuable technique as its utility is expanded.

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy.

Unique Molecular Identifiers (UMIs) are random oligonucleotide barcodes that are increasingly used in high-throughput sequencing experiments. Through a UMI, identical copies arising from distinct molecules can be distinguished from those arising through PCR amplification of the same molecule. However, bioinformatic methods to leverage the information from UMIs have yet to be formalized. In particular, sequencing errors in the UMI sequence are often ignored or else resolved in an ad hoc manner. We show that errors in the UMI sequence are common and introduce network-based methods to account for these errors when identifying PCR duplicates. Using these methods, we demonstrate improved quantification accuracy both under simulated conditions and real iCLIP and single-cell RNA-seq data sets. Reproducibility between iCLIP replicates and single-cell RNA-seq clustering are both improved using our proposed network-based method, demonstrating the value of properly accounting for errors in UMIs. These methods are implemented in the open source UMI-tools software package.

Should we be talking about guidelines with patients? A qualitative analysis in metastatic breast cancer.

BACKGROUND: Little data exist on perceptions of guideline-based care in oncology. This qualitative analysis describes patients' and oncologists' views on the value of guideline-based care as well as discussing guidelines when making metastatic breast cancer (MBC) treatment decisions. PATIENTS AND METHODS: In-person interviews completed with MBC patients and community oncologists and focus groups with academic oncologists were audio-recorded and transcribed. Two coders utilized a content analysis approach to analyze transcripts independently using NVivo. Major themes and exemplary quotes were extracted. RESULTS: Participants included 20 MBC patients, 6 community oncologists, and 5 academic oncologists. Most patients were unfamiliar with the term "guidelines." All patients desired to know if they were receiving guideline-discordant treatment but were often willing to accept this treatment. Five themes emerged explaining this including trusting the oncologist, relying on the oncologist's experiences, being informed of rationale for deviation, personalized treatment, and openness to novel therapies. Physician discussions regarding the importance of guidelines revealed three themes: consistency with scientific evidence, insurance coverage, and limiting unusual practices. Oncologists identified three major limitations in using guidelines: lack of consensus, inability to "think outside the box" to personalize treatment, and lack of guideline timeliness. Although some oncologists discussed guidelines, it was often not considered a priority. CONCLUSIONS: Patients expressed a desire to know whether they were receiving guideline-based care but were amenable to guideline-discordant treatment if the rationale was made clear. Providers' preference to limit discussions of guidelines is discordant with patients' desire for this information and may limit shared decision-making.

The Search for Contributors to Low Rates of Recognition of Paternal Alcohol Use Disorders in Offspring From the San Diego Prospective Study.

BACKGROUND: The most efficient approach for establishing family histories (FHs) asks informants about disorders in their relatives (a Family History Method [FHM]). However, FHMs underestimate family diagnoses. We evaluated if accuracies of young adult offspring report of their father's alcohol use disorders (AUDs) related to the age, sex, education, and/or substance-related patterns/problems of either the young adult informants or their AUD fathers. METHODS: Data from the San Diego Prospective Study (SDPS), a multigenerational 35-year investigation, compared father/offspring pairs where the proband father's alcohol problems were correctly (Group 1) or incorrectly (Group 2) noted by offspring. In the key analysis, Group 1 versus 2 results were entered into bootstrapped backward logistic regression analyses predicting Group 1 membership. RESULTS: Five proband and one offspring characteristic were associated with correct identification of their father's alcohol problems. None of these related to age, education, or sex. Characteristics associated with correct FHM diagnoses included the father's FH of AUDs, self-report of drinking despite social/interpersonal or physical/psychological alcohol-related problems, spending much time related to alcohol, and his having a religious preference. The single offspring item predicting correct identification of the father's problems was the number of DSM alcohol problems of the offspring. CONCLUSIONS: In the SDPS, FHM sensitivity was most closely related to the father's drinking characteristics, not the offspring characteristics. While unique aspects of SDPS families potentially limit generalizability of results, the data demonstrate how the FHM can offer important initial steps in the search for genetically related AUD risks in a subset of families.

Attrition, physical integrity and insecticidal activity of long-lasting insecticidal nets in sub-Saharan Africa and modelling of their impact on vectorial capacity.

BACKGROUND: Long-lasting insecticidal nets (LLINs) are the primary malaria prevention and control intervention in many parts of sub-Saharan Africa. While LLINs are expected to last at least 3 years under normal use conditions, they can lose effectiveness because they fall out of use, are discarded, repurposed, physically damaged, or lose insecticidal activity. The contributions of these different interrelated factors to durability of nets and their protection against malaria have been unclear. METHODS: Starting in 2009, LLIN durability studies were conducted in seven countries in Africa over 5 years. WHO-recommended measures of attrition, LLIN use, insecticidal activity, and physical integrity were recorded for eight different net brands. These data were combined with analyses of experimental hut data on feeding inhibition and killing effects of LLINs on both susceptible and pyrethroid resistant malaria vectors to estimate the protection against malaria transmission-in terms of vectorial capacity (VC)-provided by each net cohort over time. Impact on VC was then compared in hypothetical scenarios where one durability outcome measure was set at the best possible level while keeping the others at the observed levels. RESULTS: There was more variability in decay of protection over time by country than by net brand for three measures of durability (ratios of variance components 4.6, 4.4, and 1.8 times for LLIN survival, use, and integrity, respectively). In some countries, LLIN attrition was slow, but use declined rapidly. Non-use of LLINs generally had more effect on LLIN impact on VC than did attrition, hole formation, or insecticide loss. CONCLUSIONS: There is much more variation in LLIN durability among countries than among net brands. Low levels of use may have a larger impact on effectiveness than does variation in attrition or LLIN degradation. The estimated entomological effects of chemical decay are relatively small, with physical decay probably more important as a driver of attrition and non-use than as a direct cause of loss of effect. Efforts to maximize LLIN impact in operational settings should focus on increasing LLIN usage, including through improvements in LLIN physical integrity. Further research is needed to understand household decisions related to LLIN use, including the influence of net durability and the presence of other nets in the household.

Efficacy of Olyset Duo, a bednet containing pyriproxyfen and permethrin, versus a permethrin-only net against clinical malaria in an area with highly pyrethroid-resistant vectors in rural Burkina Faso: a cluster-randomised controlled trial.

BACKGROUND: Substantial reductions in malaria incidence in sub-Saharan Africa have been achieved with massive deployment of long-lasting insecticidal nets (LLINs), but pyrethroid resistance threatens control. Burkina Faso is an area with intense malaria transmission and highly pyrethroid-resistant vectors. We assessed the effectiveness of bednets containing permethrin, a pyrethroid, and pyriproxyfen, an insect growth regulator, versus permethrin-only (standard) LLINs against clinical malaria in children younger than 5 years in Banfora, Burkina Faso. METHODS: In this two-group, step-wedge, cluster-randomised, controlled, superiority trial, standard LLINs were incrementally replaced with LLINs treated with permethrin plus pyriproxyfen (PPF) in 40 rural clusters in Burkina Faso. In each cluster, 50 children (aged 6 months to 5 years) were followed up by passive case detection for clinical malaria. Cross-sectional surveys were done at the start and the end of the transmission seasons in 2014 and 2015. We did monthly collections from indoor light traps to estimate vector densities. Primary endpoints were the incidence of clinical malaria, measured by passive case detection, and the entomological inoculation rate. Analyses were adjusted for clustering and for month and health centre. This trial is registered as ISRCTN21853394. FINDINGS: 1980 children were enrolled in the cohort in 2014 and 2157 in 2015. At the end of the study, more than 99% of children slept under a bednet. The incidence of clinical malaria was 2·0 episodes per child-year in the standard LLIN group and 1·5 episodes per child-year in the PPF-treated LLIN group (incidence rate ratio 0·88 [95% CI 0·77-0·99; p=0·04]). The entomological inoculation rate was 85 (95% CI 63-108) infective bites per transmission season in the standard LLIN group versus 42 (32-52) infective bites per transmission season in the PPF-treated LLIN group (rate ratio 0·49, 95% CI 0·32-0·66; p<0·0001). INTERPRETATION: PPF-treated LLINs provide greater protection against clinical malaria than do standard LLINs and could be used as an alternative to standard LLINs in areas with intense transmission of Plasmodium falciparum malaria and highly pyrethroid-resistant vectors. FUNDING: EU Seventh Framework Programme.