Demonstration of event position reconstruction based on diffusion in the NEXT-white detector

Noble element time projection chambers are a leading technology for rare event detection in physics, such as for dark matter and neutrinoless double beta decay searches. Time projection chambers typically assign event position in the drift direction using the relative timing of prompt scintillation and delayed charge collection signals, allowing for reconstruction of an absolute position in the drift direction. In this paper, alternate methods for assigning event drift distance via quantification of electron diffusion in a pure high pressure xenon gas time projection chamber are explored. Data from the NEXT-White detector demonstrate the ability to achieve good position assignment accuracy for both high- and low-energy events. Using point-like energy deposits from 83mKr calibration electron captures (E ∼ 45  keV), the position of origin of low-energy events is determined to 2 cm precision with bias < 1 mm. A convolutional neural network approach is then used to quantify diffusion for longer tracks (E ≥ 1.5  MeV), from radiogenic electrons, yielding a precision of 3 cm on the event barycenter. The precision achieved with these methods indicates the feasibility energy calibrations of better than 1% FWHM at Qββ in pure xenon, as well as the potential for event fiducialization in large future detectors using an alternate method that does not rely on primary scintillation.

Which type of forceps is better for nonrotational operative births? A simulation study comparing Thierry spatulas and Simpson-Braun and Kielland forceps

OBJECTIVE

Obstetric forceps play an important role in safe childbirth, yet there is a lack of distinction between various forceps types in clinical practice. This study aimed to evaluate and compare perineal pressure and forces on the baby during nonrotational forceps-assisted births using Simpson-Braun forceps, Kielland forceps, and Thierry spatulas on a simulation model.

METHODS

This experimental study involved six obstetricians conducting 108 forceps-assisted births on a simulation model. Instruments were assessed for their impact on perineal pressure, traction force, and operator-assessed difficulty.

RESULTS

Thierry's spatulas exerted the lowest force on the baby, while Kielland forceps exhibited the lowest perineal pressure, though not statistically significant. An experienced obstetrician demonstrated less perineal pressure with Simpson forceps. Notably, no significant differences in difficulty were observed between instruments.

CONCLUSION

This study highlights distinctions in forceps performance, with Thierry spatulas applying the least force on the fetal head, while an experienced obstetrician fared better with Simpson forceps in terms of perineal pressure. Kielland forceps remain a viable alternative for nonrotational forceps births, showing comparable outcomes.

Perspectives on technology - prostate cancer: is local anaesthetic transperineal prostate biopsy really better than transrectal biopsy?

For many years, transrectal ultrasound-guided (TRUS) prostate biopsies have been performed to establish a histological diagnosis of prostate cancer. This has been the recommended standard of care procedure, but has always carried risks, in particular the risk of post-procedural sepsis, and the associated antibiotic burden and risk of development of antibiotic resistance. Transperineal (TP) prostate biopsies performed under local anaesthetic (LA) have been proposed as a possible solution to these issues, with potentially lower infectious complications, and avoidance of need for antibiotic prophylaxis. The European Association of Urology produced guidance in 2023 with 'weak' recommendations in favour of LATP biopsy as a new standard of care, citing its safety profile. Both the National Institute for Health and Care Excellence in the UK, and the American Urological Association in the United States, have concluded for now that the body of evidence is inadequate and not offered a similar recommendation. We discuss the available evidence, pros and cons of each technique, and the status of current trials in the field. We believe that clinical equipoise remains necessary, given the disparity in national and international guidelines highlighting the need for large randomised controlled trials to answer the question: is LATP biopsy really better than TRUS biopsy?

Multi-scale datasets for monitoring Mediterranean oak forests from optical remote sensing during the SENTHYMED/MEDOAK experiment in the north of Montpellier (France)

Mediterranean forests represent critical areas that are increasingly affected by the frequency of droughts and fires, anthropic activities and land use changes. Optical remote sensing data give access to several essential biodiversity variables, such as species traits (related to vegetation biophysical and biochemical composition), which can help to better understand the structure and functioning of these forests. However, their reliability highly depends on the scale of observation and the spectral configuration of the sensor. Thus, the objective of the SENTHYMED/MEDOAK experiment is to provide datasets from leaf to canopy scale in synchronization with remote sensing acquisitions obtained from multi-platform sensors having different spectral characteristics and spatial resolutions. Seven monthly data collections were performed between April and October 2021 (with a complementary one in June 2023) over two forests in the north of Montpellier, France, comprised of two oak endemic species with different phenological dynamics (evergreen: Quercus ilex and deciduous: Quercus pubescens) and a variability of canopy cover fractions (from dense to open canopy). These collections were coincident with satellite multispectral Sentinel-2 data and one with airborne hyperspectral AVIRIS-Next Generation data. In addition, satellite hyperspectral PRISMA and DESIS were also available for some dates. All these airborne and satellite data are provided from free online download websites. Eight datasets are presented in this paper from thirteen studied forest plots: (1) overstory and understory inventory, (2) 687 canopy plant area index from Li-COR plant canopy analyzers, (3) 1475 in situ spectral reflectances (oak canopy, trunk, grass, limestone, etc.) from ASD spectroradiometers, (4) 92 soil moistures and temperatures from IMKO and Campbell probes, (5) 747 leaf-clip optical data from SPAD and DUALEX sensors, (6) 2594 in-lab leaf directional-hemispherical reflectances and transmittances from ASD spectroradiometer coupled with an integrating sphere, (7) 747 in-lab measured leaf water and dry matter content, and additional leaf traits by inversion of the PROSPECT model and (8) UAV-borne LiDAR 3-D point clouds. These datasets can be useful for multi-scale and multi-temporal calibration/validation of high level satellite vegetation products such as species traits, for current and future imaging spectroscopic missions, and by fusing or comparing both multispectral and hyperspectral data. Other targeted applications can be forest 3-D modelling, biodiversity assessment, fire risk prevention and globally vegetation monitoring.

Intra-prostatic tumour evolution, steps in metastatic spread and histogenomic associations revealed by integration of multi-region whole-genome sequencing with histopathological features

BACKGROUND

Extension of prostate cancer beyond the primary site by local invasion or nodal metastasis is associated with poor prognosis. Despite significant research on tumour evolution in prostate cancer metastasis, the emergence and evolution of cancer clones at this early stage of expansion and spread are poorly understood. We aimed to delineate the routes of evolution and cancer spread within the prostate and to seminal vesicles and lymph nodes, linking these to histological features that are used in diagnostic risk stratification.

METHODS

We performed whole-genome sequencing on 42 prostate cancer samples from the prostate, seminal vesicles and lymph nodes of five treatment-naive patients with locally advanced disease. We spatially mapped the clonal composition of cancer across the prostate and the routes of spread of cancer cells within the prostate and to seminal vesicles and lymph nodes in each individual by analysing a total of > 19,000 copy number corrected single nucleotide variants.

RESULTS

In each patient, we identified sample locations corresponding to the earliest part of the malignancy. In patient 10, we mapped the spread of cancer from the apex of the prostate to the seminal vesicles and identified specific genomic changes associated with the transformation of adenocarcinoma to amphicrine morphology during this spread. Furthermore, we show that the lymph node metastases in this patient arose from specific cancer clones found at the base of the prostate and the seminal vesicles. In patient 15, we observed increased mutational burden, altered mutational signatures and histological changes associated with whole genome duplication. In all patients in whom histological heterogeneity was observed (4/5), we found that the distinct morphologies were located on separate branches of their respective evolutionary trees.

CONCLUSIONS

Our results link histological transformation with specific genomic alterations and phylogenetic branching. These findings have implications for diagnosis and risk stratification, in addition to providing a rationale for further studies to characterise the genetic changes causally linked to morphological transformation. Our study demonstrates the value of integrating multi-region sequencing with histopathological data to understand tumour evolution and identify mechanisms of prostate cancer spread.

Vacuum-assisted birth in maternal lateral posture versus lithotomy. A simulation study

OBJECTIVE

Maternal lateral postures provide advantages during childbirth. This study aims to investigate the feasibility of assisting vacuum births in maternal lateral postures in a simulation model.

STUDY DESIGN

In a simulation model, four obstetricians and four medical students were randomly allocated to perform vacuum-assisted births first in maternal lateral posture or lithotomy. A modification of Aldo Vacca's 5-step technique was developed to assist vacuum-assisted births in lateral posture. The lateral distance, vertical distance, and distance from the cup center to the flexion point were measured for every placement of the cup.

RESULTS AND CONCLUSIONS

A total of 128 vacuum-assisted births were performed. The mean distance to the flexion point was 1.15 ± 0.71 cm for the lithotomy posture and 1.31 ± 0.82 cm for the lateral posture (P = 0.127). There were no statistically significant differences in vacuum extractor cup placement accuracy based on maternal posture. Performing vacuum-assisted births in maternal lateral posture is feasible in a simulation model. The technique is easy to learn, and the differences in cup placement between the lateral and lithotomy postures are small.

Radiotherapy for Metastatic Spinal Cord Compression with Increased Doses: Final Results of the RAMSES-01 Trial

PURPOSE/OBJECTIVE(S)

To investigate the outcomes of precision-radiotherapy (RT) with 15 × 2.633 Gy (EQD2 = 41.6 Gy for tumor cell kill, α/β = 10 Gy) or 18 × 2.333 Gy (EQD2 = 43.2 Gy) in patients with metastatic spinal cord compression (MSCC) and favorable survival prognoses (>35 points on a validated survival score). In addition, these patients were compared to a historical control group of patients with favorable prognoses treated with 10 × 3 Gy (EQD2 = 32.5 Gy).

MATERIALS/METHODS

In a multi-center phase 2 study (RAMSES-01), patients with MSCC and favorable survival prognoses receiving 15 × 2.633 Gy or 18 × 2.333 Gy of precision-RT alone (no upfront surgery) were mainly evaluated for local progression-free survival (LPFS), defined as no deterioration of motor function during RT and no in-field recurrence of MSCC following RT, at 12 months (primary endpoint). Secondary endpoints included improvement of motor and sensory functions, post-RT ambulatory status, relief of pain and distress, toxicity, and survival (OS). The maximum relative doses allowed to the spinal cord were 101.5 % of the prescribed dose for 18 × 2.333 Gy and 101.2% for 15 × 2.633 Gy, respectively (both representing an EQD2 of 46.6 Gy for myelopathy, α/β = 2 Gy). In addition, the RAMSES-cohort was compared to a historical control group (N = 266) irradiated with 10 × 3 Gy (propensity score adjusted Cox regression).

RESULTS

In the RAMSES-cohort, 50 (of 62 planned) patients were evaluable for LPFS and included in the analyses. Since OS was worse than expected, a new survival score was developed, which was more precise in predicting OS than a previous tool. As a consequence, the RAMSES-trial, which was based on the previous score, was terminated. In the 50 patients included so far, 12-month rates of LPFS and OS were 97.6% and 69.9%, respectively. Improvement of motor function occurred in 28 patients (56.0%), and 47 patients (94.0%) were ambulatory following RT. Within 3 months following RT, 12 of 21 patients (57.2%) with pre-RT sensory deficits improved, 38 of 45 patients (84.4%) with pre-RT pain experienced at least partial relief, and 39 of 50 patients (78.0%) reported relief of distress. Ten of 50 patients (20.0%) experienced grade 2 toxicities (mainly esophagitis/dysphagia) and another two patients (4.0%) grade 3 toxicities (1 diarrhea, 1 esophagitis). After propensity score adjustment, the RAMSES-cohort showed significantly better LPFS than the control group (hazard ratio = 0.125, 95% confidence interval = 0.016 - 0.962, p = 0.046) and a strong trend regarding improvement of motor function (hazard ratio = 1.943, 95% confidence interval = 0.981 - 3.850, p = 0.057). Post-RT ambulatory rates (p = 0.56) and OS rates (p = 0.62) were not significantly different.

CONCLUSION

Precision-RT with 15 × 2.633 Gy or 18 × 2.333 Gy was sufficiently well tolerated and resulted in significantly better long-term LPFS than 10 × 3 Gy in patients with MSCC and favorable survival prognoses. Thus, the dose-fractionation regimens of the RAMSES-01 trial appear preferable for these patients.

Clinical Usefulness of PSMA PET/CT Imaging in Patients with Suspected Recurrence of Prostate Cancer after Primary RT with PSA below the Phoenix Criteria Threshold: Systematic Review and Meta-Analysis

PURPOSE/OBJECTIVE(S)

To assess the detection rate and the patterns of PSMA PET/CT uptake in patients with suspected prostate cancer recurrence after primary radiotherapy with serum PSA levels below the accepted Phoenix definition criteria for biochemical recurrence.

MATERIALS/METHODS

The meta-analysis was performed according to the PRISMA statement. Studies providing data on patients with suspected prostate cancer recurrence after primary radiotherapy with serum PSA levels below the accepted Phoenix definition criteria were included.

RESULTS

Atotal of 5 studies included a total of 1334 patients, of which 489 patients with suspected BCR and serum PSA levels below the Phoenix criteria were included. The PSMA PET/CT detection rate (DR) was 60% for PSA <0.5 ng/mL, 76% for PSA 0.5-1 ng/mL, 81.03% for PSA 1-2 ng/mL, and 89.5% for PSA>2. No significant differences were found in the locations of PSMA-PET/CT uptake among those with PSA ≤2 ng/mL, compared with those meeting the Phoenix criteria. The PSMA-PET/CT uptake of local-only recurrence was more likely in patients with PSA <2 ng/mL (local-only recurrence PSA >2 ng/mL [40.07%] vs PSA <2 ng/mL [58.10%]), RR: 0.718 (95% CI: 0.579-0.892). Lymph node, bone, and visceral metastasis detection rates could be extracted from 3 studies (432 patients). For lymph nodes, the DR was 46% (95% CI: 38-54) in patients outside the Phoenix criteria threshold, and 50% (95% CI: 39-62) in patients with PSA>2 ng/mL. The DR for bone metastases was 19% (95% CI: 12-28) in patients outside the Phoenix criteria threshold, and 25% (95% CI: 19-31) in patients with PSA>2 ng/mL. The DR for visceral metastases was 3% (95% CI: 0-7) in patients outside the Phoenix criteria threshold, and 2% (95% CI: 0-4) in patients with PSA>2 ng/mL. The potentially salvageable disease was considered when all evidence of avid disease could be safely treated with local therapy. This data could be extracted from two studies (343 patients). A higher proportion of disease potentially amenable to salvage therapy was reported in patients outside the Phoenix criteria threshold [salvageable disease: PSA ≤2 ng/mL: 69% (95% CI: 57-80), and PSA >2 ng/mL: 61% (95% CI: 55-66). The pooled risk ratio meta-analysis showed no statistically significant differences between the two previous groups RR: 0.91 (95% CI: 0.75-1.10).

CONCLUSION

PSMAPET/CT can detect prostate cancer recurrence in patients with PSA levels below the Phoenix criteria threshold (reaching up to 80%). Local-only recurrence detection by PSMA PET/CT was more likely in patients with PSA <2 ng/mL. The data from the present meta-analysis shows that a critical review of the Phoenix criteria in the era of PSMA PET/CT might be warranted. Nevertheless, the lack of anatomopathological validation and the retrospective nature of the studies are some of our limitations.

Intrapartum ultrasound in maternal lateral versus semi-recumbent posture. A repeated measures study

OBJECTIVE

This study aimed to assess whether intrapartum ultrasound (ITU) measurements in maternal lateral posture are superimposable to ITU measurements in semi-recumbent position.

STUDY DESIGN

A single-center, repeated measures design was used. Women in the second stage of labor were randomized to ITU first in semi-recumbent followed by ITU in side-lying posture without and with contraction, or inversely. The angle of progression (AOP) and the head-perineum distance (HPD) between contractions (AOP1 and HPD1) and with contraction (AOP2 and HPD2) were measured in each maternal posture. The differences between AOP1 and AOP2 (dAOP), and between HPD1 and HPD2 (dHPD) were calculated.

RESULTS AND CONCLUSIONS

Forty-two women participated in the study. A generalized estimating equation model showed that AOP1 (-3.00°; 95 % CI -5.77 to -0.23; p = 0.03) and AOP2 (-4.14°; 95 % CI -7.20 to -1.08; p = 0.008) were lower in semi-recumbent compared to maternal lateral posture. HPD1 (+1.43 mm; 95 % CI 0.05-2.81; p = 0.042) and HPD2 (+1.53 mm; 95 % CI 0.17-2.89; p = 0.03) were higher in semi-recumbent position. Differences in the ITU measurements in maternal lateral posture compared to semi-recumbent position are small. Monitoring the second stage of labor with ITU in lateral maternal posture is possible.

Cohort profile: the ESC EURObservational Research Programme Non-ST-segment elevation myocardial infraction (NSTEMI) Registry

AIMS

The European Society of Cardiology (ESC) EURObservational Research Programme (EORP) Non-ST-segment elevation myocardial infarction (NSTEMI) Registry aims to identify international patterns in NSTEMI management in clinical practice and outcomes against the 2015 ESC Guidelines for the management of acute coronary syndromes in patients presenting without ST-segment-elevation.

METHODS AND RESULTS

Consecutively hospitalised adult NSTEMI patients (n = 3620) were enrolled between 11 March 2019 and 6 March 2021, and individual patient data prospectively collected at 287 centres in 59 participating countries during a two-week enrolment period per centre. The registry collected data relating to baseline characteristics, major outcomes (in-hospital death, acute heart failure, cardiogenic shock, bleeding, stroke/transient ischaemic attack, and 30-day mortality) and guideline-recommended NSTEMI care interventions: electrocardiogram pre- or in-hospital, pre-hospitalization receipt of aspirin, echocardiography, coronary angiography, referral to cardiac rehabilitation, smoking cessation advice, dietary advice, and prescription on discharge of aspirin, P2Y12 inhibition, angiotensin converting enzyme inhibitor (ACEi)/angiotensin receptor blocker (ARB), beta-blocker, and statin.

CONCLUSION

The EORP NSTEMI Registry is an international, prospective registry of care and outcomes of patients treated for NSTEMI, which will provide unique insights into the contemporary management of hospitalised NSTEMI patients, compliance with ESC 2015 NSTEMI Guidelines, and identify potential barriers to optimal management of this common clinical presentation associated with significant morbidity and mortality.

Psychoactive Substance Use Among Middle-Aged and Older Adults With Visual Impairment

Older adults with visual impairment may be at risk for developing substance use disorder (SUD) as psychoactive substance use is often used to cope with the stressors of vision loss. This study estimates the national prevalence and risk of psychoactive substance use among older adults with visual impairment. We analyzed data of respondents age ≥50 from the 2015-2019 National Survey on Drug Use and Health, an annual cross-sectional survey of a nationally representative sample of non-institutionalized individuals in the U.S. (N=43,886). We estimated and compared prevalence of past-year use of cannabis, cocaine, misuse of prescription opioids, sedatives, stimulants/tranquilizers, alcohol use disorder (AUD), any SUD, and nicotine dependence between adults with visual impairment to those without. Comparisons were conducted using chi-square and we used multivariable generalized linear models using Poisson and log link to estimate adjusted prevalence ratios (aPRs) for adults with visual impairment relative to those without, controlling for demographics and diagnosis of ≥2 chronic diseases. An estimated 6.1% experienced visual impairment. Those with visual impairment had higher prevalence of AUD, nicotine dependence, misuse of prescription opioids, tranquilizers, and stimulants, and SUDs. In adjusted analyses, vision-impaired adults had higher risk of AUD (aPR=1.71, 95% CI: 1.40-2.09), nicotine dependence (aPR =1.53, 95% CI:1.35-1.73), opioid misuse (aPR =1.54, 95% CI:1.26-1.90), and SUD (aPR=1.67, 95% CI:1.40-2.01). Psychoactive substance use adds unique health risks for older adults with vision loss, who may suffer significant psychological stress and loss of independence. Screening for substance use among all older adults with visual impairment should be considered.

Water knot: Case report of a rare complication during a urodynamic test

Intravesical catheter knotting is a rarely reported event that could lead to serious complications. We present a case that occurred during urodynamic test with two K30 tubes: a 56-year-old female with a double knot of two K30 (8.4 Fr) tubes. This case was resolved by removing the catheters with sustained traction. Because catheter knotting can be a serious complication, we recommend the use of a double-lumen catheter when possible and assessment of a safe insertion length.

Assessing deep learning methods for the identification of kidney stones in endoscopic images

Knowing the type (i.e., the biochemical composition) of kidney stones is crucial to prevent relapses with an appropriate treatment. During ureteroscopies, kidney stones are fragmented, extracted from the urinary tract, and their composition is determined using a morpho-constitutional analysis. This procedure is time-consuming (the morpho-constitutional analysis results are only available after several weeks) and tedious (the fragment extraction lasts up to an hour). Identifying the kidney stone type only with the in-vivo endoscopic images would allow for the dusting of the fragments and eneable early treatments, while the morpho-constitutional analysis is ready. Only few contributions dealing with the in vivo identification of kidney stones have been published. This paper discusses and compares five classification methods including deep convolutional neural networks (DCNN)-based approaches and traditional (non DCNN-based) ones. Even if the best method is a DCCN approach with a precision and recall of 98% and 97% over four classes, this contribution shows that an XGBoost classifier exploiting well-chosen feature vectors can closely approach the performances of DCNN classifiers for a medical application with a limited number of annotated data.

Seminal vesicle leiomyosarcoma: Case report and literature review

INTRODUCTION AND BACKGROUND

Primary leiomyosarcoma of the seminal vesicle is an extremely rare and highly malignant disease with less than 15 cases reported.

CASE DESCRIPTION

A 34-year-old man presented with acute urinary symptoms. Imagen studies showed an abdominal mass (80 mm × 65 mm × 50 mm) with contrast enhancement, compressing the right side of the bladder but with a clear cleavage level between surrounding organs. The patient underwent a transrectal US-guided biopsy which was informed as compatible with leiomyosarcoma by immunohistochemical characterization. We performed a cystoprostatectomy and pelvic lymphadenectomy plus radiotherapy. Pathology showed a 7.5 cm × 6 cm nodular para-vesical Leiomyosarcoma histological grade 2 with 0/22 lymph nodes involved. Twelve months after the surgery no recurrences have presented.

CONCLUSION

A multi-disciplinary therapeutic approach, combined with close follow-up, is mandatory to obtain good outcomes in such rare and challenging cases.

EGFR mutation and HPV infection in sinonasal inverted papilloma and squamous cell carcinoma

BACKGROUND

To evaluate the involvement of EGFR signalling and HPV infection in a cohort of inverted sinonasal papilloma (ISP) and sinonasal squamous cell carcinoma (SNSCC) and their value for prognosis and clinical treatment.

METHODS

We analysed 55 ISP, 14 SNSCC associated with ISP (SNSCC-isp) and and 60 SNSCC not associated with ISP (SNSCC-novo) for EGFR gene mutation and copy number gain, protein expression of EGFR and phosporylated EGFR (pEGFR), and HPV-infection and KRAS mutation. Findings were correlated to clinico-pathological and follow-up data.

RESULTS

We found EGFR exon 20 mutations in 38% (7/18) ISP, in 50% (6/12) SNSCC-isp and in 5% (1/19) SNSCC-novo. EGFR was expressed in 92% of ISP, while pEGFR was observed in 54% (21/39). SNSCC-isp and SNSCC-novo demonstrated comparable expression of EGFR (57% and 33%) and of pEGFR (44% and 38%). We observed an inverse relation between EGFR exon 20 mutation and pEGFR expression. Four of 39 (10%) ISP carried HPV-16. Oncogenic HPV was detected in 3/12 (25%) SNSSC-isp and in 1/8 (13%) SNSCC-novo. KRAS mutations were not detected in any of the samples. HPV infection was inversely correlated with pEGFR expression but not with EGFR mutation. ISP with EGFR activation by mutation or by phosphorylation had longer ISP-free survival, however, neither EGFR exon 20 mutation, pEGFR expression nor HPV infection demonstrated prognostic value in SNSCC.

CONCLUSIONS

EGFR exon 20 mutation is frequent in ISP and SNSCC-isp, while activation of EGFR through phosphorylation also plays an important role. Our data indicate that a large proportion of SNSCC patients could benefit from therapy with modern EGFR inhibitors.

Explore, edit and leverage genomic annotations using Python GTF toolkit

MOTIVATION

While Python has become very popular in bioinformatics, a limited number of libraries exist for fast manipulation of gene coordinates in Ensembl GTF format.

RESULTS

We have developed the GTF toolkit Python package (pygtftk), which aims at providing easy and powerful manipulation of gene coordinates in GTF format. For optimal performances, the core engine of pygtftk is a C dynamic library (libgtftk) while the Python API provides usability and readability for developing scripts. Based on this Python package, we have developed the gtftk command line interface that contains 57 sub-commands (v0.9.10) to ease handling of GTF files. These commands may be used to (i) perform basic tasks (e.g. selections, insertions, updates or deletions of features/keys), (ii) select genes/transcripts based on various criteria (e.g. size, exon number, transcription start site location, intron length, GO terms) or (iii) carry out more advanced operations such as coverage analyses of genomic features using bigWig files to create faceted read-coverage diagrams. In conclusion, the pygtftk package greatly simplifies the annotation of GTF files with external information while providing advance tools to perform gene analyses.

AVAILABILITY AND IMPLEMENTATION

pygtftk and gtftk have been tested on Linux and MacOSX and are available from https://github.com/dputhier/pygtftk under the MIT license. The libgtftk dynamic library written in C is available from https://github.com/dputhier/libgtftk.

Co-occurrence of kdr Mutations V1016I and F1534C and Its Association With Phenotypic Resistance to Pyrethroids in Aedes aegypti (Diptera: Culicidae) Populations From Costa Rica

Aedes aegypti (Linnaeus, 1762) is considered the most important mosquito vector species for several arboviruses (e.g., dengue, chikungunya, Zika) in Costa Rica. The primary strategy for the control and prevention of Aedes-borne diseases relies on insecticide-based vector control. However, the emergence of insecticide resistance in the mosquito populations presents a significant threat to these prevention actions. The characterization of the mechanisms driving the insecticide resistance in Ae. aegypti is vital for decision making in vector control programs. Therefore, we analyzed the voltage-gated sodium channel (VGSC) gene for the presence of the V1016I and F1534C kdr mutations in Ae. aegypti populations from Puntarenas and Limon provinces, Costa Rica. The CDC bottle bioassays showed that both Costa Rican Ae. aegypti populations were resistant to permethrin and deltamethrin. In the case of kdr genotyping, results revealed the co-occurrence of V1016I and F1534C mutations in permethrin and deltamethrin-resistant populations, as well as the fixation of the 1534C allele. A strong association between these mutations and permethrin and deltamethrin resistance was found in Puntarenas. Limon did not show this association; however, our results indicate that the Limon population analyzed is not under the same selective pressure as Puntarenas for the VGSC gene. Therefore, our findings make an urgent call to expand the knowledge about the insecticide resistance status and mechanisms in the Costa Rican populations of Ae. aegypti, which must be a priority to develop an effective resistance management plan.

OLOGRAM: Determining significance of total overlap length between genomic regions sets

MOTIVATION

Various bioinformatics analyses provide sets of genomic coordinates of interest. Whether two such sets possess a functional relation is a frequent question. This is often determined by interpreting the statistical significance of their overlaps. However, only few existing methods consider the lengths of the overlap, and they do not provide a resolutive p-value.

RESULTS

Here, we introduce OLOGRAM, which performs overlap statistics between sets of genomic regions described in BEDs or GTF. It uses Monte Carlo simulation, taking into account both the distributions of region and inter-region lengths, to fit a negative binomial model of the total overlap length. Exclusion of user-defined genomic areas during the shuffling is supported.

AVAILABILITY

This tool is available through the command line interface of the pygtftk toolkit. It has been tested on Linux and OSX and is available on Bioconda and from https://github.com/dputhier/pygtftk under the GNU GPL license.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Free Neurocognitive Screening Initiative: An Opportunity to Address Health Disparities and Promote Cultural Competence in Northcentral Florida

Objective

The risk for cognitive impairment is greater in individuals with low SES and limited education. In rural areas, distance and economic concerns preclude individuals from accessing care. In Alachua County, 23% of residents live below poverty and 16% are uninsured. The Neurocognitive Screening Initiative (NSI) attempts to reduce disparities in Alachua by offering free neurocognitive screening. NSI also aspires to promote cultural competence through unique training opportunities for clinical neuropsychology doctoral students.

Method

Patients learned about NSI through flyers, word of mouth, or referrals. Appointments include a clinical interview, cognitive testing, and mood questionnaires. Patients receive feedback, brain health recommendations, and referrals to community resources. Phase 1 began in November 2017 and involved selection of appropriate cognitive measures, development and dissemination of advertising materials, identification of resources, and trainee recruitment. From February 2018 to August 2018, phase 2 involved administration of cognitive screeners. Phase 3 involved continued provision of clinical services, expansion of the NSI team and increased culturally relevant outreach.

Outcomes

NSI’s greatest challenge is recruitment of the appropriate demographic. Since phase 2, we have evaluated 10 patients with diverse racial, socioeconomic, and clinical characteristics. NSI has recruited an ethnoracially diverse cohort of trainees comprised of 4 graduate students and 2 postdoctoral fellows supervised by a clinical neuropsychologist.

Discussion

Efforts to provide services to marginalized individuals have uncovered challenges in attracting patients who might benefit from these services. NSI is forging community partnerships with churches, libraries, and local organizations to reach the targeted audience. Via weekly meetings, participation in community events/outreach, and clinical work, NSI provides unique training for emerging neuropsychologists.

A-46 Impairments in Memory for “Who”, “When”, and “Where” are Detectable in Middle-Aged Adults

Objective

We conducted a cross-sectional study to examine age-¬related differences in performance on a new test assessing memory for “who, when, and where” and associations among these elements. The test was designed to assess aspects of episodic memory by simulating an everyday experience of meeting a series of different people in different places across time.

Method

Healthy young (ages 18¬-25), middle-aged (ages 40-55), and older adults (ages 60+) were asked to remember a sequence of pictures of different faces paired with different places. After viewing the sequence, the participants were asked to pair each face with the correct place and put the face-place pairs in the correct sequence. Participants also completed a battery of standardized neuropsychological tests.

Results

Young adults remembered significantly more face-place pairs in the correct sequence than middle-aged (p < .05) and older adults (p < .05). There were no significant differences between middle-aged and older adults in the number of face-place pairs in correct sequence. Furthermore, young adults remembered significantly more face-place pairs irrespective of sequence than older adults (p < .05). There were no significant differences between young and middle-aged adults or between middle-aged and older adults in the number of correct face-place pairs irrespective of sequence.

Conclusions

Using a new test that incorporates aspects of episodic memory, we found evidence for age-related differences in test performance beginning in middle age. We found that performance on the test correlated with performance on standardized measures of verbal memory and executive functioning but not visual confrontation naming.

B-26 Predictors of Cognitive Decline Over a 2-year Follow up: Olfaction and Scans Without Evidence of Dopaminergic Deficit Status (SWEDD)

Objective

Given the high discriminatory power of olfaction assessments in movement disorders, the current study sought to determine whether olfaction dysfunction differentially predicted cognitive decline in patients who have scans without evidence of dopaminergic deficit (SWEDD). Dopamine depletion is a major neuropathological feature of Parkinson’s disease (PD); however, 15% of patients with a clinical PD diagnosis have neuroimaging evidence of intact dopaminergic function. Recent work has suggested that patients with SWEDD are at a greater risk of cognitive impairment relative to those with PD.

Methods

Archival data were obtained from the Parkinson’s Progression Markers Initiative database. The total sample included three groups: PD (n = 401), SWEDD (n = 51), and HC (n = 175). Participants were categorized into non-impaired (-) or impaired (+) olfaction groups based on performance on the University of Pennsylvania Smell Identification Test, corrected for age and gender. Participants were administered the Montreal Cognitive Assessment twice and change scores were calculated to examine changes in cognition over time (baseline – two-year follow-up).

Results

A bootstrapped analysis of variance (ANOVA) revealed that the SWEDD+ group had lower MoCA scores than PD+ and HC+ groups at baseline (ps < .05). A bootstrapped ANOVA indicated that group differences were not significant at follow-up; rather, impaired baseline olfaction predicted cognitive decline across all study participants (p < .05), regardless of diagnosis.

Conclusions

Future studies are needed to assess whether the profile of motor and non-motor symptoms in SWEDD patients, including olfaction, is deserving of its own syndrome, or whether individual patients may fit better under alternative, existing diagnoses.

Non-BRCA1/2 Variants Detected in a High-Risk Chilean Cohort With a History of Breast and/or Ovarian Cancer

METHODS

Data were retrospectively collected from the registry of the High-Risk Breast and Ovarian Cancer Program at Clínica Las Condes, Santiago, Chile. Data captured included index case diagnosis, ancestry, family history, and genetic test results.

RESULTS

Three hundred fifteen individuals underwent genetic testing during the study period. The frequency of germline pathogenic and likely pathogenic variants in a breast or ovarian cancer predisposition gene was 20.3%. Of those patients who underwent testing with a panel of both high- and moderate-penetrance genes, 10.5% were found to have pathogenic or likely pathogenic variants in non-BRCA1/2 genes.

CONCLUSION

Testing for non-BRCA1 and -2 mutations may be clinically relevant for individuals who are suspected to have a hereditary breast or ovarian cancer syndrome in Chile. Comprehensive genetic testing of individuals who are at high risk is necessary to further characterize the genetic susceptibility to cancer in Chile.

First Search for Short-Baseline Neutrino Oscillations at HFIR with PROSPECT

This Letter reports the first scientific results from the observation of antineutrinos emitted by fission products of ^{235}U at the High Flux Isotope Reactor. PROSPECT, the Precision Reactor Oscillation and Spectrum Experiment, consists of a segmented 4 ton ^{6}Li-doped liquid scintillator detector covering a baseline range of 7-9 m from the reactor and operating under less than 1 m water equivalent overburden. Data collected during 33 live days of reactor operation at a nominal power of 85 MW yield a detection of 25 461±283 (stat) inverse beta decays. Observation of reactor antineutrinos can be achieved in PROSPECT at 5σ statistical significance within 2 h of on-surface reactor-on data taking. A reactor model independent analysis of the inverse beta decay prompt energy spectrum as a function of baseline constrains significant portions of the previously allowed sterile neutrino oscillation parameter space at 95% confidence level and disfavors the best fit of the reactor antineutrino anomaly at 2.2σ confidence level.

Recurrent DNA copy number alterations in intestinal-type sinonasal adenocarcinoma

BACKGROUND

Intestinal-type sinonasal adenocarcinoma (ITAC) is a rare tumour related to occupational wood dust exposure. Few studies have described recurrent genetic changes on a genome-wide scale. The aim of this study was to obtain a high resolution map of recurrent genetic alterations in ITAC.

MATERIAL AND METHODS

Copy number alterations were evaluated by microarray CGH and MLPA in 37 primary tumours. The results were correlated with pathological characteristics and clinical outcome.

RESULTS

Microarray CGH identified the following recurrent aberrations, in descending order: gains at 5p15 (22 cases, 60%), 8q24 (21 cases, 57%), 20q13 (20 cases, 54%), 20q11, and 8q21 (19 cases, 51%), 20p13, and 7p11 (16 cases, 43%), and losses at 5q11-qter, 8p12-pter, and 18q12-23 (15 cases, 40%), and 17p13, and 19p13 (13 cases, 35%). MLPA analysis confirmed this global pattern of gains and losses. Chromosomal loss at 4q32-ter and gains at 1q22, 6p22 and 3q29, as well as deletion of TIMP2 and CRK correlated with unfavourable clinical outcome.

CONCLUSION

ITACs have a unique pattern of chromosomal abnormalities. The four different histological subtypes of ITAC appeared genetically similar. Four chromosomal gains and losses and two specific genes showed prognostic value and may be involved in tumour progression.

Synthetic Renal Capsule Tailoring: A Novel Renorrhaphy Technique After Subcapsular Dissection of Renal Tumors with Severe Adherent Perirenal Fat During Laparoscopic Partial Nephrectomy

BACKGROUND

Multiple factors can account for surgical complexity during laparoscopic partial nephrectomy (LPN); severe adhesion of perirenal fat (PRF) is a crucial one. Consequent renal decapsulation can deem renorrhaphy a very challenging task. We propose a novel technique (synthetic renal capsule tailoring [SYRCT]) to facilitate renorrhaphy in decapsulated kidneys and suggest early decapsulation as a safe option in cases with severe PRF.

MATERIALS AND METHODS

We retrospectively analyzed perioperative results of this novel technique performed in cases with severe PRF. All cases were classified as high grade in the Mayo Adhesive Probability (MAP) score.

RESULTS

A total of six cases were performed with the SYRCT technique. All patients were male with a mean age of 70 years (62-76 years) and mean body mass index of 30 kg/m² (23.66-33.86). Of the six cases, five were T1a and 1 T1b. Mean tumor size was 2.83 cm (range 1.2-6 cm). Mean operative time was 121 minutes (range 74-150 minutes); mean warm ischemia time was 17.2 minutes (range 13-25 minutes). Mean operative bleeding was 128 mL (range 50-250 mL). Mean hospital stay was 2.3 days. There were no surgical complications greater or equal to Clavien II.

CONCLUSION

Performing complete renal decapsulation with subcapsular dissection and SYRCT in cases with high MAP score and severe PRF is safe and reproducible. Using this novel technique, we were able to obtain perioperative results comparable to the ones we found in LPN with normal PRF.

The efficacy of individual treatment of subjective tinnitus with cognitive behavioural therapy

INTRODUCTION

It has been a long time since subjective tinnitus cases were described for the first time but they still lack a treatment with proven effectiveness. The main goal of this study was to evaluate the effectiveness of cognitive behavioural therapy in these patients.

PATIENTS AND METHOD

Between 2012 and 2013, 310 patients that suffered from subjective tinnitus were studied. Of these, 267 were included in treatment based on cognitive behavioural therapy. The monitoring period lasted 18 months for most cases, while it lasted 21 months for 11 patients.

RESULTS

Considering patients that interrupted their treatment as failures, the percentage of recovery was 95.7%.

CONCLUSION

Cognitive behavioural therapy should always be included in the treatment of people suffering from tinnitus.

Peptides derived from the dependence receptor ALK are proapoptotic for ALK-positive tumors

ALK is a receptor tyrosine kinase with an oncogenic role in various types of human malignancies. Despite constitutive activation of the kinase through gene alterations, such as chromosomal translocation, gene amplification or mutation, treatments with kinase inhibitors invariably lead to the development of resistance. Aiming to develop new tools for ALK targeting, we took advantage of our previous demonstration identifying ALK as a dependence receptor, implying that in the absence of ligand the kinase-inactive ALK triggers or enhances apoptosis. Here, we synthesized peptides mimicking the proapoptotic domain of ALK and investigated their biological effects on tumor cells. We found that an ALK-derived peptide of 36 amino acids (P36) was cytotoxic for ALK-positive anaplastic large-cell lymphoma and neuroblastoma cell lines. In contrast, ALK-negative tumor cells and normal peripheral blood mononuclear cells were insensitive to P36. The cytotoxic effect was due to caspase-dependent apoptosis and required N-myristoylation of the peptide. Two P36-derived shorter peptides as well as a cyclic peptide also induced apoptosis. Surface plasmon resonance and mass spectrometry analysis of P36-interacting proteins from two responsive cell lines, Cost lymphoma and SH-SY5Y neuroblastoma, uncovered partners that could involve p53-dependent signaling and pre-mRNA splicing. Furthermore, siRNA-mediated knockdown of p53 rescued these cells from P36-induced apoptosis. Finally, we observed that a treatment combining P36 with the ALK-specific inhibitor crizotinib resulted in additive cytotoxicity. Therefore, ALK-derived peptides could represent a novel targeted therapy for ALK-positive tumors.