Takshan/R1 huggingface dataset:
Planning benchmark study for SBRT of early stage NSCLC : Results of the DEGRO Working Group Stereotactic Radiotherapy.Planvergleichsstudie bei der SBRT des NSCLC im Frühstadium : Ergebnisse der DEGRO AG Stereotaxie.

PURPOSE: The aim was to evaluate stereotactic body radiation therapy (SBRT) treatment planning variability for early stage nonsmall cell lung cancer (NSCLC) with respect to the published guidelines of the Stereotactic Radiotherapy Working Group of the German Society for Radiation Oncology (DEGRO). MATERIALS AND METHODS: Planning computed tomography (CT) scan and the structure sets (planning target volume, PTV; organs at risk, OARs) of 3 patients with early stage NSCLC were sent to 22 radiotherapy departments with SBRT experience: each department was asked to prepare a treatment plan according to the DEGRO guidelines. The prescription dose was 3 fractions of 15 Gy to the 65% isodose. RESULTS: In all, 87 plans were generated: 36 used intensity-modulated arc therapy (IMAT), 21 used three-dimensional conformal radiation therapy (3DCRT), 6 used static field intensity-modulated radiation therapy (SF-IMRT), 9 used helical radiotherapy and 15 used robotic radiosurgery. PTV dose coverage and simultaneously kept OARs doses were within the clinical limits published in the DEGRO guidelines. However, mean PTV dose (mean 58.0 Gy, range 52.8-66.4 Gy) and dose conformity indices (mean 0.75, range 0.60-1.00) varied between institutions and techniques (p ≤ 0.02). OARs doses varied substantially between institutions, but appeared to be technique independent (p = 0.21). CONCLUSION: All studied treatment techniques are well suited for SBRT of early stage NSCLC according to the DEGRO guidelines. Homogenization of SBRT practice in Germany is possible through the guidelines; however, detailed treatment plan characteristics varied between techniques and institutions and further homogenization is warranted in future studies and recommendations. Optimized treatment planning should always follow the ALARA (as low as reasonably achievable) principle.
Structure and function of neonatal social communication in a genetic mouse model of autism.

A critical step toward understanding autism spectrum disorder (ASD) is to identify both genetic and environmental risk factors. A number of rare copy number variants (CNVs) have emerged as robust genetic risk factors for ASD, but not all CNV carriers exhibit ASD and the severity of ASD symptoms varies among CNV carriers. Although evidence exists that various environmental factors modulate symptomatic severity, the precise mechanisms by which these factors determine the ultimate severity of ASD are still poorly understood. Here, using a mouse heterozygous for Tbx1 (a gene encoded in 22q11.2 CNV), we demonstrate that a genetically triggered neonatal phenotype in vocalization generates a negative environmental loop in pup-mother social communication. Wild-type pups used individually diverse sequences of simple and complicated call types, but heterozygous pups used individually invariable call sequences with less complicated call types. When played back, representative wild-type call sequences elicited maternal approach, but heterozygous call sequences were ineffective. When the representative wild-type call sequences were randomized, they were ineffective in eliciting vigorous maternal approach behavior. These data demonstrate that an ASD risk gene alters the neonatal call sequence of its carriers and this pup phenotype in turn diminishes maternal care through atypical social communication. Thus, an ASD risk gene induces, through atypical neonatal call sequences, less than optimal maternal care as a negative neonatal environmental factor. Molecular Psychiatry advance online publication, 15 December 2015; doi:10.1038/mp.2015.190.
Molecular subtyping of nasopharyngeal carcinoma (NPC) and a microRNA-based prognostic model for distant metastasis.

BACKGROUND: Nasopharyngeal carcinoma (NPC) is a highly invasive and metastatic cancer, with diverse molecular characteristics and clinical outcomes. This study aims to dissect the molecular heterogeneity of NPC, followed by the construction of a microRNA (miRNA)-based prognostic model for prediction of distant metastasis. METHODS: We retrieved two NPC datasets: GSE32960 and GSE70970 as training and validation cohorts, respectively. Consensus clustering was employed for cluster discovery, and support vector machine was used to build a classifier. Finally, Cox regression analysis was applied to constructing a prognostic model for predicting risk of distant metastasis. RESULTS: Three NPC subtypes (immunogenic, classical and mesenchymal) were identified that are molecularly distinct and clinically relevant, of which mesenchymal subtype (~ 36%) is associated with poor prognosis, characterized by suppressing tumor suppressor miRNAs and the activation of epithelial--mesenchymal transition. Out of the 25 most differentially expressed miRNAs in mesenchymal subtype, miR-142, miR-26a, miR-141 and let-7i have significant prognostic power (P < 0.05). CONCLUSIONS: We proposed for the first time that NPC can be stratified into three subtypes. Using a panel of 4 miRNAs, we established a prognostic model that can robustly stratify NPC patients into high- and low- risk groups of distant metastasis.
Neonatal maternal separation alters the capacity of adult neural precursor cells to differentiate into neurons via methylation of retinoic Acid receptor gene promoter.

BACKGROUND: Early life stress is thought to contribute to psychiatric disorders, but the precise mechanisms underlying this link are poorly understood. As neonatal stress decreases adult hippocampal neurogenesis, which, in turn, functionally contributes to many behavioral phenotypes relevant to psychiatric disorders, we examined how in vivo neonatal maternal separation (NMS) impacts the capacity of adult hippocampal neural precursor cells via epigenetic alterations in vitro. METHODS: Rat pups were separated from their dams for 3 hours daily from postnatal day (PND) 2 to PND 14 or were never separated from the dam (as control animals). We isolated adult neural precursor cells from the hippocampal dentate gyrus at PND 56 and assessed rates of proliferation, apoptosis, and differentiation in cell culture. We also evaluated the effect of DNA methylation at the retinoic acid receptor (RAR) promoter stemming from NMS on adult neural precursor cells. RESULTS: NMS attenuated neural differentiation of adult neural precursor cells but had no detectible effect on proliferation, apoptosis, or astroglial differentiation. The DNA methyltransferase (DNMT) inhibitor, 5-aza-dC, reversed a reduction by NMS of neural differentiation of adult neural precursor cells. NMS increased DNMT1 expression and decreased expression of RARα. An RARα agonist increased neural differentiation and an antagonist reduced retinoic acid-induced neural differentiation. NMS increased the methylated portion of RARα promoter, and the DNMT inhibitor reversed a reduction by NMS of RARα messenger RNA expression. CONCLUSIONS: NMS attenuates the capacity of adult hippocampal neural precursor cells to differentiate into neurons by decreasing expression of RARα through DNMT1-mediated methylation of its promoter.
In-plane ultrasonic needle tracking using a fiber-optic hydrophone.

PURPOSE: Accurate and efficient guidance of needles to procedural targets is critically important during percutaneous interventional procedures. Ultrasound imaging is widely used for real-time image guidance in a variety of clinical contexts, but with this modality, uncertainties about the location of the needle tip within the image plane lead to significant complications. Whilst several methods have been proposed to improve the visibility of the needle, achieving accuracy and compatibility with current clinical practice is an ongoing challenge. In this paper, the authors present a method for directly visualizing the needle tip using an integrated fiber-optic ultrasound receiver in conjunction with the imaging probe used to acquire B-mode ultrasound images. METHODS: Needle visualization and ultrasound imaging were performed with a clinical ultrasound imaging system. A miniature fiber-optic ultrasound hydrophone was integrated into a 20 gauge injection needle tip to receive transmissions from individual transducer elements of the ultrasound imaging probe. The received signals were reconstructed to create an image of the needle tip. Ultrasound B-mode imaging was interleaved with needle tip imaging. A first set of measurements was acquired in water and tissue ex vivo with a wide range of insertion angles (15°-68°) to study the accuracy and sensitivity of the tracking method. A second set was acquired in an in vivo swine model, with needle insertions to the brachial plexus. A third set was acquired in an in vivo ovine model for fetal interventions, with insertions to different locations within the uterine cavity. Two linear ultrasound imaging probes were used: a 14-5 MHz probe for the first and second sets, and a 9-4 MHz probe for the third. RESULTS: During insertions in tissue ex vivo and in vivo, the imaged needle tip had submillimeter axial and lateral dimensions. The signal-to-noise (SNR) of the needle tip was found to depend on the insertion angle. With the needle tip in water, the SNR of the needle tip varied with insertion angle, attaining values of 284 at 27° and 501 at 68°. In swine tissue ex vivo, the SNR decreased from 80 at 15° to 16 at 61°. In swine tissue in vivo, the SNR varied with depth, from 200 at 17.5 mm to 48 at 26 mm, with a constant insertion angle of 40°. In ovine tissue in vivo, within the uterine cavity, the SNR varied from 46.4 at 25 mm depth to 18.4 at 32 mm depth, with insertion angles in the range of 26°-65°. CONCLUSIONS: A fiber-optic ultrasound receiver integrated into the needle cannula in combination with single-element transmissions from the imaging probe allows for direct visualization of the needle tip within the ultrasound imaging plane. Visualization of the needle tip was achieved at depths and insertion angles that are encountered during nerve blocks and fetal interventions. The method presented in this paper has strong potential to improve the safety and efficiency of ultrasound-guided needle insertions.
Adolescents at high risk of obesity show greater striatal response to increased sugar content in milkshakes.

Background: Children of overweight or obese parents are at a high risk of developing obesity. Objective: This study sought to examine the underlying neural factors related to parental obesity risk and the relative impact of sugar and fat when consuming a palatable food, as well as the impact of obesity risk status on brain response to appetizing food images. Design: With the use of functional MRI, the responses of 108 healthy-weight adolescents [mean ± SD body mass index (kg/m2): 20.9 ± 1.9; n = 53 who were at high risk by virtue of parental obesity status, n = 55 who were low risk] to food stimuli were examined. Stimuli included 4 milkshakes, which systematically varied in sugar and fat content, a calorie-free tasteless solution, and images of appetizing foods and glasses of water. Results: High-risk compared with low-risk adolescents showed greater blood oxygen-dependent response to milkshakes (all variants collapsed) compared with the tasteless solution in the primary gustatory and oral somatosensory cortices (P-family-wise error rate < 0.05), replicating a previous report. Notably, high-risk adolescents showed greater caudate, gustatory, and oral somatosensory responses to the high-sugar milkshake than to the tasteless solution; however, no effect of risk status was observed in the high-fat milkshake condition. Responses to food images were not related to obesity risk status. Conclusion: Collectively, the data presented here suggest that parental weight status is associated with greater striatal, gustatory, and somatosensory responses to palatable foods-in particular, high-sugar foods-in their adolescent offspring, which theoretically contributes to an increased risk of future overeating. This trial was registered at www.clinicaltrials.gov as NCT01949636.
Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data.

Subcellular localisation is an important aspect of protein function, but the protein composition of many intracellular compartments is poorly characterised. For example, many nuclear bodies are challenging to isolate biochemically and thus remain inaccessible to proteomics. Here we explore covariation in proteomics data as an alternative route to subcellular proteomes. Rather than targeting a structure of interest biochemically we target it by machine learning. This becomes possible by taking data obtained for one organelle and searching it for traces of another organelle. As an extreme example and proof-of-concept we predict mitochondrial proteins based on their covariation in published interphase chromatin data. We detect about ⅓ of the known mitochondrial proteins in our chromatin data, presumably most as contaminants. However, these proteins are not present at random. We show covariation of mitochondrial proteins in chromatin proteomics data. We then exploit this covariation by Multiclassifier Combinatorial Proteomics (MCCP) to define a list of mitochondrial proteins. This list agrees well with different databases on mitochondrial composition. This benchmark test raises the possibility that, in principle, covariation proteomics may also be applicable to structures for which no biochemical isolation procedures are available. This article is protected by copyright. All rights reserved.
Associations within school-based same-sex friendship networks of children's physical activity and sedentary behaviours: a cross-sectional social network analysis.

BACKGROUND: Physical activity in children is associated with better physical and mental health but many children do not meet physical activity guidelines. Friendship groups are potentially an important influence on children's physical activity and sedentary time. This paper examines the association between children of physical activity and sedentary time in school-based same-sex friendship networks, for both moderate-to-vigorous intensity physical activity (MVPA) and sedentary time. Moreover, considering the methodological challenges of conducting and interpreting these analyses, we provide examples of how to analyse these data and interpret results to encourage further work in the area. METHODS: Accelerometer data for 1223 children, aged 8-9 years, were collected in 2015-2016 and analysed in 2017. Mean accelerometer minutes of MVPA and sedentary time were calculated. Children named up to four school friends and same-sex school-based friendship networks were constructed. Network models, which include correlation between friends, were fitted by sex. RESULTS: Both MVPA and sedentary time were found to be associated via the friendship networks, for both boys and girls. The network autocorrelation was 0.21 (95% CI: 0.15 to 0.26) for boys' MVPA, and 0.14 (95% CI: 0.07 to 0.21) for sedentary time. Network autocorrelation between girls was weaker, with 0.13 (95% CI: 0.06 to 0.19) for MVPA and 0.11 (95% CI: 0.05 to 0.17) for sedentary time. CONCLUSIONS: Physical activity and sedentary time of boys and girls are associated with the physical activity and sedentary time respectively of others within same-sex friendship networks, and these associations are comparable to other known factors. In this study, the correlation between friends was stronger for boys than girls, and stronger for MVPA than for sedentary time. These findings suggest that friendship networks play a part in understanding children's physical activity and sedentary time and could play a valuable role in developing effective interventions.
Target localization of 3D versus 4D cone beam computed tomography in lipiodol-guided stereotactic radiotherapy of hepatocellular carcinomas.

BACKGROUND: Aim of this study was to comparatively evaluate the accuracy of respiration-correlated (4D) and uncorrelated (3D) cone beam computed tomography (CBCT) in localizing lipiodolized hepatocellular carcinomas during stereotactic body radiotherapy (SBRT). METHODS: 4D-CBCT scans of eighteen HCCs were acquired during free-breathing SBRT following trans-arterial chemo-embolization (TACE) with lipiodol. Approximately 1320 x-ray projections per 4D-CBCT were collected and phase-sorted into ten bins. A 4D registration workflow was followed to register the reconstructed time-weighted average CBCT with the planning mid-ventilation (MidV) CT by an initial bone registration of the vertebrae and then tissue registration of the lipiodol. For comparison, projections of each 4D-CBCT were combined to synthesize 3D-CBCT without phase-sorting. Using the lipiodolized tumor, uncertainties of the treatment setup estimated from the absolute and relative lipiodol position to bone were analyzed separately for 4D- and 3D-CBCT. RESULTS: Qualitatively, 3D-CBCT showed better lipiodol contrast than 4D-CBCT primarily because of a tenfold increase of projections used for reconstruction. Motion artifact was observed to subside in 4D-CBCT compared to 3D-CBCT. Group mean, systematic and random errors estimated from 4D- and 3D-CBCT agreed to within 1 mm in the cranio-caudal (CC) and 0.5 mm in the anterior-posterior (AP) and left-right (LR) directions. Systematic and random errors are largest in the CC direction, amounting to 4.7 mm and 3.7 mm from 3D-CBCT and 5.6 mm and 3.8 mm from 4D-CBCT, respectively. Safety margin calculated from 3D-CBCT and 4D-CBCT differed by 2.1, 0.1 and 0.0 mm in the CC, AP, and LR directions. CONCLUSIONS: 3D-CBCT is an adequate alternative to 4D-CBCT when lipoid is used for localizing HCC during free-breathing SBRT. Similar margins are anticipated with 3D- and 4D-CBCT.
Stereotactic body radiotherapy for oligo-metastatic liver disease - Influence of pre-treatment chemotherapy and histology on local tumor control.

INTRODUCTION: Stereotactic body radiation therapy (SBRT) is applied in the oligometastatic setting to treat liver metastases. However, factors influencing tumor control probability (TCP) other than radiation dose have not been thoroughly investigated. Here we set out to investigate such factors with a focus on the influence of histology and chemotherapy prior to SBRT using a large multi-center database from the German Society of Radiation Oncology. METHODS: 452 SBRT treatments in 363 patients were analyzed after collection of patient, tumor and treatment data in a multi-center database. Histology was considered through random effects in semi-parametric and parametric frailty models. Dose prescriptions were parametrized by conversion to the maximum biologically effective dose using alpha/beta of 10Gy (BEDmax). RESULTS: After adjusting for histology, BEDmax was the strongest predictor of TCP. Larger PTV volumes, chemotherapy prior to SBRT and simple motion management techniques predicted significantly lower TCP. The model predicted a BED of 209±67Gy10 necessary for 90% TCP at 2years with no prior chemotherapy, but 286±78Gy10 when chemotherapy had been given. Breast cancer metastases were significantly more responsive to SBRT compared to other histologies with 90% TCP at 2years achievable with BEDmax of 157±80Gy10 or 80±62Gy10 with and without prior chemotherapy, respectively. CONCLUSIONS: Besides dose, histology and pretreatment chemotherapy were important factors influencing local TCP in this large cohort of liver metastases. After adjusting for prior chemotherapy, our data add to the emerging evidence that breast cancer metastases do respond better to hypofractionated SBRT compared to other histologies.
Dosimetric Implications of Residual Tracking Errors During Robotic SBRT of Liver Metastases.

PURPOSE: Although the metric precision of robotic stereotactic body radiation therapy in the presence of breathing motion is widely known, we investigated the dosimetric implications of breathing phase-related residual tracking errors. METHODS AND MATERIALS: In 24 patients (28 liver metastases) treated with the CyberKnife, we recorded the residual correlation, prediction, and rotational tracking errors from 90 fractions and binned them into 10 breathing phases. The average breathing phase errors were used to shift and rotate the clinical tumor volume (CTV) and planning target volume (PTV) for each phase to calculate a pseudo 4-dimensional error dose distribution for comparison with the original planned dose distribution. RESULTS: The median systematic directional correlation, prediction, and absolute aggregate rotation errors were 0.3 mm (range, 0.1-1.3 mm), 0.01 mm (range, 0.00-0.05 mm), and 1.5° (range, 0.4°-2.7°), respectively. Dosimetrically, 44%, 81%, and 92% of all voxels differed by less than 1%, 3%, and 5% of the planned local dose, respectively. The median coverage reduction for the PTV was 1.1% (range in coverage difference, -7.8% to +0.8%), significantly depending on correlation (P=.026) and rotational (P=.005) error.  With a 3-mm PTV margin, the median coverage change for the CTV was 0.0% (range, -1.0% to +5.4%), not significantly depending on any investigated parameter. In 42% of patients, the 3-mm margin did not fully compensate for the residual tracking errors, resulting in a CTV coverage reduction of 0.1% to 1.0%. CONCLUSIONS: For liver tumors treated with robotic stereotactic body radiation therapy, a safety margin of 3 mm is not always sufficient to cover all residual tracking errors. Dosimetrically, this translates into only small CTV coverage reductions.
An adaptable chromosome preparation methodology for use in invertebrate research organisms.

BACKGROUND: The ability to efficiently visualize and manipulate chromosomes is fundamental to understanding the genome architecture of organisms. Conventional chromosome preparation protocols developed for mammalian cells and those relying on species-specific conditions are not suitable for many invertebrates. Hence, a simple and inexpensive chromosome preparation protocol, adaptable to multiple invertebrate species, is needed. RESULTS: We optimized a chromosome preparation protocol and applied it to several planarian species (phylum Platyhelminthes), the freshwater apple snail Pomacea canaliculata (phylum Mollusca), and the starlet sea anemone Nematostella vectensis (phylum Cnidaria). We demonstrated that both mitotically active adult tissues and embryos can be used as sources of metaphase chromosomes, expanding the potential use of this technique to invertebrates lacking cell lines and/or with limited access to the complete life cycle. Simple hypotonic treatment with deionized water was sufficient for karyotyping; growing cells in culture was not necessary. The obtained karyotypes allowed the identification of differences in ploidy and chromosome architecture among otherwise morphologically indistinguishable organisms, as in the case of a mixed population of planarians collected in the wild. Furthermore, we showed that in all tested organisms representing three different phyla this protocol could be effectively coupled with downstream applications, such as chromosome fluorescent in situ hybridization. CONCLUSIONS: Our simple and inexpensive chromosome preparation protocol can be readily adapted to new invertebrate research organisms to accelerate the discovery of novel genomic patterns across the branches of the tree of life.