Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of CT-verified loco-regional recurrences after definitive IMRT for HNSCC using site of origin estimation methods

Abstract Introduction: A significant part of patients with head and neck squamous cell carcinoma (HNSCC) develop recurrent disease after curative radiotherapy. We aimed to analyze loco-regional recurrence pattern by identifying possible points of recurrence origin by three different methods in relation to treatment volumes. Material and methods: A total of 455 patients completed IMRT-based treatment for HNSCC from 2006 to 2012. A total of 159 patients had remaining cancer after IMRT, developed loco-regional recurrence or distant disease during follow-up. Among those, 69 patients with loco-regional recurrences had affirmative CT or PET/CT scan. Possible points of origin (POs) of the recurrences were identified on scans by two independent observers, estimated as center of mass and as maximum surface distance. The recurrence position was analyzed in relation to high-dose treatment volume (CTV1) and 95% of prescription dose. Results: In total, 104 loco-regional recurrences (54 in T-site and 50 in N-site) were identified in 69 patients. Median time to recurrence for the 69 patients was 10 months. No clinically relevant difference was found between the four POs, with standard deviation between POs in x, y and z axes of 3, 3 and 6 mm. For recurrences inside CTV1, 0–5 mm and 5–10 mm outside CTV1 the standard deviation of dose differences between the POs were 1, 1.4 and 1 Gy, respectively. 56% and 25% of T-site and N-site recurrences were inside CTV1, respectively. Coverage by 95% prescription dose to high-dose treatment volume was achieved in 78% of T-site and 39% of N-site recurrences. Conclusions: For recurrences identified by possible points of recurrence origin, no significant difference between observer-based or mathematically estimated methods was found. More than half of T-site recurrences were inside high-dose treatment volume, whereas N-site recurrences were mainly outside.
The Putative Role of TP53 Alterations and p53 Expression in Borderline Ovarian Tumors - Correlation with Clinicopathological Features and Prognosis: A Mini-Review

Borderline ovarian tumors (BOTs) represent an independent group among ovarian malignancies, being diagnosed at clinical stage earlier than invasive ovarian carcinomas (OCs) and characterized by a rather favorable outcome after careful surgical management. Data published worldwide showed a substantial discordance of p53 expression in BOTs. The purpose of this work was to present the current status of knowledge on the significance of TP53 gene and p53 protein product alterations in BOTs. In general, higher p53 expression patterns were reported for ovarian malignancies compared to BOTs. Serous, mucinous, and endometrioid BOTs differ substantially in relation to p53 immunostaining, but data concerning the relationship between the protein's immunoreactivity and other clinico-pathological variables are scarce. Finally, reports published to date support the view that TP53 alterations may not be commonly associated with the borderline phenotype of ovarian tumors but they probably occur during the development of invasive OCs. In light of these uncertainties, the impact of TP53 alterations and p53 expression on overall survival in women affected by BOTs requires further multi-institutional studies in large cohorts of patients.
Three new polyketides from the marine sponge-derived fungus Trichoderma sp. SCSIO41004

Abstract Three new polyketides named trichbenzoisochromen A (1), 5,7-dihydroxy-3-methyl -2-(2-oxopropyl)naphthalene-1,4-dione (2) and 7-acetyl-1,3,6-trihydroxyanthracene-9,10- dione (3) together with six known compounds (4–9) were isolated from a sponge-derived fungus Trichoderma sp. SCSIO41004. The structures of three new polyketides (1–3) were determined by the extensive spectroscopic analysis, including 1D, 2D NMR and HRESIMS data. The absolute configuration of compound 1 was confirmed by the specific optical rotation value and CD spectra analyses. Compound 4 exhibited significant inhibitory activity against EV71 with the IC50 value of 25.7 μM.
Mobile Health in the Developing World: Review of Literature and Lessons From a Case Study

The mHealth trend, which uses mobile devices and associated technology for health interventions, offers unprecedented opportunity to transform the health services available to people across the globe. In particular, the mHealth transformation can be most disruptive in the developing countries, which is often characterized by a dysfunctional public health system. Despite this opportunity, the growth of mHealth in developing countries is rather slow and no existing studies have conducted an in-depth search to identify the reasons. We present a comprehensive report about the factors hindering the growth of mHealth in developing countries. Most importantly, we outline future strategies for making mHealth even more effective. We are also the first to conduct a case study on the public health system of Pakistan showing that mHealth can offer tremendous opportunities for a developing country with a severe scarcity of health infrastructure and resources. The findings of this paper will guide the development of policies and strategies for the sustainable adoption of mHealth not only in Pakistan but also for any developing country in general.
Towards Reaching Human Performance in Pedestrian Detection

Encouraged by the recent progress in pedestrian detection, we investigate the gap between current state-of-the-art methods and the “perfect single frame detector”. We enable our analysis by creating a human baseline for pedestrian detection (over the Caltech pedestrian dataset). After manually clustering the frequent errors of a top detector, we characterise both localisation and background-versus-foreground errors. To address localisation errors we study the impact of training annotation noise on the detector performance, and show that we can improve results even with a small portion of sanitised training data. To address background/foreground discrimination, we study convnets for pedestrian detection, and discuss which factors affect their performance. Other than our in-depth analysis, we report top performance on the Caltech pedestrian dataset, and provide a new sanitised set of training and test annotations.
Palladium nanoparticle-decorated reduced graphene oxide sheets synthesized using Ficus carica fruit extract: A catalyst for Suzuki cross-coupling reactions

We present a biogenic method for the synthesis of palladium nanoparticle (PdNP)-modified by reducing graphene oxide sheets (rGO) in a one-pot strategy using Ficus carica fruit juice as the reducing agent. The synthesized material was well characterized by morphological and structural analyses, including, Ultraviolet-Visible spectroscopy (UV-Vis), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR) and Transmission Electron Microscopy (TEM) and Raman spectroscopy. The results revealed that the PdNP modified GO are spherical in shape and estimated to be a dimension of ~0.16 nm. The PdNP/graphene exhibits a great catalytic activity in Suzuki cross-coupling reactions for the synthesis of biaryl compounds with various substrates under both aqueous and aerobic conditions. The catalyst can be recovered easily and is suitable for repeated use because it retains its original catalytic activity. The PdNP/rGO catalyst synthesized by an eco-friendly protocol was used for the Suzuki coupling reactions. The method offers a mild and effective substitute to the existing methods and may significantly contribute to green chemistry.
Vocal development through morphological computation

The vocal behavior of infants changes dramatically during early life. Whether or not such a change results from the growth of the body during development—as opposed to solely neural changes—has rarely been investigated. In this study of vocal development in marmoset monkeys, we tested the putative causal relationship between bodily growth and vocal development. During the first two months of life, the spontaneous vocalizations of marmosets undergo (1) a gradual disappearance of context-inappropriate call types and (2) an elongation in the duration of context-appropriate contact calls. We hypothesized that both changes are the natural consequences of lung growth and do not require any changes at the neural level. To test this idea, we first present a central pattern generator model of marmoset vocal production to demonstrate that lung growth can affect the temporal and oscillatory dynamics of neural circuits via sensory feedback from the lungs. Lung growth qualitatively shifted vocal behavior in the direction observed in real marmoset monkey vocal development. We then empirically tested this hypothesis by placing the marmoset infants in a helium–oxygen (heliox) environment in which air is much lighter. This simulated a reversal in development by decreasing the effort required to respire, thus increasing the respiration rate (as though the lungs were smaller). The heliox manipulation increased the proportions of inappropriate call types and decreased the duration of contact calls, consistent with a brief reversal of vocal development. These results suggest that bodily growth alone can play a major role in shaping the development of vocal behavior.
Equatorial upper‐ocean dynamics and their interaction with the West African monsoon

Zonal wind anomalies in the western equatorial Atlantic during late boreal winter to early summer precondition boreal summer cold/warm events in the eastern equatorial Atlantic (EEA) that manifest in a strong interannual Atlantic cold tongue (ACT) variability. Local intraseasonal wind fluctuations, linked to the St. Helena anticyclone, contribute to the variability of cold tongue onset and strength, particularly during years with preconditioned shallow thermoclines. The impact of cold tongue sea surface temperature (SST) anomalies on the wind field in the Gulf of Guinea is assessed. It contributes to the northward migration of humidity and convection and possibly the West African monsoon (WAM) jump. Copyright © 2010 Royal Meteorological Society
ON THE CONVERGENCE OF FINITE ELEMENT

We study the convergence of monotone P1 finite element methods on unstructured meshes for fully nonlinear Hamilton–Jacobi–Bellman equations arising from stochastic optimal control problems with possibly degenerate, isotropic diffusions. Using elliptic projection operators we treat discretizations which violate the consistency conditions of the framework by Barles and Souganidis. We obtain strong uniform convergence of the numerical solutions and, under nondegeneracy assumptions, strong L2 convergence of the gradients.
Bullying Behaviors among Macanese Adolescents—Association with Psychosocial Variables

Bullying is a widespread public health problem among school students. Using a large sample of Macanese school adolescents, the present study examines psychosocial conditions and demographic characteristics in discriminating the following four subgroups of students: victims; bullies; bully-victims; and a comparison group of adolescents. Participants included 2288 adolescents from 13 primary and secondary schools in Macau whose ages ranged from 10 to 20 years. Statistical results revealed significant differences among the groups and indicated that adolescents who are involved in school bullying experience worse psychosocial adjustment. Specifically, among the four subgroups of students, bully-victims reported the strongest feelings of anxiety, depression, and negative affectivity, and expressed the lowest satisfaction with life. Compared with students who were not involved in bullying and victimization, bullies experienced more anxiety and depression and victims had lower levels of satisfaction with life. In addition, boys were more likely to engage in bullying behaviors and younger students had a greater probability of being victimized by their peers at school. Implications for future research and practice on bullying perpetration and the prevention of peer victimization are discussed.
Feasibility of Functional Near-Infrared Spectroscopy (fNIRS) to Investigate the Mirror Neuron System: An Experimental Study in a Real-Life Situation

The mirror neuron system (MNS), mainly including the premotor cortex (PMC), inferior frontal gyrus (IFG), superior parietal lobule (SPL), and rostral inferior parietal lobule (IPL), has attracted extensive attention as a possible neural mechanism of social interaction. Owing to high ecological validity, functional near-infrared spectroscopy (fNIRS) has become an ideal approach for exploring the MNS. Unfortunately, for the feasibility of fNIRS to detect the MNS, none of the four dominant regions were found in previous studies, implying a very limited capacity of fNIRS to investigate the MNS. Here, we adopted an experimental paradigm in a real-life situation to evaluate whether the MNS activity, including four dominant regions, can be detected by using fNIRS. Specifically, 30 right-handed subjects were asked to complete a table-setting task that included action execution and action observation. A double density probe configuration covered the four regions of the MNS in the left hemisphere. We used a traditional channel-based group analysis and also a ROI-based group analysis to find which regions are activated during both action execution and action observation. The results showed that the IFG, adjacent PMC, SPL, and IPL were involved in both conditions, indicating the feasibility of fNIRS to detect the MNS. Our findings provide a foundation for future research to explore the functional role of the MNS in social interaction and various disorders using fNIRS.
ACUTE PANCREATITIS IN PATIENTS WITH SEVERE HYPERTRIGLYCERIDEMIA IN A MULTI-ETHNIC MINORITY POPULATION.

OBJECTIVE To investigate the prevalence and predictors of hypertriglyceridemic acute pancreatitis (HTG-AP) in a multi-ethnic minority population. METHODS A retrospective, cross-sectional study from 2003 to 2013 of 1,157 adults with a serum triglyceride (TG) level ≥1,000 mg/dL comparing baseline characteristics and risk factors between those with and without HTG-AP. RESULTS Mean study population age was 49.2 ± 11.5 years; 75.6% were male, 31.6% African American, 38.4% Hispanic, 22.7% Caucasian, 5.7% Asian, and 1.6% Pacific Islander. Prevalence of HTG-AP was 9.2%. Patients with HTG-AP were significantly younger (41.3 years vs. 50.0 years; P<.001) than those without HTG-AP. Excessive alcohol intake (odds ratio [OR], 3.9; 95% confidence interval [CI], 2.5 to 6.0; P<.001), gallstone disease (OR, 3.9; 95% CI, 1.4 to 10.8; P = .008), and TG >2,000 mg/dL (OR, 4.8; 95% CI, 3.1 to 7.4; P<.001) remained significant independent risk factors. TG levels for patients with HTG-AP were higher (median TG, 2,394 mg/dL; interquartile range [IQR], 1,152 to 4,339 mg/dL vs. median TG, 1,406 mg/dL; IQR, 1,180.7 to 1,876.5 mg/dL). TG levels >2,000 mg/dL were associated with higher incidence of AP (22% vs. 5%). Patients with TG levels <2,000 mg/dL and no risk factors had prevalence of 2% compared to 33.6% with one risk factor and TG >2,000 mg/dL. Patients with HTG-AP had higher incidence of diabetic ketoacidosis at admission (7.5% vs. 2.5%; P = .004). CONCLUSION TG level ≥2,000 mg/dL is associated with higher HTG-AP prevalence in ethnic minorities. Presence of excessive alcohol intake and/or gallstones further accentuates risk. ABBREVIATIONS AP = acute pancreatitis; CT = computed tomography; DM = diabetes mellitus; HbA1c = hemoglobin A1c; HIV = human immunodeficiency virus; HTG = hyper-triglyceridemia; HTG-AP = hypertriglyceridemic acute pancreatitis; ROC = receiver operating characteristic; TG = triglyceride.
Genetic and small molecule inhibition of arylamine N‐acetyltransferase 1 reduces anchorage‐independent growth in human breast cancer cell line MDA‐MB‐231

Arylamine N‐acetyltransferase 1 (NAT1) expression is reported to affect proliferation, invasiveness, and growth of cancer cells. MDA‐MB‐231 breast cancer cells were engineered such that NAT1 expression was elevated or suppressed, or treated with a small molecule inhibitor of NAT1. The MDA‐MB‐231 human breast cancer cell lines were engineered with a scrambled shRNA, a NAT1 specific shRNA or a NAT1 overexpression cassette stably integrated into a single flippase recognition target (FRT) site facilitating incorporation of these different genetic elements into the same genomic location. NAT1‐specific shRNA reduced NAT1 activity in vitro by 39%, increased endogenous acetyl coenzyme A levels by 35%, and reduced anchorage‐independent growth (sevenfold) without significant effects on cell morphology, growth rates, anchorage‐dependent colony formation, or invasiveness compared to the scrambled shRNA cell line. Despite 12‐fold overexpression of NAT1 activity in the NAT1 overexpression cassette transfected MDA‐MB‐231 cell line, doubling time, anchorage‐dependent cell growth, anchorage‐independent cell growth, and relative invasiveness were not changed significantly when compared to the scrambled shRNA cell line. A small molecule (5E)‐[5‐(4‐hydroxy‐3,5‐diiodobenzylidene)‐2‐thioxo‐1,3‐thiazolidin‐4‐one (5‐HDST) was 25‐fold more selective towards the inhibition of recombinant human NAT1 than N‐acetyltransferase 2. Incubation of MDA‐MB‐231 cell line with 5‐HDST resulted in 60% reduction in NAT1 activity and significant decreases in cell growth, anchorage‐dependent growth, and anchorage‐independent growth. In summary, inhibition of NAT1 activity by either shRNA or 5‐HDST reduced anchorage‐independent growth in the MDA‐MB‐231 human breast cancer cell line. These findings suggest that human NAT1 could serve as a target for the prevention and/or treatment of breast cancer.
Estimation of the global inventory of methane hydrates in marine sediments using transfer functions

The accumulation of gas hydrates in marine sediments is essentially controlled by the accumulation of particulate organic carbon (POC) which is microbially converted into methane, the thickness of the gas hydrate stability zone (GHSZ) where methane can be trapped, the sedimentation rate (SR) that controls the time that POC and the generated methane stays within the GHSZ, and the delivery of methane from deep-seated sediments by ascending pore fluids and gas into the GHSZ. Recently, Wallmann et al. (2012) presented transfer functions to predict the gas hydrate inventory in diffusion-controlled geological systems based on SR, POC and GHSZ thickness for two different scenarios: normal and full compacting sediments. We apply these functions to global data sets of bathymetry, heat flow, seafloor temperature, POC input and SR, estimating a global mass of carbon stored in marine methane hydrates from 3 to 455 Gt of carbon (GtC) depending on the sedimentation and compaction conditions. The global sediment volume of the GHSZ in continental margins is estimated to be 60–67 × 1015 m3, with a total of 7 × 1015 m3 of pore volume (available for GH accumulation). However, seepage of methane-rich fluids is known to have a pronounced effect on gas hydrate accumulation. Therefore, we carried out a set of systematic model runs with the transport-reaction code in order to derive an extended transfer function explicitly considering upward fluid advection. Using averaged fluid velocities for active margins, which were derived from mass balance considerations, this extended transfer function predicts the enhanced gas hydrate accumulation along the continental margins worldwide. Different scenarios were investigated resulting in a global mass of sub-seafloor gas hydrates of ~ 550 GtC. Overall, our systematic approach allows to clearly and quantitatively distinguish between the effect of biogenic methane generation from POC and fluid advection on the accumulation of gas hydrate, and hence, provides a simple prognostic tool for the estimation of large-scale and global gas hydrate inventories in marine sediments.
Mutational phospho-mimicry reveals a regulatory role for the XRCC4 and XLF C-terminal tails in modulating DNA bridging during classical non-homologous end joining

XRCC4 and DNA Ligase 4 (LIG4) form a tight complex that provides DNA ligase activity for classical non-homologous end joining (the predominant DNA double-strand break repair pathway in higher eukaryotes) and is stimulated by XLF. Independently of LIG4, XLF also associates with XRCC4 to form filaments that bridge DNA. These XRCC4/XLF complexes rapidly load and connect broken DNA, thereby stimulating intermolecular ligation. XRCC4 and XLF both include disordered C-terminal tails that are functionally dispensable in isolation but are phosphorylated in response to DNA damage by DNA-PK and/or ATM. Here we concomitantly modify the tails of XRCC4 and XLF by substituting fourteen previously identified phosphorylation sites with either alanine or aspartate residues. These phospho-blocking and -mimicking mutations impact both the stability and DNA bridging capacity of XRCC4/XLF complexes, but without affecting their ability to stimulate LIG4 activity. Implicit in this finding is that phosphorylation may regulate DNA bridging by XRCC4/XLF filaments. DOI: http://dx.doi. org/10.7554/eLife.22900. 001
Compression Behavior of Zinc Contaminated Clayey Soils Solidified with Cement

This paper presents an investigation on the compressibility characteristics of cement treated zinc contaminated soil by one-dimension oedometer tests. It is found that with the increase of zinc concentration for given cement content, the compression index and yield stress decreased. The generalized state parameter void index (Iv) was adopted to discuss the effect of zinc concentration on compressibility characteristics and structure of soils. With the increase of zinc concentration, the relationship between the void index and compression pressure (Iv-logp) tends to approach and parallel to the intrinsic compression line proposed by Burland (1990). The observation shows that the presence of zinc and its concentration levels have significant influence on the compressibility and cementation structure of the cement treated zinc contaminated soils. © 2012 American Society of Civil Engineers.
Cognitive outcome in childhood of birth weight discordant monochorionic twins: the long-term effects of fetal growth restriction

Aim Intrauterine growth restriction (IUGR) is associated with poorer outcomes in later life. We used a monochorionic twin model with IUGR in one twin to determine its impact on growth and neurocognitive outcomes. Methods Monochorionic twins with ≥20% birth weight discordance born in the north of England were eligible. Cognitive function was assessed using the British Ability Scales. The Strength and Difficulties Questionnaire was used to identify behavioural problems. Auxological measurements were collected. Generalised estimating equations were used to determine the effects of birth weight on cognition. Results Fifty-one monochorionic twin pairs were assessed at a mean age of 6.3 years. Mean birth weight difference was 664 g at a mean gestation of 34.7 weeks. The lighter twin had a General Conceptual Ability (GCA) score that was three points lower (TwinL −105.4 vs TwinH −108.4, 95% CI −0.9 to −5.0), and there was a significant positive association (B 0.59) of within-pair birth weight differences and GCA scores. Mathematics and memory skills showed the largest differences. The lighter twin at school age was shorter (mean difference 2.1 cm±0.7) and lighter (mean difference 1.9 kg±0.6). Equal numbers of lighter and heavier twins were reported to have behavioural issues. Conclusions In a monochorionic twin cohort, fetal growth restriction results in lower neurocognitive scores in early childhood, and there remain significant differences in size. Longer term follow-up will be required to determine whether growth or cognitive differences persist in later child or adulthood, and whether there are any associated longer term metabolic sequelae.