Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of in-house dose claculation software for superficial x-ray therapy

OF THE THESIS Validation of In-House Dose Claculation Software for Superficial X-Ray Therapy by Christopher Daniel Johnstone Master of Science in Medical Physics San Diego State University, 2013 To model the kilovoltage (kV) x-ray source of a superficial x-ray unit and to validate a rapid and accurate in-house software (kVDoseCalc) tool for computing absorbed radiation dose from superficial x-ray therapy energies. To validate kVDoseCalc, we measured central axis percent depth-doses (PDDs) and profiles using an Xstrahl 150 x-ray system (Gulmay Medical Inc.). We also compared the measured and calculated PDDs to those from the British Journal of Radiology Supplement 25 (BJR 25). The Xstrahl source was characterized as a point spectral source with varying spatial fluence, and this source model was used in kVDoseCalc to compute absorbed radiation dose at points of interest (POIs). The spectrum was derived by inputting half-value layers (HVLs) and kVps into third party software Spektr and SpekCalc. Doses for the PDDs and profiles were measured using 2, 5, and 15 cm cone sizes at 80, 120, 140, and 150 kVp energies in a scanning water phantom (IBA Blue Phantom) using Scanditronix Wellhofer farmer-type and compact chambers of volumes 0.65 and 0.13 cc, respectively. The percent difference in the computed PDD doses compared with our measurements range from -4.76% to 4.78% with an overall mean percent difference and standard deviation of 1.52% and 0.74%, respectively. The percent difference between our PDD measurements and those from BJR 25 range from -13.98% to 15.7% with an overall mean percent difference and standard deviation of 4.94% and 2.10%, respectively; showing that our measurements agree much better with kVDoseCalc than BJR25. The range in percent difference between kVDoseCalc and measurement for profiles was -5.89% to 5.92% with an overall mean percent difference and standard deviation of 1.35% and 1.42%, respectively. The results demonstrate that using our source model, kVDoseCalc can rapidly and accurately compute absorbed radiation dose for superficial x-ray therapy. The results demonstrate that using our source model, kVDoseCalc can rapidly and accurately compute absorbed radiation dose for superficial x-ray therapy. An instruction manual for kVDoseCalc is also accompanied.
Oxytocin produces thermal analgesia via vasopressin-1a receptor by modulating TRPV1 and potassium conductance in the dorsal root ganglion neurons

Recent studies have provided several lines of evidence that peripheral administration of oxytocin induces analgesia in human and rodents. However, the exact underlying mechanism of analgesia still remains elusive. In the present study, we aimed to identify which receptor could mediate the analgesic effect of intraperitoneal injection of oxytocin and its cellular mechanisms in thermal pain behavior. We found that oxytocin-induced analgesia could be reversed by d(CH2)5[Tyr(Me)2,Dab5] AVP, a vasopressin-1a (V1a) receptor antagonist, but not by desGly-NH2-d(CH2)5[DTyr2, Thr4]OVT, an oxytocin receptor antagonist. Single cell RT-PCR analysis revealed that V1a receptor, compared to oxytocin, vasopressin-1b and vasopressin-2 receptors, was more profoundly expressed in dorsal root ganglion (DRG) neurons and the expression of V1a receptor was predominant in transient receptor potential vanilloid 1 (TRPV1)-expressing DRG neurons. Fura-2 based calcium imaging experiments showed that capsaicin-induced calcium transient was significantly inhibited by oxytocin and that such inhibition was reversed by V1a receptor antagonist. Additionally, whole cell patch clamp recording demonstrated that oxytocin significantly increased potassium conductance via V1a receptor in DRG neurons. Taken together, our findings suggest that analgesic effects produced by peripheral administration of oxytocin were attributable to the activation of V1a receptor, resulting in reduction of TRPV1 activity and enhancement of potassium conductance in DRG neurons.
Micromachined interfaces to the cellular world

This paper reviews efforts over the past three decades to apply lithography and micromachining to devices capable of interfacing with intact neural networks on a chronic basis. These efforts have mirrored developments in sensors generally and have led to advances in micromachining, on-chip circuitry, lead structures, and chip-level encapsulation. Using diffused boron etch-stops and a single-sided bulk process, two-dimensional electrode arrays can be batch fabricated and used to record extracellular multipoint single-unit neural activity over periods of several months. Similarly, stimulating probes can be used to activate neural systems with high spatial resolution and precise control of the injected charge. Using on-chip signal processing circuitry to access as many as 64 sites, such probes communicate with the outside world using five-lead silicon ribbon cables while providing on-chip signal amplification, multiplexing, current generation, and self-test. Microassembly techniques allow such probes to be stacked in three-dimensional arrays on 200-400 μm centers while displacing only about one percent of the total tissue volume. The probes can also be modified to control the local chemical environment while monitoring cellular electrical activity, facilitating important progress in neuropharmacology and in a variety of therapeutic instruments.
The multi-target search problem with environmental restrictions in swarm robotics

In this paper, we give a comprehensive and detailed introduction of the multi-target search problem in swarm robotics. Based on some assumptions, we built the idealized models of the basic search problem and three kinds of environmental restrictions. In our previous works, we have raised two searching strategies (GES and IGES) inspired from firework explosion and three restriction-handling strategies, and in this paper, we describe and analyze these strategies systematically. A series of experiments were carried out, and the results show that the strategies proposed work well on the idealized models. And it's valuable to note that, compared to GES and RPSO, IGES was more efficient and showed greater stability in searching process, greater adaptiveness in both small and large scale problems and greater compatibility with restriction-handling strategies.
Symbol Flipping Decoding Algorithms Based on Prediction for Non-Binary LDPC Codes

This paper constructs an objective function for symbol flipping decoding algorithms, considering not only soft reliability, but also hard reliability. The maximization of this objective function indicates that the flipping metric should involve both the information before and after symbol flipping, while the existing algorithms consider the information before symbol flipping. Theoretical analysis shows that such prediction mechanism, together with hard reliability, can significantly improve the error performance of symbol flipping algorithms. Simulation results show that the proposed algorithms provide effective tradeoff between error performance and complexity for decoding non-binary LDPC codes.
Very Low Calorie Diets for Weight Loss in Obese Older Adults—A Randomized Trial

Background Obesity contributes to disability in older adults, and this is offset by weight loss and exercise. Very Low Calorie Diets (VLCDs) achieve rapid weight loss; however, these have not been rigorously evaluated in older people. Methods A randomized trial was conducted from August 2012 through December 2015. The intervention was 12 weeks of thrice weekly exercise combined with either healthy eating advice (Ex/HE), hypocaloric diet (Ex/Diet), or VLCD (Ex/VLCD). Outcomes were physical function, measured by 6-minute walk test (6MWT) and De Morton Mobility Index (DEMMI). Other measures were body composition measured by Dual Energy X-Ray Absorptiometry, and nutritional parameters (albumin, vitamins B12 and D, ferritin and folate). Results 36, 40, and 41 participants were randomized to Ex/HE, Ex/Diet, and Ex/VLCD, respectively. At 12 weeks, weight was reduced by 3.7, 5.1, and 11.1% (p < .01), respectively. Ex/VLCD had significant reduction in fat (16.8%), lean mass (4.8%), and bone mineral density (1.2%), but increased relative lean mass (3.8%). DEMMI improved by 14.25, 14.25, and 13.75 points in Ex/HE, Ex/Diet, and Ex/VLCD, respectively; however, there was no between-group difference (p = .30). 6MWT improved by 53.1, 64.7, and 84.4 meters in Ex/HE, Ex/Diet, and Ex/VLCD (p = .18). Post hoc stratification for gender and adjustment for initial physical function and type 2 diabetes only revealed significant between-group differences for men in the 6MWT, with improvement by 57.8, 77.8, and 140.3 meters in Ex/HE, Ex/Diet, and Ex/VLCD, respectively (p = .01). Improvements in nutritional parameters were seen in Ex/VLCD, but not in Ex/HE and Ex/Diet. The VLCD was well tolerated. Conclusions VLCDs have potential in the treatment of obesity in older persons; of particular benefit is improvement in nutritional status. The gait speed improvement observed in men warrants further investigation.
Aboveground herbivory induced jasmonates disproportionately reduce plant reproductive potential by facilitating root nematode infestation.

Different plant feeders, including insects and parasitic nematodes, can influence each other by triggering systemic changes in their shared host plants. In most cases, however, the underlying mechanisms are unclear, and the consequences for plant fitness are not well understood. We studied the interaction between leaf feeding Manduca sexta caterpillars and root parasitic nematodes in Nicotiana attenuata. Simulated M. sexta attack increased the abundance of root parasitic nematodes in the field and facilitated Meloidogyne incognita reproduction in the glasshouse. Intact jasmonate biosynthesis was found to be required for both effects. Flower counts revealed that the jasmonate-dependent facilitation of nematode infestation following simulated leaf attack reduces the plant's reproductive potential to a greater degree than would be expected from the additive effects of the individual stresses. This work reveals that jasmonates mediate the interaction between a leaf herbivore and root parasitic nematodes and illustrates how plant-mediated interactions can alter plant's reproductive potential. The selection pressure resulting from the demonstrated fitness effects is likely to influence the evolution of plant defense traits in nature.
Skin Lesion Analysis towards Melanoma Detection Using Deep Learning Network

Skin lesions are a severe disease globally. Early detection of melanoma in dermoscopy images significantly increases the survival rate. However, the accurate recognition of melanoma is extremely challenging due to the following reasons: low contrast between lesions and skin, visual similarity between melanoma and non-melanoma lesions, etc. Hence, reliable automatic detection of skin tumors is very useful to increase the accuracy and efficiency of pathologists. In this paper, we proposed two deep learning methods to address three main tasks emerging in the area of skin lesion image processing, i.e., lesion segmentation (task 1), lesion dermoscopic feature extraction (task 2) and lesion classification (task 3). A deep learning framework consisting of two fully convolutional residual networks (FCRN) is proposed to simultaneously produce the segmentation result and the coarse classification result. A lesion index calculation unit (LICU) is developed to refine the coarse classification results by calculating the distance heat-map. A straight-forward CNN is proposed for the dermoscopic feature extraction task. The proposed deep learning frameworks were evaluated on the ISIC 2017 dataset. Experimental results show the promising accuracies of our frameworks, i.e., 0.753 for task 1, 0.848 for task 2 and 0.912 for task 3 were achieved.
Altered long non-coding RNAs predict worse outcome in osteosarcoma patients: evidence from a meta-analysis

Long non-coding RNAs (lncRNAs) are emerging as promising prognostic biomarkers in an expanding list of malignant neoplasms. Here, we sought to investigate the strength of associations between lncRNA signatures and clinical outcomes in osteosarcoma. We conducted a systematic search of the online databases from inception to July 2016. Hazard ratios (HRs) with corresponding 95% confidence intervals (CIs) for the primary endpoints of overall survival (OS), progression-free survival (PFS) or event-free survival (EFS) were extracted and meta-analyzed. Our results manifested that altered lncRNAs expression was markedly associated with worse OS (univariate analysis: HR = 3.20, 95% CI: 2.42-4.24, P = 0.000; multivariate analysis: HR = 2.66, 95% CI: 1.92-3.69, P = 0.000), PFS (HR = 2.05, 95% CI: 1.32-3.18, P = 0.001) and EFS (HR = 4.37, 95% CI: 1.64-11.66, P = 0.003) times among osteosarcoma patients. In the pooled analyses stratified by clinicopathological features, levels of lncRNAs were closely correlated with tumor size (pooled P = 0.001), tumor stage (pooled P = 0.003), and distant metastasis (pooled P = 0.002) in osteosarcoma. The results obtained in our work suggest that altered lncRNA signatures predict unfavorable clinical outcomes and are acceptable to be potential prognostic biomarkers in forecasting prognosis of osteosarcoma.
Segmentation of black ink and melanin in skin histopathological images

The black ink (India ink) and melanin are substances often found in histopathological images of skin specimens. If present in abundant quantity, they negatively affect the outcome of automatic stain deconvolution methods. We propose an automatic black ink and melanin segmentation method based on global color threshol- ding in CIELAB color space combined with a novel region growing approach. Our technique achieved sensitivity of 87 %, specificity of 99 %, and precision of 94% for black ink detection. It segmented melanin with sensitivity of 93 %, specificity of 99 %, and precision of 84 %. When excluding certain regions of images before performing color deconvolution, we observed better approximation of the stain unmixing matrix.
Severe Respiratory Illness Associated With Rhinovirus During the Enterovirus D68 Outbreak in the United States, August 2014–November 2014

Background In 2014, a nationwide outbreak of severe respiratory illness occurred in the United States, primarily associated with enterovirus D68 (EV-D68). A proportion of illness was associated with rhinoviruses (RVs) and other enteroviruses (EVs), which we aimed to characterize further. Methods Respiratory specimens from pediatric and adult patients with respiratory illness were submitted to the Centers for Disease Control and Prevention during August 2014-November 2014. While initial laboratory testing focused on identification of EV-D68, the negative specimens were typed by molecular sequencing to identify additional EV and RV types. Testing for other pathogens was not conducted. We compared available clinical and epidemiologic characteristics among patients with EV-D68 and RV species A-C identified. Results Among 2629 typed specimens, 1012 were EV-D68 (39%) and 81 (3.1%) represented 24 other EV types; 968 were RVs (37%) covering 114 types and grouped into 3 human RV species (RV-A, 446; RV-B, 133; RV-C, 389); and 568 (22%) had no RV or EV detected. EV-D68 was more frequently identified in patients who presented earlier in the investigation period. Among patients with EV-D68, RV-A, RV-B, or RV-C, the age distributions markedly differed. Clinical syndromes and intensive care unit admissions by age were largely similar. Conclusions RVs were commonly associated with severe respiratory illness during a nationwide outbreak of EV-D68, and most clinical. Characteristics were similar between groups. A better understanding of the epidemiology of RVs and EVs is needed to help inform development and use of diagnostic tests, therapeutics, and preventive measures.
Poly(malic acid) bearing Doxorubicin and N-Acetyl Galactosamine as a site-specific prodrug for targeting hepatocellular carcinoma

Abstract In the past, several systems of drug delivery carriers have been designed with a high capacity to target specific cells and/or tissues and a reduced non-specific toxicity. In this context, we synthesized and characterized novel poly(malic acid) derivatives bearing Doxorubicin (Dox), Poly(ethylene glycol) (PEG) and/or N-Acetyl Galactosamine (NAcGal) for drug delivery. These poly(malic acid) derivatives were obtained by chemical modification of the carboxylic acid lateral groups of poly(malic acid) (PMLA). The resulting nanoplatforms were evaluated for their in vitro cytotoxicity using the human HepaRG hepatoma cell line. Results reveal that the PMLA nanoplatform modified with PEG and Dox has an IC50 of 936 nM corresponding to a Dox concentration of 47 nM, while the grafting of NAcGal onto the nanoplatform reduced the IC50 to 527 nM corresponding to a Dox concentration of 26 nM. The presence of the targeting moiety, NAcGal, thus improves the cellular toxicity of the Dox.
Optimism, pessimism and self-efficacy in female cancer patients

Objective The aim of this examination was to study whether psychological resource variables (optimism and self-efficacy) decrease when cancer is present and to test the predictive power of these variables for anxiety, depression and quality of life (QoL). Methods The patient sample was comprised of 354 German women suffering from breast cancer or gynecological cancer. Participants filled in the resource assessment tools Life Orientation Test-Revised and the General Self-Efficacy Scale as well as the Hospital Anxiety and Depression Scale, the Patient Health Questionnaire-4 and the QoL instrument EORTC QLQ-C30 at two time points: (t1) during patients' hospital stay and (t2) 3 months later. Results The mean scores for optimism (total score: M = 16.2) and self-efficacy (M = 29.8) were even somewhat higher than the corresponding means of the general population. Optimism and self-efficacy were positively correlated with QoL (r between 0.15 and 0.17, P < 0.01) and negatively associated with anxiety and depression (r between -0.17 and -0.36, P < 0.01). However, only optimism was predictive of the t2 anxiety, depression and QoL scores when statistically taking into account the baseline levels of the outcome variables. Conclusions Having cancer does not generally reduce optimism and self-efficacy on the level of patients' mean scores. Cancer patients with a high level of habitual optimism will adapt to their disease better than pessimistic patients, even if the baseline levels of the outcome variables have been accounted for.
Phosphors for Solid-State White Lighting

Since the mid-1990s, phosphors have played a key role in emerging solid-state white-lighting technologies that are based on combining a III-nitride-based near-UV or blue solid-state light source with downconversion to longer wavelengths. Almost all widely used phosphors comprise a crystalline oxide, nitride, or oxynitride host that is appropriately doped with either Ce3+ or Eu2+. These ions, with [Xe] 4fn5d0 configurations (n = 1 for Ce3+ and 7 for Eu2+) have proximal excited states that are [Xe] 4fn−15d1. Optical excitation into these states and concomitant reemission can be tuned into the appropriate regions of the visible spectrum by the crystal these ions are hosted in. In this article, we review the current needs and key aspects of the conversion process. We describe some currently used families of phosphors and consider why they are suitable for solid-state lighting. Finally, we describe some empirical rules for new and improved host materials.
FPGA Based Verification for the Difficulty of Delay Based Hardware Trojan Detection

Hardware Trojan insertion during the manufacturing phase is a crucial problem for chip designers. There are several approaches to detect the Trojan in circuits without destructing the chip structure. One of them is delay based hardware Trojan detection. However, this technique suffers deeply from the variations and it is a question whether the Trojans can be detected as the variations hide the effect of the Trojan. This paper, rather than simulation tools, performs experiments on actual FPGA chips to demonstrate and verify the contribution of both inter and intra die variations as well as the effect of hardware Trojan on delay. Lastly, the ability of delay based Trojan detection backed up by the ring oscillator is investigated with different sizes of the Trojan.
“Googling” for Cancer: An Infodemiological Assessment of Online Search Interests in Australia, Canada, New Zealand, the United Kingdom, and the United States

Background The infodemiological analysis of queries from search engines to shed light on the status of various noncommunicable diseases has gained increasing popularity in recent years. Objective The aim of the study was to determine the international perspective on the distribution of information seeking in Google regarding “cancer” in major English-speaking countries. Methods We used Google Trends service to assess people’s interest in searching about “Cancer” classified as “Disease,” from January 2004 to December 2015 in Australia, Canada, New Zealand, the United Kingdom, and the United States. Then, we evaluated top cities and their relative search volumes (SVs) and country-specific “Top searches” and “Rising searches. ” We also evaluated the cross-country correlations of SVs for cancer, as well as rank correlations of SVs from 2010 to 2014 with the incidence of cancer in 2012 in the abovementioned countries. Results From 2004 to 2015, the United States (relative SV [from 100]: 63), Canada (62), and Australia (61) were the top countries searching for cancer in Google, followed by New Zealand (54) and the United Kingdom (48). There was a consistent seasonality pattern in searching for cancer in the United States, Canada, Australia, and New Zealand. Baltimore (United States), St John’s (Canada), Sydney (Australia), Otaika (New Zealand), and Saint Albans (United Kingdom) had the highest search interest in their corresponding countries. “Breast cancer” was the cancer entity that consistently appeared high in the list of top searches in all 5 countries. The “Rising searches” were “pancreatic cancer” in Canada and “ovarian cancer” in New Zealand. Cross-correlation of SVs was strong between the United States, Canada, and Australia (>.70, P<.01). Conclusions Cancer maintained its popularity as a search term for people in the United States, Canada, and Australia, comparably higher than New Zealand and the United Kingdom. The increased interest in searching for keywords related to cancer shows the possible effectiveness of awareness campaigns in increasing societal demand for health information on the Web, to be met in community-wide communication or awareness interventions.
Extrinsic information transfer charts and constituent decoder for turbo coded communications

Turbo codes have achieved near Shannon limit performance in data communication over noisy channels. Recently introduced Extrinsic Information Transfer (EXIT) Charts [1] have become an essential part of turbo code design and have also been used as a complementary design tool for the traditional bit error rate simulations. Additionally, compressive turbo codes have been shown to achieve near-entropy performance in different source coding problems [2], [3], [4]. The main objective of this paper is an extension of EXIT charts from turbo channel codes to turbo source codes, as well as extension of this technique to analog and finite precision iterative decoders.