nils-herrmann/clean_scirepeval huggingface dataset:
SU E T 246: On Augmented DVH Analysis
Year: 2013

The process of IMRT planning is an iterative inverse process, where a planner seeks to attain a desired dose distribution, specified for tumors and OARs, hence creating a plethora of competing objectives. However, the final product is rather the unpredictable outcome of a series of trial and error attempts at meeting these objectives. A key tool to inspect the quality of plans is the DVH. This inspection, however, is primarily conducted visually, hence, the chosen treatment plan is ultimately clinician dependent. In this study, we propose a quantitative method for DVH comparison based on historical data.  The treatment of one prostate case was planned by seven planners, while imposing the same clinical objectives for PTV and OARs. The resulting seven test DVHs were compared based on their deviation of from the ideal coverage, namely 100% of PTV receiving 100% of the dose. A deviation function L is proposed to measure the weighted area between the ideal and realized DVH. The weights are formed based on the distribution of past data of 100 comparable prostate cases. The frequencies were interpolated to form a continuous surface using tensor product piecewise cubic hermite interpolation. While only the dose distribution to PTV was subject to this study, the proposed method is universal and applies to other organs and/or combinations of criteria as well.  Even though none of the seven test DVHs appeared visually preferable, we measured significantly different L values: Planner 2 exhibited the lowest deviation, while the deviations of Planners 1 and 7 were far higher.  The proposed method of quantitative DVH comparison can distinguish DVHs that might otherwise visually appear similar in a clinical setting. Furthermore, the outcomes from our method are independent of planning personnel biases, providing a quantitative way of evaluating DVHs and augmenting decisions in IMRT. Joint Purdue IU Seed Grant
The Morse Sard theorem for Clarke critical values
Year: 2013

The Morse Sard theorem states that the set of critical values of a C k smooth function defined on a Euclidean space R d has Lebesgue measure zero, provided k d This result is hereby extended for (generalized) critical values of continuous selections over a compactly indexed countable family of C k functions: it is shown that these functions are Lipschitz continuous and the set of their Clarke critical values is null.
Dental microwear as a behavioral proxy for distinguishing between canids at the Upper Paleolithic (Gravettian) site of Predmosti, Czech Republic
Year: 2020

Morphological and genetic evidence put dog domestication during the Paleolithic, sometime between 40,000 and 15,000 years ago, with identification of the earliest dogs debated. We predict that these earliest dogs (referred to herein as protodogs) while potentially difficult to distinguish morphologically from wolves, experienced behavioral shifts, including changes in diet. Specifically, protodogs may have consumed more bone and other less desirable scraps within human settlement areas. Here we apply Dental Microwear Texture Analysis (DMTA) to canids from the Gravettian site of Predmosti (approx. 28,500 BP) which were previously assigned to the Paleolithic dog or Pleistocene wolf morphotypes. We test whether these groups separate out significantly by diet related variation in microwear patterning. Results are consistent with differences in dietary breadth, with the Paleolithic dog morphotype showing evidence of greater durophagy than those assigned to the wolf morphotype. This supports the presence of two morphologically and behaviorally distinct canid types at this middle Upper Paleolithic site. Our primary goal here was to test whether these two morphotypes expressed notable differences in dietary behavior. However, in the context of a major Gravettian settlement, this may also support evidence of early stage dog domestication. Dental microwear is a behavioral signal that may appear generations before morphological changes are established in a population. It shows promise for distinguishing protodogs from wolves in the Pleistocene and domesticated dogs from wolves elsewhere in the archaeological record.
Automatic aesthetic quality assessment of photographic images using deep convolutional neural network
Venue: 2016 International Conference on Information Science (ICIS)
Year: 2016

Aesthetics can be defined as the study of various emotions related to the sense of beauty. Nowadays there is a fast growth in the use of digital images which is used for representing information. With the increase in the number of photos, it has become complicated to evaluate its quality. Image aesthetic evaluation methods depends on many aesthetic features. People give more attention to the photos which are visually satisfying. Evaluation of aesthetic quality is a challenging task which require knowledge about aesthetic features. Some low level features like contrast, sharpness, colorfulness etc are used to calculate aesthetic score of an image. This paper present a system for automatic aesthetic quality assessment of photographic images using deep convolutional neural network.
CircHIPK3 Promotes Pyroptosis in Acinar Cells Through Regulation of the miR 193a 5p/GSDMD Axis
Venue: Frontiers in Medicine
Year: 2020

Acute pancreatitis (AP) especially severe acute pancreatitis (SAP) is an extremely dangerous illness with a high mortality rate. Pyroptotic cells release their cellular contents and inflammatory factors, aggravating the inflammatory response. Pyroptosis may be the main mode of acinar cell death during AP. The circular RNA circHIPK3 is expressed in pancreatic tissue and is associated with inflammatory response. In this study, we focused on the role and underlying mechanism of circHIPK3 in AP. We found that the expression of circHIPK3 was significantly elevated in serum of patients with AP and in caerulein stimulated AR42J cells and was associated with caspase 1 and caspase 11 activation. circHIPK3 silencing ameliorated caerulein induced cell damage and reduced the release of inflammatory factors IL 1b, IL 6, IL 8, and TNF a and inhibited the activation of caspase 1 and caspase 11. In addition, circHIPK3 bound to miR 193a 5p and negatively regulated its expression. Inhibition of miR 193a 5p increased the release of IL 1b, IL 6, IL 8, and TNF a and activated caspase 1 and caspase 11, thereby counteracting the effect of circHIPK3 silencing on caerulein induced cell damage. Furthermore, we identified GSDMD as a target gene of miR 193a 5p, which is the key gene for pyroptosis. Interfering with the expression of GSDMD can increase cell viability, reduce the secretion of inflammatory cytokines, and suppress the activation of cleaved caspase 1 and caspase 11. Silencing GSDMD reversed the effects of miR 193a 5p inhibitors on caerulein induced damage. In conclusion, circHIPK3 promotes pyroptosis in acinar cells through regulation of the miR 193a 5p/GSDMD axis, which eventually aggravates AP disease.
Subspace Gaussian Mixture Model for Continuous Urdu Speech Recognition using Kaldi
Venue: 2020 14th International Conference on Open Source Systems and Technologies (ICOSST)
Year: 2020

Automatic Speech Recognition Systems (ASR) have significantly improved in recent years, where deep learning is playing an important role in the development of end to end ASR's. ASR is the task of converting spoken language into computer readable text. ASRs are becoming ever more prevalent way to interact with technology, thereby significantly closing the gap in terms of how humans interact with computers, making it more natural. Urdu is an under resourced language, for which training such a system requires a huge amount of data that is not readily available. In this paper we present improvements to the architecture of a statistical automatic speech recognition system for which the components involved in a statistical ASR have been explored in great detail. We also present the results on various statistical models that are trained for Urdu language. We choose the Kaldi toolkit for training the Urdu ASR using approximately 100 hours of transcribed data. The refined Subspace Gaussian Model gives a word error rate of 9% on the test set.
Do bumper ads bump consumers? An empirical research on YouTube video viewers
Year: 2020

YouTube, the most popular present day online video platform, is also considered one of today's leading advertising media. There is an ongoing argument that YouTube measures and shares its own ad effectiveness. However, the consumer research results contradict with their measurements. The difficulty of measuring the performance of video ads on YouTube without YouTube's built in data increases the debate about its effectiveness as an advertising environment and therefore makes it more important to collect data from consumers through empirical research. This study was carried out with YouTube viewers located in Turkey, whose population is among the most online video watching Internet users in the world, to uncover the determining attitudes and the factors affecting them in the effectiveness of bumper ads, which YouTube introduced in 2016 as 6 seconds unskippable ad videos. The acquired data were tested by correlation and regression analysis under a predicted model that could explain the attitudes towards the ad. According to findings; it has been shown that the attitudes towards bumper advertisements are significantly related to the factors such as entertainment, informativeness, credibility, irritation, frequency of exposure and advertising value. However, it was found that the participants did not develop a positive attitude towards these factors, and the bumper advertisements, along with them.
A modification of the PHYLIP program: A solution for the redundant cluster problem, and an implementation of an automatic bootstrapping on trees inferred from original data.
Venue: Molecular phylogenetics and evolution
Year: 2017

Felsenstein's PHYLIP package of molecular phylogeny tools has been used globally since 1980. The programs are receiving renewed attention because of their character based user interface, which has the advantage of being scriptable for use with large scale data studies based on super computers or massively parallel computing clusters. However, occasionally we found, the PHYLIP Consense program output text file displays two or more divided bootstrap values for the same cluster in its result table, and when this happens the output Newick tree file incorrectly assigns only the last value to that cluster that disturbs correct estimation of a consensus tree. We ascertained the cause of this aberrant behavior in the bootstrapping calculation. Our rewrite of the Consense program source code outputs bootstrap values, without redundancy, in its result table, and a Newick tree file with appropriate, corresponding bootstrap values. Furthermore, we developed an add on program and shell script, add_bootstrap.pl and fasta2tre_bs.bsh, to generate a Newick tree containing the topology and branch lengths inferred from the original data along with valid bootstrap values, and to actualize the automated inference of a phylogenetic tree containing the originally inferred topology and branch lengths with bootstrap values, from multiple unaligned sequences, respectively. These programs can be downloaded at: https:/github.com/ShimadaMK/PHYLIP_enhance/
Diameter of Carbon Nanotube Directed Self Assembly of Amphiphilic Block Copolymers
Venue: Materials
Year: 2019

The cooperative self assembly of nanoparticles and amphiphilic block copolymers has attracted increasing interests as it offers effective routes to achieve nanocomposite supramolecular structures with desired structure and properties. The incorporation of nanoparticles usually tunes the self assembly structure of block copolymers, as the copolymer nanoparticle interactions may change the relative volume ratio of hydrophobic block/hydrophilic block copolymers. It should be noted that the micro size length and the strong nonpolar feature of carbon nanotubes (CNTs) may cause the block copolymer CNT interactions to differ from the the block copolymer nanoparticle interactions. Herein, we show that the diameter of CNTs and the copolymer/CNT ratio have a profound effect on the self assembly behavior of amphiphilic block copolymers. Upon the addition of carboxylated multi walled carbon nanotubes (c MWCNTs, diameter <8 nm, to the methoxy polyethylene glycol poly (D,L lactic acid) (MPEG PDLLA) solution, it is difficult to observe the c MWCNTs directly in TEM images. However, it has been found that they form supramolecular nanocomposite structures with MPEG PDLLA. Moreover, these supramolecular structures transform from core shell spherical micelles into rod like micelles and then into large composite aggregates with the increase of the c MWCNT addition. However, in the case of the addition of c MWCNTs with a diameter of 30 50 nm, the dispersed c MWCNTs and spherical core shell micelles could be observed simultaneously in the TEM images at a low c MWCNT addition, and then the micelle structure disappeared and only well dispersed c MWNTs were observed in TEM images at a high c MWCNT addition. A possible model was proposed to explain the rule of CNTs participating in the formation of copolymer/CNT nanocomposite structures. It was also shown that as prepared copolymer/CNT supramolecular nanocomposites could be used as drug carriers, enabling the adjustment of the drug loading and release time.
Antibodies and Antimatter: The Resurgence of Immuno PET
Venue: Journal of Nuclear Medicine
Year: 2009

The completion of the human genome, coupled with parallel major research efforts in proteomics and systems biology, has led to a flood of information on the roles of individual genes and proteins in normal physiologic processes and their disruptions in disease. In practical terms, this information has opened the door to increasingly targeted therapies as specific molecular markers are identified and validated. The ongoing transition from empiric to molecular medicine has engendered a need for corresponding molecular diagnostics, including noninvasive molecular imaging. Convergence of knowledge regarding key biomarkers that define normal biologic processes and disease with protein and imaging technology makes this an opportune time to revisit the combination of antibodies and PET, or immuno PET.
[Guidelines for the interpretation of fetal chromosomal karyotyping analysis]
Venue: Zhonghua yi xue yi chuan xue za zhi Zhonghua yixue yichuanxue zazhi Chinese journal of medical genetics
Year: 2021

Karyotyping analysis is a classical cytogenetic method for the prenatal diagnosis of fetal chromosomal aberrations. In order to standardize fetal chromosomal karyotyping analysis and adapt to the development of medical genetics technology, the Committee for the Prevention and Control of Birth Defect, Chinese Association of Preventive Medicine has organized the formulation of this guideline. The content has covered general requirements and standards for the analysis of fetal chromosomal karyotypes, analysis of chromosomal mosaicisms, and methods for determining the resolution of G banding, etc. with the purpose to serve the clinical practice.
Reconfigurable multi bit phase change material silicon photonics directional couplers
Year: 2021

The unique optical properties of phase change materials (PCMs) can be exploited to develop efficient reconfigurable photonic devices. Here, we design, model, and compare the performance of programmable 1X2 optical couplers based on: Ge2Sb2Te5, Ge2Sb2Se4Te1, Sb2Se3, and Sb2S3 PCMs. Once programmed, these devices are passive, which can reduce the overall power used in an ONN. In the telecommunication wavelength region (1520 to 1580 nm) the Sb2S3 directional coupler displays a minimum insertion loss of 0.04 dB and 1.1 dB, and the lowest crosstalk of 42 dB and 17 dB for the amorphous and crystalline states respectively. We also design a non volatile 2 bit low loss tuneable Sb2S3 directional coupler that can be used to set the weights of optical neural networks (ONN) Partial crystallization of Sb2S3 strips with dimensions compatible to those in the directional coupler indicate that at least four different crystalline lengths can be reliably programmed. We used this effect to design a 2 bit tuneable Sb2S3 directional coupler with a weight dynamic range close to 17 dB. The bit depth of the coupler appears to be limited by the crystallization stochasticity.
HADHA overexpression disrupts lipid metabolism and inhibits tumor growth in clear cell renal cell carcinoma.
Venue: Experimental cell research
Year: 2019

Hydroxyacyl CoA dehydrogenase alpha subunit (HADHA) is a key lipid metabolic enzyme with a novel role in carcinogenesis. We previously reported that HADHA, a prognostic marker, was downregulated in clear cell renal cell carcinoma (ccRCC) Herein, the tumor inhibitory role of HADHA overexpression in ccRCC was investigated further. The quantitative proteomic analysis displayed that a total of 1293 and 1293 proteins were identified in HADHA overexpressed 786 O hadha and vector transfected control 786 O vc cells, respectively, and 206 proteins were found to be up or downregulated. PANTHER, OmicsNet, STRING, and DAVID tools were utilized on the dysregulated proteins in order to elucidate multiple metabolic pathways (especial lipid metabolism) and lipid metabolism related proteins (e.g. ACAT1, ACLY) The dysregulation of the lipid metabolic enzymes, ACAT1, ACLY, CYB5R3 and FASN, were confirmed by Western blotting. Further assays demonstrated that HADHA overexpression significantly inhibited cell growth, induced cell apoptosis, and decreased the formation of cytoplasmic lipid droplets (LDs) moreover, it also inhibited tumor growth and lessened the formation of LDs in xenografted mouse. Collectively, these data revealed that HADHA overexpression disrupted lipid metabolism and inhibited tumor growth, which shed light on HADHA as a potential therapeutic target for clinical intervention of ccRCC.
Recomendaciones de la Asociacion Espanola de Neurogastroenterologia y Motilidad (ASENEM) para el reinicio de la actividad de los laboratorios de motilidad digestiva, tras el confinamiento por el estado de alarma decretado a raiz de la pandemia por COVID 19
Venue: Gastroenterologia y Hepatologia
Year: 2020

Resumen El coronavirus del sindrome respiratorio agudo severo tipo 2 (conocido por sus siglas en ingles, SARS CoV 2) ha sido responsable del brote de la denominada enfermedad por coronavirus de 2019 (COVID 19) que ha llegado a tener la consideracion de pandemia. Las estrategias adoptadas para su prevencion han incluido medidas de distanciamiento social, asi como la modificacion, reduccion o interrupcion de gran parte de la actividad sanitaria habitual. Esto ha afectado de forma muy notable a la asistencia prestada en las Unidades de Motilidad Digestiva. Superado el pico de mortalidad y contagios por la infeccion, se ha observado durante las ultimas semanas en Espana y otros paises europeos, una reduccion paulatina en las cifras de transmision. Sin embargo, el riesgo de reactivacion sigue siendo alto, por lo que es necesario disponer de una planificacion que permita a los centros sanitarios reiniciar con seguridad para pacientes y profesionales, las exploraciones instrumentales vinculadas al manejo de la patologia motora. La Asociacion Espanola de Neurogastroenterologia y Motilidad (ASENEM) ha elaborado una serie de recomendaciones practicas basadas en la evidencia cientifica disponible y en el consenso de un panel de expertos, y adaptadas a los riesgos inherentes a cada actividad. Se incluyen propuestas de proteccion individual, pero tambien medidas organizativas y estructurales, cuyo objetivo es permitir reanudar progresivamente las exploraciones, minimizando la posibilidad de contagio.  The severe acute respiratory syndrome coronavirus 2 (SARS CoV 2) was responsible for the outbreak of the 2019 coronavirus disease (COVID 19) which is now considered as a pandemic. The prevention strategies adopted have included social distancing measures and the modification, reduction or interruption of a large proportion of routine healthcare activity. This has had a significant impact on the care provided in Gastrointestinal Motility Units. Having passed the peak, in terms of mortality and infections, a gradual reduction in transmission figures has been observed in Spain and other European countries. The risk of reactivation, however, remains high, so it is necessary to have a plan in place that allows healthcare centres to safely resume, for their patients and professionals, instrumental examinations linked to the management of motor pathology. Based on the available scientific evidence and the consensus of a panel of experts, the Spanish Association of Neurogastroenterology and Motility (ASENEM) has drawn up a series of practical recommendations, which have been adapted to the risks inherent in each activity. These include individual protection proposals, as well as organisational and structural measures, which are conceived to allow for the gradual resumption of examinations while minimising the possibility of contagion.
Adaptive Eulerian Video Processing of Thermal Video: An Experimental Analysis
Venue: IEEE Transactions on Instrumentation and Measurement
Year: 2017

The use of spatiotemporal video processing to extract biosignals is an emerging technique. This paper aims to build upon current work through robust experimentation and analysis. A blood flow simulation model was captured by thermal and optical cameras, while hot water was pumped through the system. Additionally, five subjects were recruited to perform two experimental trials: a facial perfusion trial and an arm blood occlusion trial, for which subjects sat quietly, while video data were captured using thermal and optical cameras. Each video was subjected to region of interest selection and adaptive Eulerian video magnification (EVM) the iterative application of EVM, first with a wide temporal bandpass filter and low amplification factor and again with a narrower, targeted temporal bandpass filter and higher amplification factor. The results from the simulation experiments indicated that thermal video in conjunction with adaptive EVM processing can reveal variations in temperature indicative of pulse rate in a controlled system of known variables. This process helped to better characterize Eulerian signal enhancement versus Eulerian noise enhancement. The results from the facial perfusion experiments suggest that the adaptive EVM processing of thermal video results in signals representative of facial perfusion rate. The results from the blood occlusion experiments revealed an occlusion temperature pattern, but not a perfusion rate. This paper therefore further demonstrated the potential of thermal video in conjunction with adaptive EVM methods to extract a signal representative of facial perfusion rate, and illustrated the need for more research on thermal video and adaptive EVM.
Building Trust: How Leaders Can Engender Feelings of Trust Among Followers
Year: 2021

Trust has long been recognized across cultures, industries, and organizations as a key component of social exchange. Yet, in many communities and organizations throughout the world, there is a growing trust deficit. In this paper, we explore what leaders can do to generate trust among the individuals within their organizations to help facilitate better relationships and positive outcomes for both individuals and organizations. More specifically, we present a qualitative study in which semi structured interviews with employees at an assisted living care facility highlighted two ways that leaders can build trust within their organization: 1) demonstrating humility in their communication, and 2) exhibiting compassion in their behavior. We further highlight two characteristics, authenticity and proactivity, that can help leaders increase the effectiveness of these actions. By making these behaviors part of how they lead, leaders and managers can more successfully generate feelings of trust among the individuals within their organizations and help their organization to maintain and strengthen its competitive advantage.