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Title: 2019/20 lessons from τ(Ωc0) and τ(Ξc0) and CP asymmetry in charm decays
Our 2003 “Cicerone” had discussed charm dynamics with different directions and levels. 1 Here we focus on two items, where the “landscape” has changed sizably. (a) The lifetimes and semileptonic decays of charm hadrons show the impact of nonperturbative QCD and to which degree one can apply heavy quark expansion (HQE) for charm hadrons. It is more complex as we have learnt from 2019/20 data. (b) CP asymmetry has been established in 2019: 2 [Formula: see text] is quite an achievement by the LHCb collaboration! Our community is at the beginning of a long travel for fundamental dynamics. Can the SM account for these? We discuss the assumptions that were made up to 2018 data and new conclusions from 2019/20 ones. We need more data; however, one has to discuss correlations between different transitions. We give an Appendix, what we have learnt for large CP asymmetry in [Formula: see text].  more » « less
Award ID(s):
1820860
NSF-PAR ID:
10297318
Author(s) / Creator(s):
;
Date Published:
Journal Name:
International Journal of Modern Physics A
Volume:
35
Issue:
24
ISSN:
0217-751X
Page Range / eLocation ID:
2030013
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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  1. Obeid, I. (Ed.)
    The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue. It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do not have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools. The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”). This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels. Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA. 
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  4. Introduction Social media has created opportunities for children to gather social support online (Blackwell et al., 2016; Gonzales, 2017; Jackson, Bailey, & Foucault Welles, 2018; Khasawneh, Rogers, Bertrand, Madathil, & Gramopadhye, 2019; Ponathil, Agnisarman, Khasawneh, Narasimha, & Madathil, 2017). However, social media also has the potential to expose children and adolescents to undesirable behaviors. Research showed that social media can be used to harass, discriminate (Fritz & Gonzales, 2018), dox (Wood, Rose, & Thompson, 2018), and socially disenfranchise children (Page, Wisniewski, Knijnenburg, & Namara, 2018). Other research proposes that social media use might be correlated to the significant increase in suicide rates and depressive symptoms among children and adolescents in the past ten years (Mitchell, Wells, Priebe, & Ybarra, 2014). Evidence based research suggests that suicidal and unwanted behaviors can be promulgated through social contagion effects, which model, normalize, and reinforce self-harming behavior (Hilton, 2017). These harmful behaviors and social contagion effects may occur more frequently through repetitive exposure and modelling via social media, especially when such content goes “viral” (Hilton, 2017). One example of viral self-harming behavior that has generated significant media attention is the Blue Whale Challenge (BWC). The hearsay about this challenge is that individuals at all ages are persuaded to participate in self-harm and eventually kill themselves (Mukhra, Baryah, Krishan, & Kanchan, 2017). Research is needed specifically concerning BWC ethical concerns, the effects the game may have on teenagers, and potential governmental interventions. To address this gap in the literature, the current study uses qualitative and content analysis research techniques to illustrate the risk of self-harm and suicide contagion through the portrayal of BWC on YouTube and Twitter Posts. The purpose of this study is to analyze the portrayal of BWC on YouTube and Twitter in order to identify the themes that are presented on YouTube and Twitter posts that share and discuss BWC. In addition, we want to explore to what extent are YouTube videos compliant with safe and effective suicide messaging guidelines proposed by the Suicide Prevention Resource Center (SPRC). Method Two social media websites were used to gather the data: 60 videos and 1,112 comments from YouTube and 150 posts from Twitter. The common themes of the YouTube videos, comments on those videos, and the Twitter posts were identified using grounded, thematic content analysis on the collected data (Padgett, 2001). Three codebooks were built, one for each type of data. The data for each site were analyzed, and the common themes were identified. A deductive coding analysis was conducted on the YouTube videos based on the nine SPRC safe and effective messaging guidelines (Suicide Prevention Resource Center, 2006). The analysis explored the number of videos that violated these guidelines and which guidelines were violated the most. The inter-rater reliabilities between the coders ranged from 0.61 – 0.81 based on Cohen’s kappa. Then the coders conducted consensus coding. Results & Findings Three common themes were identified among all the posts in the three social media platforms included in this study. The first theme included posts where social media users were trying to raise awareness and warning parents about this dangerous phenomenon in order to reduce the risk of any potential participation in BWC. This was the most common theme in the videos and posts. Additionally, the posts claimed that there are more than 100 people who have played BWC worldwide and provided detailed description of what each individual did while playing the game. These videos also described the tasks and different names of the game. Only few videos provided recommendations to teenagers who might be playing or thinking of playing the game and fewer videos mentioned that the provided statistics were not confirmed by reliable sources. The second theme included posts of people that either criticized the teenagers who participated in BWC or made fun of them for a couple of reasons: they agreed with the purpose of BWC of “cleaning the society of people with mental issues,” or they misunderstood why teenagers participate in these kind of challenges, such as thinking they mainly participate due to peer pressure or to “show off”. The last theme we identified was that most of these users tend to speak in detail about someone who already participated in BWC. These videos and posts provided information about their demographics and interviews with their parents or acquaintances, who also provide more details about the participant’s personal life. The evaluation of the videos based on the SPRC safe messaging guidelines showed that 37% of the YouTube videos met fewer than 3 of the 9 safe messaging guidelines. Around 50% of them met only 4 to 6 of the guidelines, while the remaining 13% met 7 or more of the guidelines. Discussion This study is the first to systematically investigate the quality, portrayal, and reach of BWC on social media. Based on our findings from the emerging themes and the evaluation of the SPRC safe messaging guidelines we suggest that these videos could contribute to the spread of these deadly challenges (or suicide in general since the game might be a hoax) instead of raising awareness. Our suggestion is parallel with similar studies conducted on the portrait of suicide in traditional media (Fekete & Macsai, 1990; Fekete & Schmidtke, 1995). Most posts on social media romanticized people who have died by following this challenge, and younger vulnerable teens may see the victims as role models, leading them to end their lives in the same way (Fekete & Schmidtke, 1995). The videos presented statistics about the number of suicides believed to be related to this challenge in a way that made suicide seem common (Cialdini, 2003). In addition, the videos presented extensive personal information about the people who have died by suicide while playing the BWC. These videos also provided detailed descriptions of the final task, including pictures of self-harm, material that may encourage vulnerable teens to consider ending their lives and provide them with methods on how to do so (Fekete & Macsai, 1990). On the other hand, these videos both failed to emphasize prevention by highlighting effective treatments for mental health problems and failed to encourage teenagers with mental health problems to seek help and providing information on where to find it. YouTube and Twitter are capable of influencing a large number of teenagers (Khasawneh, Ponathil, Firat Ozkan, & Chalil Madathil, 2018; Pater & Mynatt, 2017). We suggest that it is urgent to monitor social media posts related to BWC and similar self-harm challenges (e.g., the Momo Challenge). Additionally, the SPRC should properly educate social media users, particularly those with more influence (e.g., celebrities) on elements that boost negative contagion effects. While the veracity of these challenges is doubted by some, posting about the challenges in unsafe manners can contribute to contagion regardless of the challlenges’ true nature. 
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  5. null (Ed.)
    We examine the uneven social and spatial distributions of COVID-19 and their relationships with indicators of social vulnerability in the U.S. epicenter, New York City (NYC). As of July 17th, 2020, NYC, despite having only 2.5% of the U.S. population, has [Formula: see text]6% of all confirmed cases, and [Formula: see text]16% of all deaths, making it a key learning ground for the social dynamics of the disease. Our analysis focuses on the multiple potential social, economic, and demographic drivers of disproportionate impacts in COVID-19 cases and deaths, as well as population rates of testing. Findings show that immediate impacts of COVID-19 largely fall along lines of race and class. Indicators of poverty, race, disability, language isolation, rent burden, unemployment, lack of health insurance, and housing crowding all significantly drive spatial patterns in prevalence of COVID-19 testing, confirmed cases, death rates, and severity. Income in particular has a consistent negative relationship with rates of death and disease severity. The largest differences in social vulnerability indicators are also driven by populations of people of color, poverty, housing crowding, and rates of disability. Results highlight the need for targeted responses to address injustice of COVID-19 cases and deaths, importance of recovery strategies that account for differential vulnerability, and provide an analytical approach for advancing research to examine potential similar injustice of COVID-19 in other U.S. cities. Significance Statement Communities around the world have variable success in mitigating the social impacts of COVID-19, with many urban areas being hit particularly hard. Analysis of social vulnerability to COVID-19 in the NYC, the U.S. national epicenter, shows strongly disproportionate impacts of the pandemic on low income populations and communities of color. Results highlight the class and racial inequities of the coronavirus pandemic in NYC, and the need to unpack the drivers of social vulnerability. To that aim, we provide a replicable framework for examining patterns of uneven social vulnerability to COVID-19- using publicly available data which can be readily applied in other study regions, especially within the U.S.A. This study is important to inform public and policy debate over strategies for short- and long-term responses that address the injustice of disproportionate impacts of COVID-19. Although similar studies examining social vulnerability and equity dimensions of the COVID-19 outbreak in cities across the U.S. have been conducted (Cordes and Castro 2020, Kim and Bostwick 2002, Gaynor and Wilson 2020; Wang et al. 2020; Choi and Unwin 2020), this study provides a more comprehensive analysis in NYC that extends previous contributions to use the highest resolution spatial units for data aggregation (ZCTAs). We also include mortality and severity rates as key indicators and provide a replicable framework that draws from the Centers for Disease Control and Prevention’s Social Vulnerability indicators for communities in NYC. 
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