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Michael Weekes

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Nick K. Jones1,2*, Lucy Rivett1,2*, Chris Workman3, Mark Ferris3, Ashley Shaw1, Cambridge COVID-19 Collaboration1,4, Paul J. Lehner1,4, Rob Howes5, Giles Wright3, Nicholas J. Matheson1,4,6¶, Michael P. Weekes1,7¶1 Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK2 Clinical Microbiology & Public Health Laboratory, Public Health England, Cambridge, UK3 Occupational Health and Wellbeing, Cambridge Biomedical Campus, Cambridge, UK4 Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK5 Cambridge COVID-19 Testing Centre and AstraZeneca, Anne Mclaren Building, Cambridge, UK6 NHS Blood and Transplant, Cambridge, UK7 Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK*Joint first authorship¶Joint last authorshipCorrespondence: mpw1001@cam.ac.ukThe UK has initiated mass COVID-19 immunisation, with healthcare workers (HCWs) given early priority because of the potential for workplace exposure and risk of onward transmission to patients. The UK’s Joint Committee on Vaccination and Immunisation has recommended maximising the number of people vaccinated with first doses at the expense of early booster vaccinations, based on single dose efficacy against symptomatic COVID-19 disease.1-3At the time of writing, three COVID-19 vaccines have been granted emergency use authorisation in the UK, including the BNT162b2 mRNA COVID-19 vaccine (Pfizer-BioNTech). A vital outstanding question is whether this vaccine prevents or promotes asymptomatic SARS-CoV-2 infection, rather than symptomatic COVID-19 disease, because sub-clinical infection following vaccination could continue to drive transmission. This is especially important because many UK HCWs have received this vaccine, and nosocomial COVID-19 infection has been a persistent problem.Through the implementation of a 24 h-turnaround PCR-based comprehensive HCW screening programme at Cambridge University Hospitals NHS Foundation Trust (CUHNFT), we previously demonstrated the frequent presence of pauci- and asymptomatic infection amongst HCWs during the UK’s first wave of the COVID-19 pandemic.4 Here, we evaluate the effect of first-dose BNT162b2 vaccination on test positivity rates and cycle threshold (Ct) values in the asymptomatic arm of our programme, which now offers weekly screening to all staff.Vaccination of HCWs at CUHNFT began on 8th December 2020, with mass vaccination from 8th January 2021. Here, we analyse data from the two weeks spanning 18thto 31st January 2021, during which: (a) the prevalence of COVID-19 amongst HCWs remained approximately constant; and (b) we screened comparable numbers of vaccinated and unvaccinated HCWs. Over this period, 4,408 (week 1) and 4,411 (week 2) PCR tests were performed from individuals reporting well to work. We stratified HCWs <12 days or > 12 days post-vaccination because this was the point at which protection against symptomatic infection began to appear in phase III clinical trial.226/3,252 (0·80%) tests from unvaccinated HCWs were positive (Ct<36), compared to 13/3,535 (0·37%) from HCWs <12 days post-vaccination and 4/1,989 (0·20%) tests from HCWs ≥12 days post-vaccination (p=0·023 and p=0·004, respectively; Fisher’s exact test, Figure). This suggests a four-fold decrease in the risk of asymptomatic SARS-CoV-2 infection amongst HCWs ≥12 days post-vaccination, compared to unvaccinated HCWs, with an intermediate effect amongst HCWs <12 days post-vaccination.A marked reduction in infections was also seen when analyses were repeated with: (a) inclusion of HCWs testing positive through both the symptomatic and asymptomatic arms of the programme (56/3,282 (1·71%) unvaccinated vs 8/1,997 (0·40%) ≥12 days post-vaccination, 4·3-fold reduction, p=0·00001); (b) inclusion of PCR tests which were positive at the limit of detection (Ct>36, 42/3,268 (1·29%) vs 15/2,000 (0·75%), 1·7-fold reduction, p=0·075); and (c) extension of the period of analysis to include six weeks from December 28th to February 7th 2021 (113/14,083 (0·80%) vs 5/4,872 (0·10%), 7·8-fold reduction, p=1x10-9). In addition, the median Ct value of positive tests showed a non-significant trend towards increase between unvaccinated HCWs and HCWs > 12 days post-vaccination (23·3 to 30·3, Figure), suggesting that samples from vaccinated individuals had lower viral loads.We therefore provide real-world evidence for a high level of protection against asymptomatic SARS-CoV-2 infection after a single dose of BNT162b2 vaccine, at a time of predominant transmission of the UK COVID-19 variant of concern 202012/01 (lineage B.1.1.7), and amongst a population with a relatively low frequency of prior infection (7.2% antibody positive).5This work was funded by a Wellcome Senior Clinical Research Fellowship to MPW (108070/Z/15/Z), a Wellcome Principal Research Fellowship to PJL (210688/Z/18/Z), and an MRC Clinician Scientist Fellowship (MR/P008801/1) and NHSBT workpackage (WPA15-02) to NJM. Funding was also received from Addenbrooke’s Charitable Trust and the Cambridge Biomedical Research Centre. We also acknowledge contributions from all staff at CUHNFT Occupational Health and Wellbeing and the Cambridge COVID-19 Testing Centre.

Guangming Wang

and 4 more

Tam Hunt

and 1 more

Tam Hunt [1], Jonathan SchoolerUniversity of California Santa Barbara Synchronization, harmonization, vibrations, or simply resonance in its most general sense seems to have an integral relationship with consciousness itself. One of the possible “neural correlates of consciousness” in mammalian brains is a combination of gamma, beta and theta synchrony. More broadly, we see similar kinds of resonance patterns in living and non-living structures of many types. What clues can resonance provide about the nature of consciousness more generally? This paper provides an overview of resonating structures in the fields of neuroscience, biology and physics and attempts to coalesce these data into a solution to what we see as the “easy part” of the Hard Problem, which is generally known as the “combination problem” or the “binding problem.” The combination problem asks: how do micro-conscious entities combine into a higher-level macro-consciousness? The proposed solution in the context of mammalian consciousness suggests that a shared resonance is what allows different parts of the brain to achieve a phase transition in the speed and bandwidth of information flows between the constituent parts. This phase transition allows for richer varieties of consciousness to arise, with the character and content of that consciousness in each moment determined by the particular set of constituent neurons. We also offer more general insights into the ontology of consciousness and suggest that consciousness manifests as a relatively smooth continuum of increasing richness in all physical processes, distinguishing our view from emergentist materialism. We refer to this approach as a (general) resonance theory of consciousness and offer some responses to Chalmers’ questions about the different kinds of “combination problem.”  At the heart of the universe is a steady, insistent beat: the sound of cycles in sync…. [T]hese feats of synchrony occur spontaneously, almost as if nature has an eerie yearning for order. Steven Strogatz, Sync: How Order Emerges From Chaos in the Universe, Nature and Daily Life (2003) If you want to find the secrets of the universe, think in terms of energy, frequency and vibration.Nikola Tesla (1942) I.               Introduction Is there an “easy part” and a “hard part” to the Hard Problem of consciousness? In this paper, we suggest that there is. The harder part is arriving at a philosophical position with respect to the relationship of matter and mind. This paper is about the “easy part” of the Hard Problem but we address the “hard part” briefly in this introduction.  We have both arrived, after much deliberation, at the position of panpsychism or panexperientialism (all matter has at least some associated mind/experience and vice versa). This is the view that all things and processes have both mental and physical aspects. Matter and mind are two sides of the same coin.  Panpsychism is one of many possible approaches that addresses the “hard part” of the Hard Problem. We adopt this position for all the reasons various authors have listed (Chalmers 1996, Griffin 1997, Hunt 2011, Goff 2017). This first step is particularly powerful if we adopt the Whiteheadian version of panpsychism (Whitehead 1929).  Reaching a position on this fundamental question of how mind relates to matter must be based on a “weight of plausibility” approach, rather than on definitive evidence, because establishing definitive evidence with respect to the presence of mind/experience is difficult. We must generally rely on examining various “behavioral correlates of consciousness” in judging whether entities other than ourselves are conscious – even with respect to other humans—since the only consciousness we can know with certainty is our own. Positing that matter and mind are two sides of the same coin explains the problem of consciousness insofar as it avoids the problems of emergence because under this approach consciousness doesn’t emerge. Consciousness is, rather, always present, at some level, even in the simplest of processes, but it “complexifies” as matter complexifies, and vice versa. Consciousness starts very simple and becomes more complex and rich under the right conditions, which in our proposed framework rely on resonance mechanisms. Matter and mind are two sides of the coin. Neither is primary; they are coequal.  We acknowledge the challenges of adopting this perspective, but encourage readers to consider the many compelling reasons to consider it that are reviewed elsewhere (Chalmers 1996, Griffin 1998, Hunt 2011, Goff 2017, Schooler, Schooler, & Hunt, 2011; Schooler, 2015).  Taking a position on the overarching ontology is the first step in addressing the Hard Problem. But this leads to the related questions: at what level of organization does consciousness reside in any particular process? Is a rock conscious? A chair? An ant? A bacterium? Or are only the smaller constituents, such as atoms or molecules, of these entities conscious? And if there is some degree of consciousness even in atoms and molecules, as panpsychism suggests (albeit of a very rudimentary nature, an important point to remember), how do these micro-conscious entities combine into the higher-level and obvious consciousness we witness in entities like humans and other mammals?  This set of questions is known as the “combination problem,” another now-classic problem in the philosophy of mind, and is what we describe here as the “easy part” of the Hard Problem. Our characterization of this part of the problem as “easy”[2] is, of course, more than a little tongue in cheek. The authors have discussed frequently with each other what part of the Hard Problem should be labeled the easier part and which the harder part. Regardless of the labels we choose, however, this paper focuses on our suggested solution to the combination problem.  Various solutions to the combination problem have been proposed but none have gained widespread acceptance. This paper further elaborates a proposed solution to the combination problem that we first described in Hunt 2011 and Schooler, Hunt, and Schooler 2011. The proposed solution rests on the idea of resonance, a shared vibratory frequency, which can also be called synchrony or field coherence. We will generally use resonance and “sync,” short for synchrony, interchangeably in this paper. We describe the approach as a general resonance theory of consciousness or just “general resonance theory” (GRT). GRT is a field theory of consciousness wherein the various specific fields associated with matter and energy are the seat of conscious awareness.  A summary of our approach appears in Appendix 1.  All things in our universe are constantly in motion, in process. Even objects that appear to be stationary are in fact vibrating, oscillating, resonating, at specific frequencies. So all things are actually processes. Resonance is a specific type of motion, characterized by synchronized oscillation between two states.  An interesting phenomenon occurs when different vibrating processes come into proximity: they will often start vibrating together at the same frequency. They “sync up,” sometimes in ways that can seem mysterious, and allow for richer and faster information and energy flows (Figure 1 offers a schematic). Examining this phenomenon leads to potentially deep insights about the nature of consciousness in both the human/mammalian context but also at a deeper ontological level.

Susanne Schilling*^

and 9 more

Jessica mead

and 6 more

The construct of wellbeing has been criticised as a neoliberal construction of western individualism that ignores wider systemic issues including increasing burden of chronic disease, widening inequality, concerns over environmental degradation and anthropogenic climate change. While these criticisms overlook recent developments, there remains a need for biopsychosocial models that extend theoretical grounding beyond individual wellbeing, incorporating overlapping contextual issues relating to community and environment. Our first GENIAL model \cite{Kemp_2017} provided a more expansive view of pathways to longevity in the context of individual health and wellbeing, emphasising bidirectional links to positive social ties and the impact of sociocultural factors. In this paper, we build on these ideas and propose GENIAL 2.0, focusing on intersecting individual-community-environmental contributions to health and wellbeing, and laying an evidence-based, theoretical framework on which future research and innovative therapeutic innovations could be based. We suggest that our transdisciplinary model of wellbeing - focusing on individual, community and environmental contributions to personal wellbeing - will help to move the research field forward. In reconceptualising wellbeing, GENIAL 2.0 bridges the gap between psychological science and population health health systems, and presents opportunities for enhancing the health and wellbeing of people living with chronic conditions. Implications for future generations including the very survival of our species are discussed.  

Mark Ferris

and 14 more

IntroductionConsistent with World Health Organization (WHO) advice [1], UK Infection Protection Control guidance recommends that healthcare workers (HCWs) caring for patients with coronavirus disease 2019 (COVID-19) should use fluid resistant surgical masks type IIR (FRSMs) as respiratory protective equipment (RPE), unless aerosol generating procedures (AGPs) are being undertaken or are likely, when a filtering face piece 3 (FFP3) respirator should be used [2]. In a recent update, an FFP3 respirator is recommended if “an unacceptable risk of transmission remains following rigorous application of the hierarchy of control” [3]. Conversely, guidance from the Centers for Disease Control and Prevention (CDC) recommends that HCWs caring for patients with COVID-19 should use an N95 or higher level respirator [4]. WHO guidance suggests that a respirator, such as FFP3, may be used for HCWs in the absence of AGPs if availability or cost is not an issue [1].A recent systematic review undertaken for PHE concluded that: “patients with SARS-CoV-2 infection who are breathing, talking or coughing generate both respiratory droplets and aerosols, but FRSM (and where required, eye protection) are considered to provide adequate staff protection” [5]. Nevertheless, FFP3 respirators are more effective in preventing aerosol transmission than FRSMs, and observational data suggests that they may improve protection for HCWs [6]. It has therefore been suggested that respirators should be considered as a means of affording the best available protection [7], and some organisations have decided to provide FFP3 (or equivalent) respirators to HCWs caring for COVID-19 patients, despite a lack of mandate from local or national guidelines [8].Data from the HCW testing programme at Cambridge University Hospitals NHS Foundation Trust (CUHNFT) during the first wave of the UK severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic indicated a higher incidence of infection amongst HCWs caring for patients with COVID-19, compared with those who did not [9]. Subsequent studies have confirmed this observation [10, 11]. This disparity persisted at CUHNFT in December 2020, despite control measures consistent with PHE guidance and audits indicating good compliance. The CUHNFT infection control committee therefore implemented a change of RPE for staff on “red” (COVID-19) wards from FRSMs to FFP3 respirators. In this study, we analyse the incidence of SARS-CoV-2 infection in HCWs before and after this transition.

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Report of Two cases of Schaaf-Yang Syndrome: Same Genotype, Different Phenotype Ana Maria Rodriguez,a MD, Katherine Schain,a MS, CGC, Parul Jayakar,aMD,MS,FACMG, Meredith S. Wright,b,c PhD., Shimul Chowdhury,b PhD., Daria Salyakina,ePhD.a Division of Genetics and Metabolism, Nicklaus Children’s Hospital Pediatric Specialists, Miami, (FL,) USA.b Rady Children’s Institute for Genomic Medicine, San Diego, (CA,) USA. c Keck Graduate Institute, Claremont, (CA,) USA. d Personalized Medicine & Health Outcomes Research, Nicklaus Children’s Hospital Pediatric Specialists, Miami, (FL,) USACorresponding Author: Ana Maria Rodriguez BarretoDivision of Genetics and Metabolism, Nicklaus Children’s Hospital Pediatric Specialists, Miami, (FL,). 3100 SW 62nd Avenue, Miami, FL, 33155, USA. Tel: 786-624-4717. Fax : 786-624-4704. E-mail: anamaria.rodriguezbarreto@nicklaushealth.orgCo-authors: Katherine Schain: Katherine.Schain@Nicklaushealth.orgParul Jayakar: Parul.Jayakar@Nicklaushealth.orgMeredith S. Wright: MWright3@rchsd.orgShimul Chowdhury: schowdhury@bluestargenomics.comDaria Salyakina: Daria.Salyakina@Nicklaushealth.orgConflicts of Interests Statement: We know of no conflicts of interests associated with this publication, and there has been no significant financial support for this work that could have influenced its outcome. As Corresponding Author, I confirm that the manuscript has been read and approved for submission by all the named authors.Informed Consent : Written informed consent was obtained from both patients parents.Ethics Declaration: The study was conducted according to the guidelines of the Declaration of Helsinki and approved by The Institutional Review Board (or Ethics Committee) of Nicklaus Children’s Hospital Pediatric Specialists.

Zuhat Urakci

and 7 more

Flagella dermatitis is a rare skin lesion due to bleomycin use: A Case ReportZuhat Urakçı1,Yasin Sezgin2,Oğur Karhan3,Suat Morkuzu4,Zeynep Oruç1,Mehmet Küçüköner1,Muhammet Ali Kaplan1,Abdurrahman Işıkdoğan11Dicle University Department of Medical Oncology, Diyarbakir,Turkey2Siirt University, Department of Medical Oncology,Siirt,Turkey3Liv Hospital, Department of Medical Oncology, Gaziantep,Turkey4Institute for Reconstructive Surgery,Houston Methodist Hospital,Houston,Texas,USAAbstract: Flagella dermatitis is a rare skin lesion that appears due to bleomycin use. It is generally seen in itchy and linear styles. Here, we present a case of flagella dermatitis in a male patient who was on bleomycin therapy with a diagnosis of germ cell tumor. When itchy skin lesions develop in patients using bleomycin, it should be kept in mind among the differential diagnoses.Keywords: Flagella dermatitis,bleomycin,germ cell tumor.Introduction: Bleomycin is a glycopeptide-structured cytotoxic drug obtained from Streptomyces verticillus (1). It is often used in the treatment of some malignant tumors, such as Hodgkin lymphoma, squamous cell carcinoma, and germ cell tumors (1). While various side effects occur in the gastrointestinal tract, respiratory system, and skin due to bleomycin, general symptoms such as fever and weakness can also be seen. Skin reactions are common side effects and usually occur as a late finding. On the skin, erythema, hyperkeratosis, rash, vesicle, hyperpigmentation, alopecia, and, in rare cases, Flagella dermatitis (FD) can be seen (2). FD was defined by Moulin et al. in 1970 as linear hyperpigmentation after bleomycin use (1). Its incidence has been reported to be between 8 and 20% in patients using bleomycin (3). Here, a case of FD developed in a 21-year-old male patient using bleomycin due to a germ cell tumor is presented.Case report: A twenty-one-year-old male patient was admitted to our clinic with complaints of shortness of breath and cough that started about 45 days ago. A patient was diagnosed with a mediastinal mass, and a biopsy was performed. The patient, who was reported as a germ cell tumor as a result of a biopsy, was given every 21 days from when bleomycin (30 mg/day, 1, 8 and 15 days), etoposide (100 mg / m2, 1-5 days) and cisplatin (20 mg / m2, 1-5 days), was started. In our patient, hyperpigmented skin lesions that developed with itching, mostly in the chest, abdomen, and back, developed after the 2nd dose of bleomycin (Figure 1.2). Due to the development of the lesions after bleomycin, and in a linear style, FD was considered in our patient. The patient was given oral antihistamine therapy. The dexamethasone that was given before each chemotherapy cycle was continued. During the follow-up, the patient’s itching passed and the skin lesions regressed. The patient’s bleomycin treatment was continued, and there was no itching again.Discussion: The term ”Flagella dermatitis” is used because the hyperpigmented eruptions on the body appear to be whipped (4). In the case of HIV infection, FD may also develop after the consumption of some poisonous mushrooms or after the use of certain chemotherapeutic agents such as peplomycin and docetaxel (5). Bleomycin is an anti-neoplastic drug belonging to the group of glycopeptides, and bleomycin is destroyed by hydrolase. The concentration of the bleomycin hydrolase enzyme is significantly lower in the skin and lungs. Therefore, the accumulation of bleomycin in the skin and lungs is higher and related toxicities develop. Generally, when the cumulative dose reaches 90–285 mg, bleomycin toxicity begins to occur. However, in some cases, it has been reported that toxicity develops at as low as 15 mg intravenously (6). Multiple lesions occur suddenly in many parts of the body. Generally, it develops between the 1st and 9th weeks of bleomycin treatment, but this period may take up to 6 months (7). In our case, FD developed at week 4. Although FD can rarely be asymptomatic, it usually progresses with itching, redness, and darkening of the skin. Indeed, in our case, there was severe itching, redness, and hyperpigmentation of the skin. The diagnosis is made according to the characteristic features of the skin lesions. Linear-style eruptions occur as if they were whipped, characteristically on the skin. The lesions are itchy and usually occur on the upper body and extremities (8). Linear hyperpigmented skin lesions are generally localized in areas where itching and pressure are applied (9). The development mechanism of FD is not known precisely. However, it has been suggested that locally increased melanogenesis, insufficient pigmentation secondary to inflammation, change in normal pigmentation pattern, and neutrophilic eccrine hydradenitis can be caused (10). Patients usually benefit from corticosteroids and anti-histaminics used in treatment. It reduces itching and limits the lesions to the skin. These lesions usually limit themselves after 3-4 months of discontinuation and begin to regress and disappear after 6-8 months. However, after the use of bleomycin again, the lesions may reappear (11). In our case, corticosteroid and anti-histaminic therapy completely alleviated the symptoms.Conclusion: When itchy lesions develop in patients using bleomycin, FD should be kept in mind among the differential diagnoses, and physicians should be careful about the toxicity of bleomycin.Conflict of interest: The authors declared that there is no conflict of interest.

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Mulugeta Tuji Dugda

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Large earthquakes, especially those occurring in a city or population centers, create devastation and havoc, and often times kindle several deaths and injuries, and significant infrastructure damage that lead to several billions of dollars in losses. Marine earthquakes are the leading cause of large tsunamis which cause deaths, destruction, displacement of population, and a possible nuclear meltdown. Thus, prediction of earthquake or its aftershocks or earthquake early warning system has a great potential to mitigate the loss of life as well as different kinds of damage. Earthquake prediction would mean forecasting the occurrence of an earthquake by providing both its magnitude estimate and accurate location. Earthquake prediction has been an important area of seismology research for quite a while, and it looks like it will continue to be an important area of research. Recently, with the implementation of deep learning in seismology, scientists have been able to detect, predict, and model seismic waves and earthquake aftershocks. Earthquake aftershocks are generally triggered by changes in stress formed by large earthquakes that happen within, or surrounding a given fault network system. The main goal of this study is to investigate the improvement of aftershock pattern predictions with the implementation of tuning and optimizing of deep learning parameters. To achieve these goals, we have developed an algorithm that can help first gather mainshock-aftershock sequence data. Some of the criteria used in identifying earthquakes that initiate an aftershock is to look at earthquakes that happen within a certain radius, the values we attempted are within about 0.5 degrees range, and within a certain period, from few seconds to several weeks of the occurrence of the main shock. For the sequence identification, we have been using seismic data from the United States Geological Survey (USGS)-National Earthquake Information Center (NEIC). We are also looking at different open-source data gathered by researchers for a similar study. The deep neural networks we are implementing make use of Keras python Toolkit, and Theano and Tensorflow libraries, with a plan to use PyTorch python library instead of Theano library in the future because of some maintenance issues. To this point our attempts have shown a good progress.

Mulugeta Tuji Dugda

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Seismology is a data-driven science with a huge amount of data gathered for over a century. Though seismic data recording started in 1900, the growth of seismic data has obviously been exponentially in the last three decades. This data growth can be easily noticed if one takes a close look at just one of the largest seismological data centers in the US, the Data Management Center (DMC) of the Integrated Research Institutions in Seismology (IRIS). Data at the DMC grew from less than 10 Tebibytes in 1992 to about 800 Tebibytes in 2022. With the availability of such a large amount of seismic data, it is paramount to develop new seismic data processing and management tools to help analyze and find new and better seismic models. Developing new big seismic data processing and management tools will be helpful to make the best use of such growing big seismological data sets. The main goal of this investigation is the development of efficient data manipulation and processing tools for retrieval, processing, merging, aggregation, and management of big seismic data from disparate data sources. In this study, such big seismic data processing tools are being developed using python programming language and open source python libraries, and the tools we are developing will be helpful to extract, split, and convert, merge and process big seismic data. In addition, python is very suitable for data science and has powerful libraries to process and manage data and applications. Significant contributions have been made in recent python based libraries for seismic data processing, though there are still some rooms for improvement when it comes to seismic applications to merge, convert, manage  and process big seismic data from disparate data sources and converting different file formats. Seismic data from different networks surrounding the Rio Grande Valley have been collected from different data sources. Our attempt is to test the developed tools and evaluate their performance. This study has made important progress in this regard and the results are promising. 

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