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1.
Nat Protoc ; 2024 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-38565959

RESUMO

Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries and/or databases. A researcher may also be using multiple different tools that require different versions of the same supporting materials. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging and containerization are different approaches to satisfy this need by delivering omics tools already wrapped in additional software that makes the tools easier to install and use. In this systematic review, we describe and compare the features of prominent packaging and containerization platforms. We outline the challenges, advantages and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers and system administrators. We also propose principles to make the distribution of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.

2.
Genome Biol ; 25(1): 49, 2024 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-38365730

RESUMO

Nanopore sequencing generates noisy electrical signals that need to be converted into a standard string of DNA nucleotide bases using a computational step called basecalling. The performance of basecalling has critical implications for all later steps in genome analysis. Therefore, there is a need to reduce the computation and memory cost of basecalling while maintaining accuracy. We present RUBICON, a framework to develop efficient hardware-optimized basecallers. We demonstrate the effectiveness of RUBICON by developing RUBICALL, the first hardware-optimized mixed-precision basecaller that performs efficient basecalling, outperforming the state-of-the-art basecallers. We believe RUBICON offers a promising path to develop future hardware-optimized basecallers.


Assuntos
Aprendizado Profundo , Nanoporos , Análise de Sequência de DNA , Genômica , Nucleotídeos , DNA/genética
3.
BMC Cancer ; 24(1): 183, 2024 Feb 07.
Artigo em Inglês | MEDLINE | ID: mdl-38326766

RESUMO

BACKGROUND: Lung cancer (LC) has poor survival outcomes mainly due to diagnosis at late stages. This study explored the anticipated time to seek medical advice for possible LC symptoms and barriers to early presentation in Palestine. METHODS: This cross-sectional study recruited adult participants from hospitals, primary healthcare centers, and public spaces of 11 governorates using convenience sampling. A modified, translated-into-Arabic version of the validated LC awareness measure was used to assess LC symptom awareness, the time needed to seek medical advice and barriers to early presentation. RESULTS: A total of 4762 participants were included. The proportion that would immediately seek medical advice for possible LC symptoms varied according to the symptoms' nature. For respiratory symptoms, this ranged from 15.0% for 'painful cough' to 37.0% for 'coughing up blood'. For non-respiratory symptoms, this ranged from '4.2% for 'unexplained loss of appetite' to 13.8% for 'changes in the shape of fingers or nails'. Participants with good LC symptom awareness were more likely to seek medical advice within a week of recognizing most LC symptoms. About 13.0% would delay their visit to see a doctor after recognizing an LC symptom. The most reported barriers were emotional with 'disliking the visit to healthcare facilities' (59.8%) as the leading barrier. CONCLUSION: LC respiratory symptoms were more likely to prompt early seeking of medical advice. Good LC symptom awareness was associated with a higher likelihood of help-seeking within a week. Educational interventions are needed to promote LC awareness and address the perceived barriers to early presentation in low-resource settings, such as Palestine.


Assuntos
Neoplasias Pulmonares , Humanos , Adulto , Neoplasias Pulmonares/diagnóstico , Neoplasias Pulmonares/epidemiologia , Estudos Transversais , Conhecimentos, Atitudes e Prática em Saúde , Projetos de Pesquisa , Emoções , Aceitação pelo Paciente de Cuidados de Saúde/psicologia
4.
JCO Glob Oncol ; 10: e2300470, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38386956

RESUMO

PURPOSE: To assess colorectal cancer (CRC) awareness and its influence on attitudes toward colonoscopy in Palestine. MATERIALS AND METHODS: Convenience sampling was used to recruit Palestinian adults from hospitals, primary health care centers, and public spaces across 11 governorates. To evaluate the awareness of CRC signs/symptoms, risk factors, and mythical causes, the Bowel Cancer Awareness Measure and Cancer Awareness Measure-Mythical Causes Scale were used after translation into Arabic. For each correctly recognized item, one point was given. The total awareness score of each domain was calculated and categorized into tertiles; the top tertile was considered high awareness, and the other two tertiles were considered low awareness. RESULTS: A total of 4,623 questionnaires were included. Only 1,849 participants (40.0%) exhibited high awareness of CRC signs/symptoms. High awareness of CRC symptoms was associated with higher likelihood of showing positive attitudes toward colonoscopy (odds ratio [OR], 1.21 [95% CI, 1.07 to 1.37]). A total of 1,840 participants (38.9%) demonstrated high awareness of CRC risk factors. Participants with high awareness of CRC risk factors were more likely to display positive attitudes toward colonoscopy (OR, 1.20 [95% CI, 1.07 to 1.37]). Only 219 participants (4.7%) demonstrated high awareness of CRC causation myths. There was no association between awareness of CRC causation myths and positive attitudes toward colonoscopy. CONCLUSION: Awareness of CRC was poor with less than half of the study participants demonstrating high awareness of CRC signs/symptoms and risk factors, and a minority (<5%) displaying high awareness of CRC causation myths. High awareness of CRC signs/symptoms and risk factors was associated with greater likelihood of demonstrating positive attitudes toward colonoscopy. Educational initiatives are needed to address knowledge gaps and dispel misconceptions surrounding CRC.


Assuntos
Neoplasias Colorretais , Adulto , Humanos , Neoplasias Colorretais/diagnóstico , Árabes , Detecção Precoce de Câncer , Fatores de Risco , Colonoscopia
5.
JCO Glob Oncol ; 10: e2300400, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38386954

RESUMO

PURPOSE: To compare colorectal cancer (CRC) awareness between vegetarians and nonvegetarians in Palestine. MATERIALS AND METHODS: The validated Bowel Cancer Awareness Measure and Cancer Awareness Measure-Mythical Causes Scale were translated into Arabic and used to assess awareness of CRC signs/symptoms, risk factors, and mythical causes. The total awareness score of each domain was calculated and categorized into tertiles; the top tertile was considered as good awareness. Multivariable logistic regression analysis was used to examine the association between being a vegetarian and displaying good awareness in each domain. RESULTS: This study included 4,623 participants: 560 vegetarians (12.1%) and 4,063 nonvegetarians (87.9%). Lump in the abdomen was the most recognized CRC sign/symptom among both nonvegetarians (n = 2,969, 73.1%) and vegetarians (n = 452, 80.7%). Vegetarians were less likely than nonvegetarians to display good awareness of CRC signs/symptoms (odds ratio, 0.59 [95% CI, 0.48 to 0.72]). Lack of physical activity was the most identified modifiable CRC risk factor in both nonvegetarians (n = 3,368, 82.9%) and vegetarians (n = 478, 85.4%). Similarly, having a bowel disease was the most identified nonmodifiable risk factor among both nonvegetarians (n = 2,889, 71.1%) and vegetarians (n = 431, 77.0%). There were no associated differences between both groups in the awareness levels of CRC risk factors. The most recognized food-related CRC causation myth in nonvegetarians was drinking from plastic bottles (n = 1,023, 25.2%), whereas it was eating burnt food in vegetarians (n = 176, 31.4%). Having a physical trauma was the most recognized food-unrelated myth in both nonvegetarians (n = 2,356, 58.0%) and vegetarians (n = 396, 70.7%). There were no associated differences in the awareness of CRC causation myths between both groups. CONCLUSION: Awareness of CRC was notably low in both Palestinian vegetarians and nonvegetarians. Particularly, vegetarians demonstrated lower awareness of CRC signs and symptoms.


Assuntos
Neoplasias Colorretais , Dieta Vegetariana , Humanos , Estudos Transversais , Árabes , Vegetarianos , Neoplasias Colorretais/diagnóstico , Neoplasias Colorretais/epidemiologia
6.
JCO Glob Oncol ; 10: e2300373, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38386955

RESUMO

PURPOSE: Examining the association of breast cancer (BC) symptom awareness with time to help seeking and exploring barriers to timely presentation may enhance the effectiveness of BC awareness campaigns and early detection efforts. This study aimed to assess the anticipated time for seeking medical advice when experiencing a potential BC symptom among women in Palestine and to identify their barriers to early presentation. MATERIALS AND METHODS: A convenience sampling method was used to recruit adult women from hospitals, primary health care facilities, and public areas across 11 governorates in Palestine. A translated-into-Arabic version of the validated BC Awareness Measure was used. The questionnaire consisted of three sections: sociodemographic information, recognition of 13 BC symptoms and reporting time for seeking medical advice, and barriers to early presentation. RESULTS: A total of 5,257 questionnaires were included. The proportion of participants who would seek medical advice immediately varied on the basis of the nature of BC symptoms. For symptoms related to the breast, the proportion ranged from 25.7% for redness of the breast skin to 53.5% for a lump or thickening in the breast. For symptoms related to the nipple, the proportion ranged from 30.7% for nipple rash to 48.0% for discharge or bleeding from the nipple. Exhibiting good BC symptom awareness was associated with a higher likelihood of seeking medical advice within a week for all BC symptoms. Emotional barriers were the most frequently reported barriers. There was no association between increasing levels of BC awareness and reporting fewer or more barriers. CONCLUSION: The nature of BC symptoms had an impact on help-seeking behaviors. Participants with good BC symptom awareness were more likely to seek medical advice earlier.


Assuntos
Neoplasias da Mama , Adulto , Humanos , Feminino , Neoplasias da Mama/diagnóstico , Neoplasias da Mama/terapia , Estudos Transversais , Árabes , Conhecimentos, Atitudes e Prática em Saúde , Aceitação pelo Paciente de Cuidados de Saúde
7.
BMC Public Health ; 24(1): 189, 2024 01 16.
Artigo em Inglês | MEDLINE | ID: mdl-38229049

RESUMO

BACKGROUND: Cervical cancer (CC) myths and beliefs can negatively impact women's preventive behaviors, including vaccination against human papillomavirus and having regular screening tests. This study aimed to examine awareness of Palestinian women about myths related to CC causation and investigated factors associated with good awareness. METHODS: A national cross-sectional study was conducted to recruit adult Palestinian women from hospitals, primary healthcare facilities, and public areas in 11 Palestinian governorates. A translated-into-Arabic version of the Cancer Awareness Measure-Mythical Causes Scale was used to collect data. Awareness level was determined based on the number of CC myths around CC causation recognized to be incorrect: poor (0-4), fair (5-9), and good (10-13). RESULTS: A total of 7058 questionnaires were included. Myths unrelated to food were more commonly recognized as incorrect compared to those related to food. The most recognized food-unrelated myth was 'having a physical trauma' (n = 3714, 52.6%), whereas the least recognized was 'using mobile phones' (n = 2238, 31.7%). The most recognized food-related myth was 'drinking from plastic bottles' (n = 2708, 38.4%), whereas the least recognized was 'eating food containing additives' (n = 1118, 15.8%). Only 575 participants (8.1%) displayed good awareness and promptly recognized at least 10 out of 13 myths around CC causation as incorrect. Factors associated with lower likelihood of displaying good awareness of myths around CC causation included living in the West Bank and Jerusalem, being married, widowed or divorced, knowing someone with cancer, and visiting hospitals or primary healthcare centers. CONCLUSIONS: A very small proportion of Palestinian women recognized 10 or more myths around CC causes as incorrect. Initiatives addressing CC myths are needed in the Palestinian community.


Assuntos
Neoplasias do Colo do Útero , Adulto , Humanos , Feminino , Neoplasias do Colo do Útero/epidemiologia , Neoplasias do Colo do Útero/etiologia , Neoplasias do Colo do Útero/prevenção & controle , Estudos Transversais , Árabes , Conhecimentos, Atitudes e Prática em Saúde , Oriente Médio , Inquéritos e Questionários
8.
JCO Glob Oncol ; 10: e2300295, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38166235

RESUMO

PURPOSE: To explore public awareness of myths around colorectal cancer (CRC) causation in Palestine and to examine factors associated with good awareness. MATERIALS AND METHODS: Convenience sampling was used to recruit adult Palestinians from governmental hospitals, primary health care centers, and public spaces. Recognizing 13 myths around CRC causation was assessed using a translated-into-Arabic version of the Cancer Awareness Measure-Mythical Causes Scale. Awareness level was determined based on the number of CRC mythical causes recognized: poor (0-4), fair (5-9), and good (10-13). Multivariable logistic regression was used to examine the association between sociodemographic characteristics and displaying good awareness. It adjusted for age group, sex, education, occupation, monthly income, residence, marital status, having chronic diseases, being a vegetarian, knowing someone with cancer, and site of data collection. RESULTS: Of 5,254 participants approached, 4,877 agreed to participate (response rate, 92.3%). A total of 4,623 questionnaires were included in the final analysis: 2,700 from the West Bank and Jerusalem (WBJ) and 1,923 from the Gaza Strip. Only 219 participants (4.7%) demonstrated good awareness of myths around CRC causation. WBJ participants were twice more likely than those from the Gaza Strip to display good recognition (5.9% v 3.1%). Male sex, living in the WBJ, and visiting hospitals were all associated with an increase in the likelihood of displaying good awareness. Conversely, knowing someone with cancer was associated with a decrease in the likelihood of displaying good awareness. Having a physical trauma was the most recognized CRC causation myth (n = 2,752, 59.5%), whereas eating food containing additives was the least (n = 456, 9.8%). CONCLUSION: Only 4.7% displayed good ability to recognize myths around CRC causation. Future educational interventions are needed to help the public distinguish the evidence-based versus mythical causes of CRC.


Assuntos
Árabes , Neoplasias Colorretais , Adulto , Humanos , Masculino , Estudos Transversais , Oriente Médio/epidemiologia , Inquéritos e Questionários , Neoplasias Colorretais/diagnóstico , Neoplasias Colorretais/epidemiologia , Neoplasias Colorretais/etiologia
9.
JCO Glob Oncol ; 9: e2300184, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-38085044

RESUMO

PURPOSE: Having an accurate knowledge of what truly increases the likelihood of developing lung cancer (LC) may help people make better decisions about lifestyle changes that could potentially lower their risk. This study assessed current beliefs in LC causation myths among Palestinians and explored factors associated with displaying good recognition of such myths. METHODS: A national cross-sectional study was conducted from July 2019 to March 2020. A modified version of the Cancer Awareness Measure-Mythical Causes Scale was used for data collection. The awareness level of LC causation myths was determined based on the number of myths recognized to be incorrect: poor (0-4), fair (5-9), and good (10-13). RESULTS: A total of 4,817 participants completed the questionnaire of 5,174 approached (response rate = 93.1%). In total, 4,762 participants were included in the final analysis. Myths unrelated to food were more commonly recognized than food-related myths. The food-related myth most frequently recognized was eating burnt food (n = 1,427; 30.0%) followed by drinking from plastic bottles (n = 1,389; 29.2%). The food-related myth least commonly recognized was eating food containing additives (n = 737; 15.5%). The most frequently recognized myth unrelated to food was having a physical trauma (n = 2,903; 61%), whereas the least was using cleaning products (n = 1,140; 23.9%). Only 287 participants (6%) displayed good awareness. Having a chronic disease and knowing someone with cancer were associated with a decrease in the likelihood of displaying good awareness. Conversely, participants who were smoking cigarettes/shisha and those recruited from hospitals had an associated increase in the likelihood of displaying good awareness. CONCLUSION: This study found very poor awareness of LC causation myths, with only 6% recognizing ≥10 myths. Initiatives addressing LC mythical causes are needed.


Assuntos
Neoplasias Pulmonares , Humanos , Neoplasias Pulmonares/epidemiologia , Neoplasias Pulmonares/etiologia , Estudos Transversais , Árabes , Inquéritos e Questionários
10.
BMC Public Health ; 23(1): 2370, 2023 11 29.
Artigo em Inglês | MEDLINE | ID: mdl-38031084

RESUMO

BACKGROUND: The discussion about breast cancer (BC) causation continues to be surrounded by a number of myths and misbeliefs. If efforts are misdirected towards reducing risk from false mythical causes, individuals might be less likely to consider and adopt risk-reducing behaviors for evidence-based BC causes. This national study aimed to assess the awareness of BC causation myths and misbeliefs among Palestinian women, and examine the factors associated with having good awareness. METHODS: This national cross-sectional study recruited adult women from government hospitals, primary healthcare centers, and public spaces in 11 governorates in Palestine. A modified version of the Cancer Awareness Measure-Mythical Causes Scale was used to collect data. The level of awareness of BC causation myths was determined based on the number of myths recognized to be incorrect: poor (0-5), fair (6-10), or good (11-15). RESULTS: A total of 5,257 questionnaires were included. Only 269 participants (5.1%) demonstrated good awareness (i.e., recognizing more than 10 out of 15 BC mythical causes). There were no notable differences in displaying good awareness between the main areas of Palestine, the Gaza Strip and the West Bank and Jerusalem (5.1% vs. 5.1%). Having chronic disease as well as visiting hospitals and primary healthcare centers were associated with a decrease in the likelihood of displaying good awareness. Myths related to food were less frequently recognized as incorrect than food-unrelated myths. 'Eating burnt food' was the most recognized food-related myth (n = 1414, 26.9%), while 'eating food containing additives' was the least recognized (n = 599, 11.4%). 'Having a physical trauma' was the most recognized food-unrelated myth (n = 2795, 53.2%), whereas the least recognized was 'wearing tight bra' (n = 1018, 19.4%). CONCLUSIONS: A very small proportion of Palestinian women could recognize 10 or more myths around BC causation. There is a substantial need to include clear information about BC causation in future educational interventions besides focusing on BC screening, signs and symptoms, and risk factors.


Assuntos
Neoplasias da Mama , Adulto , Humanos , Feminino , Neoplasias da Mama/epidemiologia , Neoplasias da Mama/etiologia , Neoplasias da Mama/diagnóstico , Estudos Transversais , Árabes , Oriente Médio/epidemiologia , Inquéritos e Questionários , Conhecimentos, Atitudes e Prática em Saúde
11.
BMC Cancer ; 23(1): 975, 2023 Oct 13.
Artigo em Inglês | MEDLINE | ID: mdl-37833659

RESUMO

BACKGROUND: Several factors contribute to delayed presentation with ovarian cancer (OC) symptoms including poor symptom awareness and barriers to seeking help. This study explored the anticipated time to seek medical advice for possible OC symptoms and its association with OC symptom awareness. In addition, it examined perceived barriers that may delay help-seeking among Palestinian women. METHODS: A cross-sectional study was conducted among adult women (≥ 18 years) recruited from hospitals, primary healthcare centers, and public spaces in 11 Palestinian governorates. A modified version of the OC awareness measure was used to collect data in face-to-face interviews. The questionnaire comprised three sections: sociodemographic details, awareness of 11 OC symptoms and time to seek medical advice, and barriers to early presentation. RESULTS: Of 6095 participants approached, 5618 completed the OCAM (response rate = 92.1%). The proportion of participants who would immediately seek medical advice for a possible OC symptom varied based on the symptom's nature. For OC symptoms with pain, the proportion that reported immediate seeking of medical advice ranged from 7.9% for 'persistent low back pain' to 13.6% for 'persistent pain in the pelvis'. For non-specific potential OC symptoms, the proportion that reported immediate seeking of medical advice ranged from 2.3% for 'feeling full persistently' to 15.8% for 'increased abdominal size on most days'. Good OC symptom awareness was associated with higher likelihood of seeking medical advice within a week from recognizing 10 out of 11 OC symptoms. Emotional barriers were the most common barriers with 'feeling scared' as the most reported barrier (n = 1512, 52.4%). Displaying good OC symptom awareness was associated with a lower likelihood of reporting ≥ 4 emotional barriers (OR = 0.61, 95% CI: 0.38-0.98). CONCLUSION: Participants with good OC symptom awareness were more likely to seek medical advice earlier and to display fewer emotional barriers. Establishing educational interventions to raise OC awareness may help in promoting earlier help-seeking and, thus, facilitate earlier diagnosis and improved prognosis.


Assuntos
Árabes , Neoplasias Ovarianas , Adulto , Humanos , Feminino , Estudos Transversais , Detecção Precoce de Câncer , Conhecimentos, Atitudes e Prática em Saúde , Neoplasias Ovarianas/diagnóstico , Neoplasias Ovarianas/epidemiologia , Neoplasias Ovarianas/psicologia , Aceitação pelo Paciente de Cuidados de Saúde/psicologia , Dor
13.
Sci Rep ; 13(1): 6871, 2023 04 27.
Artigo em Inglês | MEDLINE | ID: mdl-37105988

RESUMO

This study explored the anticipated time to seek medical advice for possible colorectal cancer (CRC) signs/symptoms and its association with CRC symptom awareness. In addition, it examined perceived barriers that may delay seeking medical advice. Palestinian adults were recruited from hospitals, primary healthcare centers, and public spaces in 11 governorates. A modified, translated-into-Arabic version of the validated Bowel Cancer Awareness Measure was used. The questionnaire comprised three sections: sociodemographics, assessment of CRC symptom awareness and time to seek medical advice, and barriers to early presentation. A total of 4623 participants were included. The proportion that reported seeking immediate medical advice for possible CRC signs/symptoms with blood or mass ranged from 47.1% for 'blood in stools' to 59.5% for 'bleeding from back passage'. Less than half of the participants reported immediate seeking of medical advice for non-specific symptoms (ranging from 5.4% for 'loss of appetite' to 42.0% for 'anemia') and other gastrointestinal symptoms (ranging from 7.7% for 'feeling persistently full' to 35.7% for 'change in bowel habits'). Good CRC symptom awareness was associated with higher likelihood of seeking medical advice within a week from recognizing a CRC symptom. About 13.0% reported a delay to visit their doctor after recognizing a CRC symptom. The most reported barriers were practical with 'would try some herbs first' (50.9%) as the leading barrier. CRC symptoms with blood or mass prompted earlier help seeking. Participants with good CRC awareness were more likely to seek medical advice within a week.


Assuntos
Árabes , Neoplasias Colorretais , Adulto , Humanos , Conhecimentos, Atitudes e Prática em Saúde , Neoplasias Colorretais/diagnóstico , Inquéritos e Questionários , Aconselhamento
14.
Bioinformatics ; 39(5)2023 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-36961334

RESUMO

MOTIVATION: Pairwise sequence alignment is a very time-consuming step in common bioinformatics pipelines. Speeding up this step requires heuristics, efficient implementations, and/or hardware acceleration. A promising candidate for all of the above is the recently proposed GenASM algorithm. We identify and address three inefficiencies in the GenASM algorithm: it has a high amount of data movement, a large memory footprint, and does some unnecessary work. RESULTS: We propose Scrooge, a fast and memory-frugal genomic sequence aligner. Scrooge includes three novel algorithmic improvements which reduce the data movement, memory footprint, and the number of operations in the GenASM algorithm. We provide efficient open-source implementations of the Scrooge algorithm for CPUs and GPUs, which demonstrate the significant benefits of our algorithmic improvements. For long reads, the CPU version of Scrooge achieves a 20.1×, 1.7×, and 2.1× speedup over KSW2, Edlib, and a CPU implementation of GenASM, respectively. The GPU version of Scrooge achieves a 4.0×, 80.4×, 6.8×, 12.6×, and 5.9× speedup over the CPU version of Scrooge, KSW2, Edlib, Darwin-GPU, and a GPU implementation of GenASM, respectively. We estimate an ASIC implementation of Scrooge to use 3.6× less chip area and 2.1× less power than a GenASM ASIC while maintaining the same throughput. Further, we systematically analyze the throughput and accuracy behavior of GenASM and Scrooge under various configurations. As the best configuration of Scrooge depends on the computing platform, we make several observations that can help guide future implementations of Scrooge. AVAILABILITY AND IMPLEMENTATION: https://github.com/CMU-SAFARI/Scrooge.


Assuntos
Algoritmos , Computadores , Genoma , Genômica , Biologia Computacional
15.
Bioinformatics ; 39(5)2023 05 04.
Artigo em Inglês | MEDLINE | ID: mdl-36971586

RESUMO

MOTIVATION: Sequence alignment is a memory bound computation whose performance in modern systems is limited by the memory bandwidth bottleneck. Processing-in-memory (PIM) architectures alleviate this bottleneck by providing the memory with computing competencies. We propose Alignment-in-Memory (AIM), a framework for high-throughput sequence alignment using PIM, and evaluate it on UPMEM, the first publicly available general-purpose programmable PIM system. RESULTS: Our evaluation shows that a real PIM system can substantially outperform server-grade multi-threaded CPU systems running at full-scale when performing sequence alignment for a variety of algorithms, read lengths, and edit distance thresholds. We hope that our findings inspire more work on creating and accelerating bioinformatics algorithms for such real PIM systems. AVAILABILITY AND IMPLEMENTATION: Our code is available at https://github.com/safaad/aim.


Assuntos
Algoritmos , Software , Alinhamento de Sequência , Biologia Computacional , Análise de Sequência de DNA , Sequenciamento de Nucleotídeos em Larga Escala
16.
NAR Genom Bioinform ; 5(1): lqad004, 2023 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-36685727

RESUMO

Generating the hash values of short subsequences, called seeds, enables quickly identifying similarities between genomic sequences by matching seeds with a single lookup of their hash values. However, these hash values can be used only for finding exact-matching seeds as the conventional hashing methods assign distinct hash values for different seeds, including highly similar seeds. Finding only exact-matching seeds causes either (i) increasing the use of the costly sequence alignment or (ii) limited sensitivity. We introduce BLEND, the first efficient and accurate mechanism that can identify both exact-matching and highly similar seeds with a single lookup of their hash values, called fuzzy seed matches. BLEND (i) utilizes a technique called SimHash, that can generate the same hash value for similar sets, and (ii) provides the proper mechanisms for using seeds as sets with the SimHash technique to find fuzzy seed matches efficiently. We show the benefits of BLEND when used in read overlapping and read mapping. For read overlapping, BLEND is faster by 2.4×-83.9× (on average 19.3×), has a lower memory footprint by 0.9×-14.1× (on average 3.8×), and finds higher quality overlaps leading to accurate de novo assemblies than the state-of-the-art tool, minimap2. For read mapping, BLEND is faster by 0.8×-4.1× (on average 1.7×) than minimap2. Source code is available at https://github.com/CMU-SAFARI/BLEND.

17.
BMJ Open ; 13(1): e061110, 2023 01 17.
Artigo em Inglês | MEDLINE | ID: mdl-36653053

RESUMO

OBJECTIVES: To evaluate lung cancer (LC) risk factor awareness among Palestinians and identify factors associated with good awareness. DESIGN: Cross-sectional study. SETTINGS: Participants were recruited using convenience sampling from hospitals, primary healthcare centres (PHCs) and public spaces located at 11 governorates in Palestine. PARTICIPANTS: Of 5174 approached, 4817 participants completed the questionnaire (response rate=93.1%). A total of 4762 questionnaires were included: 2742 from the West Bank and Jerusalem (WBJ) and 2020 from the Gaza Strip. Exclusion criteria were working or studying in a health-related field, having a nationality other than Palestinian and visiting oncology departments or clinics at the time of data collection. TOOL: A modified version of the validated LC Awareness Measure was used for data collection. PRIMARY AND SECONDARY OUTCOMES: The primary outcome was LC risk factor awareness level as determined by the number of factors recognised: poor (0-3), fair (4-7) and good (8-10). Secondary outcomes include the recognition of each LC risk factor. RESULTS: Smoking-related risk factors were more often recognised than other LC risk factors. The most recognised risk factors were 'smoking cigarettes' (n=4466, 93.8%) and 'smoking shisha (waterpipes)' (n=4337, 91.1%). The least recognised risk factors were 'having a close relative with LC' (n=2084, 43.8%) and 'having had treatment for any cancer in the past' (n=2368, 49.7%).A total of 2381 participants (50.0%) displayed good awareness of LC risk factors. Participants from the WBJ and the Gaza Strip had similar likelihood to display good awareness (50.6% vs 49.1%). Being≥45 years, having higher education and monthly income, knowing someone with cancer and visiting hospitals and PHCs seemed to have a positive impact on displaying good awareness. CONCLUSION: Half of study participants displayed good awareness of LC risk factors. Educational interventions are warranted to further improve public awareness of LC risk factors, especially those unrelated to smoking.


Assuntos
Árabes , Neoplasias Pulmonares , Humanos , Estudos Transversais , Fatores de Risco , Inquéritos e Questionários , Neoplasias Pulmonares/epidemiologia , Neoplasias Pulmonares/etiologia
18.
JCO Glob Oncol ; 8: e2200087, 2022 12.
Artigo em Inglês | MEDLINE | ID: mdl-36508704

RESUMO

PURPOSE: This study aimed to assess awareness of Palestinian women about breast cancer (BC) age-related and lifetime risks and its risk factors and to identify factors associated with good awareness. MATERIALS AND METHODS: Adult women were recruited from government hospitals, primary health care centers, and public spaces in 11 governorates in Palestine. Recognition of 14 BC risk factors was assessed using a translated-into-Arabic version of the validated BC awareness measure. The level of BC risk factor awareness was determined on the basis of the number of risk factors recognized: poor (0-4), fair (5-9), and good (10-14). RESULTS: Of 6,269 potential participants approached, 5,434 agreed and completed the questionnaire (response rate = 86.7%). A total of 5,257 questionnaires were included: 2,706 from the West Bank and Jerusalem and 2,551 from the Gaza Strip. Only 173 participants (3.3%) recognized the age-related risk of BC. More than one quarter (n = 1,465; 27.9%) recognized the lifetime risk of BC. The most recognized modifiable risk factor was not breastfeeding (n = 4,937; 93.9%), whereas the least recognized was having children later on in life or not at all (n = 1,755; 33.4%). The most recognized nonmodifiable risk factor was radiation exposure (n = 4,579; 87.1%), whereas the least recognized was starting the periods at an early age (n = 1,030; 19.6%). In total, 2,024 participants (38.4%) demonstrated good BC risk factor awareness. Participants from the Gaza Strip had a higher likelihood than participants from the West Bank and Jerusalem to have good awareness (42.0% v 35.2%). Age ≥ 40 years, postsecondary education, and visiting hospitals and primary health care centers were all associated with an increase in the likelihood of having good BC risk factor awareness. CONCLUSION: The awareness of BC risk factors was suboptimal. These findings highlight the need for implementing health education programs combined with consistent use of ad hoc opportunities to raise awareness by health care providers.


Assuntos
Neoplasias da Mama , Adulto , Criança , Humanos , Feminino , Neoplasias da Mama/epidemiologia , Estudos Transversais , Conhecimentos, Atitudes e Prática em Saúde , Árabes , Fatores de Risco
19.
Comput Struct Biotechnol J ; 20: 4579-4599, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36090814

RESUMO

We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently exist major computational bottlenecks and inefficiencies throughout the entire genome analysis pipeline, because state-of-the-art genome sequencing technologies are still not able to read a genome in its entirety. We describe the ongoing journey in significantly improving the performance, accuracy, and efficiency of genome analysis using intelligent algorithms and hardware architectures. We explain state-of-the-art algorithmic methods and hardware-based acceleration approaches for each step of the genome analysis pipeline and provide experimental evaluations. Algorithmic approaches exploit the structure of the genome as well as the structure of the underlying hardware. Hardware-based acceleration approaches exploit specialized microarchitectures or various execution paradigms (e.g., processing inside or near memory) along with algorithmic changes, leading to new hardware/software co-designed systems. We conclude with a foreshadowing of future challenges, benefits, and research directions triggered by the development of both very low cost yet highly error prone new sequencing technologies and specialized hardware chips for genomics. We hope that these efforts and the challenges we discuss provide a foundation for future work in making genome analysis more intelligent.

20.
BMC Womens Health ; 22(1): 352, 2022 08 19.
Artigo em Inglês | MEDLINE | ID: mdl-35986304

RESUMO

BACKGROUND: Progress has been made in the reduction of morbidity and mortality of cervical cancer by the implementation of human papillomavirus (HPV) vaccination programs. This study aimed to assess the awareness of Palestinian women about HPV as well as their knowledge and acceptability of the HPV vaccine and to examine the factors associated with good awareness. METHODS: This was a national cross-sectional study. Adult women were recruited from hospitals, primary healthcare centers, and public spaces in 11 Palestinian governorates using convenience sampling. A structured questionnaire was used for data collection. For each correctly answered question, one point was given. The total score was calculated and categorized into poor (0-10) and good awareness (11-21). RESULTS: The questionnaire was completed by 7223 women out of 8086 who were approached (response rate = 89.3%). A total of 7058 questionnaires were included in the final analysis; 4403 from the West Bank and Jerusalem (WBJ) and 2655 from the Gaza Strip. Women recruited from the Gaza Strip were younger, getting lower monthly incomes, and with fewer chronic diseases than women recruited from the WBJ. Only 33 women (0.5%) displayed good awareness of HPV and its vaccine with 0.7% of women from WBJ and only 0.2% of women from the Gaza Strip. Completing post-secondary education, being employed or a student, and having a higher monthly income were associated with an increase in the likelihood of having good awareness. Among women who had heard of HPV (n = 571, 8.1%), only 46 women (8.1%) reported familiarity with its vaccine. Women from the WBJ were more likely than women from the Gaza Strip to have heard about the HPV vaccine (0.9% vs. 0.2%). Most women agreed to receive the HPV vaccine themselves or for their daughters if it was given without cost or with a co-payment. No differences were found in the likelihood of agreeing to receive the HPV vaccine among women in the WBJ versus the Gaza Strip. CONCLUSION: The overall awareness of HPV and its vaccine was extremely low. Inclusion of the HPV vaccine in the national immunization program could change this, especially as the HPV vaccine appeared to be acceptable.


Assuntos
Alphapapillomavirus , Infecções por Papillomavirus , Vacinas contra Papillomavirus , Neoplasias do Colo do Útero , Adulto , Árabes , Estudos Transversais , Feminino , Conhecimentos, Atitudes e Prática em Saúde , Humanos , Papillomaviridae , Infecções por Papillomavirus/prevenção & controle , Vacinas contra Papillomavirus/uso terapêutico , Aceitação pelo Paciente de Cuidados de Saúde , Políticas , Inquéritos e Questionários , Neoplasias do Colo do Útero/prevenção & controle , Vacinação
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