Critical Assessment of Metagenome Interpretation: the second round of challenges.

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II challenge engaged the community to assess methods on realistic and complex datasets with long- and short-read sequences, created computationally from around 1,700 new and known genomes, as well as 600 new plasmids and viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due to long-read data. Related strains still were challenging for assembly and genome recovery through binning, as was assembly quality for the latter. Profilers markedly matured, with taxon profilers and binners excelling at higher bacterial ranks, but underperforming for viruses and Archaea. Clinical pathogen detection results revealed a need to improve reproducibility. Runtime and memory usage analyses identified efficient programs, including top performers with other metrics. The results identify challenges and guide researchers in selecting methods for analyses.

A framework for high-throughput sequence alignment using real processing-in-memory systems.

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.

Scrooge: a fast and memory-frugal genomic sequence aligner for CPUs, GPUs, and ASICs.

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.

Anticipated time to seek medical advice for possible lung cancer symptoms and barriers to timely presentation in Palestine: a national cross-sectional study.

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.

Understanding the interplay of colorectal cancer awareness and attitudes among Palestinians: a national cross-sectional study.

BACKGROUND: In Palestine, colorectal cancer (CRC) is the second most common cause of cancer-related mortality after lung cancer. No studies have examined the relationship between CRC awareness and attitudes. This study aimed to investigate the interplay between CRC awareness and attitudes among the Palestinian population. METHODS: A nationwide cross-sectional survey was carried out between July 2019 and March 2020. Convenience sampling was used to collect data from hospitals, primary healthcare facilities, and public areas in 11 governorates. Modified, translated-into-Arabic versions of the validated Bowel Cancer Awareness Measure and Cancer Awareness Measure-Mythical Causes Scale were utilized to assess the awareness of CRC signs/symptoms, risk factors, and causation myths. The cumulative awareness score for each domain was computed and stratified into tertiles. The top tertile denoted 'high' awareness, while the remaining two tertiles denoted 'low' awareness. RESULTS: The final analysis included 4,623 participants; of whom, 3115 (67.4%) reported positive attitudes toward CRC. In total, 1,849 participants (40.0%) had high awareness of CRC signs/symptoms. There was no association between displaying a high awareness of CRC signs/symptoms and having positive attitudes toward CRC. A total of 1,840 participants (38.9%) showed high awareness of CRC risk factors. Participants with high CRC risk factor awareness were more likely to display positive attitudes toward CRC (OR = 1.22, 95% CI: 1.07-1.39). Only 219 participants (4.7%) had high awareness of CRC causation myths. Participants with high awareness of CRC causation myths were more likely to exhibit positive attitudes toward CRC (OR = 2.48, 95% CI: 1.71-3.58). CONCLUSION: A high awareness level of CRC risk factors and causation myths was associated with a greater likelihood of demonstrating positive attitudes toward CRC in terms of perceived susceptibility, importance of early detection, and consequences of developing the disease. Future educational interventions should focus on raising public awareness about CRC, with a particular emphasis on risk factors and causation myths, to maximize the potential for shaping favorable attitudes toward the disease.

Common misconceptions and myths about ovarian cancer causation: a national cross-sectional study from palestine.

BACKGROUND: Women's inability to recognize ovarian cancer (OC) causation myths to be incorrect may lead to behavioral changes that could distract them from actual risk factors and impact their treatment decision making. This study examined Palestinian women's recognition of OC mythical causes, and explored factors associated with good recognition. METHODS: A national cross-sectional study was conducted. Adult Palestinian women were recruited from hospitals, primary healthcare facilities, and public areas in 11 governorates. The Cancer Awareness Measure-Mythical Causes Scale was modified and utilized for data collection. Awareness level was determined based on the number of myths around OC causation recognized to be incorrect: poor (0-4), fair (5-9), and good (10-13). RESULTS: A total of 5618 participants agreed and completed the questionnaire out of 6095 approached (response rate = 92.1%), and 5411 questionnaires were included in the final analysis. The most recognized food-related myth was 'drinking from plastic bottles' (n = 1370, 25.3%) followed by 'eating burnt food' (n = 1298, 24.0%). The least recognized food-related myth was 'eating food containing additives' (n = 611, 11.3%). The most recognized food-unrelated myth was 'having a physical trauma' (n = 2899, 53.6%), whereas the least recognized was 'using mobile phones' (n = 1347, 24.9%). Only 273 participants (5.1%) had good awareness of OC causation myths as incorrect. Earning higher monthly incomes as well as visiting governmental healthcare facilities were associated with a decrease in the likelihood of exhibiting good awareness. CONCLUSION: The overall recognition of OC causation myths was low. Addressing mythical beliefs should be included in OC prevention strategies and public health interventions to improve women's understanding of OC risk factors versus mythical causes.

Myths and common misbeliefs about cervical cancer causation among Palestinian women: a national cross-sectional study.

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.

Differences in colorectal cancer awareness between screening eligible vs. ineligible Palestinians: a national cross-sectional study.

BACKGROUND: This study aimed to compare colorectal cancer (CRC) awareness between screening-eligible and ineligible individuals in Palestine. METHODS: Convenience sampling was utilized to recruit Palestinian adults from diverse settings, including hospitals, primary healthcare centers and public spaces across 11 governorates. The evaluation of CRC awareness in terms of signs/symptoms, risk factors and causation myths was conducted using Arabic-translated, modified versions of the validated instruments, the Bowel Cancer Awareness Measure and the Cancer Awareness Measure-Mythical Causes Scale. RESULTS: The final analysis included 2698 participants, with 2158 (80.9%) eligible for CRC screening and 540 (19.1%) ineligible for it. The most recognized CRC sign/symptom was 'lump in the abdomen' in both screening-eligible (n = 386, 71.5%) and ineligible (n = 1582, 73.3%) groups. 'Lack of physical activity' was the most recognized risk factor in both groups (eligible: n = 451, 83.5%; ineligible: n = 1766, 81.8%). The most reported causation myth in both groups was 'having a physical trauma' (eligible: n = 340, 63.0%; ineligible: n = 1353, 62.7%). In the screening-eligible group, only 210 participants (38.9%) demonstrated high awareness of CRC signs/symptoms, 213 participants (39.4%) showed high awareness of CRC risk factors and only 46 participants (8.5%) displayed high awareness of CRC causation myths. There were no significant associations between being eligible for screening colonoscopy and the awareness levels of CRC signs/symptoms, risk factors and causation myths. CONCLUSION: Overall, awareness levels of CRC signs/symptoms, risk factors and causation myths were notably low among screening-eligible participants. There were no differences in awareness levels between individuals eligible for colonoscopy and those who were not.

Anticipated time to seek medical advice for possible ovarian cancer symptoms and perceived barriers to early presentation among Palestinian women: a national cross-sectional study.

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.

Common myths and misconceptions about breast cancer causation among Palestinian women: a national cross-sectional study.

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.

SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs.

MOTIVATION: We introduce SneakySnake, a highly parallel and highly accurate pre-alignment filter that remarkably reduces the need for computationally costly sequence alignment. The key idea of SneakySnake is to reduce the approximate string matching (ASM) problem to the single net routing (SNR) problem in VLSI chip layout. In the SNR problem, we are interested in finding the optimal path that connects two terminals with the least routing cost on a special grid layout that contains obstacles. The SneakySnake algorithm quickly solves the SNR problem and uses the found optimal path to decide whether or not performing sequence alignment is necessary. Reducing the ASM problem into SNR also makes SneakySnake efficient to implement on CPUs, GPUs and FPGAs. RESULTS: SneakySnake significantly improves the accuracy of pre-alignment filtering by up to four orders of magnitude compared to the state-of-the-art pre-alignment filters, Shouji, GateKeeper and SHD. For short sequences, SneakySnake accelerates Edlib (state-of-the-art implementation of Myers's bit-vector algorithm) and Parasail (state-of-the-art sequence aligner with a configurable scoring function), by up to 37.7× and 43.9× (>12× on average), respectively, with its CPU implementation, and by up to 413× and 689× (>400× on average), respectively, with FPGA and GPU acceleration. For long sequences, the CPU implementation of SneakySnake accelerates Parasail and KSW2 (sequence aligner of minimap2) by up to 979× (276.9× on average) and 91.7× (31.7× on average), respectively. As SneakySnake does not replace sequence alignment, users can still obtain all capabilities (e.g. configurable scoring functions) of the aligner of their choice, unlike existing acceleration efforts that sacrifice some aligner capabilities. AVAILABILITYAND IMPLEMENTATION: https://github.com/CMU-SAFARI/SneakySnake. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Awareness of human papillomavirus and acceptability of the vaccine among women in Palestine: is it time for policy adjustment?

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.

Awareness of Palestinians about lung cancer symptoms: a national cross-sectional study.

BACKGROUND: The majority of lung cancer (LC) cases are diagnosed at an advanced stage. Poor awareness of LC symptoms is a contributor to late diagnosis. This study aimed to assess the awareness of LC symptoms among Palestinians, and to examine the factors associated with displaying good awareness. METHODS: Participants were recruited from hospitals, primary healthcare centers and public spaces using convenience sampling. A translated-into-Arabic version of the validated LC awareness measure was used to assess recognition of 14 LC symptoms. One point was given for each recognized symptom. The total score was calculated and categorized based on the number of symptoms recognized: poor (0-4), fair (5-9), and good (10-14). Multivariable logistic regression was used to examine the association between participant characteristics and having good awareness. The multivariable analysis adjusted for age-group, gender, education, monthly income, occupation, residence, marital status, any chronic disease, knowing someone with cancer, smoking history, and site of data collection. RESULTS: Of 5174 potential participants approached, 4817 completed the questionnaire (response rate = 93.1%) and 4762 were included in the final analysis. Of these, 2742 (56.9%) were from the West Bank and Jerusalem (WBJ) and 2020 (43.1%) were from the Gaza Strip. Participants from the WBJ were older, had higher monthly income but lower education, and suffered from more chronic diseases. The most recognized respiratory LC symptom was 'worsening in an existing cough'(n = 3884, 81.6%) while the least recognized was 'a cough that does not go away for two or three weeks'(n = 2951, 62.0%). The most recognized non-respiratory LC symptom was 'persistent tiredness or lack of energy'(n = 3205, 67.3%) while the least recognized was 'persistent shoulder pain'(n = 1170, 24.6%). A total of 2466 participants (51.8%) displayed good awareness of LC symptoms. Participants from both the Gaza Strip and the WBJ had similar likelihoods to have good awareness levels. Factors associated with a higher likelihood to display good awareness included female gender, having post-secondary education, being employed, knowing someone with cancer, and visiting hospitals and primary healthcare centers. CONCLUSION: About half of the study participants displayed a good level of awareness of LC symptoms. Further improvement in public awareness of LC symptoms by educational interventions might reduce LC mortality by promoting early diagnosis.

Awareness of colorectal cancer signs and symptoms: a national cross-sectional study from Palestine.

BACKGROUND: In low-resource settings, the awareness level of colorectal cancer (CRC) signs and symptoms plays a crucial role in early detection and treatment. This study examined the public awareness level of CRC signs and symptoms in Palestine and investigated the factors associated with good awareness. METHODS: This was a national cross-sectional study conducted at hospitals, primary healthcare centers, and public spaces in 11 governorates across Palestine between July 2019 and March 2020. A translated-into-Arabic version of the validated bowel cancer awareness measure (BoCAM) was utilized to assess the awareness level of CRC signs and symptoms. For each correctly identified CRC sign/symptom, one point was given. The total score (ranging from 0 to 12) was calculated and categorized into three categories based on the number of symptoms recognized: poor (0 to 4), fair (5 to 8), and good awareness (9 to 12). RESULTS: Of 5254 approached, 4877 participants completed the questionnaire (response rate = 92.3%). A total of 4623 questionnaires were included in the analysis; 1923 were from the Gaza Strip and 2700 from the West Bank and Jerusalem (WBJ). Participants from the Gaza Strip were younger, gained lower monthly income, and had less chronic diseases than participants in the WBJ. The most frequently identified CRC sign/symptom was 'lump in the abdomen' while the least was 'pain in the back passage'. Only 1849 participants (40.0%, 95% CI: 39.0%-41.0%) had a good awareness level of CRC signs/symptoms. Participants living in the WBJ were more likely to have good awareness than participants living in the Gaza Strip (42.2% vs. 37.0%; p = 0.002). Knowing someone with cancer (OR = 1.37, 95% CI: 1.21-1.55; p < 0.001) and visiting hospitals (OR = 1.46, 95% CI: 1.25-1.70; p < 0.001) were both associated with higher likelihood of having good awareness. However, male gender (OR = 0.80, 95% CI: 0.68-0.94; p = 0.006) and following a vegetarian diet (OR = 0.59, 95% CI: 0.48-0.73; p < 0.001) were both associated with lower likelihood of having good awareness. CONCLUSION: Less than half of the study participants had a good awareness level of CRC signs and symptoms. Future education interventions are needed to improve public awareness of CRC in Palestine.

Women's awareness of breast cancer symptoms: a national cross-sectional study from Palestine.

BACKGROUND: Early diagnosis is crucial to reduce the morbidity and mortality associated with breast cancer (BC). Awareness of BC symptoms plays a key role in this. This study aimed to evaluate the Palestinian women's awareness of BC symptoms and determine factors associated with good awareness. METHODS: This was a national cross-sectional study conducted from July 2019 to March 2020 in Palestine. Convenience sampling was used to recruit adult women from hospitals, primary healthcare centers, and public spaces located in 11 governorates. A translated-into-Arabic version of the validated BC awareness measure was utilized for data collection. The awareness level was categorized based on the number of symptoms recognized into: poor (0 to 4), fair (5 to 9), and good (10 to 13). RESULTS: Of 6269 approached, 5434 participants completed the questionnaire (response rate = 86.7%). A total of 5257 questionnaires were included in the analysis: 2551 from the Gaza Strip and 2706 from the West Bank and Jerusalem (WBJ). Participants living in the WBJ were more likely to be older, have higher monthly income, and suffer from more chronic diseases than participants living in the Gaza Strip. The most frequently identified BC symptom was 'lump or thickening in the breast' (n = 4887, 92.9%) followed by 'lump or thickening under the armpit' (n = 4394, 83.6%). The least frequently identified symptoms were 'pulling in of the nipple' (n = 2665, 50.7%) and 'change in the position of the nipple' (n = 2710, 51.6%). A total of 2191 participants (41.7%) demonstrated good awareness of BC symptoms. Participants from the Gaza Strip were more likely than participants from the WBJ to have good awareness (47.0.0% vs. 36.7%). On the multivariable analysis, being ≥ 40 years, completing a post-secondary education, knowing someone with cancer, and visiting hospitals and primary healthcare centers were all associated with an increase in the likelihood of having good awareness. However, living in the WBJ was associated with a decrease in the likelihood of having good awareness. CONCLUSION: Less than half of women included in this study showed good awareness of BC symptoms. More targeted educational interventions are needed to promote Palestinian women's awareness of BC symptoms to facilitate early diagnosis.

Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm.

MOTIVATION: Third-generation sequencing technologies can sequence long reads that contain as many as 2 million base pairs. These long reads are used to construct an assembly (i.e. the subject's genome), which is further used in downstream genome analysis. Unfortunately, third-generation sequencing technologies have high sequencing error rates and a large proportion of base pairs in these long reads is incorrectly identified. These errors propagate to the assembly and affect the accuracy of genome analysis. Assembly polishing algorithms minimize such error propagation by polishing or fixing errors in the assembly by using information from alignments between reads and the assembly (i.e. read-to-assembly alignment information). However, current assembly polishing algorithms can only polish an assembly using reads from either a certain sequencing technology or a small assembly. Such technology-dependency and assembly-size dependency require researchers to (i) run multiple polishing algorithms and (ii) use small chunks of a large genome to use all available readsets and polish large genomes, respectively. RESULTS: We introduce Apollo, a universal assembly polishing algorithm that scales well to polish an assembly of any size (i.e. both large and small genomes) using reads from all sequencing technologies (i.e. second- and third-generation). Our goal is to provide a single algorithm that uses read sets from all available sequencing technologies to improve the accuracy of assembly polishing and that can polish large genomes. Apollo (i) models an assembly as a profile hidden Markov model (pHMM), (ii) uses read-to-assembly alignment to train the pHMM with the Forward-Backward algorithm and (iii) decodes the trained model with the Viterbi algorithm to produce a polished assembly. Our experiments with real readsets demonstrate that Apollo is the only algorithm that (i) uses reads from any sequencing technology within a single run and (ii) scales well to polish large assemblies without splitting the assembly into multiple parts. AVAILABILITY AND IMPLEMENTATION: Source code is available at https://github.com/CMU-SAFARI/Apollo. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Knowledge of cervical cancer risk factors among Palestinian women: a national cross-sectional study.

BACKGROUND: High awareness of cervical cancer (CC) risk factors is important to decrease the morbidity and mortality associated with CC. This study aimed to assess the knowledge level of Palestinian women about CC risk factors and to determine the factors associated with good knowledge. METHODS: This was a national cross-sectional study. Adult women from hospitals, primary healthcare centers, and public spaces of 11 governorates in Palestine were recruited using a stratified convenience sampling. A translated-into-Arabic version of the validated CC awareness measure (CeCAM) was used to assess the knowledge about the 11 CC risk factors. For each correctly identified risk factor, the participant was given one point. The total score was calculated and was categorized into three categories: poor knowledge (0-3), fair knowledge (4-7), and good knowledge (8-11). RESULTS: A total of 7223 participants completed the Arabic CeCAM (response rate = 89.3%) and 7058 questionnaires were included in the final analysis: 2655 from the Gaza Strip and 4403 from the West Bank and Jerusalem. Participants recruited from the Gaza Strip were younger, getting lower monthly incomes, and with less chronic diseases than participants recruited from the West Bank and Jerusalem. The most frequently identified risk factor was 'having a weakened immune system' (n = 5458, 77.3%) followed by 'infection with a sexually transmitted infection' (n = 5388, 76.3%). The least identified risk factor was 'having many children' (n = 1597, 22.6%). Only 1670 women (23.7%) had good knowledge of CC risk factors. Women living in the Gaza Strip were more likely than women living in the West Bank and Jerusalem to have good knowledge (25.2% vs 22.7%). Completing a secondary or diploma degree, being employed, and having a monthly income of ≥ 1450 NIS (around $450) were all associated with lower likelihood of having good knowledge of CC risk factors. Conversely, knowing someone with cancer was associated with higher likelihood of having good knowledge. CONCLUSION: The overall awareness of CC risk factors was low. There is a substantial need to establish educational programs to promote Palestinian women's awareness of CC.

Knowledge of ovarian cancer symptoms among women in Palestine: a national cross-sectional study.

INTRODUCTION: Ovarian cancer (OC) is often diagnosed at advanced stages. This study aimed to assess the Palestinian women's knowledge about OC symptoms and determine the factors associated with having good knowledge. METHODS: A cross-sectional study was conducted from July 2019 to March 2020 in the two main areas of Palestine: the West Bank and Jerusalem as well as the Gaza Strip. A translated-into-Arabic version of the validated OC awareness measure (OCAM) was utilized for data collection. Stratified convenience sampling was used to recruit adult women attending hospitals, primary healthcare centers, and public spaces at 11 governorates. The knowledge level was categorized into three categories based on the number of symptoms recognized: poor (0 to 4), fair (5 to 8), and good (9 to 11). RESULTS: Of 6095 approached, 5618 participants completed the Arabic OCAM (response rate = 92.1%).A total of 5411 questionnaires were included in the analysis: 2278 from the Gaza Strip and 3133 from the West Bank and Jerusalem. Participants living in the West Bank and Jerusalem were older, of higher monthly income, and with more chronic diseases than those living in the Gaza Strip. The most frequently identified symptoms were 'extreme generalized fatigue' (n = 3821, 70.6%), 'unexplained weight loss' (n = 3607, 66.7%), and 'increased abdominal size on most days' (n = 3252, 60.1%). On the other hand, the least recognized symptoms were 'feeling full persistently' (n = 1553, 28.7%) and 'difficulty eating on most days' (n = 1971, 36.4%). Only 943 participants (17.4%) displayed good knowledge of OC symptoms. Participants from the Gaza Strip had a higher likelihood than participants from the West Bank and Jerusalem to have a good level of knowledge (21.0% vs. 14.8%). Being married, knowing someone with cancer, and visiting hospitals were all associated with a higher likelihood of having good knowledge level. However, living in the West Bank and Jerusalem was associated with a lower likelihood of having good knowledge. CONCLUSION: The overall knowledge of OC symptoms in this study was low. Educational interventions are needed to improve Palestinian women's knowledge about OC symptoms.

Knowledge of Palestinian women about cervical cancer warning signs: a national cross- sectional study.

BACKGROUND: Timely presentation and diagnosis of cervical cancer (CC) are crucial to decrease its mortality especially in low- and middle-income countries like Palestine. This study aimed to evaluate the knowledge of Palestinian women about CC warning signs and determine the factors associated with good knowledge. METHODS: This was a national cross-sectional study conducted between July 2019 and March 2020 in Palestine. Stratified convenience sampling was used to recruit adult women from hospitals, primary healthcare centers, and public spaces of 11 governorates. A translated-into-Arabic version of the validated CC awareness measure (CeCAM) was used to assess women's knowledge of 12 CC warning signs. RESULTS: Of 8086 approached, 7223 participants completed the CeCAM (response rate = 89.3%). A total of 7058 questionnaires were included in the analysis: 2655 from the Gaza Strip and 4403 from the West Bank and Jerusalem (WBJ). The median age [interquartile range] for all participants was 34.0 [24.0, 42.0] years. Participants recruited from the WBJ were older, getting higher monthly income, and having more chronic diseases than those recruited from the Gaza Strip. The most frequently identified warning sign was 'vaginal bleeding after menopause' (n = 5028, 71.2%) followed by 'extreme generalized fatigue' (n = 4601, 65.2%) and 'unexplained weight loss' (n = 4578, 64.9%). Only 1934 participants (27.4%) demonstrated good knowledge of CC warning signs. Participants from the Gaza Strip were slightly more likely than participants from the WBJ to have a good level of knowledge. Factors associated with having good knowledge included having a bachelor or postgraduate degree, being married, divorced, or widowed as well as knowing someone with cancer. CONCLUSION: The overall awareness of CC warning signs was low. Educational interventions are needed to increase Palestinian women's awareness of CC warning signs.

Shouji: a fast and efficient pre-alignment filter for sequence alignment.

MOTIVATION: The ability to generate massive amounts of sequencing data continues to overwhelm the processing capability of existing algorithms and compute infrastructures. In this work, we explore the use of hardware/software co-design and hardware acceleration to significantly reduce the execution time of short sequence alignment, a crucial step in analyzing sequenced genomes. We introduce Shouji, a highly parallel and accurate pre-alignment filter that remarkably reduces the need for computationally-costly dynamic programming algorithms. The first key idea of our proposed pre-alignment filter is to provide high filtering accuracy by correctly detecting all common subsequences shared between two given sequences. The second key idea is to design a hardware accelerator that adopts modern field-programmable gate array (FPGA) architectures to further boost the performance of our algorithm. RESULTS: Shouji significantly improves the accuracy of pre-alignment filtering by up to two orders of magnitude compared to the state-of-the-art pre-alignment filters, GateKeeper and SHD. Our FPGA-based accelerator is up to three orders of magnitude faster than the equivalent CPU implementation of Shouji. Using a single FPGA chip, we benchmark the benefits of integrating Shouji with five state-of-the-art sequence aligners, designed for different computing platforms. The addition of Shouji as a pre-alignment step reduces the execution time of the five state-of-the-art sequence aligners by up to 18.8×. Shouji can be adapted for any bioinformatics pipeline that performs sequence alignment for verification. Unlike most existing methods that aim to accelerate sequence alignment, Shouji does not sacrifice any of the aligner capabilities, as it does not modify or replace the alignment step. AVAILABILITY AND IMPLEMENTATION: https://github.com/CMU-SAFARI/Shouji. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.