Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Papillomavirus Infection Rate by Genotype and Vaccination Rates in Canada: Canadian Health Measures Survey 2009 to 2013

Background An infection with certain HPV genotypes can lead to cancer or genital warts. HPV can be detected with PCR-based tests, and some genotypes can be prevented by vaccines. However, since the infection rates of various HPV genotypes have not been well reported, the present study aims to provide this information. Methods The Canadian Health Measures Survey (CHMS) is an ongoing biannual national survey. Between 2009 and 2011, it sampled a nationally representative sample of females aged 14 to 59 years to determine the infection rates of 46 HPV genotypes. Females aged 9 to 29 years and 9 to 59 years were asked whether they received HPV vaccines between 2009 to 2011 (cycle 2) and 2012 to 2013 (cycle 3), respectively. The reported infection rates and vaccination proportions were weighted and adjusted for the survey design. Results Among the estimated 10,592,968 females aged 14 to 59 years at cycle 2, the HPV genotypes with the highest infection rates were 16, 62, 74, and 54, and the rates were 3.42% (95% CI = 1.67% to 5.17%), 2.14% (95% CI = 0.68% to 3.59%), 2.1% (95% CI = 0.51% to 3.69%), and 2.04% (95% CI = 0.38% to 3.7%), respectively. There were an estimated 6,569,100 and 11,603,752 females aged 9 to 29 and 9 to 59 years at cycles 2 and 3, respectively. The proportions receiving a HPV vaccine were 13.55% (11.18% to 15.92%) and 12.3% (9.8% to 14.79%), respectively. The estimated numbers of females that received HPV vaccines were 890,197 and 1,427,000, respectively. Conclusion Canada is one of the few countries that conduct national surveys to determine HPV infection rates by genotype, which are not limited to the surveillance of carcinogenic genotypes. Our study found discrepancies between the HPV genotypes whose infections were the most common, that could be detected by PCR tests, that were carcinogenic, and that could be prevented by vaccines. For example, 5 of the 7 genotypes (42, 54, 62, 66, and 74) with infection rates of more than 1% cannot be detected by PCR tests and are not targeted by vaccines. HPV 51 is carcinogenic, associated with genital warts, and can be detected by PCR tests, but it is not targeted by vaccines. We recommend a better alignment of the genotypes targeted by HPV tests and vaccines with those genotypes with the highest infection rates in Canada.
Surveillance of zoonotic Brugia pahangi in monastery cats, Samphran district, Nakhon Pathom, Thailand

The mosquito-borne filarial nematode parasites Brugia pahangi and B. malayi have been proposed as potential zoonotic pathogens, with dogs and cats being the main reservoir hosts. The monasteries where both stray and semi-domesticated animals live often serve as areas where humans are exposed to these reservoirs. In Thailand, the prevalence of B. pahangi , particularly in infected monastery cats, is underreported. In this study, we investigated B. pahangi prevalence in cats at 24 temples in the Samphran district, Nakhon Pathom province, central Thailand. In total, 196 blood samples were collected from the cats and examined using the hematocrit capillary tube technique. Then, modified Wright–Giemsa staining was used to morphologically identify microfilaria at the genus level. We then used the polymerase chain reaction (PCR) to target the mitochondrial cytochrome oxidase I ( COI ) gene and perform sequencing to confirm the species level of the filarial nematode parasite. The results were highly similar to B . pahangi COI (100%). A phylogenetic analysis was then conducted using MEGA X software. The B. pahangi infection prevalence at the study sites was 4.08% (8/196). Most infected cats exhibited no clinical signs and gender and monastery location were non-risk factors for infection. Our study indicated that molecular techniques and phylogenetic analyses are useful tools for identifying filarial parasites and understanding their evolution. Importantly, going forward, our findings will help improve the diagnosis, treatment, control and prevention of zoonotic filarial nematode parasite infections.
Krüppel-like Factor 9 (KLF9) Promotes hepatic Cytochrome P450 (CYP) 2D6 Expression during Pregnancy in CYP2D6-humanized Mice Role of KLF9 in CYP2D6 induction during pregnancy

CYP2D6, a major drug-metabolizing enzyme, is responsible for metabolism of approximately 25% of marketed drugs. Clinical evidence indicates that metabolism of CYP2D6 substrates is increased during pregnancy, but the underlying mechanisms remain unclear. To identify transcription factors potentially responsible for CYP2D6 induction during pregnancy, a panel of genes differentially expressed in the livers of pregnant vs. nonpregnant CYP2D6-humanized (tg- CYP2D6) mice was compiled via microarray experiments followed by qRT-PCR verification. As a result, seven transcription factors (ATF5, EGR1, FOXA3, JUNB, KLF9, KLF10, and REV-ERB α ) were found to be upregulated in liver during pregnancy. Results from transient transfection and promoter reporter gene assays indicate that KLF9 itself is a weak transactivator of CYP2D6 promoter but significantly enhances CYP2D6 promoter transactivation by HNF4 α , a known transcriptional activator of CYP2D6 expression. The results from deletion and mutation analysis of CYP2D6 promoter activity identified a KLF9 putative binding motif at -22/-14 region to be critical in the potentiation of HNF4 α -induced transactivation of CYP2D6. Electrophoretic mobility shift assays revealed a direct binding of KLF9 to the putative KLF binding motif. Results from chromatin immunoprecipitation assay showed increased recruitment of KLF9 to CYP2D6 promoter in the livers of tg- CYP2D6 mice during pregnancy. Taken together, our data suggest that increased KLF9 expression is in part responsible for CYP2D6 induction during pregnancy via the potentiation of HNF4 α transactivation of CYP2D6. role of promoter contexts in modulating HNF4 α transactivation of its target genes and the presence of additional regulatory factors potentially involved in CYP2D6 regulation during pregnancy. In this study, we show that KLF9 expression is upregulated during pregnancy in the livers of tg-CYP2D6 mice. The roles of KLF9 in HNF4 α transactivation of the CYP2D6 promoter as well as in CYP2D6 induction during pregnancy were investigated. Our results illustrate the interplay among hepatic transcription factors KLF9, HNF4 α , and SHP contributing to the regulation of CYP2D6 expression during pregnancy. Affymetrix GeneChip list differentially genes at term postpartum, compared control group (virgin). prediction of putative factor binding sites performed using These results may provide a basis to improve drug therapy during pregnancy. Also, considering the roles of CYP2D6 in the pathophysiology of neurological diseases (in addition to drug metabolism), better understanding of the regulation of CYP2D6 expression may allow for the identification of new drug targets. In this regard, whether the regulatory pathways involving KLF9, SHP, and HNF4 α play a role in governing CYP2D6 expression in non-pregnant subjects is currently being investigated.
Bimodal Expression Patterns, and Not Viral Burst Sizes, Predict the Effects of Vpr on HIV-1 Proviral Populations in Jurkat Cells

A bedrock assumption in HIV-1 population modeling is that all active cells release the same amount of virus. However, the findings here revealed that when HIV-infected cells expand into clones, each clone differs in virus production. ABSTRACT Integration site landscapes, clonal dynamics, and latency reversal with or without vpr were compared in HIV-1-infected Jurkat cell populations, and the properties of individual clones were defined. Clones differed in fractions of long terminal repeat (LTR)-active daughter cells, with some clones containing few to no LTR-active cells, while almost all cells were LTR active for others. Clones varied over 4 orders of magnitude in virus release per active cell. Proviruses in largely LTR-active clones were closer to preexisting enhancers and promoters than low-LTR-active clones. Unsurprisingly, major vpr+ clones contained fewer LTR-active cells than vpr− clones, and predominant vpr+ proviruses were farther from enhancers and promoters than those in vpr− pools. Distances to these marks among intact proviruses previously reported for antiretroviral therapy (ART)-suppressed patients revealed that patient integration sites were more similar to those in the vpr+ pool than to vpr− integrants. Complementing vpr-defective proviruses with vpr led to the rapid loss of highly LTR-active clones, indicating that the effect of Vpr on proviral populations occurred after integration. However, major clones in the complemented pool and its vpr− parent population did not differ in burst sizes. When the latency reactivation agents prostratin and JQ1 were applied separately or in combination, vpr+ and vpr− population-wide trends were similar, with dual-treatment enhancement being due in part to reactivated clones that did not respond to either drug applied separately. However, the expression signatures of individual clones differed between populations. These observations highlight how Vpr, exerting selective pressure on proviral epigenetic variation, can shape integration site landscapes, proviral expression patterns, and reactivation properties. IMPORTANCE A bedrock assumption in HIV-1 population modeling is that all active cells release the same amount of virus. However, the findings here revealed that when HIV-infected cells expand into clones, each clone differs in virus production. Reasoning that this variation in expression patterns constituted a population of clones from which differing subsets would prevail under differing environmental conditions, the cytotoxic HIV-1 protein Vpr was introduced, and population dynamics and expression properties were compared in the presence and absence of Vpr. The results showed that whereas most clones produced fairly continuous levels of virus in the absence of Vpr, its presence selected for a distinct subset of clones with properties reminiscent of persistent populations in patients, suggesting the possibility that the interclonal variation in expression patterns observed in culture may contribute to proviral persistence in vivo.
Risks of deep vein thrombosis, pulmonary embolism, and bleeding after covid-19: nationwide self-controlled cases series and matched cohort study

Abstract Objective To quantify the risk of deep vein thrombosis, pulmonary embolism, and bleeding after covid-19. Design Self-controlled case series and matched cohort study. Setting National registries in Sweden. Participants 1 057 174 people who tested positive for SARS-CoV-2 between 1 February 2020 and 25 May 2021 in Sweden, matched on age, sex, and county of residence to 4 076 342 control participants. Main outcomes measures Self-controlled case series and conditional Poisson regression were used to determine the incidence rate ratio and risk ratio with corresponding 95% confidence intervals for a first deep vein thrombosis, pulmonary embolism, or bleeding event. In the self-controlled case series, the incidence rate ratios for first time outcomes after covid-19 were determined using set time intervals and the spline model. The risk ratios for first time and all events were determined during days 1-30 after covid-19 or index date using the matched cohort study, and adjusting for potential confounders (comorbidities, cancer, surgery, long term anticoagulation treatment, previous venous thromboembolism, or previous bleeding event). Results Compared with the control period, incidence rate ratios were significantly increased 70 days after covid-19 for deep vein thrombosis, 110 days for pulmonary embolism, and 60 days for bleeding. In particular, incidence rate ratios for a first pulmonary embolism were 36.17 (95% confidence interval 31.55 to 41.47) during the first week after covid-19 and 46.40 (40.61 to 53.02) during the second week. Incidence rate ratios during days 1-30 after covid-19 were 5.90 (5.12 to 6.80) for deep vein thrombosis, 31.59 (27.99 to 35.63) for pulmonary embolism, and 2.48 (2.30 to 2.68) for bleeding. Similarly, the risk ratios during days 1-30 after covid-19 were 4.98 (4.96 to 5.01) for deep vein thrombosis, 33.05 (32.8 to 33.3) for pulmonary embolism, and 1.88 (1.71 to 2.07) for bleeding, after adjusting for the effect of potential confounders. The rate ratios were highest in patients with critical covid-19 and highest during the first pandemic wave in Sweden compared with the second and third waves. In the same period, the absolute risk among patients with covid-19 was 0.039% (401 events) for deep vein thrombosis, 0.17% (1761 events) for pulmonary embolism, and 0.101% (1002 events) for bleeding. Conclusions The findings of this study suggest that covid-19 is a risk factor for deep vein thrombosis, pulmonary embolism, and bleeding. These results could impact recommendations on diagnostic and prophylactic strategies against venous thromboembolism after covid-19.
Dynamic Changes in Breast Milk Microbiome in the Early Postpartum Period of Kenyan Women Living with HIV Are Influenced by Antibiotics but Not Antiretrovirals

Breastfeeding has important benefits for long-term infant health, particularly in establishing and shaping the infant gut microbiome. However, the impact of combination antiretroviral therapy exposure and antibiotics on the breast milk microbiome in women living with HIV is not known. ABSTRACT Shared bacteria between maternal breast milk and infant stool, infers that transfer of maternal breast milk microbiota through breastfeeding seeds the establishment of the infant gut microbiome. Whether combination antiretroviral therapy (cART) impacts the breast milk microbiota in women living with HIV is unknown. Since current standard of care for people living with HIV includes cART, it has been difficult to evaluate the impact of cART on the microbiome. Here, we performed a next-generation sequencing retrospective study from pre-ART era clinical trials in Nairobi, Kenya (between 2003–2006 before cART was standard of care) that tested the effects of ART regimens to prevent mother-to-child HIV transmission. Kenyan women living with HIV were randomized to receive either no ART during breastfeeding (n = 24) or cART (zidovudine, nevirapine, lamivudine; n = 25) postpartum. Using linear mixed-effects models, we found that alpha diversity and beta diversity of the breast milk bacterial microbiome changed significantly over time during the first 4 weeks postpartum (alpha diversity P < 0.0007; beta diversity P = 0.005). There was no statistically significant difference in diversity, richness, and composition of the bacterial microbiome between cART-exposed and cART-unexposed women. In contrast, antibiotic use influenced the change of beta diversity of the bacterial microbiome over time. Our results indicate that while early postpartum time predicts breast milk microbiome composition, cART does not substantially alter the breast milk microbiota in women living with HIV. Hence, cART has minimal impact on the breast milk microbiome compared to antibiotics use. IMPORTANCE Breastfeeding has important benefits for long-term infant health, particularly in establishing and shaping the infant gut microbiome. However, the impact of combination antiretroviral therapy exposure and antibiotics on the breast milk microbiome in women living with HIV is not known. Here, in a longitudinal retrospective study of Kenyan women living with HIV from the pre-antiretroviral therapy era, we found that antibiotic use significantly influenced breast milk microbiome beta diversity, but antiretrovirals exposure did not substantially alter the microbiome. Given the protective role of breastfeeding in maternal-infant health, these findings fill an important knowledge gap of the impact of combination antiretroviral therapy on the microbiome of women living with HIV.
Differential Dopamine Dynamics in Adolescents and Adults

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Title: Sourdoughs fermented by autochthonous Lactobacillus strains improve the quality of gluten-free bread Short Title: Fermented sourdoughs improve the quality of GF bread

1 Department of Food Biotechnology, Branch for Northwest & West region, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Tabriz, Iran. 2 Department of Food Science and Technology, Tabriz Branch, Islamic Azad University, Tabriz, Iran. 3 Department of Food Science and Technology, Gorgan University of Agriculture Sciences and Natural Resources.
Exploring Outdoor Recreation Activities as a Facilitator for College Student Diversity Experiences

Racial intolerance and violence in the United States, and on college campuses specifically, has created a dire need for universities to bridge gaps between students of diverse backgrounds and beliefs. Campus recreation programs offer promising environments for students from diverse identities to engage with each other and learn about peers, while increasing their openness to diversity. Despite this potential, little is known about how students engage with diversity in recreation contexts. This phenomenological study uncovered the experiences of students attending diversity-focused outdoor adventure trips and examined the facets of this recreation environment that contributed to engagement with diverse peers. Campus recreation administrators can use these findings to consider parallel experiences throughout recreation programs that can bring students from diverse backgrounds together.
Development of lightweight and low-cost microwave components for remote-sensing applications

To my mother Zenaida and to my family for the unconditional love and support. ACKNOWLEDGMENTS First and foremost, I would like to express my deepest gratitude to my advisor, Dr. John Papapolymerou, for the enormous support he provided throughout my PhD studies at Geor-gia Tech. The amount of freedom to pursue my ideas and remarkable opportunities he has provisioned (and keeps facilitating) have surpassed all the professional expectations I used to have as a young Panamanian engineer. His advise, which has gone beyond the technical realm in many occasions, has helped me to mature as a person and as a researcher, and to appreciate the value of hard work and dedication in academia. Smith, from Georgia Tech. Their teachings, character, wisdom and challenging classes fostered and reinforced my fascination for electromagnetism and wireless technologies. I also give a special recognition to my mentor Prof. Ing. Anselmo Araolaza and the personnel of the National Centre of Metrology of Panama (CENAMEP) for instructing me in the art of measurements, and for providing me with the necessary intuition and skills to confront the toughest laboratory challenges throughout my PhD research. I would like to thank my sponsors for financially supporting my research. I thank the National Space Administration (NASA) for supporting my work on the development of a lightweight-phased-arrays technology for the study of cold-land processes. Without a doubt, this was the most challenging, interesting and exciting project I have undertaken in my professional career. I would like to thank, besides the Mirctech members who were involved, the multidisciplinary team that helped this project to become a real success. In particular, I deeply value the contributions of Dr. John Cressler and his research group members Christopher Coen and Dr. John Poh for the endless hours of dedication and lab action. I would also like to thank Dr. Ted Heath and Bill Wilson from the Georgia Tech Research Institute for making me feel as welcome as I could be in their hi-tech facilities. iv I thank Nanowave Technologies for funding the final projects of my research. Especially , I would like to acknowledge the constructive support of Dr. Justin Miller and Dr. Huifang Gu in the development of the sponsored projects. I deeply appreciate the encouragement to pursue design creativity, which was at the same time greatly benefited with their input. The interactions with them have been the first real exposure I have had …
Training Fully Connected Neural Networks is ∃R-Complete

We consider the problem of finding weights and biases for a two-layer fully connected neural network to fit a given set of data points as well as possible, also known as EmpiricalRiskMinimization. Our main result is that the associated decision problem is $\exists\mathbb{R}$-complete, that is, polynomial-time equivalent to determining whether a multivariate polynomial with integer coefficients has any real roots. Furthermore, we prove that algebraic numbers of arbitrarily large degree are required as weights to be able to train some instances to optimality, even if all data points are rational. Our result already applies to fully connected instances with two inputs, two outputs, and one hidden layer of ReLU neurons. Thereby, we strengthen a result by Abrahamsen, Kleist and Miltzow [NeurIPS 2021]. A consequence of this is that a combinatorial search algorithm like the one by Arora, Basu, Mianjy and Mukherjee [ICLR 2018] is impossible for networks with more than one output dimension, unless $\mathsf{NP}=\exists\mathbb{R}$.
Computer Science Analyzing the Code Coverage of Android Apps using the Exerciser Monkey

With a market share of 72.84% [1] in June 2021, Android is the worlds most used operating system for mobile devices. In order for developers to test the applications they create, random testing can be an attractive option. Additionally, when third-party applications have to be tested that the source code is not available for, automated testing is a good approach. Exerciser Monkey [2] is Google’s oﬃcial tool that uses a simple random approach in order to test Android apps. Prior studies show that Monkey’s simple approach to testing beats more sophisticated tools. However, these types of tools almost never fully explore an application. Earlier work on Monkey’s code coverage usually does not test many diﬀerent parameter combinations. In order to maximize the code coverage of an application that gets covered by Monkey, in this paper, the code coverage obtained by the diﬀerent parameters and runtimes of Monkey are investigated and compared, as well as the amount of applications that crash while being tested. The experiment is tested on a dataset of 50 applications with 10 diﬀerent parameter options. It is shown that changing the parameters of Monkey can have a positive inﬂuence on code coverage and application crashes found.