niryuu/sni-each-converted huggingface dataset:
Paragraph: Endoribonuclease-prepared siRNA (esiRNA) is an alternative tool to chemical synthetic siRNA for gene silencing. Since esiRNAs are directed against long target sequences, the genetic variations in the target sequences will have little influence on their effectiveness. The ability of esiRNAs to inhibit hepatitis B virus (HBV) gene expression and replication was tested. EsiRNAs targeting the coding region of HBV surface antigen (HBsAg) and the nucleocapsid (HBcAg) inhibited specifically the expression of HBsAg and HBcAg when cotransfected with the respective expression plasmids. Both esiRNAs reduced the HBV transcripts and replication intermediates in transient transfected cells and cells with HBV genomes integrated stably. Compared with synthetic siRNA, esiRNA targeting HBsAg was less effective than the selected synthetic siRNA in terms of the inhibition of HBV gene expression and replication. However, while the ability of synthetic siRNAs for specific gene silencing was impaired strongly by the nucleotide substitutions within the target sequences. The efficiency of gene silencing by esiRNAs was not influenced by sequence variation. The transfection of esiRNA did not induce interferon-stimulated genes (ISGs) like STAT1 and ISG15, indicating the absence of off-target effects. In general, esiRNAs strongly inhibited HBV gene expression and replication and may have an advantage against HBV strains which are variable genetically. 
 Title: Inhibition of hepatitis B virus gene expression and replication by endoribonuclease-prepared siRNA
Output: True
Paragraph: Teaser This review provides an update of recent advances in intracellular delivery and reports mechanisms that could help drugs reach their target efficiently, resulting in smarter drugs that reach their target still with the original bioavailability. The intracellular delivery of nanomaterials and drugs has been attracting increasing research interest, mainly because of their important effects and functions in several organelles. Targeting specific organelles can help treat or decrease the symptoms of diabetes, cancer, infectious, and autoimmune diseases. Tuning biological and chemical properties enables the creation of functionalized nanomaterials with enhanced intracellular uptake, ability to escape premature lysosome degradation, and to reach a specific target. Here, we provide an update of recent advances in the intracellular delivery mechanisms that could help drugs reach their target more efficiently. 
 Title: Strategies for the enhanced intracellular delivery of nanomaterials
Output: True
Paragraph: publicly funded repositories, such as the WHO COVID database with rights for unrestricted research re-use and analyses in any form or by any means with acknowledgement of the original source. These permissions are granted for free by Elsevier for as long as the COVID-19 resource centre remains active. J. Dairy Sci. 96 :981-992 http://dx. Farmers attempting to reduce first-calving age (FCA) need to understand which rearing management factors influence FCA and first-lactation milk production (FLP). Reduced FCA might be associated with lower FLP. This study describes the association between herd FCA, FLP, and several herd-level health and rearing management variables and describes the association between FCA and FLP at the cow level. It uses data from a 2010 survey of 100 Dutch dairy farms about general management, colostrum and milk feeding, housing, cleanliness, healthcare, disease, and breeding. It also used available data on FCA and 305-d FLP at both cow and herd level. The associations between median FCA and median FLP of the herd and herd-level health and rearing management variables were determined using multivariate regression analysis. The median FCA was associated with minimum age of first insemination, feeding of waste milk, and the amount of milk given preweaning. The median FLP was associated with median FCA and vaccination status for bovine respiratory syncytial virus. The association between FCA and FLP (based on 8,454 heifers) was analyzed with a single-effect linear mixed model, where the dependent variable was either FCA or relative FCA (defined as the difference between FCA of the heifer and median FCA of the herd to which they belonged). Heifers having an FCA of 24 mo produced, on average, 7,164 kg of milk per 305 d, and calving 1 mo earlier gave 143 kg less milk per 305 d. When FCA did not deviate from the median herd FCA, heifers produced, on average, 7,272 kg of milk per 305 d. From the median FCA of the herd, heifers calving 1 mo earlier produced 90 kg of milk per 305 d less, and heifers calving 1 mo later produced 86 kg per 305 d more. This is the first study that explained FLP using relative FCA. It assumes that heifers raised within the same farm have similar development because they are similarly managed. Similar management is reflected by the median FCA of the herd, with a deviation of the heifer's FCA from median FCA reflecting the heifer's development relative to the herd's average. The advantage of using relative FCA was that it accounts for between-farm differences in rearing management. It showed that earlier insemination without adjusting management to ensure sufficient development lowers FLP. An economic optimum exists between rearing costs, FCA, and FLP and, as a consequence, decisions with regard to young stock management should be made with care. 
 Title: First-calving age and first-lactation milk production on Dutch dairy farms
Output: False
Paragraph: Background: On 31 March 2013, the first human infections with the novel influenza A/H7N9 virus were reported in Eastern China. The outbreak expanded rapidly in geographic scope and size, with a total of 132 laboratoryconfirmed cases reported by 3 June 2013, in 10 Chinese provinces and Taiwan. The incidence of A/H7N9 cases has stalled in recent weeks, presumably as a consequence of live bird market closures in the most heavily affected areas. Here we compare the transmission potential of influenza A/H7N9 with that of other emerging pathogens and evaluate the impact of intervention measures in an effort to guide pandemic preparedness. We used a Bayesian approach combined with a SEIR (Susceptible-Exposed-Infectious-Removed) transmission model fitted to daily case data to assess the reproduction number (R) of A/H7N9 by province and to evaluate the impact of live bird market closures in April and May 2013. Simulation studies helped quantify the performance of our approach in the context of an emerging pathogen, where human-to-human transmission is limited and most cases arise from spillover events. We also used alternative approaches to estimate R based on individual-level information on prior exposure and compared the transmission potential of influenza A/H7N9 with that of other recent zoonoses. Results: Estimates of R for the A/H7N9 outbreak were below the epidemic threshold required for sustained human-to-human transmission and remained near 0.1 throughout the study period, with broad 95% credible intervals by the Bayesian method (0.01 to 0.49). The Bayesian estimation approach was dominated by the prior distribution, however, due to relatively little information contained in the case data. We observe a statistically significant deceleration in growth rate after 6 April 2013, which is consistent with a reduction in A/H7N9 transmission associated with the preemptive closure of live bird markets. Although confidence intervals are broad, the estimated transmission potential of A/H7N9 appears lower than that of recent zoonotic threats, including avian influenza A/H5N1, swine influenza H3N2sw and Nipah virus. Conclusion: Although uncertainty remains high in R estimates for H7N9 due to limited epidemiological information, all available evidence points to a low transmission potential. Continued monitoring of the transmission potential of A/H7N9 is critical in the coming months as intervention measures may be relaxed and seasonal factors could promote disease transmission in colder months. 
 Title: Transmission potential of influenza A/H7N9
Output: False
Paragraph: Graphical Abstract Highlights d The young, functional de novo protein Bsc4 has a rudimentary ability to fold d Bsc4 forms compact oligomers with high b sheet content and a hydrophobic core d Bsc4 lacks a specific quaternary state and binds dyes suggestive of amyloid oligomers d Young de novo proteins can have some structural order and native-like properties In Brief Recent studies have shown that new protein-coding genes can arise ''de novo'' from noncoding DNA. The properties of the brand new proteins encoded by these genes remain poorly understood. Here, Bungard et al. show that a very young de novo protein from yeast folds to a partially ordered three-dimensional structure. The de novo evolution of protein-coding genes from noncoding DNA is emerging as a source of molecular innovation in biology. Studies of random sequence libraries, however, suggest that young de novo proteins will not fold into compact, specific structures typical of native globular proteins. Here we show that Bsc4, a functional, natural de novo protein encoded by a gene that evolved recently from noncoding DNA in the yeast S. cerevisiae, folds to a partially specific three-dimensional structure. Bsc4 forms soluble, compact oligomers with high b sheet content and a hydrophobic core, and undergoes cooperative, reversible denaturation. Bsc4 lacks a specific quaternary state, however, existing instead as a continuous distribution of oligomer sizes, and binds dyes indicative of amyloid oligomers or molten globules. The combination of native-like and non-native-like properties suggests a rudimentary fold that could potentially act as a functional intermediate in the emergence of new folded proteins de novo. 
 Title: Foldability of a Natural De Novo Evolved Protein Article Foldability of a Natural De Novo Evolved Protein
Output: False
Paragraph: Common cold viruses create significant health and financial burdens, and understanding key loci of transmission would help focus control strategies. This study (1) examines factors that influence when individuals transition from a negative to positive test (acquisition) or a positive to negative test (loss) of rhinovirus (HRV) and other respiratory tract viruses in 26 households followed weekly for one year, (2) investigates evidence for intrahousehold and interhousehold transmission and the characteristics of individuals implicated in transmission, and (3) builds data-based simulation models to identify factors that most strongly affect patterns of prevalence. We detected HRV, coronavirus, paramyxovirus, influenza and bocavirus with the FilmArray polymerase chain reaction (PCR) platform (BioFire Diagnostics, LLC). We used logistic regression to find covariates affecting acquisition or loss of HRV including demographic characteristics of individuals, their household, their current infection status, and prevalence within their household and across the population. We apply generalized linear mixed models to test robustness of results. Acquisition of HRV was less probable in older individuals and those infected with a coronavirus, and higher with a higher proportion of other household members infected. Loss of HRV is reduced with a higher proportion of other household members infected. Within households, only children and symptomatic individuals show evidence for transmission, while between households only a higher number of infected older children (ages 5-19) increases the probability of acquisition. Coronaviruses, paramyxoviruses and bocavirus also show evidence of intrahousehold transmission. Simulations show that age-dependent susceptibility and transmission have the largest effects on mean HRV prevalence. 
 Title: Transmission of rhinovirus in the Utah BIG- LoVE families: Consequences of age and household structure
Output: True
Paragraph: The genome of coronaviruses contains structural and non-structural genes, including several so-called accessory genes. All group 1b coronaviruses encode a single accessory protein between the spike and envelope genes, except for human coronavirus (HCoV) 229E. The prototype virus has a split gene, encoding the putative ORF4a and ORF4b proteins. To determine whether primary HCoV-229E isolates exhibit this unusual genome organization, we analyzed the ORF4a/b region of five current clinical isolates from The Netherlands and three early isolates collected at the Common Cold Unit (CCU) in Salisbury, UK. Results: All Dutch isolates were identical in the ORF4a/b region at amino acid level. All CCU isolates are only 98% identical to the Dutch isolates at the nucleotide level, but more closely related to the prototype HCoV-229E (>98%). Remarkably, our analyses revealed that the laboratory adapted, prototype HCoV-229E has a 2-nucleotide deletion in the ORF4a/b region, whereas all clinical isolates carry a single ORF, 660 nt in size, encoding a single protein of 219 amino acids, which is a homologue of the ORF3 proteins encoded by HCoV-NL63 and PEDV. Conclusion: Thus, the genome organization of the group 1b coronaviruses HCoV-NL63, PEDV and HCoV-229E is identical. It is possible that extensive culturing of the HCoV-229E laboratory strain resulted in truncation of ORF4. This may indicate that the protein is not essential in cell culture, but the highly conserved amino acid sequence of the ORF4 protein among clinical isolates suggests that the protein plays an important role in vivo. 
 Title: Virology Journal Human coronavirus 229E encodes a single ORF4 protein between the spike and the envelope genes
Output: False
Paragraph: Pertussis, commonly referred to as "whooping cough," is a highly contagious acute respiratory infection that has exhibited cyclical outbreaks throughout the last century. Although vaccines have provided some immunity, many populations, including infants and pregnant women, remain at risk for serious illness. Through the use of the novel "Identify, Isolate, Inform" (3I) tool, emergency department (ED) providers can readily recognize key symptoms of the disease and risk factors for exposure, thus curbing its transmission through early initiation of antimicrobial therapy and post-exposure prophylaxis. The three classic stages of pertussis include an initial catarrhal stage, characterized by nonspecific upper respiratory infection symptoms, which may advance to the paroxysmal stage, revealing the distinctive "whooping cough." This cough can persist for weeks to months leading into the convalescent stage. Household contacts of patients with suspected pertussis or other asymptomatic, high-risk populations (infants, pregnant women in their third trimester, and childcare workers) may benefit from post-exposure prophylactic therapy. The Pertussis 3I tool can also alert healthcare professionals to the proper respiratory droplet precautions during contact with a symptomatic patient, as well as isolation practices until antimicrobial treatment is in progress. ED personnel should then inform local public health departments of any suspected cases. All of these actions will ultimately aid public health in controlling the incidence of pertussis cases, thus ensuring the protection of the general public from this re-emerging respiratory illness. [West J Emerg Med. 2019;20(2)191-197.]  
 Title: Pertussis: The Identify, Isolate, Inform Tool Applied to a Re-emerging Respiratory Illness
Output: False
Paragraph: Virus discovery based on cDNA-AFLP (amplified fragment length polymorphism) (VIDISCA) is a novel approach that provides a fast and effective tool for amplification of unknown genomes, e.g., of human pathogenic viruses. The VIDISCA method is based on double restriction enzyme processing of a target sequence and ligation of oligonucleotide adaptors that subsequently serve as priming sites for amplification. As the method is based on the common presence of restriction sites, it results in the generation of reproducible, species-specific amplification patterns. The method allows amplification and identification of viral RNA/DNA, with a lower cutoff value of 10 5 copies/ml for DNA viruses and 10 6 copies/ml for the RNA viruses. Previously, we described the identification of a novel human coronavirus, HCoV-NL63, with the use of the VIDISCA method. 
 Title: Detection of New Viruses by VIDISCA Virus Discovery Based on cDNA-Amplified Fragment Length Polymorphism
Output: True
Paragraph: H9N2 Avian influenza virus has repeatedly infected humans and other mammals, which highlights the need to determine the pathogenicity and the corresponding mechanism of this virus for mammals. In this study, we found two H9N2 viruses with similar genetic background but with different pathogenicity in mice. The A/duck/Nanjing/06/2003 (NJ06) virus was highly pathogenic for mice, with a 50% mouse lethal dose (MLD 50 ) of 10 2.83 50% egg infectious dose (EID 50 ), whereas the A/duck/Nanjing/01/1999 (NJ01) virus was low pathogenic for mice, with a MLD 6.81 50 of >10 EID 50 . Further studies showed that the NJ06 virus grew faster and reached significantly higher titers than NJ01 in vivo and in vitro. Moreover, the NJ06 virus induced more severe lung lesions, and higher levels of inflammatory cellular infiltration and cytokine response in lungs than NJ01 did. However, only 12 different amino acid residues (HA-K157E, NA-A9T, NA-R435K, PB2-T149P, PB2-K627E, PB1-R187K, PA-L548M, PA-M550L, NP-G127E, NP-P277H, NP-D340N, NS1-D171N) were found between the two viruses, and all these residues except for NA-R435K were located in the known functional regions involved in interaction of viral proteins or between the virus and host factors. Summary, our results suggest that multiple amino acid differences may be responsible for the higher pathogenicity of the NJ06 virus for mice, resulting in lethal infection, enhanced viral replication, severe lung lesions, and excessive inflammatory cellular infiltration and cytokine response in lungs. These observations will be helpful for better understanding the pathogenic potential and the corresponding molecular basis of H9N2 viruses that might pose threats to human health in the future. 
 Title: Two Genetically Similar H9N2 Influenza A Viruses Show Different Pathogenicity in Mice
Output: False
Paragraph: A recombinant baculovirus containing a cDNA which encodes haemagglutininneuraminidase (HN) of Newcastle disease virus (NDV) was constructed. Spodqteru frugiperda cells infected with this recombinant virus produced a large amount of HN glycoprotein similar to the authentic HN in size. The recombinant HN glycoprotein was localized on the surface of the infected cells and conserved its haemadsorption and neuraminidase activities. The antigenic properties of the recombinant HN glycoprotein seemed to be slightly different from the authentic one, as judging by the reactivity with a panel of monoclonal antibodies specific to the antigenic sites responsible for neutralization of viral infectivity. Chickens inoculated with the cells infected with the recombinant virus developed haemagglutination-inhibition and virus neutralization antibodies, and were completely protected from the NDV challenge. Correspondence tot M. Niikura, 
 Title: Characterization of haemagglutinin-neuraminidase glycoprotein of Newcastle disease virus expressed by a recombinant baculovirus
Output: True
Paragraph: Cell culture Buffalo green monkey (BGM) kidney cells, HeLa R19 cells, and rhabdomyosarcoma RD cells were grown at 37°C, 5% CO 2 in DMEM Ready Mix (PAA) containing 10% fetal bovine serum or in DMEM (Lonza) supplemented with 10% fetal bovine serum. Vero, HeLa H and BGM cells used in the multicycle antiviral assays were grown in MEM supplemented with 10% FCS (Integro), 2 mM Lglutamine and 20 mM HEPES. HAP1 cells (Carette et al., 2011) (provided by Thijn Brummelkamp, NKI, Amsterdam, The Netherlands) were grown in IMDM supplemented with 10% fetal bovine serum. 
 Title: SUPPLEMENTAL INFORMATION TO: Itraconazole inhibits enterovirus replication by targeting the oxysterol-binding protein (OSBP)
Output: False
Paragraph: Wuhan, China. The number of cases has increased rapidly but information on the clinical characteristics of SARS-CoV-2 pneumonia compared to normal controls in Chinese Han population is limited. Our objective is to describe the clinical characteristics of SARS-CoV-2 pneumonia compared to normal controls in the Chinese Han population. In this case series of 752 patients, the full spectrum of cases is described. Fever was present in 86-90% of the patients. The second most common symptom was cough (49.1-51.0%), fatigue (25.2-27.1%), sputum (20.0-23.1%), and headache (9.8-11.1%). the mortality rate is 4.6% in Wuhan, 1.9% in Beijing, and 0.9% in Shanghai. Our findings showed that the levels of lymphocytes were 0.8 (IQR, 0.6-1.1) 10 9 /L in Wuhan, 1.0 (IQR, 0.7-1.4) 10 9 /L in Beijing, and 1.1 (IQR, 0.8-1.5) 10 9 /L in Shanghai before admission to hospitals, respectively, indicating that cellular immune function might relate to the mortality. Based on the reference ranges of normal Chinese Han population and the data of the critically ill patients we have observed, it is recommended that reference ranges of people at high risk of COVID-19 infection are CD3 + lymphocytes below 900 cells/mm 3 , CD4 + lymphocytes below 500 cells/mm 3 , and CD8 + lymphocytes below 300 cells/mm 3 . All rights reserved. No reuse allowed without permission. author/funder, who has granted medRxiv a license to display the preprint in perpetuity. 
 Title: Mortality of COVID-19 is Associated with Cellular Immune Function Compared to Immune Function in Chinese Han Population
Output: True
Paragraph: Hypertension is a diverse illness interlinked with cerebral, cardiovascular (CVS) and renal abnormalities. Presently, the malady is being treated by focusing on Renin-angiotensin system (RAS), voltage-gated calcium channels, peripheral vasodilators, renal and sympathetic nervous systems. Cardiovascular and renal abnormalities are associated with the overactivation of RAS, which can be constrained by angiotensin-converting enzyme inhibitors (ACEIs), angiotensin II (Ang-II) -AT1 receptor blockers (ARBs) and renin inhibitors. The latter is a new player in the old system. The renin catalyzes the conversion of angiotensinogen to Angiotensin I (Ang-I). This can be overcome by inhibiting renin, a preliminary step, eventually hinders the occurrence of the cascade of events in the RAS. Various peptidomimetics, the first-generation renin inhibitors developed six decades ago have limited drug-like properties as they suffered from poor intestinal absorption, high liver first-pass metabolism and low oral bioavailability. The development of chemically diverse molecules from peptides to nonpeptides expanded the horizon to achieving direct renin inhibition. Aliskiren, a blockbuster drug that emerged as a clinical candidate and got approved by the US FDA in 2007 was developed by molecular modeling studies. Aliskiren indicated superior to average efficacy and with minor adverse effects relative to other RAS inhibitors. However, its therapeutic use is limited by poor oral bioavailability of less than 2% that is similar to first-generation peptidic compounds. In this review, we present the development of direct renin inhibitors (DRIs) from peptidic to nonpeptidics that lead to the birth of aliskiren, its place in the treatment of cardiovascular diseases and its limitations. 
 Title: Decades-old renin inhibitors are still struggling to find a niche in antihypertensive therapy. A fleeting look at the old and the promising new molecules
Output: False
Paragraph: • Segregated spatial domain and individual-based linkage are incorporated into SIS model. • Activating a small number of individual-based linkage between different spatial domains can prompt the outbreak of epidemic globally. • Narrowing segregated spatial domain and reducing mobility are conducive to suppression of infectious disease. a b s t r a c t By incorporating segregated spatial domain and individual-based linkage into the SIS (susceptible-infected-susceptible) model, we propose a generalized epidemic model which can change from the territorial epidemic model to the networked epidemic model. The role of the individual-based linkage between different spatial domains is investigated. As we adjust the timescale parameter τ from 0 to unity, which represents the degree of activation of the individual-based linkage, three regions are found. Within the region of 0 < τ < 0.02, the epidemic is determined by local movement and is sensitive to the timescale τ . Within the region of 0.02 < τ < 0.5, the epidemic is insensitive to the timescale τ . Within the region of 0.5 < τ < 1, the outbreak of the epidemic is determined by the structure of the individual-based linkage. As we keep an eye on the first region, the role of activating the individual-based linkage in the present model is similar to the role of the shortcuts in the two-dimensional small world network. Only activating a small number of the individualbased linkage can prompt the outbreak of the epidemic globally. The role of narrowing segregated spatial domain and reducing mobility in epidemic control is checked. These two measures are found to be conducive to curbing the spread of infectious disease only when the global interaction is suppressed. A log-log relation between the change in the number of infected individuals and the timescale τ is found. By calculating the epidemic threshold * L.-X. Zhong et al. / Physica A 436 (2015) 482-491 483 and the mean first encounter time, we heuristically analyze the microscopic characteristics of the propagation of the epidemic in the present model. 
 Title: Physica A Coupled effects of local movement and global interaction on contagion
Output: True
Paragraph: This article describes methods of treatment for avian zoonoses, modern antibiotic therapy and drug resistance of selected pathogens, which pose a threat to the population's health. A tabular form has been used to present the current data from the European Union from 2011 to 2017 regarding human morbidity and mortality and the costs incurred by national health systems for the treatment of zoonoses occurring in humans and animals. Moreover, the paper includes descriptions of selected diseases, which indirectly affect birds. Scientists can obtain information regarding the occurrence of particular diseases, their aetiology, epidemiology, incubation period and symptoms caused by dangerous microorganisms and parasites. This information should be of particular interest for people who have frequent contact with birds, such as ornithologists, as well as veterinarians, farm staff, owners of accompanying animals and zoological workers. This paper presents a review used for identification and genetic characterization of bacterial strains isolated from a variety of environmental sources, e.g., bird feathers along with their practical application. We describe the bacterial, viral and fungal serotypes present on avian feathers after the slaughter process. This review also enables us to effectively identify several of the early stages of infectious diseases from heterogeneous avian research material. 
 Title: Bird feathers as potential sources of pathogenic microorganisms: a new look at old diseases
Output: False
Paragraph: Background: Cats are susceptible to feline panleukopenia virus (FPV) and canine parvovirus (CPV) variants 2a, 2b and 2c. Detection of FPV and CPV variants in apparently healthy cats and their persistence in white blood cells (WBC) and other tissues when neutralising antibodies are simultaneously present, suggest that parvovirus may persist long-term in the tissues of cats post-infection without causing clinical signs. The aim of this study was to screen a population of 54 cats from Sardinia (Italy) for the presence of both FPV and CPV DNA within buffy coat samples using polymerase chain reaction (PCR). The DNA viral load, genetic diversity, phylogeny and antibody titres against parvoviruses were investigated in the positive cats. Results: Carnivore protoparvovirus 1 DNA was detected in nine cats (16.7%). Viral DNA was reassembled to FPV in four cats and to CPV (CPV-2b and 2c) in four cats; one subject showed an unusually high genetic complexity with mixed infection involving FPV and CPV-2c. Antibodies against parvovirus were detected in all subjects which tested positive to DNA parvoviruses. Conclusions: The identification of FPV and CPV DNA in the WBC of asymptomatic cats, despite the presence of specific antibodies against parvoviruses, and the high genetic heterogeneity detected in one sample, confirmed the relevant epidemiological role of cats in parvovirus infection. 
 Title: Molecular analysis of carnivore Protoparvovirus detected in white blood cells of naturally infected cats
Output: True
Paragraph: Disease spreads as a result of people moving and coming in contact with each other. Thus the mobility patterns of individuals are crucial in understanding disease dynamics. Here we study the impact of human mobility on HIV transmission in different parts of Kenya. We build an SIR metapopulation model that incorporates the different regions within the country. We parameterise the model using census data, HIV data and mobile phone data adopted to track human mobility. We found that movement between different regions appears to have a relatively small overall effect on the total increase in HIV cases in Kenya. However, the most important consequence of movement patterns was transmission of the disease from high infection to low prevalence areas. Mobility slightly increases HIV incidence rates in regions with initially low HIV prevalences and slightly decreases incidences in regions with initially high HIV prevalence. We discuss how regional HIV models could be used in public-health planning. This paper is a first attempt to model spread of HIV using mobile phone data, and we also discuss limitations to the approach. 
 Title: The Impact of Human Mobility on HIV Transmission in Kenya
Output: True
Paragraph: In the era of globalization, internationalized representations of infectious disease threats have profound implications for understandings of infectious disease problems and their management in developing countries, particularly in Sub-Saharan Africa. By examining the policy implications of the key narratives around public health, animal health and trade, it becomes possible to clarify the relationship between global understandings of infectious disease risk and their impact on the development of local responses to disease problems. We highlight the tensions that resource-constrained countries face in the nexus of animal healthpublic health and trade, including the perception that resource-constrained countries are both source and victims of potential infectious disease threats. Given this scenario, it is important to think about how developing countries, particularly those in Sub-Saharan Africa, can approach infectious disease risk management as it relates to pandemic scale threats such as avian and pandemic influenza. We outline some of the key considerations in defining and assessing disease risk using avian and pandemic influenza in Zambia as an example. We conclude that the key to the feasibility of the analysis of the risk of multi-sectoral affecting emerging infectious diseases such as zoonotic avian influenza is flexibility in how risk is framed across the public health, animal health and trade systems. 
 Title: Globalized Perspectives on Infectious Disease Management and Trade in Africa: A Conceptual Framework for Assessing Risk in Developing Country Settings
Output: False
Paragraph: Candida auris has emerged in the past decade as a multi-drug resistant public health threat causing health care outbreaks. Here we report epidemiological, clinical, and microbiological investigations of a C. auris outbreak in a regional Omani hospital between April 2018 and April 2019. The outbreak started in the intensive care areas (intensive care unit (ICU), coronary care unit (CCU), and high dependency unit) but cases were subsequently diagnosed in other medical and surgical units. In addition to the patients' clinical and screening samples, environmental swabs from high touch areas and from the hands of 35 staff were collected. All the positive samples from patients and environmental screening were confirmed using MALDI-TOF, and additional ITS-rDNA sequencing was done for ten clinical and two environmental isolates. There were 32 patients positive for C. auris of which 14 (43.8%) had urinary tract infection, 11 (34.4%) had candidemia, and 7 (21.8%) had asymptomatic skin colonization. The median age was 64 years (14-88) with 17 (53.1%) male and 15 (46.9%) female patients. Prior to diagnosis, 21 (65.6%) had been admitted to the intensive care unit, and 11 (34.4%) had been nursed in medical or surgical wards. The crude mortality rate in our patient's cohort was 53.1. Two swabs collected from a ventilator in two different beds in the ICU were positive for C. auris. None of the health care worker samples were positive. Molecular typing showed that clinical and environmental isolates were genetically similar and all belonged to the South Asian C. auris clade I. Most isolates had non-susceptible fluconazole (100%) and amphotericin B (33%) 
 Title: Ongoing Challenges with Healthcare-Associated Candida auris Outbreaks in Oman
Output: False
Paragraph: As the world faces its first influenza pandemic in 40 years, it has been argued that we have never been better prepared. Concern about emerging infectious diseases has fuelled significant public health and political developments, such as the coming into force of the International Health Regulations (IHR). Since the turn of the century, the World Health Organization (WHO) has documented a historically unprecedented number of emerging infectious disease outbreaks, and lessons drawn from their management have confirmed the critical importance of effective communications, specifically through formal channels such as WHO and in the public domain. In concert with novel emerging infectious diseases, the communication landscape itself has also changed radically. We now live in an era of real-time electronic communications; consequently, approaches to surveillance are being transformed. Data sources, information messengers, mechanisms of data and information transfer and audiences are all changing. Instant and global transmission of information has become a powerful ally, along with peer pressure, for WHO in ensuring that member states comply with new obligations to swiftly declare outbreaks considered to be of public health importance. There is now significant global attention and accompanying investment which should, the authors suggest, be used as an opportunity to improve strategic and operational communication capacity to respond not only to pandemic influenza but also to other public health threats. There are many concepts of communication in relation to risk associated with outbreaks. As these are relatively new concepts, this article will consider approaches relating to highlighting public health threats and supporting operational management, addressing these as the communication of risk and subsequent risk management. Strategic considerations are critical to both, although information, messengers, communication tools and audiences may differ. The communication of risk refers to the process by which information regarding outbreaks is identified and shared with the purpose of increasing awareness amongst key stakeholders of the threat. Key stakeholders for public health threats include WHO, national governments and the public. Risk management, by contrast, refers to the management processes associated with response to the outbreak, for which communication is crucial at each stage. Three examples are used to explore the challenges and demands of communicating effectively and coherently given this changing landscape. This brief paper will attempt to show the progress made, draw lessons to be learned and outline the ways forward. 
 Title: Risk communication and management in public health crises
Output: True
Paragraph: The concurrent use of N95 filtering facepiece respirators with powered air-purifying respirators during aerosol-generating medical procedures in patients with severe respiratory pathogens has been promoted as offering additional protection against infectious agents. The purpose of this article is to examine the impact of this additional respiratory equipment upon protection and personal performance. The presumed additive protective effect of an N95 filtering facepiece respirator used concurrently with a powered air-purifying respirator has not been subjected to rigorous scientific investigation. The burden imposed by additional respiratory protective equipment should not be discounted, and the potentially minor contribution to protection may be offset by the negative impact on personal performance. Novel uses of protective equipment occasionally are spawned during crisis situations, but their generalized applicability to healthcare workers should ultimately be evidence-based. (Am J Infect Control 2008;36:135-41.)  
 Title: Evaluation of the rationale for concurrent use of N95 filtering facepiece respirators with loose-fitting powered air-purifying respirators during aerosol-generating medical procedures
Output: False
Paragraph: Immune sera from convalescent patients have been shown to be effective in the treatment of patients infected with Severe Acute Respiratory Syndrome Virus (SARS-CoV) making passive immune therapy with human monoclonal antibodies an attractive treatment strategy for SARS. Previously, using Xenomouse (Amgen British Columbia Inc), we produced a panel of neutralizing Human monoclonal antibodies (HmAbs) that could specifically bind to the ectodomain of the SARS-CoV spike (S) glycoprotein. Some of the HmAbs were S1 domain specific, while some were not. In this study, we describe non-S1 binding neutralizing HmAbs that can specifically bind to the conserved S2 domain of the S protein. However, unlike the S1 specific HmAbs, the S2 specific HmAbs can neutralize pseudotyped viruses expressing different S proteins containing receptor binding domain sequences of various clinical isolates. These data indicate that HmAbs which bind to conserved regions of the S protein are more suitable for conferring protection against a wide range of SARS-CoV variants and have implications for generating therapeutic antibodies or subunit vaccines against other enveloped viruses. Citation: Elshabrawy HA, Coughlin MM, Baker SC, Prabhakar BS (2012) Human Monoclonal Antibodies against Highly Conserved HR1 and HR2 Domains of the SARS-CoV Spike Protein Are More Broadly Neutralizing. PLoS ONE 7(11): e50366. 
 Title: Human Monoclonal Antibodies against Highly Conserved HR1 and HR2 Domains of the SARS-CoV Spike Protein Are More Broadly Neutralizing
Output: False
Paragraph: Through a prospective cohort study the relationship between travellers' awareness of MERS-CoV, and compliance with preventive measures and exposure to camels was evaluated among Australian Hajj pilgrims who attended Hajj in 2015. Only 28% of Australian Hajj pilgrims were aware of MERS-CoV in Saudi Arabia. Those who were aware of MERS-CoV were more likely to receive recommended vaccines [odds ratio (OR) 3.1, 95% confidence interval (CI): 1.5-5.9, P < 0.01], but there was no significant difference in avoiding camels or their raw products during Hajj between those who were aware of MERS-CoV and those who were not (OR 1.2, 95% CI: 0.3-5.2, P ¼ 0.7). Hajj pilgrims' awareness is reflected in some of their practices but not in all. 
 Title: Association between Australian Hajj Pilgrims' awareness of MERS-CoV, and their compliance with preventive measures and exposure to camels
Output: False
Paragraph: Infectious diseases are acknowledged as one of the most critical threats to global public health today. Climate change, unprecedented population growth with accelerated rates of antimicrobial resistance, have resulted in both the emergence of novel pathogenic organisms and the re-emergence of infections that were once controlled. The consequences have led to an increased vulnerability to infectious diseases globally. The ability to rapidly monitor the spread of diseases is key for prevention, intervention and control, however several limitations exist for current surveillance systems and the capacity to cope with the rapid population growth and environmental changes. Wastewater-Based Epidemiology (WBE) is a new epidemiology tool that has potential to act as a complementary approach for current infectious disease surveillance systems and an early warning system for disease outbreaks. WBE postulates that through the analysis of population pooled wastewater, infectious disease and resistance spread, the emergence of new disease outbreak to the community level can be monitored comprehensively and in real-time. This manuscript provides critical overview of current infectious disease surveillance status, as well as it introduces WBE and its recent advancements. It also provides recommendations for further development required for WBE application as an effective tool for infectious disease surveillance. 
 Title: Journal Pre-proofs Future Perspectives of Wastewater-Based Epidemiology: Monitoring Infec- tious Disease Spread and Resistance to the Community Level Future Perspectives of Wastewater-Based Epidemiology: Monitoring Infectious Disease Spread and Resistance to the Community Level
Output: True
Paragraph: The SARS-CoV spike glycoprotein (S) is the main target of the protective immune response in humans and animal models of SARS. Here, we demonstrated that efficient expression of S from the wild-type spike gene in cultured cells required the use of improved plasmid vectors containing donor and acceptor splice sites, as well as heterologous viral RNA export elements, such as the CTE of Mazon-Pfizer monkey virus or the PRE of Woodchuck hepatitis virus (WPRE). The presence of both splice sites and WPRE markedly improved the immunogenicity of S-based DNA vaccines against SARS. Upon immunization of mice with low doses (2 μg) of naked DNA, only intron and WPRE-containing vectors could induce neutralizing anti-S antibodies and provide protection against challenge with SARS-CoV. Our observations are likely to be useful for the construction of plasmid and viral vectors designed for optimal expression of intronless genes derived from cytoplasmic RNA viruses. 
 Title: Heterologous viral RNA export elements improve expression of severe acute respiratory syndrome (SARS) coronavirus spike protein and protective efficacy of DNA vaccines against SARS
Output: False
Paragraph: The spike (S) protein of coronavirus, mouse hepatitis virus (MHV), mediates attachment and fusion during viral entry and cell-to-cell fusion later in infection. By analogy with other viral proteins that induce cell fusion the MHV S protein would be expected to have a hydrophobic stretch of amino acids that serves as a fusion peptide. Sequence analysis suggests that the S protein falls within the group of fusion proteins having internal rather than N-terminal fusion peptides. Based on the features of known viral fusion peptides, we identified two regions (PEP1 and PEP2) of MHV-A59 S2 as possible fusion peptides. Site-directed mutagenesis and an in vitro cell-to-cell fusion assay were used to evaluate the roles of PEP1 and PEP2, as well as a third previously identified putative fusion domain (PEP3) in membrane fusion. Substitution of bulky hydrophobic residues with charged residues within PEP1 affects the fusion activity of the S protein without affecting processing and surface expression. Similar substitutions within PEP2 result in a fusion-negative phenotype; however, these mutant S proteins also exhibit defects in protein processing and surface expression which likely explain the loss of the ability to induce fusion. Thus PEP1 remains a candidate fusion peptide, while PEP2 may play a significant role in the overall structure or oligomerization of the S protein. PEP3 is an unlikely putative fusion peptide since it is not conserved among coronaviruses and nonconservative amino acid substitutions in PEP3 have minimal effects on cell-to-cell fusion. 
 Title: Roles in Cell-to-Cell Fusion of Two Conserved Hydrophobic Regions in the Murine Coronavirus Spike Protein
Output: True
Paragraph: Background Assessment of the eff ect of infl uenza on populations, including risk of infection, illness if infected, illness severity, and consultation rates, is essential to inform future control and prevention. We aimed to compare the community burden and severity of seasonal and pandemic infl uenza across diff erent age groups and study years and gain insight into the extent to which traditional surveillance underestimates this burden. Methods Using preseason and postseason serology, weekly illness reporting, and RT-PCR identifi cation of infl uenza from nasal swabs, we tracked the course of seasonal and pandemic infl uenza over fi ve successive cohorts (England 2006-11; 5448 person-seasons' follow-up). We compared burden and severity of seasonal and pandemic strains. We weighted analyses to the age and regional structure of England to give nationally representative estimates. We compared symptom profi les over the fi rst week of illness for diff erent strains of PCR-confi rmed infl uenza and non-infl uenza viruses using ordinal logistic regression with symptom severity grade as the outcome variable. (13-34) , suggesting most infl uenza infections are asymptomatic. 25% (18-35) of all people with serologically confi rmed infections had PCR-confi rmed disease. 17% (10-26) of people with PCR-confi rmed infl uenza had medically attended illness. These fi gures did not diff er signifi cantly when comparing pandemic with seasonal infl uenza. Of PCR-confi rmed cases, people infected with the 2009 pandemic strain had markedly less severe symptoms than those infected with seasonal H3N2. Interpretation Seasonal infl uenza and the 2009 pandemic strain were characterised by similar high rates of mainly asymptomatic infection with most symptomatic cases self-managing without medical consultation. In the community the 2009 pandemic strain caused milder symptoms than seasonal H3N2. www.thelancet.com/respiratory Vol 
 Title: Articles Comparative community burden and severity of seasonal and pandemic infl uenza: results of the Flu Watch cohort study
Output: False
Paragraph: Human coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1 are common respiratory viruses associated with acute respiratory infection. They have a global distribution. Rapid and accurate diagnosis of HCoV infection is important for the management and treatment of hospitalized patients with HCoV infection. Here, we developed a melting curve-based multiplex RT-qPCR assay for simultaneous detection of the four HCoVs. In the assay, SYTO 9 was used to replace SYBR Green I as the fluorescent dye, and GC-modified primers were designed to improve the melting temperature (Tm) of the specific amplicon. The four HCoVs were clearly distinguished by characteristic melting peaks in melting curve analysis. The detection sensitivity of the assay was 3 × 10 2 copies for HCoV-OC43, and 3 × 10 1 copies for HCoV-NL63, HCoV-229E and HCoV-HKU1 per 30 µL reaction. Clinical evaluation and sequencing confirmation demonstrated that the assay was specific and reliable. The assay represents a sensitive and reliable method for diagnosis of HCoV infection in clinical samples. 
 Title: A Melting Curve-Based Multiplex RT-qPCR Assay for Simultaneous Detection of Four Human Coronaviruses
Output: True