ResearchPad - note https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[ <b>CSA:</b> A high-throughput <b>c</b>hromosome-<b>s</b>cale <b>a</b>ssembly pipeline for vertebrate genomes]]> https://www.researchpad.co/article/elastic_article_12663 Easy-to-use and fast bioinformatics pipelines for long-read assembly that go beyond the contig level to generate highly continuous chromosome-scale genomes from raw data remain scarce.ResultChromosome-Scale Assembler (CSA) is a novel computationally highly efficient bioinformatics pipeline that fills this gap. CSA integrates information from scaffolded assemblies (e.g., Hi-C or 10X Genomics) or even from diverged reference genomes into the assembly process. As CSA performs automated assembly of chromosome-sized scaffolds, we benchmark its performance against state-of-the-art reference genomes, i.e., conventionally built in a laborious fashion using multiple separate assembly tools and manual curation. CSA increases the contig lengths using scaffolding, local re-assembly, and gap closing. On certain datasets, initial contig N50 may be increased up to 4.5-fold. For smaller vertebrate genomes, chromosome-scale assemblies can be achieved within 12 h using low-cost, high-end desktop computers. Mammalian genomes can be processed within 16 h on compute-servers. Using diverged reference genomes for fish, birds, and mammals, we demonstrate that CSA calculates chromosome-scale assemblies from long-read data and genome comparisons alone. Even contig-level draft assemblies of diverged genomes are helpful for reconstructing chromosome-scale sequences. CSA is also capable of assembling ultra-long reads.ConclusionsCSA can speed up and simplify chromosome-level assembly and significantly lower costs of large-scale family-level vertebrate genome projects. ]]> <![CDATA[COVID-19 preparedness: Clinical pharmacy services remote staffing in a quaternary, level I trauma and comprehensive stroke center]]> https://www.researchpad.co/article/elastic_article_12485 In an effort to expedite the publication of articles related to the COVID-19 pandemic, AJHP is posting these manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time.PurposeThe rapid spread of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes coronavirus disease 2019 (COVID-19), has strained the resources of healthcare systems around the world. In accordance with recommendations from the World Health Organization, Centers for Disease Control and Prevention, and US Department of Defense, Intermountain Medical Center (IMED) in Murray, UT, has developed a plan to provide remote clinical pharmacy services to protect the health of pharmacy caregivers while maintaining appropriate clinical pharmacy coverage to optimally care for patients.SummaryThe utilization of telemedicine technology permits clinical pharmacists to readily communicate with nurses, physicians, other caregivers, and patients. We have identified strategies to allow clinical pharmacists to continue to participate in daily rounds, provide consultations under collaborative practice agreements, verify medication orders, collect medication histories, provide antimicrobial stewardship, and deliver medication education to patients from off-site locations. The pharmacy department at IMED proactively tested telemedicine technologies, defined the roles of clinical pharmacists, and identified communication strategies prior to a rapid rise of COVID-19 in the state of Utah.ConclusionThe proactive measures described can help ensure that pharmacy caregivers have appropriate remote access and are capable of confidently using the resources. These steps allow for optimal care of hospitalized patients and promote social distancing, which may have the added benefit of decreasing the spread of SARS-CoV-2 among patients and caregivers. ]]> <![CDATA[Evaluation of Oxytetracycline Metabolites Cross-Reactivity with Oxytetracycline Enzyme-Linked Immunosorbent Assay (ELISA)]]> https://www.researchpad.co/article/elastic_article_11729 Antibiotics have been successfully used for the control of several plant diseases for many years. Recently, streptomycin and oxytetracycline have been approved for the treatment of Huanglongbing (HLB) in Florida. The enzyme-linked immunosorbent assay (ELISA) is the most commonly used assay for the detection of these antibiotics because it is quick, simple, and can be used to analyze many samples at the same time. However, ELISA can react with the metabolites of the parent compound and its structurally related compounds. In this study, we investigated the cross-reactivity of the oxytetracycline ACCEL ELISA kitTM with three of oxytetracycline metabolites (4-epi-oxytetracycline, α-apo-oxytetracycline, and β-apo-oxytetracycline). The α-apo-oxytetracycline and β-apo-oxytetracycline metabolite did not show any cross-reactivity in the linear range (1.5–50 ng mL−1) of the assay. Whereas 4-epi-oxytetracycline showed high cross-reactivity, and its response was similar to oxytetracycline. Our results indicated that the oxytetracycline ELISA kits estimate the level of oxytetracycline as well as its main metabolite, 4-epi-oxytetracycline.

]]>
<![CDATA[The association of low serum salivary and pancreatic amylases with the increased use of lipids as an energy source in non-obese healthy women]]> https://www.researchpad.co/article/elastic_article_11248 It is unknown whether low serum levels of salivary and pancreatic amylases are associated with the high combustion of carbohydrates or lipids for energy. Elevated blood ketones and a low respiratory quotient (RQ) can reflect the preferential combustion of lipids relative to carbohydrates. Therefore, using the data from our previous study, we investigated if low levels of serum amylases were associated with a high serum ketone level and low RQ in 60 healthy non-obese young women aged 20–39 years old.ResultsSerum ketones [3-hydroxybutyric acid (3-HBA) and acetoacetic acid (AA)] were inversely correlated with RQs, but not body mass index (BMI) or glycated haemoglobin (HbA1c) levels. Logistic regression analysis showed that high levels of serum ketones (3-HBA ≥ 24 μmol/L and AA ≥ 17 μmol/L) and a low RQ (< 0.766) were significantly associated with low serum salivary (< 60 U/L) and pancreatic (< 29 U/L) amylase levels, respectively. These associations were not altered by further adjustments for age, BMI, HbA1c, and estimated glomerular filtration rate. These results confirm the high combustion of lipids for energy in individuals with low serum amylase levels, suggesting a close relationship between circulating amylases and internal energy production. ]]> <![CDATA[Measuring and Comparing Municipal Policy Responses to COVID-19]]> https://www.researchpad.co/article/elastic_article_11121 Municipal governments are experts in social non-distancing. From swimming pools to libraries, streetcars to public parks, municipalities bring residents together and move them around—services vital to a vibrant community in ordinary times, but potentially disastrous in a pandemic. Municipal decisions to shutter these services and enforce social distancing are thus crucial for a successful COVID-19 response.

]]>
<![CDATA[How Right-Leaning Media Coverage of COVID-19 Facilitated the Spread of Misinformation in the Early Stages of the Pandemic in the U.S.]]> https://www.researchpad.co/article/elastic_article_11119 We have yet to know the ultimate global impact of the novel coronavirus pandemic. However, we do know that delays, denials and misinformation about COVID-19 have exacerbated its spread and slowed pandemic response, particularly in the U.S. (e.g., Abutaleb et al., 2020).

]]>
<![CDATA[Opportunities, Challenges and Directions in Science and Technology for Tackling COVID-19]]> https://www.researchpad.co/article/elastic_article_10718 The ongoing global crisis due to Coronavirus disease-2019 (COVID-19) pandemic has caused an enormous socioeconomic burden. A novel coronavirus causing severe acute respiratory syndrome (SARS-CoV-2) that evolved from a virus infecting bats is responsible for COVID-19, first reported in the Chinese city of Wuhan. In the absence of any specific scientifically proven and clinically tested drug or vaccine against SARS-CoV-2, the virus is wreaking havoc across the world, claiming more than 2,50,000 lives in less than 5 months, and posed a global health emergency. The scientific community is relentlessly working on the design and testing of vaccines and antiviral drugs against the novel coronavirus, several of which have reached advanced stages of testing and are undergoing clinical trials. Here we discuss the recent advances and developments in understanding the etiology and epidemiology of the COVID-19 pandemic, the factors influencing the disease transmission, and the countermeasures adopted to combat and stop further spread of the disease.

]]>
<![CDATA[From micro to nano: evolution and impact of drug delivery in treating disease]]> https://www.researchpad.co/article/elastic_article_10699 Over the past 50 years, drug delivery breakthroughs have enabled the approval of several important medicines. Often, this path starts with innovation from academic collaborations amongst biologists, chemists, and engineers, followed by the formation of a start-up company driving clinical translation and approval. An early wave featured injectable (i.e., intramuscular, subcutaneous) biodegradable polymeric microspheres to control drug release profiles for peptides and small molecules (e.g., Lupron Depot®, Risperdal Consta®). With these early successes for microspheres, research shifted to exploring systemic delivery by intravenous injection, which required smaller particle sizes and modified surface properties (e.g., PEGylation) to enable long circulation times. These new innovations resulted in the nanoparticle medicines Doxil® and Abraxane®, designed to improve the therapeutic index of cytotoxic cancer agents by decreasing systemic exposure and delivering more drug to tumors. Very recently, the first siRNA lipid nanoparticle medicine, Patisiran (Onpattro®), was approved for treating hereditary transthyretin-mediated amyloidosis. In this inspirational note, we will highlight the technological evolution of drug delivery from micro- to nano-, citing some of the approved medicines demonstrating the significant impact of the drug delivery field in treating many diseases.

]]>
<![CDATA[parSMURF, a high-performance computing tool for the genome-wide detection of pathogenic variants]]> https://www.researchpad.co/article/elastic_article_10165 Several prediction problems in computational biology and genomic medicine are characterized by both big data as well as a high imbalance between examples to be learned, whereby positive examples can represent a tiny minority with respect to negative examples. For instance, deleterious or pathogenic variants are overwhelmed by the sea of neutral variants in the non-coding regions of the genome: thus, the prediction of deleterious variants is a challenging, highly imbalanced classification problem, and classical prediction tools fail to detect the rare pathogenic examples among the huge amount of neutral variants or undergo severe restrictions in managing big genomic data.ResultsTo overcome these limitations we propose parSMURF, a method that adopts a hyper-ensemble approach and oversampling and undersampling techniques to deal with imbalanced data, and parallel computational techniques to both manage big genomic data and substantially speed up the computation. The synergy between Bayesian optimization techniques and the parallel nature of parSMURF enables efficient and user-friendly automatic tuning of the hyper-parameters of the algorithm, and allows specific learning problems in genomic medicine to be easily fit. Moreover, by using MPI parallel and machine learning ensemble techniques, parSMURF can manage big data by partitioning them across the nodes of a high-performance computing cluster. Results with synthetic data and with single-nucleotide variants associated with Mendelian diseases and with genome-wide association study hits in the non-coding regions of the human genome, involhing millions of examples, show that parSMURF achieves state-of-the-art results and an 80-fold speed-up with respect to the sequential version.ConclusionsparSMURF is a parallel machine learning tool that can be trained to learn different genomic problems, and its multiple levels of parallelization and high scalability allow us to efficiently fit problems characterized by big and imbalanced genomic data. The C++ OpenMP multi-core version tailored to a single workstation and the C++ MPI/OpenMP hybrid multi-core and multi-node parSMURF version tailored to a High Performance Computing cluster are both available at https://github.com/AnacletoLAB/parSMURF. ]]> <![CDATA[Negative social interactions and coping behaviors: experiences of Japanese mothers caring for children with special needs in disaster areas]]> https://www.researchpad.co/article/elastic_article_9890 This study aims to identify the challenging experiences pertaining negative social interactions and the coping behaviors of mothers of children with special needs after two major earthquakes in Japan. A qualitative content analysis was conducted based on the interviews of 26 mothers of children with special needs who had experienced the Great East Japan Earthquake in 2011 or Kumamoto Earthquake in 2016.ResultsThe themes extracted were “perceiving pressures and unfairness,” “failing to obtain support and deeper understanding,” “realizing child’s characteristics that are difficult for others to understand,” and “tackling challenges on their own in different ways.” The experienced negative social interactions and coping behaviors were found to be similar in both earthquakes. Although the Japanese legislation was amended 2 years after the Great East Japan Earthquake, it may not have had necessarily improved the mothers’ situations. Thus, while it is important to provide specific support for families of children with special needs after natural disasters and organize food supplies with a focus on family units, it is also important to increase Japanese society’s understanding of the varied characteristics of disabilities. ]]> <![CDATA[Traumatic childhood events of parents enrolled in the Avon Longitudinal Study of Parents and Children (ALSPAC)]]> https://www.researchpad.co/article/elastic_article_9220 Background: Early life experiences can have a significant impact on an individual’s later behaviour, the way they view the world, their beliefs and their success at forming strong interpersonal relationships. These factors may subsequently influence the way that the individual may parent their children, which in turn may have an effect on their child’s behaviour, mental health and world view. Research has linked early traumatic life experiences in the parent’s childhood to disorganised attachment to their own child. In this paper we describe the data collected from parents enrolled in the Avon Longitudinal Study of Parents and Children (ALSPAC) on traumatic events experienced during their childhood, so that it can act as a resource for researchers in the future when considering outcomes on the adult, their children and grandchildren.

Methods: Data were collected via multiple questionnaires completed by parents enrolled into the ALSPAC study. During pregnancy and post-delivery, questionnaires were administered between 1990 and 1992 via post to the study mothers and their partners. Data were collected on life events including bereavement, sexual abuse, physical abuse, abandonment, neglect, memories of childhood and accidents. Other reports of traumatic events in childhood were reported by parents using free text. This can be made available to researchers for coding on request.

]]>
<![CDATA[Misconceptions about transmission, symptoms and prevention of HIV/AIDS among adolescents in Ebonyi state, South-east Nigeria]]> https://www.researchpad.co/article/elastic_article_9045 Nigeria has the second largest number of adolescents and young people living with HIV/AIDS in the world. Misconceptions about HIV/AIDS contribute to spread of HIV, and constrain uptake of preventive services. This paper explored misconceptions about HIV/AIDS among adolescents in south-east Nigeria. A qualitative study was conducted in six urban and rural local government areas of Ebonyi state. Data were collected through twelve focus group discussions (FGD) with unmarried adolescents aged 13–18 who were either attending school or out-of-school. The FGDs were conducted using a pre-tested topic guide. Data were coded manually and analyzed using a thematic framework approach.ResultsThere are persistent misconceptions about transmission of HIV/AIDS through mosquito bites and sharing of personal belongings. Some adolescents had inaccurate notions that a HIV infected person could be identified through changes in physical features such as abdominal swelling and longer fingernails. A few of them also reported that HIV could be treated with antibiotics. These misconceptions were expressed by both male and female adolescents. Adolescents have some mistaken beliefs about HIV/AIDS which constrain them from taking necessary preventive measures. Hence, the need to target adolescents with health education interventions on HIV/AIDS. ]]> <![CDATA[Functional Assessment of Lumbar Nerve Roots Using Coronal-plane Single-shot Turbo Spin-echo Diffusion Tensor Imaging]]> https://www.researchpad.co/article/elastic_article_8390 We investigated the usefulness of diffusion tensor imaging using single-shot turbo spin-echo sequence (TSE–DTI) in detecting the responsible nerve root by multipoint measurements of fractional anisotropy (FA) values. Five patients with bilateral lumbar spinal stenosis showing unilateral neurological symptoms were examined using TSE–DTI. In the spinal canal, FA values in the symptomatic side were lower than those in the asymptomatic side. TSE–DTI using multipoint measurements of FA values can differentiate the responsible lumbar nerve root.

]]>
<![CDATA[Comparison of Silent Navigator Waveform Generation Methods]]> https://www.researchpad.co/article/elastic_article_8379 The silent navigator technique utilizes a non-selective excitation and an appropriate respiratory waveform generation method is necessary for an accurate motion detection. We compared three methods for silent navigator waveform generation. The profile generation method with coil selection (prof-selection) resulted in a high cross correlation with bellows signals and a large respiration amplitude. The prof-selection method should be used for silent navigator waveform generation.

]]>
<![CDATA[Retraction Note: Optical rectification and absorption coefficients studied by a short-range topless exponential potential well with inverse square root]]> https://www.researchpad.co/article/elastic_article_8164 <![CDATA[Transoral Mandibular Tongue-Splitting Approach in Upper Cervical Epidural Abscess: A Case Report and Review of the Literature]]> https://www.researchpad.co/article/elastic_article_7222 The transoral mandibular tongue-splitting approach is typically performed for the treatment of upper cervical tumor and instability but has not been performed for the treatment of upper cervical epidural abscess (UCEA). We report the first case of UCEA successfully treated with a transoral mandibular tongue-splitting approach. Technical Note A 62-year-old man who had medical histories of tracheotomy with intubation and dermatopathy due to radiation therapy for the treatment of nasopharyngeal carcinoma presented with neck pain and limb weakness. The imaging examination revealed bone erosion of C2-C4 vertebrae and abscess at the level of C2-C4, supporting a diagnosis of UCEA. The transcervical approach could not be used for treatment; therefore, the transoral mandibular tongue-splitting approach was used successfully to perform decompression, debridement, and iliac bone grafting. Subsequently, we reviewed the literature pertaining to the use of the transoral mandibular tongue-splitting approach. The approach can be invasive and cause some complications. However, no fatal complications have been reported, and all patients demonstrated a favorable neurological outcome with reduced neurological deficits. Conclusions This case and subsequent literature review suggest that the transoral mandibular tongue-splitting approach may be effective for the improvement of neurological outcomes without fatal complications in patients with UCEA. There may be an increasing number of patients with UCEA requiring the transoral mandibular tongue-splitting approach due to the increasing prevalence of immunocompromized status and the aging population. ]]> <![CDATA[Modeling an equivalent b‐value in diffusion‐weighted steady‐state free precession]]> https://www.researchpad.co/article/elastic_article_6791 Diffusion‐weighted steady‐state free precession (DW‐SSFP) is shown to provide a means to probe non‐Gaussian diffusion through manipulation of the flip angle. A framework is presented to define an effective b‐value in DW‐SSFP.TheoryThe DW‐SSFP signal is a summation of coherence pathways with different b‐values. The relative contribution of each pathway is dictated by the flip angle. This leads to an apparent diffusion coefficient (ADC) estimate that depends on the flip angle in non‐Gaussian diffusion regimes. By acquiring DW‐SSFP data at multiple flip angles and modeling the variation in ADC for a given form of non‐Gaussianity, the ADC can be estimated at a well‐defined effective b‐value.MethodsA gamma distribution is used to model non‐Gaussian diffusion, embedded in the Buxton signal model for DW‐SSFP. Monte‐Carlo simulations of non‐Gaussian diffusion in DW‐SSFP and diffusion‐weighted spin‐echo sequences are used to verify the proposed framework. Dependence of ADC on flip angle in DW‐SSFP is verified with experimental measurements in a whole, human postmortem brain.ResultsMonte‐Carlo simulations reveal excellent agreement between ADCs estimated with diffusion‐weighted spin‐echo and the proposed framework. Experimental ADC estimates vary as a function of flip angle over the corpus callosum of the postmortem brain, estimating the mean and standard deviation of the gamma distribution as 1.50·10-4 mm2/s and 2.10·10-4 mm2/s.ConclusionDW‐SSFP can be used to investigate non‐Gaussian diffusion by varying the flip angle. By fitting a model of non‐Gaussian diffusion, the ADC in DW‐SSFP can be estimated at an effective b‐value, comparable to more conventional diffusion sequences. ]]> <![CDATA[Magnetization transfer and frequency distribution effects in the SSFP ellipse]]> https://www.researchpad.co/article/elastic_article_6701 To demonstrate that quantitative magnetization transfer (qMT) parameters can be extracted from steady‐state free‐precession (SSFP) data with no external T 1 map or banding artifacts.MethodsSSFP images with multiple MT weightings were acquired and qMT parameters fitted with a two‐stage elliptical signal model.ResultsMonte Carlo simulations and data from a 3T scanner indicated that most qMT parameters could be recovered with reasonable accuracy. Systematic deviations from theory were observed in white matter, consistent with previous literature on frequency distribution effects.ConclusionsqMT parameters can be extracted from SSFP data alone, in a manner robust to banding artifacts, despite several confounds. ]]> <![CDATA[Sociodemographic and Psychological Correlates of Compliance with the COVID-19 Public Health Measures in France]]> https://www.researchpad.co/article/N607779bd-6d97-429e-b431-6bb49c09464e The COVID-19 disease was first identified in Wuhan, China, in December 2019, having since spread rapidly across the world. The infection and mortality rates of the disease have forced governments to implement a wave of public health measures. Depending on the context, these range from the implementation of simple hygienic rules to measures such as social distancing or lockdowns that cause major disruptions in citizens’ daily lives. The success of these crucial public health measures rests on the public's willingness to comply. However, individual differences in following the official public health recommendations for stopping the spread of COVID-19 have not yet to our knowledge been assessed. This study aims to fill this gap by assessing the sociodemographic and psychological correlates of implementing public health recommendations that aim to halt the COVID-19 pandemic. We investigate these associations in the context of France, one of the countries that has been most severely affected by the pandemic, and which ended up under a nationwide lockdown on March 17. In the next sections we describe our theoretical expectations over the associations between sociodemographics, personality, ideology, and emotions with abiding by the COVID-19 public health measures. We then test these hypotheses using data from the French Election Study.

]]>
<![CDATA[Preliminary design of an innovative, simple, and easy-to-build portable ventilator for COVID-19 patients]]> https://www.researchpad.co/article/N6f644e2e-a85d-4c55-b627-509422858257 This technical note describes the preliminary design of a simple, easy-to-use, and easy-to-build ventilator with an unique design that can be used for COVID-19 patients in emergencies and to prevent massive loss of life in resource-poor environments. It can be assembled by a nonexpert as a homemade solution, without the need for specific equipment or technology. The proposed system is novel, inexpensive, has a reduced reliance on external power, and is very easy to maintain.

]]>