bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nurturing diversity and inclusion in AI in Biomedicine through a virtual summer program for high school students
Authors: Oskotsky Tomiko , Bajaj Ruchika , Burchard Jillian , Cavazos Taylor , Chen Ina , Connell Will , Eaneff Stephanie , Grant Tianna , Kanungo Ishan , Lindquist Karla , Myers-Turnbull Douglas , Naing Zun Zar Chi , Tang Alice , Vora Bianca , Wang Jon , Karim Isha , Swadling Claire , Yang Janice ,   AI4ALL Student Cohort 2020, Sirota Marina 
Published: March 2021

AbstractArtificial Intelligence (AI) has the power to improve our lives through a wide variety of applications, many of which fall into the healthcare space; however, a lack of diversity is contributing to flawed systems that perpetuate gender and racial biases, and limit how broadly AI can help people. The UCSF AI4ALL program was established in 2019 to address this issue by promoting diversity and inclusion in AI. The program targets high school students from underrepresented backgrounds in AI and gives them a chance to learn about AI with a focus on biomedicine. In 2020, the UCSF AI4ALL three-week program was held entirely online due to the COVID-19 pandemic. Thus students participated virtually to gain experience with AI, interact with diverse role models in AI, and learn about advancing health through AI. Specifically, they attended lectures in coding and AI, received an in-depth research experience through hands-on projects exploring COVID-19, and engaged in mentoring and personal development sessions with faculty, researchers, industry professionals, and undergraduate and graduate students, many of whom were women and from underrepresented racial and ethnic backgrounds. At the conclusion of the program, the students presented the results of their research projects at our final symposium. Comparison of pre- and post-program survey responses from students demonstrated that after the program, significantly more students were familiar with how to work with data and to evaluate and apply machine learning algorithms. There was also a nominally significant increase in the students’ knowing people in AI from historically underrepresented groups, feeling confident in discussing AI, and being aware of careers in AI. We found that we were able to engage young students in AI via our online training program and nurture greater inclusion in AI.
Transmission, infectivity, and antibody neutralization of an emerging SARS-CoV-2 variant in California carrying a L452R spike protein mutation
Authors: Deng Xianding , Garcia-Knight Miguel A , Khalid Mir M. , Servellita Venice , Wang Candace , Morris Mary Kate , Sotomayor-González Alicia , Glasner Dustin R , Reyes Kevin R , Gliwa Amelia S. , Reddy Nikitha P. , Sanchez San Martin Claudia , Federman Scot , Cheng Jing , Balcerek Joanna , Taylor Jordan , Streithorst Jessica A , Miller Steve , Kumar G. Renuka , Sreekumar Bharath , Chen Pei-Yi , Schulze-Gahmen Ursula , Taha Taha Y. , Hayashi Jennifer , Simoneau Camille R. , McMahon Sarah , Lidsky Peter V. , Xiao Yinghong , Hemarajata Peera , Green Nicole M. , Espinosa Alex , Kath Chantha , Haw Monica , Bell John , Hacker Jill K. , Hanson Carl , Wadford Debra A. , Anaya Carlos , Ferguson Donna , Lareau Liana F. , Frankino Phillip A. , Shivram Haridha , Wyman Stacia K. , Ott Melanie , Andino Raul , Chiu Charles Y. 
Published: March 2021

AbstractWe identified a novel SARS-CoV-2 variant by viral whole-genome sequencing of 2,172 nasal/nasopharyngeal swab samples from 44 counties in California. Named B.1.427/B.1.429 to denote its 2 lineages, the variant emerged around May 2020 and increased from 0% to >50% of sequenced cases from September 1, 2020 to January 29, 2021, exhibiting an 18.6-24% increase in transmissibility relative to wild-type circulating strains. The variant carries 3 mutations in the spike protein, including an L452R substitution. Our analyses revealed 2-fold increased B.1.427/B.1.429 viral shedding in vivo and increased L452R pseudovirus infection of cell cultures and lung organoids, albeit decreased relative to pseudoviruses carrying the N501Y mutation found in the B.1.1.7, B.1.351, and P.1 variants. Antibody neutralization assays showed 4.0 to 6.7-fold and 2.0-fold decreases in neutralizing titers from convalescent patients and vaccine recipients, respectively. The increased prevalence of a more transmissible variant in California associated with decreased antibody neutralization warrants further investigation.
COVID-19 vaccine distrust in Colombian university students: Frequency and associated variables
Authors: Campo-Arias Adalberto , Pedrozo-Pupo John Carlos 
Published: March 2021

AbstractThe study aimed to know the frequency and variables associated with COVID-19 vaccine distrust in students of a Colombian university. A cross-sectional study was carried out which participated emerging adult students of a Colombian university. A total of 1,136 students between 18 and 29 years (M= 22.0, SD = 3.0); most of them were female (66.0%), non-health students (82.8%), low-income (79.0%), and residents of urban areas (84.9%). It was frequent low institutional trust (74.8%), low cognitive, social capital (27.9%), low fear of COVID-19 (49.5%), low perceived stress related to COVID-19 (83.5%), and high COVID-19 vaccine distrust (78.9%). Non-health carrier (Adjusted OR = 3.63, 95%CI 2.58-5.10), rural residence (AOR = 1.85, 95%CI 1.13-3.04), low income (AOR = 1.84, 95%CI 1.31-2.57), and perceived stress related to COVID-19 (AOR = 1.74, 95%CI 1.20-2.54) were related to high COVID-19 vaccine distrust. In conclusion, COVID-19 vaccine distrust is high among emerging adult Colombian university students. The COVID-19 vaccine distrust is related to non-health science carriers, rural residents, low-income, and low-perceived stress related to COVID-19. The COVID-19 related health literacy should be improved in students of this university considering socio-cultural background.
Explainable AI for Retinal Prostheses: Predicting Electrode Deactivation from Routine Clinical Measures
Authors: Hu Zuying , Beyeler Michael 
Published: March 2021

AbstractTo provide appropriate levels of stimulation, retinal prostheses must be calibrated to an individual’s perceptual thresholds (‘system fitting’). Nonfunctional electrodes may then be deactivated to reduce power consumption and improve visual outcomes. However, thresholds vary drastically not just across electrodes but also over time, thus calling for a more flexible electrode deactivation strategy. Here we present an explainable artificial intelligence (XAI) model fit on a large longitudinal dataset that can 1) predict at which point in time the manufacturer chose to deactivate an electrode as a function of routine clinical measures (‘predictors’) and 2) reveal which of these predictors were most important. The model predicted electrode deactivation from clinical data with 60.8% accuracy. Performance increased to 75.3% with system fitting data, and to 84% when thresholds from follow-up examinations were available. The model further identified subject age and time since blindness onset as important predictors of electrode deactivation. An accurate XAI model of electrode deactivation that relies on routine clinical measures may benefit both the retinal implant and wider neuroprosthetics communities.
Heparin promotes fibrillation of most phenol soluble modulin peptides fromS. aureus: a possible strengthening of the bacterial biofilm
Authors: Najarzadeh Zahra , Zaman Masihuz , Serekaité Vita , Strømgaard Kristian , Andreasen Maria , Otzen Daniel E. 
Published: March 2021

ABSTRACTPhenol soluble modulins (PSMs) are virulence peptides secreted by differentStaphylococcus aureusstrains. In addition, PSMs are able to form amyloid fibrils which may strengthen the biofilm matrix. The highly sulfated glycosaminoglycan heparin promotesS.aureusinfection but the basis for this is unclear. We hypothesized that heparin promotes PSM fibrillation and in this way aids bacterial colonization. Here we address this hypothesis using a combination of different biophysical techniques along with peptide microarrays. We find that heparin accelerates fibrillation of all α-PSMs (except PSMα2) and δ-toxin, but inhibits β-PSMs’ fibrillation by blocking nucleation. Given thatS. aureussecretes higher levels of α-PSMs than β-PSMs peptidess, heparin is likely to overall promote fibrillation. Heparin binding is driven by multiple positively charged lysine residues in α-PSMs and δ-toxins, whose removal strongly reduces affinity. Binding of heparin does not alter the final fibril conformation. Rather, heparin provides a scaffold to catalyze or inhibit fibrillation. Our findings suggest that heparin may strengthen bacterial biofilm through increased PSM fibrillation.Abstract Figure
Palynofacies, environments, and climate changes in the Magdalena River Basin
Authors: Lorente M. A. 
Published: March 2021

ABSTRACTFour environments (swamp, shallow lake, alluvial flood plain, and lagoon) from the Lower Magdalena River Basin were studied for palynofacies’ quantitative characterization. Each environment has been described based on four criteria: palynomorph assemblage, organic matter concentration, organic matter palynological composition, and organic particle morphology.Shallow lakes’palynological assemblages are dominated by composite and grass pollen. The POM (particulate organic matter) morphology is characterized by a maximum at Φ 5 class (silt), and it has a sphericity histogram with bimodal distribution (peaks at 0.1 and 0.5/0.6). From a composition point of view, POM is mainly opaque amorphous materials. POM concentration is usually lower than 0.1%.Swampenvironments palynological assemblages are dominated by grass pollen with a slightly smaller amount of composite pollen. The POM is dominated by finely dispersed amorphous and indeterminate “other” types (organo-mineral gel ?), depending on the oxidation degree. The swamp concentration of organic matter a few centimeters below the water-sediment interface varies between 0.1% and 0.3%. Below that, organic concentration is usually lower than 0.1%.Lagoonassemblages are rich in species and specimens, but assemblages are highly variable. Main components are either finely dispersed amorphous or plant cuticular/epidermal or amorphous homogeneous and heterogeneous or fungal remains. Peat lithology is rich in mangrove pollen, while clay assemblages are dominated by composites, grass, and water plants together withBotryococcusalgal remains. Lagoon sediments are the richest in POM concentration, with values between 0.13% and 1% (excluding peats). Regarding particle size and shape, in this environment, they show a trend to decrease in grain size from Φ 1 to Φ 2 class (sand) dominated assemblages to Φ 5 to Φ 6 class (silt) dominated assemblages from base to top. Elongated shapes are abundant, with 30% to 50% of particles in the tabloid to elongated tabloid classes.Alluvial - fluvial flood basinsamples are often barren in palynomorphs and organic matter. Occasionally present grass pollen and fungal remains. The POM, when present, is mainly of organo-mineral gel type and has a bimodal grain size distribution, with a minor peak at Φ 7 class (v.f.silt) and a major peak at Φ 4 to Φ 2 class (c. silt to f. sand).Significant changes in quantitative palynofacies occur within the top few meters of the cores, representing the last 1000 yr of sedimentation in the area. These changes are related to shifts in climate, from colder to warmer conditions or from dry to wet periods, most probably linked with E.N.S.O. A short dry and cold period related to the “Little Ice Age” was identified in the Ayapel and Cienaga de El Medio cores.
Analysis of antibody data using Finite Mixture Models based on Scale Mixtures of Skew-Normal distributions
Authors: Domingues Tiago Dias , Mouriño Helena , Sepúlveda Nuno 
Published: March 2021

AbstractFinite mixture models have been widely used in antibody (or serological) data analysis in order to help classifying individuals into either antibody-positive or antibody-negative. The most popular models are the so-called Gaussian mixture models which assume a Normal distribution for each component of a mixture. In this work, we propose the use of finite mixture models based on a flexible class of scale mixtures of Skew-Normal distributions for serological data analysis. These distributions are sufficiently flexible to describe right and left asymmetry often observed in the distributions associated with hypothetical antibody-negative and antibody-positive individuals, respectively. We illustrate the advantage of these alternative mixture models with a data set of 406 individuals in which antibodies against six different human herpesviruses were measured in the context of Myalgic Encephalomyelitis/Chronic Fatigue Syndrome.
Single-Arm, Open-Label Phase 2 Trial of Preemptive Methylprednisolone to Avert Progression to Respiratory Failure in High-Risk Patients with COVID-19
Authors: Cabanillas Fernando , Morales Javier , G. Conde José , Bertrán-Pasarell Jorge , Fernández Ricardo , Hernandez-Silva Yaimara , Liboy Idalia , Bryan-Díaz James , Arraut-Gonzalez Juan 
Published: March 2021

AbstractIntroductionCovid-19 is a triphasic disorder first typified by a viral phase that lasts from the first onset of symptoms until seven days later. This is followed by a second and third phase, initially characterized by the appearance of lung infiltrates, followed in 20% by respiratory failure. The second phase is usually heralded by an elevation of serologic inflammatory markers including CRP, ferritin, IL-6, LDH as well as D-dimers. Approximately 20% proceed to the second phase and are usually then treated with dexamethasone, provided they are oxygen-dependent since these are the only cases that benefit from dexamethasone. If we had objective criteria to predict this 20% that develop severe illness, they could preemptively be treated with steroids. In this exploratory study we investigated the early use of preemptive steroids in the setting of early disease, in high-risk non-oxygen dependent cases.MethodsEligible patients were those 21 years or older with a diagnosis of Covid-19 and oxygen saturation ≥91%. For patients to be classified as high-risk, they had to exhibit two or more of the following abnormalities 7-10 days after first symptom: IL-6 ≥ 10 pg/ml, ferritin > 500 ng/ml, D-dimer > 1 mg/L (1,000 ng/ml), CRP > 10 mg/dL (100 mg/L), LDH above normal range lymphopenia (absolute lymphocyte count <1,000 /µL), oxygen saturation between 91-94%, or CT chest with evidence of ground glass infiltrates. Primary endpoint was progression to respiratory failure. CALL score method was used to predict the expected number of cases of respiratory failure. High risk patients received methylprednisolone (MPS) 80 mg IV daily x 5 days starting no earlier than seven days from first onset of symptoms. The primary endpoint was progression to hypoxemic respiratory failure defined as PaO2 <60 mm Hg or oxygen saturation ≤90%. Secondary endpoints included survival at 28 days from registration, admission to intensive care and live discharge from the hospital. Change in levels of inflammatory markers and length of hospitalization were also assessed.ResultsIn 76 patients, the expected number with respiratory failure was 30 (39.5%), yet only 4 (5.3%) developed that complication (p=.00001). Survival at 28 days was 98.6%.Improvement in inflammatory markers correlated with favorable outcome.ConclusionsOur results are encouraging and suggest that this approach is both effective and safe.
Ultra-small cells and DPANN genome unveiled inside an extinct vent chimney
Authors: Takamiya Hinako , Kouduka Mariko , Furutani Hitoshi , Mukai Hiroki , Yamamoto Takushi , Kato Shingo , Kodama Yu , Tomioka Naotaka , Ito Motoo , Suzuki Yohey 
Published: March 2021

AbstractChemosynthetic organisms flourish around deep-sea hydrothermal vents where energy-rich fluids are emitted from metal sulfide chimneys. In contrast to actively venting chimneys, the nature of microbial life in extinct chimneys without fluid venting remains largely unknown. Here, the occurrence of ultra-small cells in silica-filled grain boundaries inside an extinct chimney is demonstrated by high-resolution bio-signature mapping. The ultra-small cells are associated with extracellularly precipitated Cu2O nanocrystals. Single-gene analysis shows that the chimney interior is dominated by a member of Pacearchaeota known as a major phylum of DPANN. Genome-resolved metagenomic analysis reveals that the chimney Pacearchaeota member is equipped with a nearly full set of genes for fermentation-based energy generation from nucleic acids, in contrast to previously characterized Pacearchaeota members lacking many genes for nucleic acid fermentation. We infer that the ultra-small cells associated with silica and extracellular Cu2O nanocrystals in the grain boundaries are Pacearchaeota, on the basis of the experimentally demonstrated capability of silica to concentrate nucleic acids from seawater and the presence of Cu-exporting genes in a reconstructed Pacearchaeota genome. Given the existence of ~3-billion-year-old submarine hydrothermally deposited silica, proliferation of microbial life using silica-bound nucleic acids might be relevant to the primitive vent biosphere.
IsoSolve: an integrative framework to improve isotopic coverage and consolidate isotopic measurements by MS and/or NMR
Authors: Millard Pierre , Sokol Sergueï , Kohlstedt Michael , Wittmann Christoph , Létisse Fabien , Lippens Guy , Portais Jean-Charles 
Published: March 2021

ABSTRACTStable-isotope labeling experiments are widely used to investigate the topology and functioning of metabolic networks. Label incorporation into metabolites can be quantified using a broad range of mass spectrometry (MS)and nuclear magnetic resonance (NMR)spectroscopy methods, but in general, no single approach can completely cover isotopic space, even for small metabolites. The number of quantifiable isotopic species could be increased, and the coverage of isotopic space improved, by integrating measurements obtained by different methods; however, this approach has remained largely unexplored because no framework able to deal with partial, heterogeneous isotopic measurements has yet been developed. Here, we present a generic computational framework based on symbolic calculus that can integrate any isotopic dataset by connecting measurements to the chemical structure of the molecules. As a test case, we apply this framework to isotopic analyses of amino acids, which are ubiquitous to life, central to many biological questions, and can be analyzed by a broad range of MS and NMR methods. We demonstrate how this integrative framework helps to i) clarify and improve the coverage of isotopic space, ii) evaluate the complementarity and redundancy of different techniques, iii) consolidate isotopic datasets, iv) design experiments, and v) guide future analytical developments. This framework, which can be applied to any labeled element, isotopic tracer, metabolite, and analytical platform, has been implemented in IsoSolve (available athttps://github.com/MetaSysLISBP/IsoSolveandhttps://pypi.org/project/IsoSolve), an open source software that can be readily integrated into data analysis pipelines.
In vitroandin vivointeraction of caspofungin with isavuconazole againstCandida aurisplanktonic cells and biofilms
Authors: Nagy Fruzsina , Tóth Zoltán , Nyikos Fanni , Forgács Lajos , Jakab Ágnes , Borman Andrew M. , Majoros László , Kovács Renátó 
Published: March 2021

AbstractThein vitroandin vivoefficacy of caspofungin was determined in combination with isavuconazole againstCandida auris. Drug–drug interactions were assessed utilising the fractional inhibitory concentration indices (FICIs), the Bliss independence model and an immunocompromised mouse model. Median planktonic minimum inhibitory concentrations (pMICs) of 23C. aurisisolates were between 0.5 and 2 mg/L and between 0.015 and 4 mg/L for caspofungin and isavuconazole, respectively. Median pMICs for caspofungin and isavuconazole in combination showed 2–128-fold and 2–256-fold decreases, respectively. Caspofungin and isavuconazole showed synergism in 14 out of 23 planktonic isolates (FICI range 0.03–0.5; Bliss cumulative synergy volume range 0–4.83). Median sessile MICs (sMIC) of 14 biofilm-forming isolates were between 32 and >32 mg/L and between 0.5 and >2 mg/L for caspofungin and isavuconazole, respectively. Median sMICs for caspofungin and isavuconazole in combination showed 0–128-fold and 0-512-fold decreases, respectively. Caspofungin and isavuconazole showed synergistic interaction in 12 out of 14 sessile isolates (FICI range 0.023–0.5; Bliss cumulative synergy volume range 0.13–234.32). In line with thein vitrofindings, synergistic interactions were confirmed byin vivoexperiments. The fungal kidney burden decreases were more than 3 log volumes in mice treated with combination of 1 mg/kg caspofungin and 20 mg/kg isavuconazole daily; this difference was statistically significant compared with control mice (p<0.001). Despite the favourable effect of isavuconazole in combination with caspofungin, further studies are needed to confirm the therapeutic advantage of this combination when treating an infection caused byC. auris.
Cancer drug discovery as a low rank tensor completion problem
Authors: Murali Vasanth S. , Ağaç Çobanoğlu Didem , Hsieh Michael , Zinn Meyer , Malladi Venkat S. , Gesell Jonathan , Williams Noelle S. , Welf Erik S. , Raj Ganesh V. , Çobanoğlu Murat Can 
Published: March 2021

AbstractThe heterogeneity of cancer necessitates developing a multitude of targeted therapies. We propose the view that cancer drug discovery is a low rank tensor completion problem. We implement this vision by using heterogeneous public data to construct a tensor of drug-target-disease associations. We show the validity of this approach computationally by simulations, and experimentally by testing drug candidates. Specifically, we show that a novel drug candidate, SU11652, controls melanoma tumor growth, including BRAFWTmelanoma. Independently, we show that another molecule, TC-E 5008, controls tumor proliferation onex vivoER+ human breast cancer. Most importantly, we identify these chemicals with only a few computationally selected experiments as opposed to brute-force screens. The efficiency of our approach enables use ofex vivohuman tumor assays as a primary screening tool. We provide a web server, the Cancer Vulnerability Explorer (accessible athttps://cavu.biohpc.swmed.edu), to facilitate the use of our methodology.