bluuebunny/crossref_metadata_2025_split huggingface dataset:
SCOPE enables type III CRISPR-Cas diagnostics using flexible targeting and stringent CARF ribonuclease activation
Authors: Steens Jurre A. , Zhu Yifan , Taylor David W. , Bravo Jack P. K. , Prinsen Stijn H. P. , Schoen Cor D. , Keijser Bart J. F. , Ossendrijver Michel , Hofstra L. Marije , Brouns Stan J. J. , Shinkai Akeo , van der Oost John , Staals Raymond H. J. 
Published: August 2021

AbstractCharacteristic properties of type III CRISPR-Cas systems include recognition of target RNA and the subsequent induction of a multifaceted immune response. This involves sequence-specific cleavage of the target RNA and production of cyclic oligoadenylate (cOA) molecules. Here we report that an exposed seed region at the 3′ end of the crRNA is essential for target RNA binding and cleavage, whereas cOA production requires base pairing at the 5′ end of the crRNA. Moreover, we uncover that the variation in the size and composition of type III complexes within a single host results in variable seed regions. This may prevent escape by invading genetic elements, while controlling cOA production tightly to prevent unnecessary damage to the host. Lastly, we use these findings to develop a new diagnostic tool, SCOPE, for the specific detection of SARS-CoV-2 from human nasal swab samples, revealing sensitivities in the atto-molar range.
Genetic epidemiology of BRCA1- and BRCA2-associated cancer across Latin America
Authors: Herzog Josef S. , Chavarri-Guerra Yanin , Castillo Danielle , Abugattas Julio , Villarreal-Garza Cynthia , Sand Sharon , Clague-Dehart Jessica , Alvarez-Gómez Rosa M. , Wegman-Ostrosky Talia , Mohar Alejandro , Mora Pamela , Del Toro-Valero Azucena , Daneri-Navarro Adrian , Rodriguez Yenni , Cruz-Correa Marcia , Ashton-Prolla Patricia , Alemar Bárbara , Mejia Rosa , Gallardo Lenny , Shaw Robin , Yang Kai , Cervantes Aleck , Tsang Kevin , Nehoray Bita , Barrera Saldana Hugo , Neuhausen Susan , Weitzel Jeffrey N. 
Published: August 2021

AbstractThe prevalence and contribution ofBRCA1/2(BRCA) pathogenic variants (PVs) to the cancer burden in Latin America are not well understood. This study aims to address this disparity.BRCAanalyses were performed on prospectively enrolled Latin American Clinical Cancer Genomics Community Research Network participants via a combination of methods: a Hispanic Mutation Panel (HISPANEL) on MassARRAY; semiconductor sequencing; and copy number variant (CNV) detection.BRCAPV probability was calculated using BRCAPRO. Among 1,627 participants (95.2% with cancer), we detected 236 (14.5%) BRCA PVs; 160BRCA1(31% CNVs); 76BRCA2PV frequency varied by country: 26% Brazil, 9% Colombia, 13% Peru, and 17% Mexico. Recurrent PVs (seen ≥3 times), some region-specific, represented 42.8% (101/236) of PVs. There was no ClinVar entry for 14% (17/125) of unique PVs, and 57% (111/196) of unique VUS. The area under the ROC curve for BRCAPRO was 0.76. In summary, we implemented a low-costBRCAtesting strategy and documented a significant burden of non-ClinVar reportedBRCAPVs among Latin Americans. There are recurrent, population-specific PVs and CNVs, and we note that the BRCAPRO mutation probability model performs adequately. This study helps address the gap in our understanding ofBRCA-associated cancer in Latin America.
Common workflows for computing material properties using different quantum engines
Authors: Huber Sebastiaan P. , Bosoni Emanuele , Bercx Marnik , Bröder Jens , Degomme Augustin , Dikan Vladimir , Eimre Kristjan , Flage-Larsen Espen , Garcia Alberto , Genovese Luigi , Gresch Dominik , Johnston Conrad , Petretto Guido , Poncé Samuel , Rignanese Gian-Marco , Sewell Christopher J. , Smit Berend , Tseplyaev Vasily , Uhrin Martin , Wortmann Daniel , Yakutovich Aliaksandr V. , Zadoks Austin , Zarabadi-Poor Pezhman , Zhu Bonan , Marzari Nicola , Pizzi Giovanni 
Published: August 2021

AbstractThe prediction of material properties based on density-functional theory has become routinely common, thanks, in part, to the steady increase in the number and robustness of available simulation packages. This plurality of codes and methods is both a boon and a burden. While providing great opportunities for cross-verification, these packages adopt different methods, algorithms, and paradigms, making it challenging to choose, master, and efficiently use them. We demonstrate how developing common interfaces for workflows that automatically compute material properties greatly simplifies interoperability and cross-verification. We introduce design rules for reusable, code-agnostic, workflow interfaces to compute well-defined material properties, which we implement for eleven quantum engines and use to compute various material properties. Each implementation encodes carefully selected simulation parameters and workflow logic, making the implementer’s expertise of the quantum engine directly available to non-experts. All workflows are made available as open-source and full reproducibility of the workflows is guaranteed through the use of the AiiDA infrastructure.
Exploring human-genome gut-microbiome interaction in Parkinson’s disease
Authors: Wallen Zachary D. , Stone William J. , Factor Stewart A. , Molho Eric , Zabetian Cyrus P. , Standaert David G. , Payami Haydeh 
Published: August 2021

AbstractThe causes of complex diseases remain an enigma despite decades of epidemiologic research on environmental risks and genome-wide studies that have uncovered tens or hundreds of susceptibility loci for each disease. We hypothesize that the microbiome is the missing link. Genetic studies have shown that overexpression of alpha-synuclein, a key pathological protein in Parkinson’s disease (PD), can cause familial PD and variants at alpha-synuclein locus confer risk of idiopathic PD. Recently, dysbiosis of gut microbiome in PD was identified: altered abundances of three microbial clusters were found, one of which was composed of opportunistic pathogens. Using two large datasets, we found evidence that the overabundance of opportunistic pathogens in PD gut is influenced by the host genotype at the alpha-synuclein locus, and that the variants responsible modulate alpha-synuclein expression. Results put forth testable hypotheses on the role of gut microbiome in the pathogenesis of PD, the incomplete penetrance of PD susceptibility genes, and potential triggers of pathology in the gut.
Codominant IgG and IgA expression with minimal vaccine mRNA in milk of BNT162b2 vaccinees
Authors: Low Jia Ming , Gu Yue , Ng Melissa Shu Feng , Amin Zubair , Lee Le Ye , Ng Yvonne Peng Mei , Shunmuganathan Bhuvaneshwari D/O , Niu Yuxi , Gupta Rashi , Tambyah Paul Anantharajah , MacAry Paul A. , Wang Liang Wei , Zhong Youjia 
Published: August 2021

AbstractLactating women can produce protective antibodies in their milk after vaccination, which has informed antenatal vaccination programs for diseases such as influenza and pertussis. However, whether SARS-CoV-2-specific antibodies are produced in human milk as a result of COVID-19 vaccination is still unclear. In this study, we show that lactating mothers who received the BNT162b2 vaccine secreted SARS-CoV-2-specific IgA and IgG antibodies into milk, with the most significant increase at 3–7 days post-dose 2. Virus-specific IgG titers were stable out to 4–6 weeks after dose 2. In contrast, SARS-CoV-2-specific IgA levels showed substantial decay. Vaccine mRNA was detected in few milk samples (maximum of 2 ng/ml), indicative of minimal transfer. Additionally, infants who consumed post-vaccination human milk had no reported adverse effects up to 28 days post-ingestion. Our results define the safety and efficacy profiles of the vaccine in this demographic and provide initial evidence for protective immunity conferred by milk-borne SARS-CoV-2-specific antibodies. Taken together, our study supports recommendations for uninterrupted breastfeeding subsequent to mRNA vaccination against COVID-19.
Lenghu on the Tibetan Plateau as an astronomical observing site
Authors: Deng Licai , Yang Fan , Chen Xiaodian , He Fei , Liu Qili , Zhang Bo , Zhang Chunguang , Wang Kun , Liu Nian , Ren Anbing , Luo Zhiquan , Yan Zhengzhou , Tian Jianfeng , Pan Jun 
Published: August 2021

AbstractOn Earth’s surface, there are only a handful of high-quality astronomical sites that meet the requirements for very large next-generation facilities. In the context of scientific opportunities in time-domain astronomy, a good site on the Tibetan Plateau will bridge the longitudinal gap between the known best sites1,2 (all in the Western Hemisphere). The Tibetan Plateau is the highest plateau on Earth, with an average elevation of over 4,000 metres, and thus potentially provides very good opportunities for astronomy and particle astrophysics3–5. Here we report the results of three years of monitoring of testing an area at a local summit on Saishiteng Mountain near Lenghu Town in Qinghai Province. The altitudes of the potential locations are between 4,200 and 4,500 metres. An area of over 100,000 square kilometres surrounding Lenghu Town has a lower altitude of below 3,000 metres, with an extremely arid climate and unusually clear local sky (day and night)6. Of the nights at the site, 70 per cent have clear, photometric conditions, with a median seeing of 0.75 arcseconds. The median night temperature variation is only 2.4 degrees Celsius, indicating very stable local surface air. The precipitable water vapour is lower than 2 millimetres for 55 per cent of the night.
Separating microparticles by material and size using dielectrophoretic chromatography with frequency modulation
Authors: Giesler Jasper , Weirauch Laura , Thöming Jorg , Baune Michael , Pesch Georg R. 
Published: August 2021

AbstractSeparation of (biological) particles ($$\ll {10}~{\upmu }\text {m}$$

≪
10

μ
m

) according to size or other properties is an ongoing challenge in a variety of technical relevant fields. Dielectrophoresis is one method to separate particles according to a diversity of properties, and within the last decades a pool of dielectrophoretic separation techniques has been developed. However, many of them either suffer selectivity or throughput. We use simulation and experiments to investigate retention mechanisms in a novel DEP scheme, namely, frequency-modulated DEP. Results from experiments and simulation show a good agreement for the separation of binary PS particles mixtures with respect to size and more importantly, for the challenging task of separating equally sized microparticles according to surface functionalization alone. The separation with respect to size was performed using 2 $${\upmu }$$
μ
m and 3 $${\upmu }$$
μ
m sized particles, whereas separation with respect to surface functionalization was performed with 2 $${\upmu }$$
μ
m particles. The results from this study can be used to solve challenging separation tasks, for example to separate particles with distributed properties.
Elevated temperature and browning increase dietary methylmercury, but decrease essential fatty acids at the base of lake food webs
Authors: Wu Pianpian , Kainz Martin J. , Valdés Fernando , Zheng Siwen , Winter Katharina , Wang Rui , Branfireun Brian , Chen Celia Y. , Bishop Kevin 
Published: August 2021

AbstractClimate change scenarios predict increases in temperature and organic matter supply from land to water, which affect trophic transfer of nutrients and contaminants in aquatic food webs. How essential nutrients, such as polyunsaturated fatty acids (PUFA), and potentially toxic contaminants, such as methylmercury (MeHg), at the base of aquatic food webs will be affected under climate change scenarios, remains unclear. The objective of this outdoor mesocosm study was to examine how increased water temperature and terrestrially-derived dissolved organic matter supply (tDOM; i.e., lake browning), and the interaction of both, will influence MeHg and PUFA in organisms at the base of food webs (i.e. seston; the most edible plankton size for zooplankton) in subalpine lake ecosystems. The interaction of higher temperature and tDOM increased the burden of MeHg in seston (< 40 μm) and larger sized plankton (microplankton; 40–200 μm), while the MeHg content per unit biomass remained stable. However, PUFA decreased in seston, but increased in microplankton, consisting mainly of filamentous algae, which are less readily bioavailable to zooplankton. We revealed elevated dietary exposure to MeHg, yet decreased supply of dietary PUFA to aquatic consumers with increasing temperature and tDOM supply. This experimental study provides evidence that the overall food quality at the base of aquatic food webs deteriorates during ongoing climate change scenarios by increasing the supply of toxic MeHg and lowering the dietary access to essential nutrients of consumers at higher trophic levels.
Distribution of pathogens and antimicrobial resistance in ICU-bloodstream infections during hospitalization: a nationwide surveillance study
Authors: Sommerstein Rami , Damonti Lauro , Marschall Jonas , Harbarth Stephan , Gasser Michael , Kronenberg Andreas , Buetti Niccolò 
Published: August 2021

AbstractChanging microorganism distributions and decreasing antibiotic susceptibility over the duration of hospitalization have been described for the colonization or infection of selected organ systems. Few data are available on bacteremias in the intensive care unit (ICU) setting. We conducted a nationwide study on bloodstream infection (BSI) using data from the Swiss Centre for Antibiotic Resistance (ANRESIS). We analyzed data on BSI detected in the ICU from hospitals that sent information on a regular basis during the entire study period (2008–2017). We described specific trends of pathogen distribution and resistance during hospitalization duration. We included 6505 ICU- BSI isolates from 35 Swiss hospitals. We observed 2587 possible skin contaminants, 3788 bacteremias and 130 fungemias. The most common microorganism was Escherichia coli (23.2%, 910), followed by Staphylococcus aureus (18.7%, 734) and enterococci (13.1%, 515). Enterococcus spp (p < 0.0001) and Candida spp (p < 0.0001) increased in proportion, whereas E. coli (p < 0.0001) and S. aureus (p < 0.0001) proportions decreased during hospitalization. Resistances against first- and second-line antibiotics increased linearly during hospitalization. Pathogen distribution and antimicrobial resistance in ICU-BSI depends on the duration of the hospitalization. The proportion of enterococcal BSI, candidemia and resistant microorganisms against first- and second-line antibiotics increased during hospitalization.
Fine-grained data reveal segregated mobility networks and opportunities for local containment of COVID-19
Authors: Fan Chao , Lee Ronald , Yang Yang , Mostafavi Ali 
Published: August 2021

AbstractDeriving effective mobility control measures is critical for the control of COVID-19 spreading. In response to the COVID-19 pandemic, many countries and regions implemented travel restrictions and quarantines to reduce human mobility and thus reduce virus transmission. But since human mobility decreased heterogeneously, we lack empirical evidence of the extent to which the reductions in mobility alter the way people from different regions of cities are connected, and what containment policies could complement mobility reductions to conquer the pandemic. Here, we examined individual movements in 21 of the most affected counties in the United States, showing that mobility reduction leads to a segregated place network and alters its relationship with pandemic spread. Our findings suggest localized area-specific policies, such as geo-fencing, as viable alternatives to city-wide lockdown for conquering the pandemic after mobility was reduced.
A randomized-controlled neurofeedback trial in adult attention-deficit/hyperactivity disorder
Authors: Barth Beatrix , Mayer-Carius Kerstin , Strehl Ute , Wyckoff Sarah N. , Haeussinger Florian B. , Fallgatter Andreas J. , Ehlis Ann-Christine 
Published: August 2021

AbstractAttention-deficit/hyperactivity disorder (ADHD) is a childhood onset disorder persisting into adulthood for a large proportion of cases. Neurofeedback (NF) has shown promising results in children with ADHD, but randomized controlled trials in adults with ADHD are scarce. We aimed to compare slow cortical potential (SCP)- and functional near-infrared spectroscopy (fNIRS) NF to a semi-active electromyography biofeedback (EMG-BF) control condition regarding changes in symptoms and the impact of learning success, as well as changes in neurophysiological parameters in an adult ADHD population. Patients were randomly assigned to SCP-NF (n = 26), fNIRS-NF (n = 21) or EMG-BF (n = 20). Outcome parameters were assessed over 30 training sessions (pre, intermediate, post) and at 6-months follow-up (FU) including 3 booster sessions. EEG was recorded during two auditory Go/NoGo paradigms assessing the P300 and contingent negative variation (CNV). fNIRS measurements were conducted during an n-back- as well as a Go/NoGo task. All three groups showed equally significant symptom improvements suggesting placebo- or non-specific effects on the primary outcome measure. Only when differentiating between learners and non-learners, fNIRS learners displayed stronger reduction of ADHD global scores compared to SCP non-learners at FU, and fNIRS learners showed specifically low impulsivity ratings. 30.8% in the SCP-NF and 61.9% of participants in the fNIRS-NF learned to regulate the respective NF target parameter. We conclude that some adults with ADHD learn to regulate SCP amplitudes and especially prefrontal hemodynamic activity during NF. We did not find any significant differences in outcome between groups when looking at the whole sample. When evaluating learners only, they demonstrate superior effects as compared to non-learners, which suggests specific effects in addition to non-specific effects of NF when learning occurs.
Crag Martin neontology complements taphonomy at the Gorham's Cave Complex
Authors: Bensusan Keith , Holmes Tyson Lee , Perez Charles , Finlayson Geraldine , Finlayson Stewart , Guillem Rhian , Finlayson Clive 
Published: August 2021

AbstractSpecies present in the fossil record may continue to exist at an archaeological site, allowing study that fine-tunes our picture of the ecological past. A large wintering population of Eurasian Crag MartinsPtyonoprogne rupestris(ECM) roosts at the ‘Gorham’s Cave Complex’ UNESCO World Heritage site in Gibraltar, which is best known for its occupation by Neanderthals at times when ECMs were also present. Its complex geomorphology allows the study of use of different micro-sites (caves) within the roost. We used mark-recapture to test whether birds showed fidelity to micro-sites for roosting, and for differences in condition of birds across micro-sites. ECM showed very high fidelity towards micro-sites, within and between years, with > 90% chance of recapture at caves where they were first caught. Condition of birds differed between micro-sites, suggesting differences in roost quality between caves; birds were more likely to be recaptured at the micro-site where birds were in best condition, indicating higher survivorship. Our results demonstrate extremely fine-scale fidelity at the largest roosting site documented for ECM globally. Implications for conservation are discussed. The study provides current knowledge of a bird that has been using these caves since the Pleistocene and more generally on these caves as refuges.
Predicting pediatric anxiety from the temporal pole using neural responses to emotional faces
Authors: Sawalha Jeffrey , Yousefnezhad Muhammad , Selvitella Alessandro M. , Cao Bo , Greenshaw Andrew J. , Greiner Russell 
Published: August 2021

AbstractA prominent cognitive aspect of anxiety is dysregulation of emotional interpretation of facial expressions, associated with neural activity from the amygdala and prefrontal cortex. We report machine learning analysis of fMRI results supporting a key role for a third area, the temporal pole (TP) for childhood anxiety in this context. This finding is based on differential fMRI responses to emotional faces (angry versus fearful faces) in children with one or more of generalized anxiety, separation anxiety, and social phobia (n = 22) compared with matched controls (n = 23). In our machine learning (Adaptive Boosting) model, the right TP distinguished anxious from control children (accuracy = 81%). Involvement of the TP as significant for neurocognitive aspects of pediatric anxiety is a novel finding worthy of further investigation.
Hybrid nanofluid flow through a spinning Darcy–Forchheimer porous space with thermal radiation
Authors: Saeed Anwar , Jawad Muhammad , Alghamdi Wajdi , Nasir Saleem , Gul Taza , Kumam Poom 
Published: August 2021

AbstractThis work investigates numerically the solution of Darcy–Forchheimer flow for hybrid nanofluid by employing the slip conditions. Basically, the fluid flow is produced by a swirling disk and is exposed to thermal stratification along with non-linear thermal radiation for controlling the heat transfer of the flow system. In this investigation, the nanoparticles of titanium dioxide and aluminum oxide have been suspended in water as base fluid. Moreover, the Darcy–Forchheimer expression is used to characterize the porous spaces with variable porosity and permeability. The resulting expressions of motion, energy and mass transfer in dimensionless form have been solved by HAM (Homotopy analysis method). In addition, the influence of different emerging factors upon flow system has been disputed both theoretically in graphical form and numerically in the tabular form. During this effort, it has been recognized that velocities profiles augment with growing values of mixed convection parameter while thermal characteristics enhance with augmenting values of radiation parameters. According to the findings, heat is transmitted more quickly in hybrid nanofluid than in traditional nanofluid. Furthermore, it is estimated that the velocities of fluid $$f^{\prime}\left( \xi \right),g\left( \xi \right)$$

f
′

ξ

,
g

ξ

are decayed for high values of $$\phi_{1} ,\phi_{2} ,\,Fr$$

ϕ
1

,

ϕ
2

,

F
r

and $$k_{1}$$

k
1

factors.
Histology and μCT reveal the unique evolution and development of multiple tooth rows in the synapsid Endothiodon
Authors: Olroyd Savannah L. , LeBlanc Aaron R. H. , Araújo Ricardo , Angielczyk Kenneth D. , Duhamel Aliénor , Benoit Julien , Amaral Marisa 
Published: August 2021

AbstractSeveral amniote lineages independently evolved multiple rows of marginal teeth in response to the challenge of processing high fiber plant matter. Multiple tooth rows develop via alterations to tooth replacement in captorhinid reptiles and ornithischian dinosaurs, but the specific changes that produce this morphology differ, reflecting differences in their modes of tooth attachment. To further understand the mechanisms by which multiple tooth rows can develop, we examined this feature in Endothiodon bathystoma, a member of the only synapsid clade (Anomodontia) to evolve a multi-rowed marginal dentition. We histologically sampled Endothiodon mandibles with and without multiple tooth rows as well as single-rowed maxillae. We also segmented functional and replacement teeth in µ-CT scanned mandibles and maxillae of Endothiodon and several other anomodonts with ‘postcanine’ teeth to characterize tooth replacement in the clade. All anomodonts in our sample displayed a space around the tooth roots for a soft tissue attachment between tooth and jaw in life. Trails of alveolar bone indicate varying degrees of labial migration of teeth through ontogeny, often altering the spatial relationships of functional and replacement teeth in the upper and lower jaws. We present a model of multiple tooth row development in E. bathystoma in which labial migration of functional teeth was extensive enough to prevent resorption and replacement by newer generations of teeth. This model represents another mechanism by which multiple tooth rows evolved in amniotes. The multiple tooth rows of E. bathystoma may have provided more extensive contact between the teeth and a triturating surface on the palatine during chewing.