bluuebunny/crossref_metadata_2025_split huggingface dataset:
Entanglement across separate silicon dies in a modular superconducting qubit device
Authors: Gold Alysson , Paquette J. P. , Stockklauser Anna , Reagor Matthew J. , Alam M. Sohaib , Bestwick Andrew , Didier Nicolas , Nersisyan Ani , Oruc Feyza , Razavi Armin , Scharmann Ben , Sete Eyob A. , Sur Biswajit , Venturelli Davide , Winkleblack Cody James , Wudarski Filip , Harburn Mike , Rigetti Chad 
Published: September 2021

AbstractAssembling future large-scale quantum computers out of smaller, specialized modules promises to simplify a number of formidable science and engineering challenges. One of the primary challenges in developing a modular architecture is in engineering high fidelity, low-latency quantum interconnects between modules. Here we demonstrate a modular solid state architecture with deterministic inter-module coupling between four physically separate, interchangeable superconducting qubit integrated circuits, achieving two-qubit gate fidelities as high as 99.1 ± 0.5% and 98.3 ± 0.3% for iSWAP and CZ entangling gates, respectively. The quality of the inter-module entanglement is further confirmed by a demonstration of Bell-inequality violation for disjoint pairs of entangled qubits across the four separate silicon dies. Having proven out the fundamental building blocks, this work provides the technological foundations for a modular quantum processor: technology which will accelerate near-term experimental efforts and open up new paths to the fault-tolerant era for solid state qubit architectures.
Specific human cytomegalovirus signature detected in NK cell metabolic changes post vaccination
Authors: Woods Elena , Zaiatz-Bittencourt Vanessa , Bannan Ciaran , Bergin Colm , Finlay David K. , Hoffmann Matthias , Brown Anthony , Turner Bethany , Makvandi-Nejad Shokouh , Vassilev Ventzi , Capone Stefania , Folgori Antonella , Hanke Tomáš , Barnes Eleanor , Dorrell Lucy , Gardiner Clair M. ,   PEACHI Consortium
Published: September 2021

AbstractEffective vaccines for human immunodeficiency virus-1 (HIV-1) and hepatitis C virus (HCV) remain a significant challenge for these infectious diseases. Given that the innate immune response is key to controlling the scale and nature of developing adaptive immune responses, targeting natural killer (NK) cells that can promote a T-helper type 1 (Th1)-type immune response through the production of interferon-γ (IFNγ) remains an untapped strategic target for improved vaccination approaches. Here, we investigate metabolic and functional responses of NK cells to simian adenovirus prime and MVA boost vaccination in a cohort of healthy volunteers receiving a dual HCV-HIV-1 vaccine. Early and late timepoints demonstrated metabolic changes that contributed to the sustained proliferation of all NK cells. However, a strong impact of human cytomegalovirus (HCMV) on some metabolic and functional responses in NK cells was observed in HCMV seropositive participants. These changes were not restricted to molecularly defined adaptive NK cells; indeed, canonical NK cells that produced most IFNγ in response to vaccination were equally impacted in individuals with latent HCMV. In summary, NK cells undergo metabolic changes in response to vaccination, and understanding these in the context of HCMV is an important step towards rational vaccine design against a range of human viral pathogens.
A doubling of stony coral cover on shallow forereefs at Carrie Bow Cay, Belize from 2014 to 2019
Authors: de Pablo Luis X. , Lefcheck Jonathan S. , Harper Leah , Paul Valerie J. , Jones Scott , Whippo Ross , Seemann Janina , Kline David I. , Duffy J. Emmett 
Published: September 2021

AbstractTo better understand the decline of one of earth’s most biodiverse habitats, coral reefs, many survey programs employ regular photographs of the benthos. An emerging challenge is the time required to annotate the large volume of digital imagery generated by these surveys. Here, we leverage existing machine-learning tools (CoralNet) and develop new fit-to-purpose programs to process and score benthic photoquadrats using five years of data from the Smithsonian MarineGEO Network’s biodiversity monitoring program at Carrie Bow Cay, Belize. Our analysis shows that scleractinian coral cover on forereef sites (at depths of 3–10 m) along our surveyed transects increased significantly from 6 to 13% during this period. More modest changes in macroalgae, turf algae, and sponge cover were also observed. Community-wide analysis confirmed a significant shift in benthic structure, and follow-up in situ surveys of coral demographics in 2019 revealed that the emerging coral communities are dominated by fast-recruiting and growing coral species belonging to the generaAgariciaandPorites. While the positive trajectory reported here is promising, Belizean reefs face persistent challenges related to overfishing and climate change. Open-source computational toolkits offer promise for increasing the efficiency of reef monitoring, and therefore our ability to assess the future of coral reefs in the face of rapid environmental change.
Intradiscal quantitative chemical exchange saturation transfer MRI signal correlates with discogenic pain in human patients
Authors: Pelled Gadi , Salas Margaux M. , Han Pei , Gill Howard E. , Lautenschlager Karl A. , Lai Tristan T. , Shawver Cameron M. , Hoch Matthew B. , Goff Brandon J. , Betts Aaron M. , Zhou Zhengwei , Lynch Cody , Schroeder Grant , Bez Maxim , Maya Marcel M. , Bresee Catherine , Gazit Zulma , McCallin John P. , Gazit Dan , Li Debiao 
Published: September 2021

AbstractLow back pain (LBP) is often a result of a degenerative process in the intervertebral disc. The precise origin of discogenic pain is diagnosed by the invasive procedure of provocative discography (PD). Previously, we developed quantitative chemical exchange saturation transfer (qCEST) magnetic resonance imaging (MRI) to detect pH as a biomarker for discogenic pain. Based on these findings we initiated a clinical study with the goal to evaluate the correlation between qCEST values and PD results in LBP patients. Twenty five volunteers with chronic low back pain were subjected to T2-weighted (T2w) and qCEST MRI scans followed by PD. A total of 72 discs were analyzed. The average qCEST signal value of painful discs was significantly higher than non-painful discs (p = 0.012). The ratio between qCEST and normalized T2w was found to be significantly higher in painful discs compared to non-painful discs (p = 0.0022). A receiver operating characteristics (ROC) analysis indicated that qCEST/T2w ratio could be used to differentiate between painful and non-painful discs with 78% sensitivity and 81% specificity. The results of the study suggest that qCEST could be used for the diagnosis of discogenic pain, in conjunction with the commonly used T2w scan.
Protein expression reveals a molecular sexual identity of avian primordial germ cells at pre-gonadal stages
Authors: Soler Laura , Alves Sabine , Brionne Aurélien , Jacques Aurore , Guérin Vanessa , Cherif-Feildel Maeva , Combes-Soia Lucie , Fouchécourt Sophie , Thélie Aurore , Blesbois Elisabeth , McGrew Michael J. , Labas Valérie , Govoroun Marina S. 
Published: September 2021

AbstractIn poultry, in vitro propagated primordial germ cells (PGCs) represent an important tool for the cryopreservation of avian genetic resources. However, several studies have highlighted sexual differences exhibited by PGCs during in vitro propagation, which may compromise their reproductive capacities. To understand this phenomenon, we compared the proteome of pregonadal migratory male (ZZ) and female (ZW) chicken PGCs propagated in vitro by quantitative proteomic analysis using a GeLC-MS/MS strategy. Many proteins were found to be differentially abundant in chicken male and female PGCs indicating their early sexual identity. Many of the proteins more highly expressed in male PGCs were encoded by genes localised to the Z sex chromosome. This suggests that the known lack of dosage compensation of the transcription of Z-linked genes between sexes persists at the protein level in PGCs, and that this may be a key factor of their autonomous sex differentiation. We also found that globally, protein differences do not closely correlate with transcript differences indicating a selective translational mechanism in PGCs. Male and female PGC expressed protein sets were associated with differential biological processes and contained proteins known to be biologically relevant for male and female germ cell development, respectively. We also discovered that female PGCs have a higher capacity to uptake proteins from the cell culture medium than male PGCs. This study presents the first evidence of an early predetermined sex specific cell fate of chicken PGCs and their sexual molecular specificities which will enable the development of more precise sex-specific in vitro culture conditions for the preservation of avian genetic resources.
PaCO2-management in the neuro-critical care of patients with subarachnoid hemorrhage
Authors: Darkwah Oppong Marvin , Wrede Karsten H. , Müller Daniela , Santos Alejandro N. , Rauschenbach Laurèl , Dinger Thiemo F. , Ahmadipour Yahya , Pierscianek Daniela , Chihi Mehdi , Li Yan , Deuschl Cornelius , Sure Ulrich , Jabbarli Ramazan 
Published: September 2021

AbstractThe partial pressure of carbon dioxide (PaCO2) in the arterial blood is a strong vasomodulator affecting cerebral blood flow and the risk of cerebral edema and ischemia after acute brain injury. In turn, both complications are related to poor outcome in patients with aneurysmal subarachnoid hemorrhage (aSAH). We aimed to analyze the effect of PaCO2 levels on the course and outcome of aSAH. All patients of a single institution treated for aSAH over 13.5 years were included (n = 633). Daily PaCO2 values from arterial blood gas measurements were recorded for up to 2 weeks after ictus. The study endpoints were: delayed cerebral ischemia (DCI), need for decompressive craniectomy due to increased intracranial pressure > 20 mmHg refractory to conservative treatment and poor outcome at 6-months follow-up (modified Rankin scale > 2). By correlations with the study endpoints, clinically relevant cutoffs for the 14-days mean values for the lowest and highest daily PaCO2 levels were defined by receiver operating characteristic curve analysis. Association with the study endpoints for the identifies subgroups was analyzed using multivariate analysis. The optimal range for PaCO2 values was identified between 30 and 38 mmHg. ASAH patients with poor initial condition (WFNS 4/5) were less likely to show PaCO2 values within the range of 30–38 mmHg (p < 0.001, OR = 0.44). In the multivariate analysis, PaCO2 values between 30 and 38 mmHg were associated with a lower risk for decompressive craniectomy (p = 0.042, aOR = 0.27), DCI occurrence (p = 0.035; aOR = 0.50), and poor patient outcome (p = 0.004; aOR = 0.42). The data from this study shows an independent positive association between low normal mean PaCO2 values during the acute phase of aSAH and patients’ outcome. This effect might be attributed to the reduction of intracranial hypertension and alterations in the cerebral blood flow.
Detection and quantification of Mycobacterium tuberculosis antigen CFP10 in serum and urine for the rapid diagnosis of active tuberculosis disease
Authors: Seifert Marva , Vargas Eva , Ruiz-Valdepeñas Montiel Victor , Wang Joseph , Rodwell Timothy C. , Catanzaro Antonino 
Published: September 2021

AbstractOutside of the ongoing COVID-19 pandemic, tuberculosis is the leading cause of infectious disease mortality globally. Currently, there is no commercially available point-of-care diagnostic that is rapid, inexpensive, and highly sensitive for the diagnosis of active tuberculosis disease. Here we describe the development and optimization of a novel, highly sensitive prototype bioelectronic tuberculosis antigen (BETA) assay to detect tuberculosis-specific antigen, CFP10, in small-volume serum and urine samples. In this proof-of-concept study we evaluated the performance of the BETA assay using clinical specimens collected from presumptive tuberculosis patients from three independent cohorts. Circulating CFP10 antigen was detected in ALL serum (n = 19) and urine (n = 3) samples from bacteriologically confirmed tuberculosis patients who were untreated or had less than one week of treatment at time of serum collection, successfully identifying all culture positive tuberculosis patients. No CFP10 antigen was detected in serum (n = 7) or urine (n = 6) samples from individuals who were determined to be negative for tuberculosis disease. Additionally, antigen quantification using the BETA assay of paired serum samples collected from tuberculosis patients (n = 8) both before and after treatment initiation, indicate consistently declining within-person levels of CFP10 antigen during treatment. This novel, low-cost assay demonstrates potential as a rapid, non-sputum-based, point-of-care tool for the diagnosis of tuberculosis disease.
Genomic analysis of ionome-related QTLs in Arabidopsis thaliana
Authors: Shariatipour Nikwan , Heidari Bahram , Ravi Samathmika , Stevanato Piergiorgio 
Published: September 2021

AbstractIonome contributes to maintain cell integrity and acts as cofactors for catalyzing regulatory pathways. Identifying ionome contributing genomic regions provides a practical framework to dissect the genetic architecture of ionomic traits for use in biofortification. Meta-QTL (MQTL) analysis is a robust method to discover stable genomic regions for traits regardless of the genetic background. This study used information of 483 QTLs for ionomic traits identified from 12 populations for MQTL analysis inArabidopsis thaliana. The selected QTLs were projected onto the newly constructed genetic consensus map and 33 MQTLs distributed onA. thalianachromosomes were identified. The average confidence interval (CI) of the drafted MQTLs was 1.30 cM, reduced eight folds from a mean CI of 10.88 cM for the original QTLs. Four MQTLs were considered as stable MQTLs over different genetic backgrounds and environments. In parallel to the gene density over theA. thalianagenome, the genomic distribution of MQTLs over the genetic and physical maps indicated the highest density at non- and sub-telomeric chromosomal regions, respectively. Several candidate genes identified in the MQTLs intervals were associated with ion transportation, tolerance, and homeostasis. The genomic context of the identified MQTLs suggested nine chromosomal regions for Zn, Mn, and Fe control. The QTLs for potassium (K) and phosphorus (P) were the most frequently co-located with Zn (78.3%), Mn (76.2%), and Fe (88.2% and 70.6%) QTLs. The current MQTL analysis demonstrates that meta-QTL analysis is cheaper than, and as informative as genome-wide association study (GWAS) in refining the known QTLs.
The small-world network of global protests
Authors: Ferreira Leonardo N. , Hong Inho , Rutherford Alex , Cebrian Manuel 
Published: September 2021

AbstractProtest diffusion is a cascade process that can spread over different regions of the planet. The way and the extension that this phenomenon can occur is still not properly understood. Here, we empirically investigate this question using protest data from GDELT and ICEWS, two of the most extensive and longest-running data sets freely available. We divide the globe into grid cells and construct a temporal network for each data set where nodes represent cells and links are established between nodes if their protest events co-occur. We show that the temporal networks are small-world, indicating that the cells are directly linked or separated by a few steps on average. Furthermore, the average path lengths are decreasing through the years, which suggests that the world is becoming “smaller”. The persistent temporal hubs present in both data sets indicate that protests can spread faster through the hubs. This topological feature is consistent with the hypothesis that protests can quickly diffuse from one region to any other part of the globe.
Application of improved and optimized fuzzy neural network in classification evaluation of top coal cavability
Authors: Wang Meng , Tai Caiwang , Zhang Qiaofeng , Yang Zongwei , Li Jiazheng , Shen Kejun 
Published: September 2021

AbstractLongwall top coal caving technology is one of the main methods of thick coal seam mining in China, and the classification evaluation of top coal cavability in longwall top coal caving working face is of great significance for improving coal recovery. However, the empirical or numerical simulation method currently used to evaluate the top coal cavability has high cost and low-efficiency problems. Therefore, in order to improve the evaluation efficiency and reduce evaluation the cost of top coal cavability, according to the characteristics of classification evaluation of top coal cavability, this paper improved and optimized the fuzzy neural network developed by Nauck and Kruse and establishes the fuzzy neural network prediction model for classification evaluation of top coal cavability. At the same time, in order to ensure that the optimized and improved fuzzy neural network has the ability of global approximation that a neural network should have, its global approximation is verified. Then use the data in the database of published papers from CNKI as sample data to train, verify and test the established fuzzy neural network model. After that, the tested model is applied to the classification evaluation of the top coal cavability in 61,107 longwall top coal caving working face in Liuwan Coal Mine. The final evaluation result is that the top coal cavability grade of the 61,107 longwall top coal caving working face in Liuwan Coal Mine is grade II, consistent with the engineering practice.
Information flow in the rat thalamo-cortical system: spontaneous vs. stimulus-evoked activities
Authors: Ishizu Kotaro , Shiramatsu Tomoyo I. , Hitsuyu Rie , Oizumi Masafumi , Tsuchiya Naotsugu , Takahashi Hirokazu 
Published: September 2021

AbstractThe interaction between the thalamus and sensory cortex plays critical roles in sensory processing. Previous studies have revealed pathway-specific synaptic properties of thalamo-cortical connections. However, few studies to date have investigated how each pathway routes moment-to-moment information. Here, we simultaneously recorded neural activity in the auditory thalamus (or ventral division of the medial geniculate body; MGv) and primary auditory cortex (A1) with a laminar resolution in anesthetized rats. Transfer entropy (TE) was used as an information theoretic measure to operationalize “information flow”. Our analyses confirmed that communication between the thalamus and cortex was strengthened during presentation of auditory stimuli. In the resting state, thalamo-cortical communications almost disappeared, whereas intracortical communications were strengthened. The predominant source of information was the MGv at the onset of stimulus presentation and layer 5 during spontaneous activity. In turn, MGv was the major recipient of information from layer 6. TE suggested that a small but significant population of MGv-to-A1 pairs was “information-bearing,” whereas A1-to-MGv pairs typically exhibiting small effects played modulatory roles. These results highlight the capability of TE analyses to unlock novel avenues for bridging the gap between well-established anatomical knowledge of canonical microcircuits and physiological correlates via the concept of dynamic information flow.
Peptide-HLA-based immunotherapeutics platforms for direct modulation of antigen-specific T cells
Authors: Seidel Ronald D. , Merazga Zohra , Thapa Dharma Raj , Soriano Jonathan , Spaulding Emily , Vakkasoglu Ahmet S. , Ruthardt Paige , Bautista Wynona , Quayle Steven N. , Kiener Peter A. , Low Simon , Ross John F. , Cemerski Saso , Suri Anish , Almo Steven C. , Chaparro Rodolfo J. 
Published: September 2021

AbstractTargeted pharmacologic activation of antigen-specific (AgS) T cells may bypass limitations inherent in current T cell-based cancer therapies. We describe two immunotherapeutics platforms for selective delivery of costimulatory ligands and peptide-HLA (pHLA) to AgS T cells. We engineered and deployed on these platforms an affinity-attenuated variant of interleukin-2, which selectively expands oligoclonal and polyfunctional AgS T cells in vitro and synergizes with CD80 signals for superior proliferation versus peptide stimulation.
Role of catalytic nitrile decomposition in tricopper complex mediated direct partial oxidation of methane to methanol
Authors: Moharreri Ehsan , Jafari Tahereh , Rathnayake Dinithi , Khanna Harshul , Kuo Chung-Hao , Suib Steven L. , Nandi Partha 
Published: September 2021

AbstractSynthetic homogeneous system known to date performing methane to methanol conversion using O2 as terminal oxidant is unique and based on copper complex with piperazine-based ligand (Cu3L in Fig. 1) in a medium of acetonitrile. Prior work have shown that in order to achieve catalytic turnover, hydrogen peroxide is needed to regenerate the active site. We show in this paper that reaction solvent based on organic nitrile decompose concurrently with methane activation and that in the absence of either acetonitrile, Cu complex or hydrogen peroxide, the catalytic turnover does not happen. We show in this manuscript that the direct methane oxidation to methanol might have been mediated by catalytic Radziszewski oxidation between acetonitrile and H2O2. Additionally we have discovered that in the absence of methane, peroxide mediated acetonitrile decomposition also makes methanol via a background reaction which was hitherto unknown.
Natural selection at the RASGEF1C (GGC) repeat in human and divergent genotypes in late-onset neurocognitive disorder
Authors: Jafarian Z. , Khamse S. , Afshar H. , Khorshid H.R. Khorram , Delbari A. , Ohadi M. 
Published: September 2021

AbstractExpression dysregulation of the neuron-specific gene,RASGEF1C(RasGEF Domain Family Member 1C), occurs in late-onset neurocognitive disorders (NCDs), such as Alzheimer’s disease. This gene contains a (GGC)13, spanning its core promoter and 5′ untranslated region (RASGEF1C-201 ENST00000361132.9). Here we sequenced the (GGC)-repeat in a sample of human subjects (N = 269), consisting of late-onset NCDs (N = 115) and controls (N = 154). We also studied the status of this STR across various primate and non-primate species based on Ensembl 103. The 6-repeat allele was the predominant allele in the controls (frequency = 0.85) and NCD patients (frequency = 0.78). The NCD genotype compartment consisted of an excess of genotypes that lacked the 6-repeat (divergent genotypes) (Mid-P exact = 0.004). A number of those genotypes were not detected in the control group (Mid-P exact = 0.007). TheRASGEF1C(GGC)-repeat expanded beyond 2-repeats specifically in primates, and was at maximum length in human. We conclude that there is natural selection for the 6-repeat allele of theRASGEF1C(GGC)-repeat in human, and significant divergence from that allele in late-onset NCDs. STR alleles that are predominantly abundant and genotypes that deviate from those alleles are underappreciated features, which may have deep evolutionary and pathological consequences.