bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cleaning our own dust: simulating and separating galactic dust foregrounds with neural networks
Authors: Aylor K , Haq M , Knox L , Hezaveh Y , Perreault-Levasseur L 
Published: October 2020

ABSTRACT
Separating galactic foreground emission from maps of the cosmic microwave background (CMB) and quantifying the uncertainty in the CMB maps due to errors in foreground separation are important for avoiding biases in scientific conclusions. Our ability to quantify such uncertainty is limited by our lack of a model for the statistical distribution of the foreground emission. Here, we use a deep convolutional generative adversarial network (DCGAN) to create an effective non-Gaussian statistical model for intensity of emission by interstellar dust. For training data we use a set of dust maps inferred from observations by the Planck satellite. A DCGAN is uniquely suited for such unsupervised learning tasks as it can learn to model a complex non-Gaussian distribution directly from examples. We then use these simulations to train a second neural network to estimate the underlying CMB signal from dust-contaminated maps. We discuss other potential uses for the trained DCGAN, and the generalization to polarized emission from both dust and synchrotron.
Fast radio bursts: do repeaters and non-repeaters originate in statistically similar ensembles?
Authors: Cui Xiang-Han , Zhang Cheng-Min , Wang Shuang-Qiang , Zhang Jian-Wei , Li Di , Peng Bo , Zhu Wei-Wei , Wang Na , Strom Richard , Ye Chang-Qing , Wang De-Hua , Yang Yi-Yan 
Published: October 2020

ABSTRACT
Fast radio bursts (FRBs) are the short, strong radio pulses lasting several milliseconds. They are subsequently identified, for the most part, as emanating from unknown objects at cosmological distances. At present, over 100 FRBs have been verified, and they are classified into two groups: repeating bursts (20 samples) and apparently non-repeating bursts (91 samples). Their origins, however, are still hotly debated. Here, we investigate the statistical classifications for the two groups of samples to see if the non-repeating and repeating FRBs have different origins by employing Anderson–Darling (A–D) test and Mann–Whitney–Wilcoxon (M–W–W) test. First, by taking the pulse width as a statistical variant, we found that the repeating samples do not follow the Gaussian statistics (may belong to a χ-square distribution), although the overall data and non-repeating group do follow the Gaussian. Meanwhile, to investigate the statistical differences between the two groups, we turn to M–W–W test and notice that the two distributions have different origins. Secondly, we consider the FRB radio luminosity as a statistical variant, and find that both groups of samples can be regarded as the Gaussian distributions under the A–D test, although they have different origins according to M–W–W tests. Therefore, statistically, we can conclude that our classifications of both repeaters and non-repeaters are plausible, that the two FRB classes have different origins, or that each has experienced distinctive phases or been subject to its own physical processes.
Final design and on-sky testing of the iLocater SX acquisition camera: broad-band single-mode fibre coupling
Authors: Crass J , Bechter A , Sands B , King D , Ketterer R , Engstrom M , Hamper R , Kopon D , Smous J , Crepp J R , Montoya M , Durney O , Cavalieri D , Reynolds R , Vansickle M , Onuma E , Thomes J , Mullin S , Shelton C , Wallace K , Bechter E , Vaz A , Power J , Rahmer G , Ertel S 
Published: October 2020

ABSTRACT
Enabling efficient injection of light into single-mode fibres (SMFs) is a key requirement in realizing diffraction-limited astronomical spectroscopy on ground-based telescopes. SMF-fed spectrographs, facilitated by the use of adaptive optics (AO), offer distinct advantages over comparable seeing-limited designs, including higher spectral resolution within a compact and stable instrument volume, and a telescope independent spectrograph design. iLocater is an extremely precise radial velocity (EPRV) spectrograph being built for the Large Binocular Telescope (LBT). We have designed and built the front-end fibre injection system, or acquisition camera, for the SX (left) primary mirror of the LBT. The instrument was installed in 2019 and underwent on-sky commissioning and performance assessment. In this paper, we present the instrument requirements, acquisition camera design, as well as results from first-light measurements. Broad-band SMF coupling in excess of 35 per cent (absolute) in the near-infrared (0.97–1.31 ${\mu {\rm m}}$) was achieved across a range of target magnitudes, spectral types, and observing conditions. Successful demonstration of on-sky performance represents both a major milestone in the development of iLocater and in making efficient ground-based SMF-fed astronomical instruments a reality.
Photoionization feedback in turbulent molecular clouds
Authors: Sartorio Nina S , Vandenbroucke Bert , Falceta-Goncalves Diego , Wood Kenneth 
Published: October 2020

ABSTRACT
We present a study of the impact of photoionization feedback from young massive stars on the turbulent statistics of star-forming molecular clouds. This feedback is expected to alter the density structure of molecular clouds and affect future star formation. Using the AMUN-Rad code, we first generate a converged isothermal forced turbulent density structure inside a periodic box. We then insert an ionizing source in this box and inject photoionization energy using a two-temperature pseudo-isothermal equation of state. We study the impact of sources at different locations in the box and of different source luminosities. We find that photoionization has a minor impact on the 2D and 3D statistics of turbulence when turbulence continues to be driven in the presence of a photoionizing source. Photoionization is only able to disrupt the cloud if the turbulence is allowed to decay. In the former scenario, the presence of an H ii region inside our model cloud does not lead to a significant impact on observable quantities, independent of the source parameters.
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions
Authors: Caudron-Herger Maiwen , Jansen Ralf E , Wassmer Elsa , Diederichs Sven 
Published: October 2020

Abstract
RNA–protein complexes have emerged as central players in numerous key cellular processes with significant relevance in health and disease. To further deepen our knowledge of RNA-binding proteins (RBPs), multiple proteome-wide strategies have been developed to identify RBPs in different species leading to a large number of studies contributing experimentally identified as well as predicted RBP candidate catalogs. However, the rapid evolution of the field led to an accumulation of isolated datasets, hampering the access and comparison of their valuable content. Moreover, tools to link RBPs to cellular pathways and functions were lacking. Here, to facilitate the efficient screening of the RBP resources, we provide RBP2GO (https://RBP2GO.DKFZ.de), a comprehensive database of all currently available proteome-wide datasets for RBPs across 13 species from 53 studies including 105 datasets identifying altogether 22 552 RBP candidates. These are combined with the information on RBP interaction partners and on the related biological processes, molecular functions and cellular compartments. RBP2GO offers a user-friendly web interface with an RBP scoring system and powerful advanced search tools allowing forward and reverse searches connecting functions and RBPs to stimulate new research directions.
HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells
Authors: Zaidan Nur Zafirah , Sridharan Rupa 
Published: October 2020

Abstract
The heterochromatin protein 1 (HP1) family members are canonical effectors and propagators of gene repression mediated by histone H3 lysine 9 (H3K9) methylation. HP1γ exhibits an increased interaction with active transcription elongation-associated factors in embryonic stem cells (ESCs) compared to somatic cells. However, whether this association has a functional consequence remains elusive. Here we find that genic HP1γ colocalizes and enhances enrichment of transcription elongation-associated H3K36me3 rather than H3K9me3. Unexpectedly, sustained H3K36me3 deposition is dependent on HP1γ. HP1γ-deleted ESCs display reduced H3K36me3 enrichment, concomitant with decreased expression at shared genes which function to maintain cellular homeostasis. Both the H3K9me3-binding chromodomain and histone binding ability of HP1γ are dispensable for maintaining H3K36me3 levels. Instead, the chromoshadow together with the hinge domain of HP1γ that confer protein and nucleic acid-binding ability are sufficient because they retain the ability to interact with NSD1, an H3K36 methyltransferase. HP1γ-deleted ESCs have a slower self-renewal rate and an impaired ability to differentiate towards cardiac mesoderm. Our findings reveal a requirement for HP1γ in faithful establishment of transcription elongation in ESCs, which regulates pluripotency.
Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations
Authors: Regy Roshan Mammen , Dignon Gregory L , Zheng Wenwei , Kim Young C , Mittal Jeetain 
Published: October 2020

AbstractRibonucleoprotein (RNP) granules are membraneless organelles (MLOs), which majorly consist of RNA and RNA-binding proteins and are formed via liquid–liquid phase separation (LLPS). Experimental studies investigating the drivers of LLPS have shown that intrinsically disordered proteins (IDPs) and nucleic acids like RNA and other polynucleotides play a key role in modulating protein phase separation. There is currently a dearth of modelling techniques which allow one to delve deeper into how polynucleotides play the role of a modulator/promoter of LLPS in cells using computational methods. Here, we present a coarse-grained polynucleotide model developed to fill this gap, which together with our recently developed HPS model for protein LLPS, allows us to capture the factors driving protein-polynucleotide phase separation. We explore the capabilities of the modelling framework with the LAF-1 RGG system which has been well studied in experiments and also with the HPS model previously. Further taking advantage of the fact that the HPS model maintains sequence specificity we explore the role of charge patterning on controlling polynucleotide incorporation into condensates. With increased charge patterning we observe formation of structured or patterned condensates which suggests the possible roles of polynucleotides in not only shifting the phase boundaries but also introducing microscopic organization in MLOs.
Discovery and characterization of a fourth class of guanidine riboswitches
Authors: Lenkeit Felina , Eckert Iris , Hartig Jörg S , Weinberg Zasha 
Published: October 2020

AbstractRiboswitches are RNAs that specifically sense a small molecule and regulate genes accordingly. The recent discovery of guanidine-binding riboswitches revealed the biological significance of this compound, and uncovered genes related to its biology. For example, certain sugE genes encode guanidine exporters and are activated by the riboswitches to reduce toxic levels of guanidine in the cell. In order to study guanidine biology and riboswitches, we applied a bioinformatics strategy for discovering additional guanidine riboswitches by searching for new candidate motifs associated with sugE genes. Based on in vitro and in vivo experiments, we determined that one of our six best candidates is a new structural class of guanidine riboswitches. The expression of a genetic reporter was induced 80-fold in response to addition of 5 mM guanidine in Staphylococcus aureus. This new class, called the guanidine-IV riboswitch, reveals additional guanidine-associated protein domains that are extremely rarely or never associated with previously established guanidine riboswitches. Among these protein domains are two transporter families that are structurally distinct from SugE, and could represent novel types of guanidine exporters. These results establish a new metabolite-binding RNA, further validate a bioinformatics method for finding riboswitches and suggest substrate specificities for as-yet uncharacterized transporter proteins.
PD-1+ Monocytes Mediate Cerebral Vasospasm Following Subarachnoid Hemorrhage
Authors: Jackson Christopher M , Choi John , Routkevitch Denis , Pant Ayush , Saleh Laura , Ye Xiaobu , Caplan Justin M , Huang Judy , McDougall Cameron G , Pardoll Drew M , Brem Henry , Tamargo Rafael J , Lim Michael 
Published: October 2020

Abstract

BACKGROUND
Cerebral vasospasm is a major source of morbidity and mortality following aneurysm rupture and has limited treatment options.

OBJECTIVE
To evaluate the role of programmed death-1 (PD-1) in cerebral vasospasm.

METHODS
Endovascular internal carotid artery perforation (ICAp) was used to induce cerebral vasospasm in mice. To evaluate the therapeutic potential of targeting PD-1, programmed death ligand-1 (PD-L1) was administered 1 h after ICAp and vasospasm was measured histologically at the level of the ICA bifurcation bilaterally. PD-1 expressing immune cell populations were evaluated by flow cytometry. To correlate these findings to patients and evaluate the potential of PD-1 as a biomarker, monocytes were isolated from the peripheral blood and analyzed by flow cytometry in a cohort of patients with ruptured cerebral aneurysms. The daily frequency of PD-1+ monocytes in the peripheral blood was correlated to transcranial Doppler velocities as well as clinical and radiographic vasospasm.

RESULTS
We found that PD-L1 administration prevented cerebral vasospasm by inhibiting ingress of activated Ly6c+ and CCR2+ monocytes into the brain. Human correlative studies confirmed the presence of PD-1+ monocytes in the peripheral blood of patients with ruptured aneurysms and the frequency of these cells corresponded with cerebral blood flow velocities and clinical vasospasm.

CONCLUSION
Our results identify PD-1+ monocytes as mediators of cerebral vasospasm and support PD-1 agonism as a novel therapeutic strategy.
The causal effect of interleukin-17 on the risk of psoriatic arthritis: a Mendelian randomization study
Authors: Wu Dongze , Wong Priscilla , Lam Steven H M , Li Edmund K , Qin Ling , Tam Lai-Shan , Gu Jieruo 
Published: October 2020

AbstractObjectiveTo determine causal associations between genetically predicted TNF-α, IL-12p70 and IL-17 levels and risk of PsA.MethodsThe publicly available summary-level findings from genome-wide association studies (GWAS) was used to identify loci influencing normal physiological concentrations of TNF-α, IL-12p70 and IL-17 (n = 8293) among healthy individuals as exposure and a GWAS for PsA from the UK Biobank (PsA = 900, control = 462 033) as the outcome. A two-sample Mendelian randomization (MR) analysis was performed using the inverse-variance weighted (IVW), weighted median and MR–Egger regression methods. Sensitivity analysis and MR–Egger regression analysis were performed to evaluate the heterogeneity and pleiotropic effects of each variant.ResultsSingle-nucleotide polymorphisms (SNPs) at genome-wide significance from GWASs on TNF-α, IL-12p70 and IL-17 were identified as the instrumental variables. The IVW method indicated a causal association between increased IL-17 level and risk of PsA (β = −0.00186 per allele, s.e. = 0.00043, P = 0.002). Results were consistent in the weighted median method (β = −0.00145 per allele, s.e. = 0.00059, P = 0.014) although the MR–Egger method suggested a non-significant association (β = −0.00133 per allele, s.e. = 0.00087; P = 0.087). Single SNP MR results revealed that the C allele of rs117556572 was robustly associated with risk of PsA (β = 0.00210, s.e. = 0.00069, P = 0.002). However, no evidence for a causal effect was observed between TNF-α, IL-12p70, decreased IL-17 levels and risk of PsA.ConclusionOur findings provide preliminary evidence that genetic variants predisposing to higher physiological IL-17 level are associated with decreased risk of PsA.
Using In Situ Simulations to Improve Pediatric Patient Safety in Emergency Departments
Authors: Lee Moon O. , Schertzer Kimberly , Khanna Kajal , Wang N. Ewen , Camargo Carlos A. , Sebok-Syer Stefanie S. 
Published: October 2020

Problem
Given the complex interaction among patients, individual providers, health care teams, and the clinical environment, patient safety events with serious consequences are most likely to occur in intensive care units, operating rooms, and emergency departments (EDs). With low-frequency, high-risk events such as pediatric resuscitations, health care teams working in EDs may not have the clinical opportunity to identify deficiencies, review and reinforce knowledge and skills, and problem solve in authentic clinical conditions. Without creating opportunities to safely practice, hospitals run the risk of having health care teams and environments that are not prepared to provide optimal patient care.

Approach
Researchers employed a case series design and used a train-the-trainer model for in situ simulation. They trained health care professionals (instructors) in 3 general, nonacademic EDs in the San Francisco Bay area of California to perform pediatric resuscitation in situ simulations in 2018–2019. In situ simulations occur in the clinical work environment with simulation participants (teams) who are health care professionals taking care of actual patients.

Outcomes
Teams made up of physicians, nurses, and ED technicians were evaluated for clinical performance, teamwork, and communication during in situ simulations conducted by instructors at baseline, 6 months, and 12 months. Debriefing after the simulations identified multiple latent safety threats (i.e., unidentified potential safety hazards) that were previously unknown. Each ED’s pediatric readiness—its ability to provide emergency care for children—was evaluated at baseline and 12 months.

Next Steps
The authors will continue to monitor and examine the impact and sustainability of the pediatric in situ simulation program on pediatric readiness scores and its possible translation to other high-risk clinical settings, as well as explore the relationship between in situ simulations and patient outcomes.
A case report of lineage switch from T-cell acute leukemia to B-cell acute leukemia
Authors: Zhu Yejing , Liu Hui , Zhang Shuna , Liang Yanyan , Xiao Meng , Hao Yunliang , Guan Yun 
Published: October 2020

Abstract

Rationale:
ALL is the most common form of leukemia (75% to 80%), it is characterized by clonal expansion of the lymphoid blasts in bone marrow, blood, and other tissues, which can be divided into T lineage and B lineage. Although relapse of acute leukemia is common, a change of immunophenotype at relapse only occurs rarely. Some of these cases have been labeled “lineage switch”.

Patient concerns:
A 31-year-old man had multiple lymph nodes in the neck, and the lymph nodes on the right side adhered to the surrounding tissues. His lymphocytes ratio in blood was up to 86.3%. Flow cytometry of the bone marrow aspirate showed positive results for CD2, CD5, CD7, cCD3, TDT, CD4, CD8, and CD10, negative results for CD34, CD117, CD33, HLA-DR, CD19, and CD20. Twenty six months later, the patient felt pain in the neck and shoulder after touching. His lymphocytes of blood were 109.9×109 /L. 43 fusion genes and positive BCR/ABL was detected. Flow cytometry of the bone marrow aspirate showed pro B lymphocytes accounted for 85.54%, and positive expression of CD38, CD10, CD34, CD33, TDT, CD9, and HLA-DR. Moreover, the RT-PCR data showed the patient expressed high level of T cell and B cell development transcription factors.

Diagnoses:
Upon examination, the patient was initially diagnosed with T-lineage pro cell ALL. BM morphologic analysis presented complete remission (CR) after systemic chemotherapy. Twenty six months later, we discovered the patient was diagnosed with B-lineage acute lymphocytic leukemia.

Interventions:
Systemic chemotherapy is first given when a patient was diagnosed with T-cell acute lymphoblastic leukemia. After the patient happened linage switch, we adjusted the treatment plan, and the patient was complete remission after 1 course of treatment.

Outcomes:
Our case provides information of lineage switch from T-ALL to B-ALL in this report, which is never seen in our knowledge.

Lessons:
This lineage switch from T-ALL to B-ALL is never reported beforemoreover, the RT-PCR data showed the patient expressed high level of T cell and B cell development transcription factors. Its early recognition can let doctor provides appropriate therapy to patient.
Local infiltration vs epidural analgesia for postoperative pain control after total knee or hip arthroplasty
Authors: Liu Xian , Zhang Haijing , Zhang Huan , Guo Mengzhuo , Gao Yuanchao , Du Chunyan 
Published: October 2020

Abstract

Background:
Inconsistent results have been obtained regarding postoperative pain control using local infiltration and epidural analgesia for patients after total knee or hip arthroplasty (TKA and THA). We therefore conducted a meta-analysis of randomized controlled trials (RCTs) to assess the efficacy and safety of local infiltration vs epidural analgesia for TKA and THA.

Methods:
Electronic searches were conducted on PubMed, EmBase, and the Cochrane library to identify eligible RCTs conducted up to February 2020. Weighted mean difference (WMD) and relative risk with 95% confidence interval (95%CI) were applied to calculate pooled effect estimates between local infiltration and epidural analgesia using the random-effects model.

Results:
Seven RCTs including a total of 412 TKA patients, and three RCTs including a total of 200 THA patients were selected for this meta-analysis. We noted that local infiltration was associated with lower visual analog scale (VAS) scores at rest after 48 hours (WMD: −1.31; 95%CI: −2.44 to −0.18; P = .024) and 72 hours (WMD: −0.95; 95%CI: −1.39 to −0.52; P < .001) for patients with TKA, while local infiltration significantly reduced VAS scores at rest after 12 hours for patients with THA (WMD: −1.00; 95%CI: −1.49 to −0.51; P < .001). Moreover, local infiltration was associated with lower VAS scores during movement after 48 hours in TKA patients (WMD: −1.08; 95%CI: −1.86 to −0.29; P = .007), while there were higher VAS scores during movement after 24 hours for patients with THA (WMD: 1.06; 95%CI: 0.67 to 1.45; P < .001). Furthermore, we noted that local infiltration was associated with higher flexion angles compared with epidural analgesia after 24 hours (WMD: 7.11; 95%CI: 2.30–11.93; P = .004), 48 hours (WMD: 6.69; 95%CI: 3.78 to 9.59; P < .001), and 72 hours (WMD: 5.19; 95%CI: 0.95–9.44; P = .016). There were no significant differences between local infiltration and epidural analgesia for the length of hospital stay, nausea, or wound infection.

Conclusions:
Local infiltration is superior to epidural analgesia for postoperative pain control after TKA, whereas for THA patients inconsistent results were obtained at various times.