bluuebunny/crossref_metadata_2025_split huggingface dataset:
A machine learning approach for GRB detection in AstroSat CZTI data
Authors: Abraham Sheelu , Mukund Nikhil , Vibhute Ajay , Sharma Vidushi , Iyyani Shabnam , Bhattacharya Dipankar , Rao A R , Vadawale Santosh , Bhalerao Varun 
Published: April 2021

ABSTRACT
We present a machine learning (ML) based method for automated detection of Gamma-Ray Burst (GRB) candidate events in the range 60–250 keV from the AstroSat Cadmium Zinc Telluride Imager data. We use density-based spatial clustering to detect excess power and carry out an unsupervised hierarchical clustering across all such events to identify the different light curves present in the data. This representation helps us to understand the instrument’s sensitivity to the various GRB populations and identify the major non-astrophysical noise artefacts present in the data. We use Dynamic Time Warping (DTW) to carry out template matching, which ensures the morphological similarity of the detected events with known typical GRB light curves. DTW alleviates the need for a dense template repository often required in matched filtering like searches. The use of a similarity metric facilitates outlier detection suitable for capturing previously unmodelled events. We briefly discuss the characteristics of 35 long GRB candidates detected using the pipeline and show that with minor modifications such as adaptive binning, the method is also sensitive to short GRB events. Augmenting the existing data analysis pipeline with such ML capabilities alleviates the need for extensive manual inspection, enabling quicker response to alerts received from other observatories such as the gravitational-wave detectors.
Radio properties of 10 nearby ultraluminous infrared galaxies with signatures of luminous buried active galactic nuclei
Authors: Hayashi Takayuki J , Hagiwara Yoshiaki , Imanishi Masatoshi 
Published: April 2021

ABSTRACT
We present the results of our multifrequency observations for 10 ultraluminous infrared galaxies (ULIRGs) made by the Karl G. Jansky Very Large Array at 1.4, 5.5, 9.0, and 14.0 GHz. Our sample is selected from ULIRGs whose active galactic nuclei (AGNs) are not found at optical wavelengths (∼70 per cent of the total ULIRGs), but whose presence is suggested by mid-infrared or submillimetre observations (&gt;50 per cent of the non-AGN ULIRGs at optical wavelengths). The statistical properties of the targets are similar to those of the entire ULIRG sample, which implies that ULIRGs have common radiative processes regardless of the presence of optical AGNs, and thus AGNs might equally contribute to the radio emission of every ULIRG. Although their spectra are mainly explained by starbursts and/or merger activity, some individual sources suggest contributions from AGNs. IRAS 00188−0856, whose optical morphology is not disturbed, shows a large non-thermal fraction and a spectral break at high frequency, which can be explained by synchrotron ageing of non-thermal plasma emitted from AGNs. In addition, we find 100-kpc-scale extended emission associated with IRAS 01004−2237. The two-sided morphology and absence of extended X-ray emission suggest that this system is not induced by a merger in a cluster but originates from AGN activity.
Effects of periodicity in observation scheduling on parameter estimation of pulsar glitches
Authors: Dunn L , Lower M E , Melatos A 
Published: April 2021

ABSTRACT
In certain pulsar timing experiments, where observations are scheduled approximately periodically (e.g. daily), timing models with significantly different frequencies (including but not limited to glitch models with different frequency increments) return near-equivalent timing residuals. The average scheduling aperiodicity divided by the phase error due to time-of-arrival uncertainties is a useful indicator when the degeneracy is important. Synthetic data are used to explore the effect of this degeneracy systematically. It is found that phase-coherent tempo2 or temponest-based approaches are biased sometimes towards reporting small glitch sizes regardless of the true glitch size. Local estimates of the spin frequency alleviate this bias. A hidden Markov model is free from bias towards small glitches and announces explicitly the existence of multiple glitch solutions but sometimes fails to recover the correct glitch size. Two glitches in the UTMOST public data release are reassessed, one in PSR J1709−4429 at MJD 58178 and the other in PSR J1452−6036 at MJD 58600. The estimated fractional frequency jump in PSR J1709−4429 is revised upward from Δf/f = (54.6 ± 1.0) × 10−9 to (2432.2 ± 0.1) × 10−9 with the aid of additional data from the Parkes radio telescope. We find that the available UTMOST data for PSR J1452−6036 are consistent with Δf/f = 270 × 10−9 + N/(fT) with N = 0, 1, and 2, where $T \approx 1\, \text{sidereal day}$ is the observation scheduling period. Data from the Parkes radio telescope can be included, and the N = 0 case is selected unambiguously with a combined data set.
The Evolution of Calcification in Reef-Building Corals
Authors: Wang Xin , Zoccola Didier , Liew Yi Jin , Tambutte Eric , Cui Guoxin , Allemand Denis , Tambutte Sylvie , Aranda Manuel 
Published: April 2021

AbstractCorals build the structural foundation of coral reefs, one of the most diverse and productive ecosystems on our planet. Although the process of coral calcification that allows corals to build these immense structures has been extensively investigated, we still know little about the evolutionary processes that allowed the soft-bodied ancestor of corals to become the ecosystem builders they are today. Using a combination of phylogenomics, proteomics, and immunohistochemistry, we show that scleractinian corals likely acquired the ability to calcify sometime between ∼308 and ∼265 Ma through a combination of lineage-specific gene duplications and the co-option of existing genes to the calcification process. Our results suggest that coral calcification did not require extensive evolutionary changes, but rather few coral-specific gene duplications and a series of small, gradual optimizations of ancestral proteins and their co-option to the calcification process.
ReFOLD3: refinement of 3D protein models with gradual restraints based on predicted local quality and residue contacts
Authors: Adiyaman Recep , McGuffin Liam J 
Published: April 2021

Abstract
ReFOLD3 is unique in its application of gradual restraints, calculated from local model quality estimates and contact predictions, which are used to guide the refinement of theoretical 3D protein models towards the native structures. ReFOLD3 achieves improved performance by using an iterative refinement protocol to fix incorrect residue contacts and local errors, including unusual bonds and angles, which are identified in the submitted models by our leading ModFOLD8 model quality assessment method. Following refinement, the likely resulting improvements to the submitted models are recognized by ModFOLD8, which produces both global and local quality estimates. During the CASP14 prediction season (May–Aug 2020), we used the ReFOLD3 protocol to refine hundreds of 3D models, for both the refinement and the main tertiary structure prediction categories. Our group improved the global and local quality scores for numerous starting models in the refinement category, where we ranked in the top 10 according to the official assessment. The ReFOLD3 protocol was also used for the refinement of the SARS-CoV-2 targets as a part of the CASP Commons COVID-19 initiative, and we provided a significant number of the top 10 models. The ReFOLD3 web server is freely available at https://www.reading.ac.uk/bioinf/ReFOLD/.
An integrative analysis of genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA detects noninvasive diagnostic markers for gliomas
Authors: Cai Jiajun , Zeng Chang , Hua Wei , Qi Zengxin , Song Yanqun , Lu Xingyu , Li Dongdong , Zhang Zhou , Cui Xiaolong , Zhang Xin , Yang Zixiao , Zhang Jinsen , Quan Kai , Zhu Wei , Cai Jiabin , He Chuan , Cheng Shi-Yuan , Zhang Wei , Mao Ying 
Published: April 2021

Abstract

Background
Gliomas, especially the high-grade glioblastomas (GBM), are highly aggressive tumors in the central nervous system (CNS) with dismal clinical outcomes. Effective biomarkers, which are not currently available, may improve clinical outcomes through early detection. We sought to develop a noninvasive diagnostic approach for gliomas based on 5-hydroxymethylcytosines (5hmC) in circulating cell-free DNA (cfDNA).

Methods
We obtained genome-wide 5hmC profiles using the 5hmC-Seal technique in cfDNA samples from 111 prospectively enrolled patients with gliomas and 111 age-, gender-matched healthy individuals, which were split into a training set and a validation set. Integrated models comprised 5hmC levels summarized for gene bodies, long noncoding RNAs (lncRNAs), cis-regulatory elements, and repetitive elements were developed using the elastic net regularization under a case–control design.

Results
The integrated 5hmC-based models differentiated healthy individuals from gliomas (area under the curve [AUC] = 84%; 95% confidence interval [CI], 74–93%), GBM patients (AUC = 84%; 95% CI, 74–94%), WHO II-III glioma patients (AUC = 86%; 95% CI, 76–96%), regardless of IDH1 (encoding isocitrate dehydrogenase) mutation status or other glioma-related pathological features such as TERT, TP53 in the validation set. Furthermore, the 5hmC biomarkers in cfDNA showed the potential as an independent indicator from IDH1 mutation status and worked in synergy with IDH1 mutation to distinguish GBM from WHO II-III gliomas. Exploration of the 5hmC biomarkers for gliomas revealed relevance to glioma biology.

Conclusions
The 5hmC-Seal in cfDNA offers the promise as a noninvasive approach for effective detection of gliomas in a screening program.
MR spectroscopic imaging predicts early response to anti-angiogenic therapy in recurrent glioblastoma
Authors: Talati Pratik , El-Abtah Mohamed , Kim Daniel , Dietrich Jorg , Fu Melanie , Wenke Michael , He Julian , Natheir Sharif N , Vangel Mark , Rapalino Otto , Vaynrub Anna , Arrillaga-Romany Isabel , Forst Deborah A , Yen Yi-Fen , Andronesi Ovidiu , Kalpathy-Cramer Jayashree , Rosen Bruce , Batchelor Tracy T , Gonzalez R Gilberto , Gerstner Elizabeth R , Ratai Eva-Maria 
Published: April 2021

AbstractBackgroundDetermining failure to anti-angiogenic therapy in recurrent glioblastoma (GBM) (rGBM) remains a challenge. The purpose of the study was to assess treatment response to bevacizumab-based therapy in patients with rGBM using MR spectroscopy (MRS).MethodsWe performed longitudinal MRI/MRS in 33 patients with rGBM to investigate whether changes in N-acetylaspartate (NAA)/Choline (Cho) and Lactate (Lac)/NAA from baseline to subsequent time points after treatment can predict early failures to bevacizumab-based therapies.ResultsAfter stratifying based on 9-month survival, longer-term survivors had increased NAA/Cho and decreased Lac/NAA levels compared to shorter-term survivors. ROC analyses for intratumoral NAA/Cho correlated with survival at 1 day, 2 weeks, 8 weeks, and 16 weeks. Intratumoral Lac/NAA ROC analyses were predictive of survival at all time points tested. At the 8-week time point, 88% of patients with decreased NAA/Cho did not survive 9 months; furthermore, 90% of individuals with an increased Lac/NAA from baseline did not survive at 9 months. No other metabolic ratios tested significantly predicted survival.ConclusionsChanges in metabolic levels of tumoral NAA/Cho and Lac/NAA can serve as early biomarkers for predicting treatment failure to anti-angiogenic therapy as soon as 1 day after bevacizumab-based therapy. The addition of MRS to conventional MR methods can provide better insight into how anti-angiogenic therapy affects tumor microenvironment and predict patient outcomes.
Viral Load Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2 in Hospitalized Individuals With Coronavirus Disease 2019
Authors: Regan James , Flynn James P , Rosenthal Alexandra , Jordan Hannah , Li Yijia , Chishti Rida , Giguel Francoise , Corry Heather , Coxen Kendyll , Fajnzylber Jesse , Gillespie Elizabeth , Kuritzkes Daniel R , Hacohen Nir , Goldberg Marcia B , Filbin Michael R , Yu Xu G , Baden Lindsey , Ribeiro Ruy M , Perelson Alan S , Conway Jessica M , Li Jonathan Z ,   MGH COVID-19 Collection & Processing Teams, Abayneh Betelihem A , Allen Patrick , Alter Galit , Antille Diane , Armstrong Katrina , Balazs Alejandro , Bals Julia , Barbash Max , Bartsch Yannic , Boucau Julie , Boyce Siobhan , Braley Joan , Branch Karen , Broderick Katherine , Carney Julia , Chan Andrew , Chevalier Josh , Chowdhury Fatema , Daley George , Davidson Susan , Dougan Michael , Drew David , Einkauf Kevin , Elliman Ashley , Fallon Jon , Fedirko Liz , Finn Kelsey , Flaherty Keith , Flannery Jeanne , Forde Pamela , Garcia-Broncano Pilar , Gettings Elise , Golan David , Griffin Amanda , Grimmel Sheila , Grinke Kathleen , Hall Kathryn , Hartana Ciputra , Healy Meg , Heller Howard , Henault Deborah , Holland Grace , Jiang Chenyang , Jilg Nikolaus , Kaplonek Paulina , Karpell Marshall , Kayitesi Chantal , Lam Evan C , LaValle Vlasta , Lefteri Kristina , Lian Xiaodong , Lichterfeld Mathias , Lingwood Daniel , Liu Hang , Liu Jinqing , Lu Yiting , Luthern Sarah , Ly Natasha , Marchewka Jordan , Martino Britanni , McNamara Roseann , Michell Ashlin , Millstrom Ilan , Miranda Noah , Nambu Christian , Nelson Susan , Noone Marjorie , O’Callaghan Claire , Ommerborn Christine , Osborn Mathew , Pacheco Lois Chris , Phan Nicole , Pillai Shiv , Porto Falisha A , Rassadkina Yelizaveta , Reissis Alexandra , Rosenthal Alex , Ruzicka Francis , Ryan Edward , Seiger Kyra , Selleck Kathleen , Sessa Libera , Sharpe Arlene , Sharr Christianne , Shin Sally , Singh Nishant , Slaughenhaupt Sue , Sheppard Kimberly Smith , Sun Weiwei , Sun Xiaoming , Suschana Elizabeth , Ticheli Hannah , Trocha-Piechocka Alicja , Wilson Vivine , Wong Colline , Worrall Daniel , Zhu Alex , Hill Zachary Manickas , Demers Edward , Judge Kelly , Walker Bruce , Lai Peggy , Li Jonathan , Ghebremichael Musie S 
Published: April 2021

Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) kinetics remain understudied, including the impact of remdesivir. In hospitalized individuals, peak sputum viral load occurred in week 2 of symptoms, whereas viremia peaked within 1 week of symptom-onset, suggesting early systemic seeding of SARS-CoV-2. Remdesivir treatment was associated with faster viral decay.
Radial Artery Access for Cerebral Angiography: 2-Dimensional Operative Video
Authors: Chen Stephanie H , Suazo Roberto , Saini Vasu , Abecassis Isaac Josh , Yavagal Dileep , Starke Robert M , Peterson Eric C 
Published: April 2021

Abstract
A number of studies have demonstrated that the radial artery is a safer access site than the femoral artery for endovascular procedures.
1-4
In the prospective randomized studies comparing transradial and transfemoral approaches for cardiac procedures, there was a 60% reduction in access site complications as well as significant decreases in all-cause mortality with the transradial approach as compared to transfemoral, which has led to the adoption of a radial first strategy.
5-7
Neurointerventional studies have demonstrated similar safety benefits as well as improved patient preference.
8-14

In this video, a patient presented with an unruptured anterior communicating artery aneurysm and consented to a transradial artery diagnostic cerebral angiogram. This technical video demonstrates the key preprocedural preparation, room setup, patient positioning, steps for radial artery, and distal radial artery puncture and sheath placement. Distal transradial artery access is our preferred approach for diagnostic cerebral angiography because of an improved safety profile and procedural ergonomics. In cases in which a larger radial artery is advantageous such as for neurointerventions requiring larger systems, a standard transradial approach may be performed.
9
In this video, a full 6-vessel cerebral angiogram is performed, followed by our arteriotomy closure technique using our standard equipment including a 10-cm 5 French Glidesheath Slender (Terumo, Japan), 100-cm hydrophilic coated 5 French Simmons 1 catheter (Merit OEM), 0.035 hydrophilic coated guidewire, and SafeGuard closure device (Merit, Salt Lake City, Utah).
Repair of Giant Anterior Skull Base Encephalocele Containing Intralesional Eloquent Brain: Technical Note
Authors: Kobets Andrew J , Redett Richard J , Walsh Jonathan M , Lopez Joseph , Guryildirim Melike , Cohen Alan R 
Published: April 2021

Abstract

BACKGROUND
Encephaloceles are herniations of intracranial neural tissue and meninges through defects in the skull. Basal encephaloceles are rare anterior skull base defects incident in 1 in 35,000 live births. Sphenoethmoidal encephaloceles are even more uncommon, with an incidence of 1 in 700,000 live births. Anterior skull base encephaloceles may be life-threatening in infants, presenting as airway obstruction and respiratory compromise. They can also present with cerebrospinal fluid (CSF) rhinorrhea, purulent nasal drainage, or meningitis.

OBJECTIVE
To report a novel technique for repairing a giant sphenoethmoidal encephalocele containing eloquent neural tissue.

METHODS
A 16-mo-old girl presented with progressive airway obstruction from a giant sphenoethmoidal encephalocele that filled her oral cavity. She had multiple congenital anomalies including agenesis of the corpus callosum and cleft lip and palate. Computed tomography showed complete absence of the bony anterior cranial base, and magnetic resonance imaging demonstrated the presence of the pituitary gland and hypothalamus in the hernia sac.

RESULTS
We repaired the encephalocele using a combined microsurgical and endoscopic multidisciplinary approach working through transcranial, transnasal, and transpalatal corridors. The procedure was completed in a single stage, during which the midline cleft lip was also repaired. The child made an excellent neurological and aesthetic recovery with preservation of pituitary and hypothalamic function, without evidence of CSF fistula.

CONCLUSION
The authors describe a novel multidisciplinary technique for treating a giant sphenoethmoidal encephalocele containing eloquent brain. The cleft lip was also repaired at the same time. The ability to work through multiple corridors can enhance the safety and efficacy of an often-treacherous operative endeavor.
Microsurgical Anatomy of the Inferior Petroclival Vein and its Relation to Surrounding Structures: A Cadaveric and Radiological Study
Authors: Matsuo Satoshi , Komune Noritaka , Amano Toshiyuki , Nakamizo Akira 
Published: April 2021

Abstract

BACKGROUND
The inferior petroclival vein (IPV) courses along the extracranial surface of the petroclival fissure. It is occasionally involved in vascular diseases and has recently been used for vascular access to the cavernous sinus. However, detailed descriptions of its anatomy are currently lacking.

OBJECTIVE
To define the anatomic relationship between the IPV and its surrounding structures based on cadaveric dissection and radiological analysis.

METHODS
A dry skull and an injected cadaver head were examined to reveal the relationships between the IPV and its surrounding structures. The existence of the IPV and its relationships with other venous structures were also examined by contrast-enhanced, fat-suppressed T1-weighted magnetic resonance imaging in 26 patients (51 sides).

RESULTS
The entire course of the IPV was shown via stepwise cadaver dissection from below. Its relationships with surrounding structures, such as the jugular bulb, sigmoid sinus, inferior petrosal sinus, petrosal venous confluence, and the posterior, lateral, and anterior condylar veins, were also shown. In the radiological analysis, the IPV was identified on all sides. The rostral end of the vein was connected to the venous plexus around the carotid artery on all sides. The vein drained into the caudal end of the inferior petrosal sinus (49/51 sides, 96.1%) or into the anterior condylar vein (2/51 sides, 3.9%).

CONCLUSION
A precise understanding of the anatomy of the IPV will enable endovascular and skull base surgeons to achieve diagnoses and gain safe access to lesions involving the IPV.
Coaxial Access for Microcatheter Stabilization During Aneurysm Coiling: 2-Dimensional Operative Video
Authors: Kim Miri , Shanker Rachyl , Kam Anthony , Reynolds Matthew , Serrone Joseph C 
Published: April 2021

Abstract
Coaxial support is a fundamental technique utilized by neurointerventionalists to optimize distal catheter control within the intracranial circulation. Here we present a 41-yr-old woman with a previously coiled ruptured anterior communicating artery aneurysm with progressive recurrence harboring tortuous internal carotid anatomy to demonstrate the utility of coaxial support. Raymond-Roy classification of initial aneurysm coiling of class 1 resulted as class 3b over the 21 mo from initial treatment.
1
The patient consented to stent-assisted coiling for retreatment of this aneurysm. Coaxial support was advanced as distally as possible in the proximal vasculature to improve catheter control, reducing dead space within which the microcatheter could move, decreasing angulations within proximal vasculature, limiting the movement of the native vessels, and providing a surface of lower friction than the endothelium. As the risk of recurrent subarachnoid hemorrhage in previously treated coiled aneurysms approaches 3%, retreatment occurs in 16.4% within 6 yr
2
and in 17.4% of patients within 10 yr.
3
Rerupture is slightly higher in patients who underwent coiling vs clipping, with the rerupture risk inversely proportional to the degree of aneurysm occlusion,
4
further substantiating that coaxial support provides technical advantage in selected patients where additional microcatheter control is necessary for optimal occlusion. Pitfalls of this technique include vasospasm and vascular injury, which can be ameliorated by pretreatment of the circulation with vasodilators to prevent catheter-induced vasospasm. This case and model demonstration illustrates the technique of coaxial access in the stent-assisted coiling of a recurrent anterior communicating artery aneurysm and identification and management of catheter-induced vasospasm.