bluuebunny/crossref_metadata_2025_split huggingface dataset:
Artificial intelligence analysis of three-dimensional imaging data derives factors associated with postoperative recurrence in patients with radiologically solid-predominant small-sized lung cancers
Authors: Kudo Yujin , Shimada Yoshihisa , Matsubayashi Jun , Kitamura Yoshiro , Makino Yojiro , Maehara Sachio , Hagiwara Masaru , Park Jinho , Yamada Takafumi , Takeuchi Susumu , Kakihana Masatoshi , Nagao Toshitaka , Ohira Tatsuo , Masumoto Jun , Ikeda Norihiko 
Published: December 2021

Abstract

OBJECTIVES
Indications of limited resection, such as segmentectomy, have recently been reported for patients with solid-predominant lung cancers ≤2 cm. This study aims to identify unfavourable prognostic factors using three-dimensional imaging analysis with artificial intelligence (AI) technology.

METHODS
A total of 157 patients who had clinical N0 non-small cell lung cancer with a radiological size ≤2 cm, and a consolidation tumour ratio &gt; 0.5, who underwent anatomical lung resection between 2011 and 2017 were enrolled. To evaluate the three-dimensional structure, the ground-glass nodule/Solid Automatic Identification AI software Beta Version (AI software; Fujifilm Corporation, Japan) was used.

RESULTS
Maximum standardized uptake value (SUVmax) and solid-part volume measured by AI software (AI-SV) showed significant differences between the 139 patients with adenocarcinoma and the 18 patients with non-adenocarcinoma. Among the adenocarcinoma patients, 42 patients (30.2%) were found to be pathological upstaging. Multivariable analysis demonstrated that high SUVmax, high carcinoembryonic antigen level and high AI-SV were significant prognostic factors for recurrence-free survival (RFS; P &lt; 0.05). The 5-year RFS was compared between patients with tumours showing high SUVmax and those showing low SUVmax (67.7% vs 95.4%, respectively, P &lt; 0.001). The 5-year RFS was 91.0% in patients with small AI-SV and 68.1% in those with high AI-SV (P = 0.001).

CONCLUSIONS
High AI-SV, high SUVmax and abnormal carcinoembryonic antigen level were unfavourable prognostic factors of patients with solid-predominant lung adenocarcinoma with a radiological size ≤2 cm. Our results suggest that lobectomy should be preferred to segmentectomy for patients with these prognostic factors.
C1. A “ Ping-Pong ” Ball Left Atrial Thrombus Mimicking Left Atrial Myxoma : A Case Report
Authors: Hargiyanto E D , Baktijasa B 
Published: December 2021

Abstract

Background
Valvular heart disease has a high prevalence, especially in developing countries, even though there is actually no exact number for prevalence in Indonesia. The prevalence of left atrial thrombus is around 17% in patients with severe mitral stenosis and will increase about 2 times in patients with atrial fibrillation. Although left atrial thrombus is common in mitral stenosis, left atrial thrombus mimicking myxoma is rarely reported

Case Summary
47-year-old woman came to Dr. Soetomo cardiology outpatient clinic. She complained of palpitation and shortness of breath. Her electrocardiogram was showed atrial fibrillation. Echocardiography showed severe mitral stenosis and free moving, round shape, left atrial mass. She then immediately planned for Mitral Valve Replacement (MVR) surgery and evacuation of the mass. We found a solid wall spherical mass, layered and easily separate. Microscopic examination revealed extensive fibrin, hemorrhage and mononuclear inflammatory cells with the conclusion of a thrombus

Discussion
Left atrial thrombus and myxoma often look the same on echocardiography, especially when the thrombus is free-moving and round shape. Echocardiography in this case showed a free-moving mass, round shape, like a "ping-pong" ball. The mass also has solid wall suggesting a myxoma. After surgery, we found tha the mass is multilayered which looks like a myxoma. However, microscopically confirmed that the mass is a thrombus. This suggests that a left atrial thrombus may mimicking a myxoma on echocardiography. Therefore, the gold standard for diagnosing intracardiac mass is by histopathology
Implantable cardioverter-defibrillators for hypertrophic cardiomyopathy: The Times They Are a-Changin’
Authors: Francia Pietro , Olivotto Iacopo , Lambiase Pier D , Autore Camillo 
Published: December 2021

AbstractThe implantable cardioverter-defibrillator (ICD) is a life-saving therapy in patients with hypertrophic cardiomyopathy (HCM) at high risk of sudden cardiac death. The heterogeneity of clinical scenarios in HCM and the availability of ICDs with distinct characteristics emphasizes the need for selecting the right device for the right patient. There is growing awareness that unnecessarily complex devices can lead to short- and long-term complications without adding significant clinical benefits. Young patients have the greatest potential years of life gained from the ICD but are also most exposed to device-related complications. This increases the complexity of decision-making of ICD prescription in these often otherwise well patients in whom device selection should be tailored to preserve survival benefit without introducing morbidity. In the light of the multiple clinical phenotypes characterizing HCM, the present article offers evidence-based perspectives helpful in predicting the individual impact of the ICD and choosing the most appropriate device.
‘Mead from Riga’: The Trade and Consumption of a Hanse Cultural Good in the Late Medieval Baltic
Authors: Whelan Mark 
Published: December 2021

Abstract
This article represents the first study of the trade and consumption of mead, the alcoholic beverage brewed by fermenting honey with water, in the late medieval Baltic. Focusing on the Teutonic Order and the Hanse settlements in the region, the article argues that the consumption of mead was culturally embedded in German-speaking communities, heightening the status of the beverage, turning it into a vital resource in the exercise of power and influencing the government and administrations of cities and lordships. From a broader perspective, a close study of the drink underlines the cultural and economic significance attached to bee produce in the later medieval period, with ecology and cultural practice combining to make honey and its pre-eminent product, mead, a distinctive international export that enjoyed high esteem and significant demand across Hanse trading networks.
Local Law for Singular Values of Oscillatory Matrices
Authors: Adhikari Arka , Lemm Marius 
Published: December 2021

AbstractWe continue the study of spectra of oscillatory random matrices with fully dependent rows. Motivated by the $d$-dimensional skew-shift dynamics from ergodic theory, we introduce the $N\times N$ random matrices $$ \begin{align*} &X_{j,k}=\exp\left(2\pi \textrm{i} \sum_{q=1}^d\ \omega_{j,q} k^q\right), \end{align*}$$where $\{\omega _{j,q}\}_{1\leq j\leq N, 1\leq q\leq d}$ is a collection of i.i.d. random variables and $d$ is a fixed integer. We prove that as $N\to \infty $ the distribution of singular values converges to the local Marchenko–Pastur law up to scales $N^{-\theta _d}$ for an explicit $\theta _d&gt;0$, as long as $d\geq 18$. Our approach provides a novel mechanism—deterministic oscillatory cancellations—for universal spectral laws. The proof blends techniques from random matrix theory, harmonic analysis, and analytic number theory such as strong estimates on the number of solutions to Diophantine equations in the form of Vinogradov’s main conjecture, proved by Bourgain–Demeter–Guth.
Effects of dietary spray-dried plasma protein on nutrient digestibility and growth performance in nursery pigs
Authors: Kim Hansol , Lee Seung Hyung , Kim Beob Gyun 
Published: December 2021

AbstractThe objectives were to determine the digestible energy and standardized ileal digestibility of amino acids (AA; Exp. 1) and to determine growth performance (Exp. 2) of two sources of dietary spray-dried plasma protein (SDPP) in nursery pigs. In Exp. 1, twelve nursery barrows (9.8 ± 0.9 kg) were assigned to a quadruplicated 3 × 2 Latin square design with three diets and two periods. Each period consisted of 5 d of adaptation, 2 d of fecal sampling, and 2 d of ileal collection. A basal diet was composed of corn, soybean meal, whey, and sucrose as the sole energy and AA sources. Experimental diets were prepared by replacing 15% of the energy and AA sources in the basal diet with SDPP 1 (manufactured in the United States; 78.2% crude protein and 4,862 kcal gross energy/kg as-is) or SDPP 2 (manufactured in Korea; 74.3% crude protein and 4,636 kcal gross energy/kg as-is). Spray-dried plasma protein 1 had greater digestible energy (P &lt; 0.05), but less (P &lt; 0.05) standardized ileal digestibility of Lys, Met, Trp, and Thr compared with SDPP 2. In Exp. 2, eighty-four nursery pigs (7.9 ± 0.7 kg) were allotted to three dietary treatments in a randomized complete block design with seven replicate pens and four pigs per pen. Three corn–soybean meal–whey–based diets contained fish meal (6% and 3.5% for days 0 to 14 and 14 to 28, respectively), SDPP 1 (4.5% and 2.7%), or SDPP 2 (5.0% and 3.0%) to maintain same energy and nutrient concentrations. During days 0 to 14 and overall period, pigs fed the diets containing SDPP gained more weight (P &lt; 0.05) than those fed the fish meal diet with no difference between two SDPP sources. In conclusion, SDPP 1 contains greater digestible energy but less AA digestibility compared with SDPP 2. Growth-promoting effects of both SDPP sources in nursery diets have been clearly demonstrated in this work.
Micelle silymarin supplementation to sows’ diet from day 109 of gestation to entire lactation period enhances reproductive performance and affects serum hormones and metabolites
Authors: Zhang Qianqian , Ahn Je Min , Kim In Ho 
Published: December 2021

Abstract
The aim of the present study was to explore the influences of varying doses of micelle silymarin (0%, 0.05%, 0.1%, and 0.2%) supplementation on sows’ feed intake, milk yields, serum hormones, and litter growth using 40 multiparous sows (Landrace × Yorkshire, parity from 3 to 5) from the 109th prenatal day to the 21st postnatal day. Each treatment included 10 sows and each sow was used as an experimental unit. On weaning day, litter weight and litter weight gain were linearly improved (P &lt; 0.01, both), corresponding to the increasing dose of silymarin micelle in the diet. Also, litter weight, litter weight gain, and average daily gain (ADG) of piglets born to treated sows exceeded (P &lt; 0.05) those of offspring from the control sows (0% micelle silymarin). Feed intake in week 1, week 2, and the entire lactation period was increased (linear, P &lt; 0.01) as micelle silymarin dose increased. Body weight (BW) loss of sows during lactation was linearly reduced (P = 0.003) with the increasing amounts of micelle silymarin. Average daily milk yields during lactation were also linearly increased (P = 0.002) in treated sows, exceeding (P = 0.046) that of control sows. Also, uniform increases were observed (P = 0.037) in fat content in milk produced by treated sows on day 14 of lactation. Epinephrine concentrations and aspartate aminotransferase (AST) activity in sow serum on day 21 postpartum were linearly declined (P = 0.010) as micelle silymarin dose increased, and were both declined (P &lt; 0.05) in treated sows compared with the control. In addition, treated sows’ serum had higher activity of superoxide dismutase (SOD) at parturition and glutathione peroxidase (GSH-Px), lower oxidized glutathione (GSSG) concentrations, and GSSG/GSH (glutathione) ratio (all, P &lt; 0.01) on day 21 of lactation. Moreover, offspring from micelle silymarin-treated sows tended to (0.05 &lt; P &lt;0.1) have higher serum catalase (CAT) activity and total antioxidant capacity (T-AOC) concentrations. Taken together, the results showed that sows fed increasing levels of micelle silymarin from the 109th prenatal day to the 21st postnatal day had an incremental dose-dependent effect on higher feed intake, diminished BW loss, greater milk yields, and greater litter weight at weaning, and 0.2% of micelle silymarin could be optimal to achieve the better effect.
Novel RAF Fusions in Pediatric Low-Grade Gliomas Demonstrate MAPK Pathway Activation
Authors: Lind Katherine T , Chatwin Hannah V , DeSisto John , Coleman Philip , Sanford Bridget , Donson Andrew M , Davies Kurtis D , Willard Nicholas , Ewing Calvin A , Knox Aaron J , Mulcahy Levy Jean M , Gilani Ahmed , Green Adam L 
Published: December 2021

Abstract
Brain tumors are the most common solid tumor in children, and low-grade gliomas (LGGs) are the most common childhood brain tumor. Here, we report on 3 patients with LGG harboring previously unreported or rarely reported RAF fusions: FYCO1-RAF1, CTTNBP2-BRAF, and SLC44A1-BRAF. We hypothesized that these tumors would show molecular similarity to the canonical KIAA1549-BRAF fusion that is the most widely seen alteration in pilocytic astrocytoma (PA), the most common pediatric LGG variant, and that this similarity would include mitogen-activated protein kinase (MAPK) pathway activation. To test our hypothesis, we utilized immunofluorescent imaging and RNA-sequencing in normal brain, KIAA1549-BRAF-harboring tumors, and our 3 tumors with novel fusions. We performed immunofluorescent staining of ERK and phosphorylated ERK (p-ERK), identifying increased p-ERK expression in KIAA1549-BRAF fused PA and the novel fusion samples, indicative of MAPK pathway activation. Geneset enrichment analysis further confirmed upregulated downstream MAPK activation. These results suggest that MAPK activation is the oncogenic mechanism in noncanonical RAF fusion-driven LGG. Similarity in the oncogenic mechanism suggests that LGGs with noncanonical RAF fusions are likely to respond to MEK inhibitors.
The Return of Biblical Theology: Rabbi Lord Jonathan Sacks and the Theological-Literary Movement
Authors: Jotkowitz Alan 
Published: December 2021

Abstract
Lord Rabbi Jonathan Sacks, the former Chief Rabbi of the British Empire, is probably the most important and well-known Jewish theologian of the twenty-first century. He believed passionately that Jewish values have relevance for all of mankind. What is somewhat surprising is the source of R. Sacks's theology. Orthodox Jewish theology has traditionally been anchored in either the perspective of Talmudic Rabbis as transmitted through the halacha and the aggadda, or based on the works of the great medieval Jewish philosophers such as the Rambam, Crescas and Yehuda Halevi. In contradistinction to these approaches, R. Sacks turned to the Bible as the primary source of his theology. This “returning to the bible” is consistent with other trends in orthodox Jewish scholarship which also emphasizes a return to intensive study of the biblical text using modern methodologies. However, since biblical theology is open to a myriad of differing and even contradictory opinions, the role of rabbinic tradition is of utmost importance. Thus, for Rabbi Sacks's theology to have lasting impact it needs to be based on, and a natural extension of, the timeless Jewish tradition. This essay will explore these issues.
Evaluation of the classification of pre-solar silicon carbide grains using consensus clustering with resampling methods: An assessment of the confidence of grain assignments
Authors: Hystad Grethe , Boujibar Asmaa , Liu Nan , Nittler Larry R , Hazen Robert M 
Published: December 2021

ABSTRACTWe report the use of several cluster analysis techniques to evaluate the classification of pre-solar silicon carbide (SiC) grains. The stability of clusters and the confidence of individual cluster assignments of grains are assessed using consensus clustering with resampling methods. Our analysis shows that pre-solar SiC grains can be divided into seven groups that are found to be highly stable with most of the grains being assigned to the same cluster for at least 90 per cent of the time over multiple aggregated clustering. Among the seven groups, two groups are dominated by AB grains, three groups by MS grains, one group by Z grains, and one group by X grains. The further division of X grains into two groups is highly dependent on the chosen algorithm and is therefore uncertain. Z and Y grains are clustered jointly with MS grains, with one group dominated by Z grains, pointing to their common origins from low-mass asymptotic giant branch stars. The most stable N grain-containing clusters are dominated by 15N-rich AB grains. However, some methods assign N grains with X grains, but in less stable clusters. The suggested genetic relationship among 15N-rich AB, N, and X grains is in line with the recent proposal that all three types of pre-solar SiC grains came from core collapse supernovae. We discuss the results from different clustering techniques based on our assessment of the cluster stabilities and the extent to which the cluster assignments overlap across the different methods.
The GALAH Survey: chemical tagging and chrono-chemodynamics of accreted halo stars with GALAH+ DR3 andGaiaeDR3
Authors: Buder Sven , Lind Karin , Ness Melissa K , Feuillet Diane K , Horta Danny , Monty Stephanie , Buck Tobias , Nordlander Thomas , Bland-Hawthorn Joss , Casey Andrew R , De Silva Gayandhi M , D’Orazi Valentina , Freeman Ken C , Hayden Michael R , Kos Janez , Martell Sarah L , Lewis Geraint F , Lin Jane , Schlesinger Katharine J , Sharma Sanjib , Simpson Jeffrey D , Stello Dennis , Zucker Daniel B , Zwitter Tomaž , Ciucă Ioana , Horner Jonathan , Kobayashi Chiaki , Ting (丁源森) Yuan-Sen , Wyse Rosemary F G ,   the GALAH collaboration
Published: December 2021

ABSTRACTSince the advent of Gaia astrometry, it is possible to identify massive accreted systems within the Galaxy through their unique dynamical signatures. One such system, Gaia-Sausage-Enceladus (GSE), appears to be an early ‘building block’ given its virial mass $\gt 10^{10}\, \mathrm{M_\odot }$ at infall (z ∼ 1−3). In order to separate the progenitor population from the background stars, we investigate its chemical properties with up to 30 element abundances from the GALAH+ Survey Data Release 3 (DR3). To inform our choice of elements for purely chemically selecting accreted stars, we analyse 4164 stars with low-α abundances and halo kinematics. These are most different to the Milky Way stars for abundances of Mg, Si, Na, Al, Mn, Fe, Ni, and Cu. Based on the significance of abundance differences and detection rates, we apply Gaussian mixture models to various element abundance combinations. We find the most populated and least contaminated component, which we confirm to represent GSE, contains 1049 stars selected via [Na/Fe] versus [Mg/Mn] in GALAH+ DR3. We provide tables of our selections and report the chrono-chemodynamical properties (age, chemistry, and dynamics). Through a previously reported clean dynamical selection of GSE stars, including $30 \lt \sqrt{J_R / \, \mathrm{kpc\, km\, s^{-1}}} \lt 55$, we can characterize an unprecedented 24 abundances of this structure with GALAH+ DR3. With our chemical selection we characterize the dynamical properties of the GSE, for example mean $\sqrt{J_R / \, \mathrm{kpc\, km\, s^{-1}}} =$$26_{-14}^{+9}$. We find only $(29\pm 1){{\ \rm per\ cent}}$ of the GSE stars within the clean dynamical selection region. Our methodology will improve future studies of accreted structures and their importance for the formation of the Milky Way.
MODOMICS: a database of RNA modification pathways. 2021 update
Authors: Boccaletto Pietro , Stefaniak Filip , Ray Angana , Cappannini Andrea , Mukherjee Sunandan , Purta Elżbieta , Kurkowska Małgorzata , Shirvanizadeh Niloofar , Destefanis Eliana , Groza Paula , Avşar Gülben , Romitelli Antonia , Pir Pınar , Dassi Erik , Conticello Silvestro G , Aguilo Francesca , Bujnicki Janusz M 
Published: December 2021

Abstract
The MODOMICS database has been, since 2006, a manually curated and centralized resource, storing and distributing comprehensive information about modified ribonucleosides. Originally, it only contained data on the chemical structures of modified ribonucleosides, their biosynthetic pathways, the location of modified residues in RNA sequences, and RNA-modifying enzymes. Over the years, prompted by the accumulation of new knowledge and new types of data, it has been updated with new information and functionalities. In this new release, we have created a catalog of RNA modifications linked to human diseases, e.g., due to mutations in genes encoding modification enzymes. MODOMICS has been linked extensively to RCSB Protein Data Bank, and sequences of experimentally determined RNA structures with modified residues have been added. This expansion was accompanied by including nucleotide 5′-monophosphate residues. We redesigned the web interface and upgraded the database backend. In addition, a search engine for chemically similar modified residues has been included that can be queried by SMILES codes or by drawing chemical molecules. Finally, previously available datasets of modified residues, biosynthetic pathways, and RNA-modifying enzymes have been updated. Overall, we provide users with a new, enhanced, and restyled tool for research on RNA modification. MODOMICS is available at https://iimcb.genesilico.pl/modomics/.
Zebularine induces enzymatic DNA–protein crosslinks in 45S rDNA heterochromatin of Arabidopsis nuclei
Authors: Prochazkova Klara , Finke Andreas , Tomaštíková Eva Dvořák , Filo Jaroslav , Bente Heinrich , Dvořák Petr , Ovečka Miroslav , Šamaj Jozef , Pecinka Ales 
Published: December 2021

Abstract
Loss of genome stability leads to reduced fitness, fertility and a high mutation rate. Therefore, the genome is guarded by the pathways monitoring its integrity and neutralizing DNA lesions. To analyze the mechanism of DNA damage induction by cytidine analog zebularine, we performed a forward-directed suppressor genetic screen in the background of Arabidopsis thaliana zebularine-hypersensitive structural maintenance of chromosomes 6b (smc6b) mutant. We show that smc6b hypersensitivity was suppressed by the mutations in EQUILIBRATIVE NUCLEOSIDE TRANSPORTER 3 (ENT3), DNA METHYLTRANSFERASE 1 (MET1) and DECREASE IN DNA METHYLATION 1 (DDM1). Superior resistance of ent3 plants to zebularine indicated that ENT3 is likely necessary for the import of the drug to the cells. Identification of MET1 and DDM1 suggested that zebularine induces DNA damage by interference with the maintenance of CG DNA methylation. The same holds for structurally similar compounds 5-azacytidine and 2-deoxy-5-azacytidine. Based on our genetic and biochemical data, we propose that zebularine induces enzymatic DNA–protein crosslinks (DPCs) of MET1 and zebularine-containing DNA in Arabidopsis, which was confirmed by native chromatin immunoprecipitation experiments. Moreover, zebularine-induced DPCs accumulate preferentially in 45S rDNA chromocenters in a DDM1-dependent manner. These findings open a new avenue for studying genome stability and DPC repair in plants.
Deriving on-shell open string field amplitudes without using Feynman rules
Authors: Masuda Toru , Matsunaga Hiroaki 
Published: December 2021

Abstract
We present a series of new gauge-invariant quantities in Witten’s open string field theory. They are defined for a given set of open string states which satisfy the physical state condition around a classical solution. For known classical solutions, we demonstrate that these gauge-invariant quantities compute on-shell tree-level scattering amplitudes around the corresponding D-brane configuration.