bluuebunny/crossref_metadata_2025_split huggingface dataset:
The distribution of dust in edge-on galaxies: I. The global structure
Authors: Mosenkov Aleksandr V , Usachev Pavel A , Shakespear Zacory , Guerrette Jacob , Baes Maarten , Bianchi Simone , Xilouris Emmanuel M , Gontcharov George A , Il’in Vladimir B , Marchuk Alexander A , Savchenko Sergey S , Smirnov Anton A 
Published: July 2022

ABSTRACT
In this first paper in a series we present a study of the global dust emission distribution in nearby edge-on spiral galaxies. Our sample consists of 16 angularly large and 13 less spatially resolved galaxies selected from the DustPedia sample. To explore the dust emission distribution, we exploit the Herschel photometry in the range 100–500 $\mu $m. We employ Sérsic and 3D disc models to fit the observed 2D profiles of the galaxies. Both approaches give similar results. Our analysis unequivocally states the case for the presence of extraplanar dust in between 6 and 10 large galaxies. The results reveal that both the disc scale length and height increase as a function of wavelength between 100 and 500 $\mu $m. The dust disc scale height positively correlates with the dust disc scale length, similar to what is observed for the stellar discs. We also find correlations between the scale lengths and scale heights in the near- and far-infrared which suggest that the stellar discs and their dust counterparts are tightly connected. Furthermore, the intrinsic flattening of the dust disc is inversely proportional to the maximum rotation velocity and the dust mass of the galaxy: more massive spiral galaxies host, on average, relatively thinner dust discs. Also, there is a tendency for the dust-to-stellar scale height ratio to decrease with the dust mass and rotation velocity. We conclude that low-mass spiral galaxies host a diffuse, puffed-up dust disc with a thickness similar to that of the stellar disc.
Revisiting bright δ Scuti stars and their period–luminosity relation with TESS and Gaia DR3
Authors: Barac Natascha , Bedding Timothy R , Murphy Simon J , Hey Daniel R 
Published: July 2022

ABSTRACT
We have used NASA’s TESS mission to study catalogued δ Scuti stars. We examined TESS light curves for 434 stars, including many for which few previous observations exist. We found that 62 are not δ Scuti pulsators, with most instead showing variability from binarity. For the 372 δ Scuti stars, we provide a catalogue of the period and amplitude of the dominant pulsation mode. Using Gaia DR3 parallaxes, we place the stars in the period–luminosity (P–L) diagram and confirm previous findings that most stars lie on a ridge that corresponds to pulsation in the fundamental radial mode, and that many others fall on a second ridge that is a factor two shorter in period. This second ridge is seen more clearly than before, thanks to the revised periods and distances. We demonstrate the value of the P–L diagram in distinguishing δ Scuti stars from short-period RR Lyrae stars, and we find several new examples of high-frequency δ Scuti stars with regular sequences of overtone modes, including XX Pyx and 29 Cyg. Finally, we revisit the sample of δ Scuti stars observed by Kepler and show that they follow a tight period–density relation, with a pulsation constant for the fundamental mode of Q = 0.0315 d.
The response of a red supergiant to a common envelope jets supernova (CEJSN) impostor event
Authors: Ragoler Nitzan , Bear Ealeal , Schreier Ron , Hillel Shlomi , Soker Noam 
Published: July 2022

ABSTRACT
Using a 1D stellar evolution code, we simulate the response of a red supergiant (RSG) star to injection of energy and to mass removal. We take the values of the energy that we inject and the mass that we remove according to our previous 3D hydrodynamical simulations of a neutron star (NS) on a highly eccentric orbit that enters the envelope of an RSG star for half a year and launches jets as it accretes mass via an accretion disc. We find that for injected energies of $\simeq 10^{47} {--} 10^{48} {~\rm erg}$ and removed mass of $\simeq 0.03{--}0.6\, {\rm M}_\odot$ the RSG envelope expands to a large radius. Therefore, we expect the NS to continue to orbit inside this massive inflated envelope for several more months, up to about twice the initial RSG radius, to continue to accrete mass and launch jets for a prolonged period. Although these late jets are weaker than the jets that the NS launches while inside the original RSG envelope, the late jets might actually be more influential on the light curve, leading to a long, several months to few years, and bright, about $\gtrsim10^8\, {\rm L}_\odot$, transient event. The RSG returns to more or less a relaxed structure after about 10 yr, and so another transient event might occur in the next periastron passage of the NS. Our results add to the already rich variety of jet-driven explosions/outbursts that might account for many puzzling transient events.
Magnetic field measurement in TMC-1C using 22.3 GHz CCS Zeeman splitting
Authors: Koley Atanu , Roy Nirupam , Momjian Emmanuel , Sarma Anuj P , Datta Abhirup 
Published: July 2022

ABSTRACT
Measurement of magnetic fields in dense molecular clouds is essential for understanding the fragmentation process prior to star formation. Radio interferometric observations of CCS 22.3 GHz emission, from the starless core TMC-1C, have been carried out with the Karl G. Jansky Very Large Array to search for Zeeman splitting of the line in order to constrain the magnetic field strength. Toward a region offset from the dust peak, we report a detection of the Zeeman splitting of the CCS 21–10 transition, with an inferred magnetic field of ∼2 mG. If we interpret the dust peak to be the core of TMC-1C, and the region where we have made a detection of the magnetic field to be the envelope, then our observed value for the magnetic field is consistent with a subcritical mass-to-flux ratio envelope around a core with supercritical mass-to-flux ratio. The ambipolar diffusion time-scale for the formation of the core is consistent with the relevant time-scale based on chemical modelling of the TMC-1C core. This work demonstrates the potential of deep CCS observation to carry out future measurements of magnetic field strengths in dense molecular clouds and, in turn, understand the role of the magnetic field in star formation.
A Phylogeny-aware GWAS Framework to Correct for Heritable Pathogen Effects on Infectious Disease Traits
Authors: Nadeau Sarah , Thorball Christian W , Kouyos Roger , Günthard Huldrych F , Böni Jürg , Yerly Sabine , Perreau Matthieu , Klimkait Thomas , Rauch Andri , Hirsch Hans H , Cavassini Matthias , Vernazza Pietro , Bernasconi Enos , Fellay Jacques , Mitov Venelin , Stadler Tanja ,   Swiss HIV Cohort Study (SHCS), Abela I , Aebi-Popp K , Anagnostopoulos A , Battegay M , Bernasconi E , Braun DL , Bucher HC , Calmy A , Cavassini M , Ciuffi A , Dollenmaier G , Egger M , Elzi L , Fehr J , Fellay J , Furrer H , Fux CA , Günthard HF , Hachfeld A , Haerry D , Hasse B , Hirsch HH , Hoffmann M , Hösli I , Huber M , Kahlert CR , Kaiser L , Keiser O , Klimkait T , Kouyos RD , Kovari H , Kusejko K , Martinetti G , Martinez de Tejada B , Marzolini C , Metzner KJ , Müller N , Nemeth J , Nicca D , Paioni P , Pantaleo G , Perreau M , Rauch A , Schmid P , Speck R , Stöckle M , Tarr P , Trkola A , Wandeler G , Yerly S 
Published: August 2022

Abstract
Infectious diseases are particularly challenging for genome-wide association studies (GWAS) because genetic effects from two organisms (pathogen and host) can influence a trait. Traditional GWAS assume individual samples are independent observations. However, pathogen effects on a trait can be heritable from donor to recipient in transmission chains. Thus, residuals in GWAS association tests for host genetic effects may not be independent due to shared pathogen ancestry. We propose a new method to estimate and remove heritable pathogen effects on a trait based on the pathogen phylogeny prior to host GWAS, thus restoring independence of samples. In simulations, we show this additional step can increase GWAS power to detect truly associated host variants when pathogen effects are highly heritable, with strong phylogenetic correlations. We applied our framework to data from two different host–pathogen systems, HIV in humans and X. arboricola in A. thaliana. In both systems, the heritability and thus phylogenetic correlations turn out to be low enough such that qualitative results of GWAS do not change when accounting for the pathogen shared ancestry through a correction step. This means that previous GWAS results applied to these two systems should not be biased due to shared pathogen ancestry. In summary, our framework provides additional information on the evolutionary dynamics of traits in pathogen populations and may improve GWAS if pathogen effects are highly phylogenetically correlated amongst individuals in a cohort.
Assessing Human Genome-wide Variation in the Massim Region of Papua New Guinea and Implications for the Kula Trading Tradition
Authors: Liu Dang , Peter Benjamin M , Schiefenhövel Wulf , Kayser Manfred , Stoneking Mark 
Published: August 2022

AbstractThe Massim, a cultural region that includes the southeastern tip of mainland Papua New Guinea (PNG) and nearby PNG offshore islands, is renowned for a trading network called Kula, in which different valuable items circulate in different directions among some of the islands. Although the Massim has been a focus of anthropological investigation since the pioneering work of Malinowski in 1922, the genetic background of its inhabitants remains relatively unexplored. To characterize the Massim genomically, we generated genome-wide SNP data from 192 individuals from 15 groups spanning the entire region. Analyzing these together with comparative data, we found that all Massim individuals have variable Papuan-related (indigenous) and Austronesian-related (arriving ∼3,000 years ago) ancestries. Individuals from Rossel Island in southern Massim, speaking an isolate Papuan language, have the highest amount of a distinct Papuan ancestry. We also investigated the recent contact via sharing of identical by descent (IBD) genomic segments and found that Austronesian-related IBD tracts are widely distributed geographically, but Papuan-related tracts are shared exclusively between the PNG mainland and Massim, and between the Bismarck and Solomon Archipelagoes. Moreover, the Kula-practicing groups of the Massim show higher IBD sharing among themselves than do groups that do not participate in Kula. This higher sharing predates the formation of Kula, suggesting that extensive contact between these groups since the Austronesian settlement may have facilitated the formation of Kula. Our study provides the first comprehensive genome-wide assessment of Massim inhabitants and new insights into the fascinating Kula system.
Long-term safety and efficacy of filgotinib treatment for rheumatoid arthritis in Japanese patients naïve to MTX treatment (FINCH 3)
Authors: Atsumi Tatsuya , Tanaka Yoshiya , Matsubara Tsukasa , Amano Koichi , Ishiguro Naoki , Sugiyama Eiji , Yamaoka Kunihiro , Westhovens René , Ching Daniel W T , Messina Osvaldo Daniel , Burmester Gerd R , Genovese Mark , Bartok Beatrix , Pechonkina Alena , Kondo Akira , Yin Zhaoyu , Gong Qi , Tasset Chantal , Takeuchi Tsutomu 
Published: August 2022

ABSTRACT

Objectives
To evaluate the long-term safety and efficacy of filgotinib (FIL) for Japanese patients with rheumatoid arthritis (RA) and limited/no prior methotrexate (MTX) exposure. We present a Japanese population subanalysis of a global randomised-controlled trial at Week 52 and interim long-term extension (LTE) to Week 48 through June 2020.

Methods
Patients were randomised to FIL 200 mg plus MTX, FIL 100 mg plus MTX, FIL 200 mg, or MTX for 52 weeks. At completion, eligible patients could enrol in the LTE. Those receiving FIL continued; those receiving MTX were rerandomised (blinded) to FIL 200 or 100 mg upon discontinuation of MTX. After a 4-week washout period, MTX could be re-added.

Results
Adverse event rates at Week 52 and in the LTE to Week 48 were comparable across treatment groups. Week 52 American College of Rheumatology 20% improvement (ACR20) rates were 83% (19/23), 82% (9/11), 75% (9/12), and 76% (19/25) for FIL 200 mg plus MTX, FIL 100 mg plus MTX, FIL 200 mg, and MTX, respectively. Through LTE Week 48, ACR20 rates were maintained.

Conclusions
In the 56 Japanese patients treated with FIL, efficacy was maintained through Week 52 and beyond, with no increases in the incidence of adverse events.
Protracted febrile myalgia as a first and challenging manifestation of familial Mediterranean fever
Authors: Arslanoglu Aydin Elif , Baglan Esra , Bagrul Ilknur , Tuncez Serife , Ozdel Semanur , Bulbul Mehmet 
Published: August 2022

ABSTRACT

Objectives
Familial Mediterranean fever (FMF) is an auto-inflammatory disease that causes recurrent episodes of fever, abdominal pain, chest pain, and arthritis. Although FMF is well known, protracted febrile myalgia syndrome (PFMS) is a clinical condition that is rare and difficult to diagnose than other symptoms of FMF. PFMS causes fever, myalgia, and acute phase reactant elevation that lasts 2–4 weeks if corticosteroid treatment is not given. In some cases, fever may not be seen. The purpose of this report is to share our experience with PFMS patients in our clinic.

Methods
This is an observational, retrospective, single-centre study. We evaluated patients who had been diagnosed with PFMS at our paediatric rheumatology clinic.

Results
Protracted febrile myalgia syndrome was observed in 14 patients. Nine of the patients were female. The median age at the time of diagnosis of PFMS was 10 years. Only three patients had previously been diagnosed with FMF. Most of our patients were patients who had no previous complaint of FMF. PFMS attack was seen as the first clinical manifestation of FMF in 11 patients. Two patients who did not respond to steroid treatment improved with anakinra treatment.

Conclusions
PFMS is a rare condition of FMF disease. It may be the first clinical manifestation of FMF disease. Fever may not be seen in all patients. Clinicians should be aware of this situation.
Outcomes and risk factors for mortality in Pneumocystis pneumonia patients with rheumatoid arthritis: A multicentre retrospective cohort study
Authors: Mori Shunsuke , Ueki Yukitaka , Miyamura Tomoya , Ishii Koji , Hidaka Toshihiko , Yoshitama Tamami , Nakamura Kazuyoshi , Suenaga Yasuo 
Published: August 2022

ABSTRACT

Objectives
The aim is to evaluate outcomes and risk factors for death in patients with rheumatoid arthritis (RA) who developed Pneumocystis pneumonia (PCP).

Methods
We included RA patients who were diagnosed with PCP at seven participating community hospitals between July 2005 and October 2020. Clinical features were compared between survivors and non-survivors. Disease-modifying antirheumatic drugs (DMARDs) before PCP onset and after PCP recovery were also examined.

Results
Seventy RA patients developed PCP, and among them, 60 (85.7%) received methotrexate (MTX) monotherapy (40%) or MTX combination therapy with other DMARDs (45.7%). PCP was more likely to occur after 12 months of MTX monotherapy and within 3 months of MTX combination therapy. Thirteen patients (18.6%) died despite PCP treatment. Multivariable logistic regression analysis revealed that coexisting RA-associated interstitial lung disease (odds ratio, 6.18; 95% confidence interval, 1.17–32.63) and delayed PCP treatment with anti-Pneumocystis drugs (odds ratio, 15.29; 95% confidence interval, 1.50–156.15) are significant risk factors for PCP mortality in RA patients. Most survivors successfully resumed DMARD therapy without PCP prophylaxis; one recurrent PCP case was observed during follow-up (median, 4.1 years).

Conclusions
To avoid a treatment delay, RA patients should be followed up for signs and symptoms of PCP development, especially those with RA-associated interstitial lung disease.
Intratracheally administered LNA gapmer antisense oligonucleotides induce robust gene silencing in mouse lung fibroblasts
Authors: Shin Minwook , Chan Io Long , Cao Yuming , Gruntman Alisha M , Lee Jonathan , Sousa Jacquelyn , Rodríguez Tomás C , Echeverria Dimas , Devi Gitali , Debacker Alexandre J , Moazami Michael P , Krishnamurthy Pranathi Meda , Rembetsy-Brown Julia M , Kelly Karen , Yukselen Onur , Donnard Elisa , Parsons Teagan J , Khvorova Anastasia , Sontheimer Erik J , Maehr René , Garber Manuel , Watts Jonathan K 
Published: August 2022

Abstract
The lung is a complex organ with various cell types having distinct roles. Antisense oligonucleotides (ASOs) have been studied in the lung, but it has been challenging to determine their effectiveness in each cell type due to the lack of appropriate analytical methods. We employed three distinct approaches to study silencing efficacy within different cell types. First, we used lineage markers to identify cell types in flow cytometry, and simultaneously measured ASO-induced silencing of cell-surface proteins CD47 or CD98. Second, we applied single-cell RNA sequencing (scRNA-seq) to measure silencing efficacy in distinct cell types; to the best of our knowledge, this is the first time scRNA-seq has been applied to measure the efficacy of oligonucleotide therapeutics. In both approaches, fibroblasts were the most susceptible to locally delivered ASOs, with significant silencing also in endothelial cells. Third, we confirmed that the robust silencing in fibroblasts is broadly applicable by silencing two targets expressed mainly in fibroblasts, Mfap4 and Adam33. Across independent approaches, we demonstrate that intratracheally administered LNA gapmer ASOs robustly induce gene silencing in lung fibroblasts. ASO-induced gene silencing in fibroblasts was durable, lasting 4–8 weeks after a single dose. Thus, lung fibroblasts are well aligned with ASOs as therapeutics.
Alteration of DNA supercoiling serves as a trigger of short-term cold shock repressed genes ofE. coli
Authors: Dash Suchintak , Palma Cristina S D , Baptista Ines S C , Almeida Bilena L B , Bahrudeen Mohamed N M , Chauhan Vatsala , Jagadeesan Rahul , Ribeiro Andre S 
Published: August 2022

AbstractCold shock adaptability is a key survival skill of gut bacteria of warm-blooded animals. Escherichia coli cold shock responses are controlled by a complex multi-gene, timely-ordered transcriptional program. We investigated its underlying mechanisms. Having identified short-term, cold shock repressed genes, we show that their responsiveness is unrelated to their transcription factors or global regulators, while their single-cell protein numbers’ variability increases after cold shock. We hypothesized that some cold shock repressed genes could be triggered by high propensity for transcription locking due to changes in DNA supercoiling (likely due to DNA relaxation caused by an overall reduction in negative supercoiling). Concomitantly, we found that nearly half of cold shock repressed genes are also highly responsive to gyrase inhibition (albeit most genes responsive to gyrase inhibition are not cold shock responsive). Further, their response strengths to cold shock and gyrase inhibition correlate. Meanwhile, under cold shock, nucleoid density increases, and gyrases and nucleoid become more colocalized. Moreover, the cellular energy decreases, which may hinder positive supercoils resolution. Overall, we conclude that sensitivity to diminished negative supercoiling is a core feature of E. coli’s short-term, cold shock transcriptional program, and could be used to regulate the temperature sensitivity of synthetic circuits.
Racial disparities in inpatient clinical presentation, treatment, and outcomes in brain metastasis
Authors: McCray Edwin , Waguia Romaric , de la Garza Ramos Rafael , Price Meghan J , Williamson Theresa , Dalton Tara , Sciubba Daniel M , Yassari Reza , Goodwin Andrea N , Fecci Peter , Johnson Margaret O , Chaichana Kaisorn , Goodwin C Rory 
Published: July 2022

Abstract

Background
Few studies have assessed the impact of race on short-term patient outcomes in the brain metastasis population. The goal of this study is to evaluate the association of race with inpatient clinical presentation, treatment, in-hospital complications, and in-hospital mortality rates for patients with brain metastases (BM).

Method
Using data collected from the National Inpatient Sample between 2004 and 2014, we retrospectively identified adult patients with a primary diagnosis of BM. Outcomes included nonroutine discharge, prolonged length of stay (pLOS), in-hospital complications, and mortality.

Results
Minority (Black, Hispanic/other) patients were less likely to receive surgical intervention compared to White patients (odds ratio [OR] 0.70; 95% confidence interval [CI] 0.66–0.74, p &lt; 0.001; OR 0.88; 95% CI 0.84–0.93, p &lt; 0.001). Black patients were more likely to develop an in-hospital complication than White patients (OR 1.35, 95% CI 1.28–1.41, p &lt; 0.001). Additionally, minority patients were more likely to experience pLOS than White patients (OR 1.48; 95% CI 1.41–1.57, p &lt; 0.001; OR 1.34; 95% CI 1.27–1.42, p &lt; 0.001). Black patients were more likely to experience a nonroutine discharge (OR 1.25; 95% CI 1.19–1.31, p &lt; 0.001) and higher in-hospital mortality than White (OR 1.13; 95% CI 1.03–1.23, p = 0.008).

Conclusion
Our analysis demonstrated that race is associated with disparate short-term outcomes in patients with BM. More efforts are needed to address these disparities, provide equitable care, and allow for similar outcomes regardless of care.
Overexpression of Chloroplast Triosephosphate Isomerase Marginally Improves Photosynthesis at Elevated CO2 Levels in Rice
Authors: Suzuki Yuji , Shiina Mizuki , Takegahara-Tamakawa Yuki , Miyake Chikahiro , Makino Amane 
Published: August 2022

AbstractWe recently suggested that chloroplast triosephosphate isomerase (cpTPI) has moderate control over the rate of CO2 assimilation (A) at elevated CO2 levels via the capacity for triose phosphate utilization (TPU) in rice (Oryza sativa L.) from its antisense-suppression study. In the present study, the effects of cpTPI overexpression on photosynthesis were examined in transgenic rice plants overexpressing the gene encoding cpTPI. The amounts of cpTPI protein in the two lines of transgenic plants were 4.8- and 12.1-folds higher than in wild-type plants, respectively. The magnitude of the increase approximately corresponded to the increase in transcript levels of cpTPI. A at CO2 levels of 100 and 120 Pa increased by 6–9% in the transgenic plants, whereas those at ambient and low CO2 levels were scarcely affected. Similar increases were observed for TPU capacity estimated from the CO2 response curves of A. These results indicate that the overexpression of cpTPI marginally improved photosynthesis at elevated CO2 levels via improvement in TPU capacity in rice. However, biomass production at a CO2 level of 120 Pa did not increase in transgenic plants, suggesting that the improvement in photosynthesis by cpTPI overexpression was not sufficient to improve biomass production in rice.