bluuebunny/crossref_metadata_2025_split huggingface dataset:
Is there a prognostic difference among patients with T3N0-3M0 non-small-cell lung cancer with different T3 descriptors?
Authors: Cai Jing-Sheng , Yang Fan , Wang Xun 
Published: December 2022

AbstractOBJECTIVESOur goal was to evaluate the survival disparities among the patients with T3N0-3M0 non-small-cell lung cancer with different T3 descriptors and to further externally validate the current T3 category.METHODSOverall survival and cancer-specific survival were compared using the Kaplan–Meier method with a log-rank test. A univariable and a multivariable Cox regression model were performed to determine the prognostic factors.RESULTSA series of 28,519 eligible cases was included. There were 17,971 cases with tumours that were larger than 5 cm but equal to or less than 7 cm (T-size group); 3,028 cases with tumours with chest wall/pericardium/phrenic nerve invasion (T-invasion group); 4,600 cases with tumours with additional tumour nodules in the same lobe (T-add group); and 2,900 cases with tumours that had at least 2 T3 descriptors (T-multiple group). The survival data indicated that patients in the T-add group had the best survival rates compared with other patients both in the entire cohort and in the subgroup analyses. Multivariable Cox models indicated that T3 descriptor was an important prognostic factor. Of the patients with different T3 descriptors, patients in the T-add group had the best prognosis, followed by patients in the T-size and in the T-invasion groups, and patients in the T-multiple group had the worst prognosis both in the pathological and clinical tumor-node-metastasis (TNM) stage cohorts.CONCLUSIONSPatients with T3N0-3M0 non-small-cell lung cancer with different T descriptors had inconsistent survival rates. T-add yielded the best survivals, followed by T-size and T-invasion, and T-multiple was associated with the worst survivals. Our results were exploratory in nature and need to be further validated.
How does power shape district health management team responsiveness to public feedback in low- and middle-income countries: an interpretive synthesis
Authors: Kagwanja Nancy , Molyneux Sassy , Whyle Eleanor , Tsofa Benjamin , Gilson Lucy 
Published: December 2022

AbstractResponsiveness is a core element of World Health Organization’s health system framework, considered important for ensuring inclusive and accountable health systems. System-wide responsiveness requires system-wide action, and district health management teams (DHMTs) play critical governance roles in many health systems. However, there is little evidence on how DHMTs enhance health system responsiveness. We conducted this interpretive literature review to understand how DHMTs receive and respond to public feedback and how power influences these processes. A better understanding of power dynamics could strengthen responsiveness and improve health system performance. Our interpretive synthesis drew on English language articles published between 2000 and 2021. Our search in PubMed, Google Scholar and Scopus combined terms related to responsiveness (feedback and accountability) and DHMTs (district health manager) yielding 703 articles. We retained 21 articles after screening. We applied Gaventa’s power cube and Long’s actor interface frameworks to synthesize insights about power. Our analysis identified complex power practices across a range of interfaces involving the public, health system and political actors. Power dynamics were rooted in social and organizational power relationships, personal characteristics (interests, attitudes and previous experiences) and world-views (values and beliefs). DHMTs’ exercise of ‘visible power’ sometimes supported responsiveness; however, they were undermined by the ‘invisible power’ of public sector bureaucracy that shaped generation of responses. Invisible power, manifesting in the subconscious influence of historical marginalization, patriarchal norms and poverty, hindered vulnerable groups from providing feedback. We also identified ‘hidden power’ as influencing what feedback DHMTs received and from whom. Our work highlights the influence of social norms, structures and discrimination on power distribution among actors interacting with, and within, the DHMT. Responsiveness can be strengthened by recognising and building on actors' life-worlds (lived experiences) while paying attention to the broader context in which these life-worlds are embedded.
Two distinct population clusters of northern sand lance (Ammodytes dubius) on the northwest Atlantic shelf revealed by whole genome sequencing
Authors: Jones Lucas F , Lou R Nicolas , Murray Christopher S , Robert Dominique , Bourne Christina M , Bouchard Caroline , Kučka Marek , Chan Y Frank , Carlon David B , Wiley David N , Therkildsen Nina O , Baumann Hannes 
Published: December 2022

AbstractNorthern sand lance (Ammodytes dubius) are essential forage fish in most offshore, temperate-to-polar waters on the Northwest Atlantic shelf (NWA), but their population structure and genetic separation from the American sand lance (A. americanus) remain unresolved. We assembled a reference genome for A. dubius (first in the Ammodytidae) and then used low-coverage whole genome sequencing on 262 specimens collected across the species distribution (Mid-Atlantic Bight to Greenland) to quantify genetic differentiation between geographic regions based on single nucleotide polymorphisms. We found strong separation between A. dubius from locations north and south of the Scotian Shelf, largely due to massive genetic differentiation spanning most of chromosomes 21 and 24. Genetic distance increased with geographic distance in the smaller southern cluster but not in the larger northern cluster, where genetic homogeneity appeared across large geographic distances (&gt;103 km). The two genetic clusters coincide with a clear break in winter sea surface temperature, suggesting that differential offspring survival, rather than limited transport, causes a break in realized connectivity. Nuclear and mitochondrial DNA both clearly delineated A. dubius from A. americanus, thereby confirming a species boundary through spatial niche partitioning into inshore (A. americanus) and offshore (A. dubius) sand lance species on the NWA.
Characterizing SARS-CoV-2 Transcription of Subgenomic and Genomic RNAs During Early Human Infection Using Multiplexed Droplet Digital Polymerase Chain Reaction
Authors: Hwang Hyon S , Lo Che-Min , Murphy Michael , Grudda Tanner , Gallagher Nicholas , Luo Chun Huai , Robinson Matthew L , Mirza Agha , Conte Madison , Conte Abigail , Zhou Ruifeng , Vergara Candelaria , Brooke Christopher B , Pekosz Andrew , Mostafa Heba H , Manabe Yukari C , Thio Chloe L , Balagopal Ashwin 
Published: December 2022

Abstract

Background
Control of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission requires understanding SARS-CoV-2 replication dynamics.

Methods
We developed a multiplexed droplet digital polymerase chain reaction (ddPCR) assay to quantify SARS-CoV-2 subgenomic RNAs (sgRNAs), which are only produced during active viral replication, and discriminate them from genomic RNAs (gRNAs). We applied the assay to specimens from 144 people with single nasopharyngeal samples and 27 people with &gt;1 sample. Results were compared to quantitative PCR (qPCR) and viral culture.

Results
sgRNAs were quantifiable across a range of qPCR cycle threshold (Ct) values and correlated with Ct values. The ratio sgRNA:gRNA was stable across a wide range of Ct values, whereas adjusted amounts of N sgRNA to a human housekeeping gene declined with higher Ct values. Adjusted sgRNA and gRNA amounts were quantifiable in culture-negative samples, although levels were significantly lower than in culture-positive samples. Daily testing of 6 persons revealed that sgRNA is concordant with culture results during the first week of infection but may be discordant with culture later in infection. sgRNA:gRNA is constant during infection despite changes in viral culture.

Conclusions
Ct values from qPCR correlate with active viral replication. More work is needed to understand why some cultures are negative despite presence of sgRNA.
Identification of Six Small Heat Shock Protein Genes in Ostrinia furnacalis (Lepidoptera: Pyralidae) and Analysis of Their Expression Patterns in Response to Environmental Stressors
Authors: Ruan Hong-Yun , Meng Jian-Yu , Yang Chang-Li , Zhou Lv , Zhang Chang-Yu 
Published: December 2022

Abstract
Ostrinia furnacalis (Guenée) is a major insect pest in maize production that is highly adaptable to the environment. Small heat shock proteins (sHsps) are a class of chaperone proteins that play an important role in insect responses to various environmental stresses. The present study aimed to clarify the responses of six O. furnacalis sHsps to environmental stressors. In particular, we cloned six sHsp genes, namely, OfHsp24.2, OfHsp21.3, OfHsp20.7, OfHsp21.8, OfHsp29.7, and OfHsp19.9, from O. furnacalis. The putative proteins encoded by these genes contained a typical α-crystallin domain. Real-time quantitative polymerase chain reaction was used to analyze the differences in the expression of these genes at different developmental stages, in different tissues of male and female adults, and in O. furnacalis under UV-A and extreme temperature stresses. The six OfsHsp genes were expressed at significantly different levels based on the developmental stage and tissue type in male and female adults. Furthermore, all OfsHsp genes were significantly upregulated in both male and female adults under extreme temperature and UV-A stresses. Thus, O. furnacalis OfsHsp genes play important and unique regulatory roles in the developmental stages of the insect and in response to various environmental stressors.
Gallbladder agenesis a rare and underdiagnosed congenital anomaly: a case report and literature review
Authors: Piltcher-da-Silva Rodrigo , Sasaki Vivian Laís , Felisberto Dóroty Eva Garcia , Bodanese Beatriz Carolina Schuta , Piltcher-Recuero Mariana , Bodanese Bianca Vitória Schuta , Bettini Luiz Francisco Cravo , Aguilera Yan Sacha Hass , da Costa Marco Raeder , Coelho Júlio Cezar Uili 
Published: December 2022

Abstract
Gallbladder agenesis (GA) is a rare congenital anomaly with conflicting epidemiology described in the literature. When present, it is misinterpreted as cholelitiasis, a highly prevalent condition. Nevertheless, surgeons and radiologists must be aware of it since it can lead to unnecessary invasive procedures. Diagnosis of GA is challenging due to the anatomical structures that sometimes resemble a shrunken gallbladder. We report the case of a 55-year-old man with preoperative diagnosis of cholelitiasis and further intraoperative find of GA. Since cholecystectomy is one of the most common surgeries worldwide, it demonstrates how relevant this case is to emphasize the need to recognize this diagnosis and be aware of its management to avoid unnecessary surgery.
Plant host domestication and soil nutrient availability determine positive plant microbial response across the Solanum genus
Authors: Miao Max , Lankau Richard 
Published: December 2022

Abstract
Domestication of crops has changed how crops shape their associated microbial communities compared with their progenitors. However, studies testing how crop domestication-driven differences in rhizosphere microbial communities affect plant health are limited mostly to specific symbiont pairings. By conducting a soil manipulation greenhouse study, we examined plant growth and yield in response to differences in microbial communities and nutrient availability across a variety of wild, landrace, and commercially available ‘Modern’ potatoes. Coupled with this, we conducted 16S and internal transcribed spacer (ITS) amplicon sequencing to examine plant host- and soil treatment-driven differences in microbial community composition on potato plant roots. We found that the plant response to microbes (PRM) was context dependent. In low nutrient conditions, landraces responded positively to the presence of live soil microbial inocula. Conversely, modern potato varieties responded positively only in high nutrient conditions. Amplicon sequencing found differences in bacterial communities due to environmental and temporal factors. However, potato clade (e.g. Andigenum, Chiletanum, Solanum berthaultii, and ‘Modern’) alone did not lead to differences in microbial communities that accounted for PRM differences. Differences in PRM between landraces and modern potatoes, and the correlation of PRM to microbial diversity, suggest that domestication and subsequent breeding have altered the S. tuberosum response to rhizosphere microbiomes between Andigenum, Chiletanum, and North American potato varieties.
The stability of Uranus Trojans over the age of the Solar system
Authors: Wood Jeremy 
Published: December 2022

ABSTRACT
The stability of eight nominal fictitious Uranus Trojan orbits over the age of the Solar system has been measured. The initial inclinations, i0, were 0°, 5°, 15°, and 30° relative to the ecliptic plane. Initial eccentricities ranged from 0 to 0.1 for i0 = 0° and 5°, and 0 to 0.2 for i0 = 15° and 30°. Half of the orbits were in the L4 swarm, and half were in the L5 swarm. Orbits in the L4 swarm had mean longitudes 8.8° from the nominal L4 Lagrange point, and orbits in the L5 swarm had mean longitudes 18.2° from the nominal L5 point. I integrated 10 000 massless clones per nominal orbit in the six-body problem (Sun, test particle, and four giant planets) for 4.5 Gyr and calculated the half-life for each orbit. A total of 1291 test particles survived for the entire integration time. Of these survivors, 99 per cent were associated with the nominal orbit with i0 = 0° in the L4 swarm. These surviving test particles had initial eccentricities in the range e0 &lt; 0.07. The half-lives associated with L4 orbits were 1258, 286, 56, and 237 Myr for nominal orbits with i0 = 0°, 5°, 15°, and 30°, respectively. The half-lives associated with L5 orbits were 103, 281, 25, and 46 Myr, respectively. The overall results showed that the ecliptic plane is one good place to search for primordial Uranus Trojans.
Scattering variability detected from the circumsource medium of FRB 20190520B
Authors: Ocker Stella Koch , Cordes James M , Chatterjee Shami , Li Di , Niu Chen-Hui , McKee James W , Law Casey J , Anna-Thomas Reshma 
Published: December 2022

ABSTRACT
Fast radio bursts (FRBs) are millisecond-time-scale radio transients, the origins of which are predominantly extragalactic and likely involve highly magnetized compact objects. FRBs undergo multipath propagation, or scattering, from electron density fluctuations on sub-parsec scales in ionized gas along the line of sight. Scattering observations have located plasma structures within FRB host galaxies, probed Galactic and extragalactic turbulence, and constrained FRB redshifts. Scattering also inhibits FRB detection and biases the observed FRB population. We report the detection of scattering times from the repeating FRB 20190520B that vary by up to a factor of 2 or more on minutes to days-long time-scales. In one notable case, the scattering time varied from 7.9 ± 0.4 ms to less than 3.1 ms ($95{{\ \rm per\ cent}}$ confidence) over 2.9 min at 1.45 GHz. The scattering times appear to be uncorrelated between bursts or with dispersion and rotation measure variations. Scattering variations are attributable to dynamic, inhomogeneous plasma in the circumsource medium, and analogous variations have been observed from the Crab pulsar. Under such circumstances, the frequency dependence of scattering can deviate from the typical power law used to measure scattering. Similar variations may therefore be detectable from other FRBs, even those with inconspicuous scattering, providing a unique probe of small-scale processes within FRB environments.
MOSEL survey: extremely weak outflows in EoR analogues at z = 3−4
Authors: Gupta Anshu , Tran Kim-Vy , Mendel Trevor , Harshan Anishya , Forrest Ben , Davies R L , Wisnioski Emily , Nanayakkara Themiya , Kacprzak Glenn G , Kewley Lisa J 
Published: December 2022

ABSTRACT
This paper presents deep K-band spectroscopic observations of galaxies at z = 3 − 4 with composite photometric rest-frame H β+[O iii] 5007 equivalent widths (EW0) &gt; 600 Å, comparable to the EW of galaxies observed during the epoch of reionization (EoR, z &gt; 6). The typical spectroscopic [O iii] 5007 EW0 and stellar mass of our targets is ∼700 Å and log (M*/M⊙) = 8.98. By stacking the [O iii] 5007 emission profiles, we find evidence of a weak broad component with $\rm F_{broad}/F_{narrow} \sim 0.2$ and velocity width σbroad ∼ 170 km s−1. The strength and velocity width of the broad component does not change significantly with stellar mass and [O iii] 5007 EW0 of the stacked sample. Assuming similar broad component profiles for [O iii] 5007 and Hα emission, we estimate a mass loading factor ∼0.2, similar to low stellar mass galaxies at z &gt; 1 even if the star formation rates of our sample is 10 times higher. We hypothesize that either the multiphase nature of supernovae driven outflows or the suppression of winds in the extreme star-forming regime is responsible for the weak signature of outflows in the EoR analogues.
The disappearances of six supernova progenitors
Authors: Van Dyk Schuyler D , de Graw Asia , Baer-Way Raphael , Zheng WeiKang , Filippenko Alexei V , Fox Ori D , Smith Nathan , Brink Thomas G , de Jaeger Thomas , Kelly Patrick L , Vasylyev Sergiy S 
Published: December 2022

ABSTRACT
As part of a larger completed Hubble Space Telescope (HST) Snapshot program, we observed the sites of six nearby core-collapse supernovae (SNe) at high spatial resolution: SN 2012A, SN 2013ej, SN 2016gkg, SN 2017eaw, SN 2018zd, and SN 2018aoq. These observations were all conducted at sufficiently late times in each SN’s evolution to demonstrate that the massive-star progenitor candidate identified in each case in pre-explosion imaging data had indeed vanished and was therefore most likely the actual progenitor. However, we have determined for SN 2016gkg that the progenitor candidate was most likely a blend of two objects: the progenitor, which itself has likely vanished, and another closely neighbouring star. We thus provide a revised estimate of that progenitor’s properties: a binary system with a hydrogen-stripped primary star at explosion with effective temperature ≈6300–7900 K, bolometric luminosity ≈104.65 L⊙, radius ≈118–154 R⊙, and initial mass 9.5–11 M⊙. Utilizing late-time additional archival HST data nearly contemporaneous with our Snapshots, we also show that SN 2017eaw had a luminous ultraviolet excess, which is best explained as a result of ongoing interaction of the SN shock with pre-existing circumstellar matter. We offer the caveat, particularly in the case of SN 2013ej, that obscuration from SN dust may be compromising our conclusions. This sample adds to the growing list of confirmed or likely core-collapse SN progenitors.
A general relativistic extension to mesh-free methods for hydrodynamics
Authors: Lupi Alessandro 
Published: December 2022

ABSTRACT
The detection of gravitational waves has opened a new era for astronomy, allowing for the combined use of gravitational wave and electromagnetic emissions to directly probe the physics of compact objects, still poorly understood. So far, the theoretical modelling of these sources has mainly relied on standard numerical techniques as grid-based methods or smoothed particle hydrodynamics, with only a few recent attempts at using new techniques as moving-mesh schemes. Here, we introduce a general relativistic extension to the mesh-less hydrodynamic schemes in the code gizmo, which benefits from the use of Riemann solvers and at the same time perfectly conserves angular momentum thanks to a generalized leap-frog integration scheme. We benchmark our implementation against many standard tests for relativistic hydrodynamics, either in one or three dimensions, and also test the ability to preserve the equilibrium solution of a Tolman–Oppenheimer–Volkoff compact star. In all the presented tests, the code performs extremely well, at a level at least comparable to other numerical techniques.
Swift J1728.9−3613 is a black hole X-ray binary: a spectral and timing study usingNICER
Authors: Saha Debasish , Mandal Manoj , Pal Sabyasachi 
Published: December 2022

ABSTRACTWe have studied different timing and spectral properties of the new Galactic X-ray transient Swift J1728.9−3613 using NICER and Swift, discovered by the Burst Alert Telescope on the Neil Gehrels Swift Observatory. The source went through multiple transitions to different spectral states during the outburst, and the complete evolution created a ‘q’-shaped track in the hardness-intensity diagram. A partial hysteresis is also observed in the RMS-intensity diagram, which is another well-defined feature of black hole transients. In soft intermediate states, power-density spectra were dominated by broad-band noise components, and two type-B quasi-periodic oscillations were detected. We have fitted 1–10 keV energy spectra obtained from NICER observations that were performed during the outburst, and the temporal evolution of spectral parameters is studied. A small-scale reflare happened near MJD 58584.69, resulting in finite changes in spectral parameters, and the 1–10 keV averaged flux also increased. We observed that the innermost radius of the accretion disc was almost constant during the soft state and we have measured the mass of the compact object to be ∼4.6 M⊙, considering a non-spinning black hole binary system. The soft-to-hard transition occurred when the bolometric luminosity was 0.01 times the Eddington luminosity. Based on our combined study of the evolution of the timing and spectral properties, we conclude that the new source Swift J1728.9−3613 is a black hole X-ray binary.
Response regulator PorX coordinates oligonucleotide signalling and gene expression to control the secretion of virulence factors
Authors: Schmitz Claus , Madej Mariusz , Nowakowska Zuzanna , Cuppari Anna , Jacula Anna , Ksiazek Miroslaw , Mikruta Katarzyna , Wisniewski Jerzy , Pudelko-Malik Natalia , Saran Anshu , Zeytuni Natalie , Mlynarz Piotr , Lamont Richard J , Usón Isabel , Siksnys Virginijus , Potempa Jan , Solà Maria 
Published: December 2022

Abstract
The PglZ family of proteins belongs to the alkaline phosphatase superfamily, which consists of metallohydrolases with limited sequence identity but similar metal-coordination architectures in otherwise divergent active sites. Proteins with a well-defined PglZ domain are ubiquitous among prokaryotes as essential components of BREX phage defence systems and two-component systems (TCSs). Whereas other members of the alkaline phosphatase superfamily are well characterized, the activity, structure and biological function of PglZ family proteins remain unclear. We therefore investigated the structure and function of PorX, an orphan response regulator of the Porphyromonas gingivalis TCS containing a putative PglZ effector domain. The crystal structure of PorX revealed a canonical receiver domain, a helical bundle, and an unprecedented PglZ domain, similar to the general organization of the phylogenetically related BREX-PglZ proteins. The PglZ domain of PorX features an active site cleft suitable for large substrates. An extensive search for substrates revealed that PorX is a phosphodiesterase that acts on cyclic and linear oligonucleotides, including signalling molecules such as cyclic oligoadenylates. These results, combined with mutagenesis, biophysical and enzymatic analysis, suggest that PorX coordinates oligonucleotide signalling pathways and indirectly regulates gene expression to control the secretion of virulence factors.