bluuebunny/crossref_metadata_2025 huggingface dataset:
The myocardial bridge: incidence, diagnosis, and prognosis of a pathology of uncertain clinical significance
Authors: Santucci Andrea , Jacoangeli Francesca , Cavallini Sara , d’Ammando Matteo , de Angelis Francesca , Cavallini Claudio
Published: November 2022

The myocardial bridge (MB) is a common anomaly of the coronary tree, very often clinically silent. The artery typically involved is the left anterior descending in its proximal and/or middle portion. MB can cause ischaemia with various mechanisms, directly proportional to the degree of compression of the intra-myocardial tract, which impairs the coronary flow. It is a dynamic phenomenon that is affected by the adrenergic tone and is therefore often brought by physical exercise. MB, when symptomatic, often begins with angina from exertion; some patients have more severe conditions such as unstable angina or myocardial infarction. Coronary vasospasm related to MB-induced endothelial dysfunction can explain a number of cases that come to observation even with catastrophic pictures such as ventricular fibrillation caused by ischaemia. The diagnostic workup includes the non-invasive study using computed tomography angiography and the invasive study of the haemodynamic impact using pressure and Doppler guides. In symptomatic cases, drug therapy with a beta-blocker is enough to manage angina. When it fails, there is the option of coronary angioplasty or surgical treatment techniques.
Treatment in patients with severe asymptomatic aortic stenosis: is it best not to wait?
Authors: Di Pietro Elena , Frittitta Valentina , Motta Silvia , Strazzieri Orazio , Valvo Roberto , Reddavid Claudia , Costa Giuliano , Tamburino Corrado
Published: November 2022

New insights into the natural history and pathophysiology of patients with aortic stenosis (AS), coupled with the dramatic evolution of transcatheter aortic valve implantation (TAVI), are fuelling intense interest in the management of asymptomatic patients with severe AS. This patient presenting for elective intervention poses a unique challenge. These patients are not traditionally offered surgical aortic valve replacement or TAVI given their lack of symptoms; however, they are at increased risk given the severity of their AS. Furthermore, clinical experience has shown that symptoms can be challenging to ascertain in many sedentary, deconditioned, and/or elderly patients. In addition, evolving data based on imaging and biomarker evidence of adverse ventricular remodelling, hypertrophy, inflammation, or fibrosis may radically transform existing clinical decision paradigms. However, management of asymptomatic severe AS is otherwise controversial and the decision to intervene requires careful assessment of the benefits and risks in an individual patient. Further randomized trials [EARLY TAVI (NCT03042104), AVATAR (NCT02436655), EVOLVED (NCT03094143)] will help determine future recommendations.
Cardiac complications of COVID-19 vaccination: now we know more
Authors: Verdecchia Paolo , Coiro Stefano , Notaristefano Francesco , Santucci Andrea , De Angelis Francesca , D’Ammando Matteo , Angeli Fabio
Published: November 2022

The proliferation of good quality observational studies on the potential adverse effects of COVID-19 vaccination has greatly increased our knowledge on myocarditis and pericarditis, and also, more recently, on arterial hypertension. According to some recent studies, the incidence of a significant increase in blood pressure after COVID-19 vaccination is about 3.2% (95% CI: 1.62–6.21). The incidence of serious hypertensive emergencies or stage III hypertension has been reported as 0.6%. It is well known that the ‘spike protein’ of the Sars-CoV-2 virus, the synthesis of which is induced by vaccines, binds to ACE2 receptors, inducing their migration towards the inside of the cell. This would result in a lack of ACE2 activity on cell surfaces and therefore a relative deficiency of angiotensin1-7 with a relative excess of angiotensin II, which could explain, at least in part, the blood pressure increases. Regarding myo-pericarditis, there is evidence that the advantages of COVID-19 vaccination over non-vaccination remain preponderant in terms of prevented hospitalizations and serious complications of COVID-19, compared with the risk of developing myocarditis. In the age group most at risk of COVID-19 vaccine myocarditis (12–29 years), for every 100 000 vaccinated, compared to about four more cases of myocarditis we have 56 fewer hospitalizations, 13.8 admissions to intensive care and 0.6 fewer deaths. Several studies have shown that post vaccine myocarditis/pericarditis are generally short-lasting phenomena with favourable clinically course.
The treatment of amyloidosis is being refined
Authors: Cantone Anna , Sanguettoli Federico , Dal Passo Beatrice , Serenelli Matteo , Rapezzi Claudio
Published: November 2022

The therapy of transthyretin (TTR)-related cardiac amyloidosis consists, on the one hand, of the prevention and management of complications (supportive therapy) and on the other of treatments aimed at interrupting or slowing down the production and deposition of fibrils (disease-modifying therapy). This definition includes drugs that act on different phases of amyloidogenesis: (i) silencing of the gene encoding TTR (small interfering RNA: patisiran, vutrisiran; antisense oligonucleotides: inotersen, eplontersen; new CRISPR Cas-9 drug technology for editing in vivo DNA); (ii) stabilization of circulating TTR to inhibit its dissociation and subsequent assembly of the resulting monomers in amyloidotic fibrils (tafamidis, acoramidis, and tolcapone); (iii) destruction and re-absorption of already formed amyloid tissue deposits. Drugs related to the latter strategy (antibodies) are still the subject of Phase 1 or 2 studies.
The cohesin complex of yeasts: sister chromatid cohesion and beyond
Authors: Choudhary Karan , Kupiec Martin
Published: November 2022

Each time a cell divides, it needs to duplicate the genome and then separate the two copies. In eukaryotes, which usually have more than one linear chromosome, this entails tethering the two newly replicated DNA molecules, a phenomenon known as sister chromatid cohesion (SCC). Cohesion ensures proper chromosome segregation to separate poles during mitosis. SCC is achieved by the presence of the cohesin complex. Besides its canonical function, cohesin is essential for chromosome organization and DNA damage repair. Surprisingly, yeast cohesin is loaded in G1 before DNA replication starts but only acquires its binding activity during DNA replication. Work in microorganisms, such as Saccharomyces cerevisiae and Schizosaccharomyces pombe has greatly contributed to the understanding of cohesin composition and functions. In the last few years, much progress has been made in elucidating the role of cohesin in chromosome organization and compaction. Here, we discuss the different functions of cohesin to ensure faithful chromosome segregation and genome stability during the mitotic cell division in yeast. We describe what is known about its composition and how DNA replication is coupled with SCC establishment. We also discuss current models for the role of cohesin in chromatin loop extrusion and delineate unanswered questions about the activity of this important, conserved complex.
Seismic wavefield reconstruction based on compressed sensing using data-driven reduced-order model
Authors: Nagata T , Nakai K , Yamada K , Saito Y , Nonomura T , Kano M , Ito S , Nagao H
Published: November 2022

Reconstruction of the distribution of ground motion due to an earthquake is one of the key technologies for the prediction of seismic damage to infrastructure. Particularly, the immediate reconstruction of the spatially continuous wavefield is valuable for decision-making of disaster response decisions in the initial phase. For a fast and accurate reconstruction, utilization of prior information is essential. In fluid mechanics, full-state recovery, which recovers the full state from sparse observation using a data-driven model reduced-order model, is actively used. In this study, the framework developed in the field of fluid mechanics is applied to seismic wavefield reconstruction. A seismic wavefield reconstruction framework based on compressed sensing using the data-driven reduced-order model (ROM) is proposed and its characteristics are investigated through numerical experiments. The data-driven ROM is generated from the data set of the wavefield using the singular value decomposition. The spatially continuous seismic wavefield is reconstructed from the sparse and discrete observation and the data-driven ROM. The observation sites used for reconstruction are effectively selected by the sensor optimization method for linear inverse problems based on a greedy algorithm. The proposed framework was applied to simulation data of theoretical waveform with the subsurface structure of the horizontally stratified three layers. The validity of the proposed method was confirmed by the reconstruction based on the noise-free observation. Since the ROM of the wavefield is used as prior information, the reconstruction error is reduced to an approximately lower error bound of the present framework, even though the number of sensors used for reconstruction is limited and randomly selected. In addition, the reconstruction error obtained by the proposed framework is much smaller than that obtained by the Gaussian process regression. For the numerical experiment with noise-contaminated observation, the reconstructed wavefield is degraded due to the observation noise, but the reconstruction error obtained by the present framework with all available observation sites is close to a lower error bound, even though the reconstructed wavefield using the Gaussian process regression is fully collapsed. Although the reconstruction error is larger than that obtained using all observation sites, the number of observation sites used for reconstruction can be reduced while minimizing the deterioration and scatter of the reconstructed data by combining it with the sensor optimization method. Hence, a better and more stable reconstruction of the wavefield than randomly selected observation sites can be realized, even if the reconstruction is carried out with a smaller number of observations with observation noise, by combining it with the sensor optimization method.
Linear Principal Minor Polynomials: Hyperbolic Determinantal Inequalities and Spectral Containment
Authors: Blekherman Grigoriy , Kummer Mario , Sanyal Raman , Shu Kevin , Sun Shengding
Published: November 2022

A linear principal minor polynomial or lpm polynomial is a linear combination of principal minors of a symmetric matrix. By restricting to the diagonal, lpm polynomials are in bijection with multiaffine polynomials. We show that this establishes a one-to-one correspondence between homogeneous multiaffine stable polynomials and PSD-stable lpm polynomials. This yields new construction techniques for hyperbolic polynomials and allows us to find an explicit degree 3 hyperbolic polynomial in six variables some of whose Rayleigh differences are not sums of squares. We further generalize the well-known Fisher–Hadamard and Koteljanskii inequalities from determinants to PSD-stable lpm polynomials. We investigate the relationship between the associated hyperbolicity cones and conjecture a relationship between the eigenvalues of a symmetric matrix and the values of certain lpm polynomials evaluated at that matrix. We refer to this relationship as spectral containment.
Back Stable K-Theory Schubert Calculus
Authors: Lam Thomas , Lee Seung Jin , Shimozono Mark
Published: November 2022

We study the back stable $K$-theory Schubert calculus of the infinite flag variety. We define back stable (double) Grothendieck polynomials and double $K$-Stanley functions and establish coproduct expansion formulae. Applying work of Weigandt, we extend our previous results on bumpless pipedreams from cohomology to $K$-theory. We study finiteness and positivity properties of the ring of back stable Grothendieck polynomials and divided difference operators in $K$-homology.
Seasonal and temporal variation in the placenta during melatonin supplementation in a bovine compromised pregnancy model
Authors: Contreras-Correa Zully E , Cochran Taylor , Metcalfe Abbie , Burnett Derris D , Lemley Caleb O
Published: November 2022

Compromised pregnancies result in a poorly functioning placenta restricting the amount of oxygen and nutrient supply to the fetus resulting in intrauterine growth restriction (IUGR). Supplementing dietary melatonin during a compromised pregnancy increased uteroplacental blood flow and prevented IUGR in a seasonal-dependent manner. The objectives were to evaluate seasonal melatonin-mediated changes in temporal alterations of the bovine placental vascularity and transcript abundance of clock genes, angiogenic factors, and nutrient sensing genes in 54 underfed pregnant Brangus heifers (Fall, n = 29; Summer, n = 25). At day 160 of gestation, heifers were assigned to treatments consisting of adequately fed (ADQ-CON; 100% NRC; n = 13), nutrient restricted (RES-CON; 60% NRC; n = 13), and ADQ or RES supplemented with 20 mg/d of melatonin (ADQ-MEL, n = 13; RES-MEL, n = 15). The animals were fed daily at 0900 hours until day 240 where Cesarean sections were performed in the morning (0500 hours) or afternoon (1300 hours) for placentome collections. In both seasons, we observed a temporal alteration of the core clock genes in the cotyledonary tissue in a season-dependent manner. In the fall, ARNTL, CLOCK, NR1D1, and RORA transcript abundance were decreased (P ≤ 0.05) in the afternoon compared to the morning; whereas in the summer, ARNTL, PER2, and RORA expression were increased (P ≤ 0.05) in the afternoon. Interestingly, in both seasons, there was a concomitant temporal increase (P ≤ 0.05) of cotyledonary blood vessel perfusion and caruncular melatonin receptor 1A transcript abundance. Melatonin supplementation did not alter the melatonin receptor 1A transcript abundance (P > 0.05), however, in the summer, melatonin supplementation increased cotyledonary VEGFA, CRY1, and RORA (P ≤ 0.05) transcript abundance. In addition, during the summer the placentomes from underfed dams had increased average capillary size and HIF1α transcript abundance compared to those adequately fed (P ≤ 0.05). In conclusion, these data indicate increased cotyledonary blood vessel size and blood distribution after feeding to better facilitate nutrient transport. Interestingly, the maternal nutritional plane appears to play a crucial role in regulating the bovine placental circadian clock. Based on these findings, the regulation of angiogenic factors and clock genes in the bovine placenta appears to be an underlying mechanism of the therapeutic effect of dietary melatonin supplementation in the summer.
Consistency of Cuticular Hydrocarbon Mixtures of Five Reticulitermes (Blattodea: Rhinotermitidae) Taxa From Northern California: Similarity Among Colonies and Seasonal Variation
Authors: Nelson Lori J , Hamud Shakeeb M , Baldwin James A , Lewis Vernard R , Haverty Michael I
Published: November 2022

Cuticular hydrocarbon (CHC) mixtures from workers of five distinct CHC phenotypes of Reticulitermes Holmgren 1913 from two locations in northern California were examined from monthly collections taken over a 3-yr period. The objectives of this study were (1) to identify and quantify variations of the CHCs of multiple colonies of each of these phenotypes (= species or subspecies) to demonstrate consistency, (2) to assess the potential of CHC mixtures to separate or identify colonies within each phenotype, and (3) to detect any temporal changes in each of the hydrocarbons in the CHC mixtures. Nonmetric multidimensional scaling of all CHC mixtures of all samples collected at both locations separated the samples into five clearly visible, different groups of CHC phenotypes (taxa or species) of Reticulitermes. The degree of variability of the CHC mixtures among colonies of each phenotype was such that nonmetric multidimensional scaling did not separate or identify colonies. Strong seasonal fluctuations were evident in some of the CHCs of all five phenotypes and were significantly consistent with a sine curve. Maximum proportions of seasonal CHCs within a phenotype occurred in all seasons of the year but occurred mostly in the winter and summer. In general, the CHCs displaying maximum values in the winter were short-chained (C23–C27) methyl-branched alkanes, whereas the CHCs displaying maximum values in the summer were long-chained (C35–C43) methyl-branched alkanes, which likely influences water retention. These consistent chemical fingerprints are probably responsible for inter-phenotype recognition patterns and are thus useful for chemical taxonomy.
CJEU clarifies that destruction of goods may be claimed irrespective of infringement type
Authors: Jacobi Jan
Published: November 2022

The Court of Justice of the European Union (CJEU) has recently ruled that the right to claim destruction of goods applies to all goods that infringe IP rights. The CJEU clarified that destruction may be sought not only of counterfeit goods but also of genuine goods that are placed on the European Economic Area market without the consent of the IP proprietor.
Fatal Fulminant Cerebral Edema in Six Children With SARS-CoV-2 Omicron BA.2 Infection in Taiwan
Authors: Lin Jainn-Jim , Tu Yi-Fang , Chen Shyi-Jou , Kuo Yung-Ting , Jeng Mei-Jy , Hsin-Ju Ko Mary , Chiu Cheng-Hsun
Published: November 2022

Acute fulminant cerebral edema in children following SARS-CoV-2 infection has been rarely reported. Such patients frequently demonstrate rapid progression and are usually fatal. In this retrospective study, we describe the detailed clinical, laboratory, and neuroimaging features of six fatal cases in Taiwan. All patients had shock initially, five showed rapid progression to multiorgan failure and disseminated intravascular coagulation, and three developed acute respiratory distress syndromes. The inflammatory biomarkers in the first 3 days, including interleukin 6, ferritin, lactate dehydrogenase, and D-dimer, showed significant elevation in all cases. The hyperinflammatory response may play a role in the pathophysiology.
An emerging probiotic with liver health benefits for smokers
Authors: Jia Wei , Zheng Xiaojiao
Published: November 2022

Cigarette smoking is considered a risk factor for nonalcoholic fatty liver disease (NAFLD). In a study recently published in Nature, Chen et al. unveiled a mechanistic role of nicotine in NAFLD progression. In addition, they identified a gut bacterium Bacteroides xylanisolvens that can reduce intestinal nicotine levels, and thus improve nicotine-induced NAFLD phenotypes in mice.
A chemical study of nine star-forming regions with evidence of infall motion
Authors: Yang Yang , Wang Yao , Jiang Zhibo , Chen Zhiwei
Published: November 2022

The study of the physical and chemical properties of gas infall motion in the molecular clumps helps us understand the initial stages of star formation. We used the FTS wide-sideband mode of the IRAM 30-m telescope to observe nine infall sources with significant double-peaked blue line profile. The observation frequency ranges are 83.7–91.5 GHz and 99.4–107.2 GHz. We have obtained numbers of molecular line data. Using xclass, a total of 7–27 different molecules and isotopic transition lines have been identified in these nine sources, including carbon chain molecules, such as CCH, c-C3H2 and HC3N. According to the radiation transfer model, we estimated the rotation temperatures and column densities of these sources. Chemical simulations adopting a physical model of HMSFRs are used to fit the observed molecular abundances. The comparison shows that most sources are in the early HMPO stage, with the inner temperature around several 10 K.
A MeerKAT look at the polarization of 47 Tucanae pulsars: magnetic field implications
Authors: Abbate F , Possenti A , Ridolfi A , Venkatraman Krishnan V , Buchner S , Barr E D , Bailes M , Kramer M , Cameron A , Parthasarathy A , van Straten W , Chen W , Camilo F , Padmanabh P V , Mao S A , Freire P C C , Ransom S M , Vleeschower L , Geyer M , Zhang L
Published: November 2022

We present the polarization profiles of 22 pulsars in the globular cluster 47 Tucanae using observations from the MeerKAT radio telescope at UHF band (544–1088 MHz) and report precise values of dispersion measure (DM) and rotation measure (RM). We use these measurements to investigate the presence of turbulence in electron density and magnetic fields. The structure function of DM shows a break at ∼30 arcsec (∼0.6 pc at the distance of 47 Tucanae) that suggests the presence of turbulence in the gas in the cluster driven by the motion of wind-shedding stars. On the other hand, the structure function of RM does not show evidence of a break. This non-detection could be explained either by the limited number of pulsars or by the effects of the intervening gas in the Galaxy along the line of sight. Future pulsar discoveries in the cluster could help confirm the presence and localize the turbulence.
Orbital and physical parameters of eclipsing binaries from the Optical Gravitational Lensing Experiment catalogue: testing the tidal circularization
Authors: Çakirli Ömür
Published: November 2022

Tidal forces are an important process in the pre-main-sequence phase (as reported by Zahn and Bouchet in their now well-known paper) and throughout the main-sequence phase of stellar evolution. Nevertheless, uncertainty over tidal forces affects estimates obtained from models of the circularization and synchronization of the orbit by tidal interactions. Here, we search for evidence of tidal circularization in close binaries using a large sample of well-characterized eclipsing systems. We searched Optical Gravitational Lensing Experiment (OGLE) photometric catalogue for the Southern hemisphere from the Southern hemisphere for eclipsing binaries in eccentric orbits. We present precise values of the eccentricity and orbital and stellar parameters of eight detached, eclipsing stars from the OGLE catalogue that were determined by jointly modelling light curves and spectral analysis. The temperatures and relative radii of their components, as well as their mass ratios, were also calculated with high accuracy. We find a clear dependence of the components' relative radii and orbital period on the eccentricity. The determination of eccentricities as a function of period potentially allows us to infer the role of tidal circularization. The (P, r1,2) distribution of the known eccentric binaries exhibits a rough trend of increasing eccentricity with period. This suggests that the secondary components in binaries with longer orbital periods may be tidally circularized significantly more efficiently than is usually assumed. Observing this effect is challenging because it requires large and well-characterized samples that include many types of systems. Here we seek evidence of the predicted dependence of circularization on the relative radii using a sample of eclipsing binaries observed by OGLE.
The demographics of obscured AGN from X-ray spectroscopy guided by multiwavelength information
Authors: Laloux Brivael , Georgakakis Antonis , Andonie Carolina , Alexander David M , Ruiz Angel , Rosario David J , Aird James , Buchner Johannes , Carrera Francisco J , Lapi Andrea , Ramos Almeida Cristina , Salvato Mara , Shankar Francesco
Published: November 2022

A complete census of active galactic nuclei (AGNs) is a prerequisite for understanding the growth of supermassive black holes across cosmic time. A significant challenge towards this goal is the whereabouts of heavily obscured AGN that remain uncertain. This paper sets new constraints on the demographics of this population by developing a methodology that combines X-ray spectral information with priors derived from multiwavelength observations. We select X-ray AGN in the Chandra COSMOS Legacy survey and fit their $2.2\!-\!500\, \mu \mathrm{m}$ spectral energy distributions with galaxy and AGN templates to determine the mid-infrared ($6\, \mu \mathrm{m}$) luminosity of the AGN component. Empirical correlations between X-ray and $6\, \mu \mathrm{m}$ luminosities are then adopted to infer the intrinsic accretion luminosity at X-rays for individual AGN. This is used as prior information in our Bayesian X-ray spectral analysis to estimate physical properties, such as line-of-sight obscuration. Our approach breaks the degeneracies between accretion luminosity and obscuration that affect X-ray spectral analysis, particularly for the most heavily obscured (Compton-Thick) AGN with low photon counts X-ray spectra. The X-ray spectral results are then combined with the selection function of the Chandra COSMOS Legacy survey to derive the AGN space density and a Compton-Thick fraction of $21.0^{+16.1}_{-9.9}{{\ \rm per\ cent}}$ at redshifts z < 0.5. At higher redshift, our analysis suggests upper limits to the Compton-Thick AGN fraction of $\lesssim 40{{\ \rm per\ cent}}$. These estimates are at the low end of the range of values determined in the literature and underline the importance of multiwavelength approaches for tackling the challenge of heavily obscured AGN demographics.
Preferential accretion and circumbinary disc precession in eccentric binary systems
Authors: Siwek Magdalena , Weinberger Rainer , Muñoz Diego J , Hernquist Lars
Published: November 2022

We present a suite of high-resolution hydrodynamic simulations of binaries immersed in circumbinary accretion discs (CBDs). For the first time, we investigate the preferential accretion rate as a function of both eccentricity eb and mass ratio qb in a densely sampled parameter space, finding that when compared with circular binaries, (i) mass ratios grow more efficiently in binaries on moderately eccentric orbits (0.0 ≲ eb ≲ 0.4), and (ii) high eccentricities (eb ≳ 0.6) suppress mass ratio growth. We suggest that this non-monotonic preferential accretion behaviour may produce an observable shift in the mass ratio distributions of stellar binaries and massive black hole binaries. We further find that the response of a CBD can be divided into three regimes, depending on eccentricity and mass ratio: (i) CBDs around circular binaries always precess freely, whereas CBDs around eccentric binaries either (ii) undergo forced precession or (iii) remain locked at an angle with respect to the binary periapsis. Forced precession in eccentric binaries is associated with strong modulation of individual accretion rates on the precession time-scale, a potentially observable signature in accreting binaries with short orbital periods. We provide CBD locking angles and precession rates as a function of eb and qb for our simulation suite.
The present-day gas content of simulated field dwarf galaxies
Authors: Herzog Georg , Benítez-Llambay Alejandro , Fumagalli Michele
Published: November 2022

We examine the gas content of field dwarf galaxies in a high-resolution cosmological simulation. In agreement with previous work, we find that galaxies inhabiting dark matter haloes with mass below a critical value, M200 ≲ Mcrit ≈ 5 × 109 M⊙, are quiescent at the present day. The gas content of these galaxies is thus insensitive to feedback from evolving stars. Almost half of these quiescent systems today have gas masses much smaller than that expected for their mass. We find that gas-deficient galaxies originate from (1) past interactions with massive hosts, in which a dwarf loses gas and dark matter via tidal and ram-pressure forces; and (2) from hydrodynamic interactions with the gaseous filaments and sheets of the cosmic web, in which a dwarf loses gas via ram pressure. We refer to these systems as ‘flybys’ and ‘COSWEBs’. Flybys locate in high-density regions, tracing the location of the most massive galaxies in the simulation. In contrast, COSWEBs are dispersed throughout the volume and trace the cosmic web. For sub-critical systems, M200 < Mcrit, the fraction of COSWEB galaxies can be as high as $35 {{\ \rm per\ cent}}$, and much higher for flybys, which make up 100 per cent of the galaxies with $M_{200}\lt 3\times 10^8 \ \rm M_{\odot }$. The deficit of gas caused by these mechanisms may preclude the detection of a large fraction of field dwarfs in future H i surveys. For galaxies inhabiting haloes with mass M200 > Mcrit, we find that cosmic web stripping, on average, shuts down star formation in more than $70{{\ \rm per\ cent}}$ of the affected systems.
Peekaboo: the extremely metal poor dwarf galaxy HIPASS J1131-31
Authors: Karachentsev I D , Makarova L N , Koribalski B S , Anand G S , Tully R B , Kniazev A Y
Published: November 2022

The dwarf irregular galaxy HIPASS J1131-31 was discovered as a source of HI emission at low redshift in such close proximity of a bright star that we call it Peekaboo. The galaxy resolves into stars in images with Hubble Space Telescope, leading to a distance estimate of 6.8 ± 0.7 Mpc. Spectral optical observations with the Southern African Large Telescope reveal HIPASS J1131-31 to be one of the most extremely metal-poor galaxies known with the gas-phase oxygen abundance 12 + log(O/H)  = 6.99 ± 0.16 dex via the direct [O iii] 4363 line method and 6.87 ± 0.07 dex from the two strong line empirical methods. The red giant branch of the system is tenuous compared with the prominence of the features of young populations in the colour-magnitude diagram, inviting speculation that star formation in the galaxy only began in the last few Gyr.
UPF1 mutants with intact ATPase but deficient helicase activities promote efficient nonsense-mediated mRNA decay
Authors: Chapman Joseph H , Craig Jonathan M , Wang Clara D , Gundlach Jens H , Neuman Keir C , Hogg J Robert
Published: November 2022

The conserved RNA helicase UPF1 coordinates nonsense-mediated mRNA decay (NMD) by engaging with mRNAs, RNA decay machinery and the terminating ribosome. UPF1 ATPase activity is implicated in mRNA target discrimination and completion of decay, but the mechanisms through which UPF1 enzymatic activities such as helicase, translocase, RNP remodeling, and ATPase-stimulated dissociation influence NMD remain poorly defined. Using high-throughput biochemical assays to quantify UPF1 enzymatic activities, we show that UPF1 is only moderately processive (<200 nt) in physiological contexts and undergoes ATPase-stimulated dissociation from RNA. We combine an in silico screen with these assays to identify and characterize known and novel UPF1 mutants with altered helicase, ATPase, and RNA binding properties. We find that UPF1 mutants with substantially impaired processivity (E797R, G619K/A546H), faster (G619K) or slower (K547P, E797R, G619K/A546H) unwinding rates, and/or reduced mechanochemical coupling (i.e. the ability to harness ATP hydrolysis for work; K547P, R549S, G619K, G619K/A546H) can still support efficient NMD of well-characterized targets in human cells. These data are consistent with a central role for UPF1 ATPase activity in driving cycles of RNA binding and dissociation to ensure accurate NMD target selection.
An updated definition of V(D)J recombination signal sequences revealed by high-throughput recombination assays
Authors: Hoolehan Walker , Harris Justin C , Byrum Jennifer N , Simpson Destiny A , Rodgers Karla K
Published: November 2022

In the adaptive immune system, V(D)J recombination initiates the production of a diverse antigen receptor repertoire in developing B and T cells. Recombination activating proteins, RAG1 and RAG2 (RAG1/2), catalyze V(D)J recombination by cleaving adjacent to recombination signal sequences (RSSs) that flank antigen receptor gene segments. Previous studies defined the consensus RSS as containing conserved heptamer and nonamer sequences separated by a less conserved 12 or 23 base-pair spacer sequence. However, many RSSs deviate from the consensus sequence. Here, we developed a cell-based, massively parallel assay to evaluate V(D)J recombination activity on thousands of RSSs where the 12-RSS heptamer and adjoining spacer region contained randomized sequences. While the consensus heptamer sequence (CACAGTG) was marginally preferred, V(D)J recombination was highly active on a wide range of non-consensus sequences. Select purine/pyrimidine motifs that may accommodate heptamer unwinding in the RAG1/2 active site were generally preferred. In addition, while different coding flanks and nonamer sequences affected recombination efficiency, the relative dependency on the purine/pyrimidine motifs in the RSS heptamer remained unchanged. Our results suggest RAG1/2 specificity for RSS heptamers is primarily dictated by DNA structural features dependent on purine/pyrimidine pattern, and to a lesser extent, RAG:RSS base-specific interactions.
The ProteomeXchange consortium at 10 years: 2023 update
Authors: Deutsch Eric W , Bandeira Nuno , Perez-Riverol Yasset , Sharma Vagisha , Carver Jeremy J , Mendoza Luis , Kundu Deepti J , Wang Shengbo , Bandla Chakradhar , Kamatchinathan Selvakumar , Hewapathirana Suresh , Pullman Benjamin S , Wertz Julie , Sun Zhi , Kawano Shin , Okuda Shujiro , Watanabe Yu , MacLean Brendan , MacCoss Michael J , Zhu Yunping , Ishihama Yasushi , Vizcaíno Juan Antonio
Published: November 2022

Mass spectrometry (MS) is by far the most used experimental approach in high-throughput proteomics. The ProteomeXchange (PX) consortium of proteomics resources (http://www.proteomexchange.org) was originally set up to standardize data submission and dissemination of public MS proteomics data. It is now 10 years since the initial data workflow was implemented. In this manuscript, we describe the main developments in PX since the previous update manuscript in Nucleic Acids Research was published in 2020. The six members of the Consortium are PRIDE, PeptideAtlas (including PASSEL), MassIVE, jPOST, iProX and Panorama Public. We report the current data submission statistics, showcasing that the number of datasets submitted to PX resources has continued to increase every year. As of June 2022, more than 34 233 datasets had been submitted to PX resources, and from those, 20 062 (58.6%) just in the last three years. We also report the development of the Universal Spectrum Identifiers and the improvements in capturing the experimental metadata annotations. In parallel, we highlight that data re-use activities of public datasets continue to increase, enabling connections between PX resources and other popular bioinformatics resources, novel research and also new data resources. Finally, we summarise the current state-of-the-art in data management practices for sensitive human (clinical) proteomics data.
CAMPR4: a database of natural and synthetic antimicrobial peptides
Authors: Gawde Ulka , Chakraborty Shuvechha , Waghu Faiza Hanif , Barai Ram Shankar , Khanderkar Ashlesha , Indraguru Rishikesh , Shirsat Tanmay , Idicula-Thomas Susan
Published: November 2022

There has been an exponential increase in the design of synthetic antimicrobial peptides (AMPs) for its use as novel antibiotics. Synthetic AMPs are substantially enriched in residues with physicochemical properties known to be critical for antimicrobial activity; such as positive charge, hydrophobicity, and higher alpha helical propensity. The current prediction algorithms for AMPs have been developed using AMP sequences from natural sources and hence do not perform well for synthetic peptides. In this version of CAMP database, along with updating sequence information of AMPs, we have created separate prediction algorithms for natural and synthetic AMPs. CAMPR4 holds 24243 AMP sequences, 933 structures, 2143 patents and 263 AMP family signatures. In addition to the data on sequences, source organisms, target organisms, minimum inhibitory and hemolytic concentrations, CAMPR4 provides information on N and C terminal modifications and presence of unusual amino acids, as applicable. The database is integrated with tools for AMP prediction and rational design (natural and synthetic AMPs), sequence (BLAST and clustal omega), structure (VAST) and family analysis (PRATT, ScanProsite, CAMPSign). The data along with the algorithms of CAMPR4 will aid to enhance AMP research. CAMPR4 is accessible at http://camp.bicnirrh.res.in/.
Lithosphere architecture characterized by crust–mantle decoupling controls the formation of orogenic gold deposits
Authors: Hou Zengqian , Wang Qingfei , Zhang Haijiang , Xu Bo , Yu Nian , Wang Rui , Groves David I , Zheng Yuanchuan , Han Shoucheng , Gao Lei , Yang Lin
Published: November 2022

This study, via combined analysis of geophysical and geochemical data, reveals a lithospheric architecture characterized by crust–mantle decoupling and vertical heat-flow conduits that control orogenic gold mineralization in the Ailaoshan gold belt on the southeastern margin of Tibet. The mantle seismic tomography indicates that the crust–mantle decoupled deformation, defined from previous seismic anisotropy analysis, was formed by upwelling and lateral flow of the asthenosphere, driven by deep subduction of the Indian continent. Our magnetotelluric and seismic images show both a vertical conductor across the Moho and high Vp/Vs anomalies both in the uppermost mantle and lowest crust, suggesting that crust–mantle decoupling promotes ponding of mantle-derived basic melts at the base of the crust via a heat-flow conduit. Noble gas isotope and halogen ratios of gold-related ore minerals indicate a mantle source of ore fluid. A rapid decrease in Cl/F ratios of lamprophyres under conditions of 1.2 GPa and 1050°C suggests that the ore fluid was derived from degassing of the basic melts. Similar lithospheric architecture is recognized in other orogenic gold provinces, implying analogous formational controls.
Introduction
Authors: Dews Peter
Published: November 2022

Since the last decades of the twentieth century, interest in developments in German philosophy immediately after Kant has increased the English-speaking world. Hegel has rightly been the focus of much attention, but so also have figures who were previously little known to anglophone philosophers. However, what became the predominant approach to Hegel and post-Kantian Idealism, associated with figures such as Robert Pippin and Terry Pinkard, was unfavorable—even hostile—to the work of Schelling, one of the three major German Idealists, besides Hegel and Fichte. This is because the approach relied on the historically implausible claim that Idealism was concerned with a “space of reasons,” or a normative domain disconnected from all ontological issues. But the atmosphere in the English-speaking world has now changed and basic metaphysical questions are back on the table. The time is right for a less-prejudiced evaluation of Schelling’s work, for a comprehensive comparison of his late philosophy with Hegel’s thought, and for an appreciation of his achievements as a philosophical diagnostician of modernity.
Agency and Absolute Identity
Authors: Dews Peter
Published: November 2022

During the later 1790s Schelling stakes out an original position in the debates concerning the relation between “rational will” (Wille), power of choice (Willkür), and freedom. Criticizing both Kant and Reinhold, he argues that our power of choice is the manifestation of the rational will under finite conditions. In the System of Transcendental Idealism (1800) he then seeks to reconcile this view with history’s teleological structure, regarded as the most general expression of rational will, arguing that aesthetic experience discloses a coincidence of free choice and rational necessity which philosophy cannot grasp theoretically. However, dissatisfaction with the dualism of “transcendental idealism” and the “philosophy of nature” leads to Schelling’s adoption of a philosophy of absolute identity, where the problem of freedom eventually emerges again for his now quasi-Spinozist position. He begins to address the problem in a new manner in the 1804 text, Philosophy and Religion, with the theorem of a “fall” (Abfall) from the absolute, which results in the finite, contingent world.
Beyond the Idea
Authors: Dews Peter
Published: November 2022

This chapter begins with a description of the structure of Schelling’s negative philosophy. It then seeks to elucidate the transition from negative to positive philosophy, as does Schelling himself, by discussing Kant’s theory of the “Ideal of Pure Reason” and his conception of absolute necessity. Schelling’s account of the move beyond the Idea generated by negative philosophy, and why this does not violate Kant’s prohibition on the derivation of existence from pure reason, is explained. The rationale for the transition beyond the absolute Idea at the end of Hegel’s Science of Logic is then compared with Schelling’s pivot from negative to positive philosophy. The chapter ends with a critique of James Kreines’ attempt to explain how Hegel can regard pure thought both as an absolute ground and as dependent on the existence of finite entities. It argues that Schelling’s late text, “On the Source of the Eternal Truths” also seeks, like Kreines, to uncouple epistemological from metaphysical monism, but proposes a more viable solution.
Reason and Revelation
Authors: Dews Peter
Published: November 2022

This chapter discusses Schelling’s Philosophy of Revelation, the second major historical component of his positive philosophy. It explores Schelling’s conception of the relation between reason and revelation, against the background of the emergence of the new sub-discipline, “philosophy of religion,” in the late eighteenth century. It then discusses Schelling’s view of Christianity as the definitive liberation of human consciousness from the mythological process. This account is compared with Hegel’s conception of the coming of Christianity as a similarly pivotal moment in human history. Schelling’s philosophical Christology is then compared with Hegel’s, with regard to their respective conceptions of freedom, and of the relation between the human and the divine. Hegel’s effort to shore up Christian doctrine philosophically, and his insistence on the role of religion in grounding the state in social existence, are compared with Schelling’s view of the trajectory of modern religious consciousness, in the light of his anticipation of what he terms “philosophical religion.”
Turn On, Tune In, Drift Off
Authors: Szabo Victor
Published: November 2022

Turn On, Tune In, Drift Off: Ambient Music’s Psychedelic Past rethinks the history and socioaesthetics of ambient music as a popular genre with roots in the psychedelic countercultures of the late twentieth century. It narrates how anglophone audio producers and DJs between the mid-1960s and century’s end commodified drone- and loop-based records as ambient audio: slow, spare, spacious audio sold as artful personal media for creating atmosphere, fostering contemplation, transforming awareness, and stilling the body. The book takes a trip through landmark ambient audio productions and related discourses, including marketing rhetoric, artist manifestos and interviews, and music criticism, that during this time plotted the conventions of what became known as ambient music. These productions include nature sounds records, experimental avant-garde pieces, “space music” radio, psychedelic and cosmic rock albums, electronic dance music compilations, and of course, explicitly “ambient” music, all of which popularized ambient audio through vivid atmospheric concepts. In paying special attention to the sound of ambient audio; to ambient audio’s relationship with the psychedelic, New Age, and rave countercultures of the United States and United Kingdom; and to the coincident coevolution of therapeutic audio and “head music” across alternative media and independent music markets, this history resituates ambient music as a hip highbrow framing and stylization of ongoing practices in crafting audio to alter consciousness, comportment, and mood. In so doing, Turn On, Tune In, Drift Off illuminates the social and aesthetic rifts and alliances informing one of today’s most popular musical experimentalisms.
A New Grammar of Dyirbal
Authors: Dixon R. M. W.
Published: November 2022

When it was published, in 1972, Professor R. M. W. Dixon’s The Dyirbal Language of North Queensland had a decisive influence in several directions. By the inclusion of culturally informative examples from texts, it helped reveal the role of language in society. Its clear organisation became a benchmark for descriptive grammars. And the analysis of ergativity opened a new theoretical window. Dixon continued fieldwork with the remaining fluent speakers almost every year through 2001, building up a considerable corpus. He refined and extended the grammatical analysis, taking full account of recent advances in typological theory (for quite a few of which he had played a significant role). A New Grammar of Dyirbal is self-contained; it does not assume any familiarity with the 1972 grammar. A special feature is that, whereas in the earlier work structural features were explained through simple sentences crafted by linguist and speakers, in this present volume almost every example comes directly from a text. In this way, the book provides insight into Dyirbal traditional culture and beliefs. A pervasive characteristic of the language is its ‘ergative syntax’—the operation of an ‘S/O pivot’—a feature which recurs in a dozen chapters. There is a split-case system; two antipassive derivations, with contrastive meanings; one derivation which can have either applicative or causative effect; two relative clause constructions with a wider functional range than in most languages. And much more.
The House Where My Soul Lives
Authors: Graham Maryemma
Published: November 2022

This chapter moves on to Margaret Walker’s return to New Orleans. In 1934, the New Orleans in which Walker spent her first official year of adulthood was a more refined version of the Jim Crow South, more brutal and unforgiving. Yet she found her creative and moral center in the midst of these myriad conflicts, gravitating toward them, almost as a duty to herself. On the one hand, the situation with her parents wore heavily on her; on the other, the social realities of New Orleans stared her in the face. What made all of this unique was her attempt at self-definition through these conflicts, one not bound to her mother, her father, or a Jim Crow world. It was the first time she had felt compelled to mark her independence, which she did, not by speaking her mind, but rather by keeping her silence. The distinction she made was a crucial one for our understanding of the kind of poet that Margaret Walker became. Hers was an intellectual and artistic awakening as much as it was a physical one that affirmed her identity as a young Black woman. Art was her sense of connection, a convergence of individual will and creative spirit bound together by the needs and expectations of her family, community, and her race.
A Year of New Beginnings
Authors: Graham Maryemma
Published: November 2022

This chapter recounts how, on the day following the Japanese attack on Pearl Harbor, in December 1941, Sigismund Walker handed his daughter a telegram from President W. J. Trent of Livingstone College in Salisbury, North Carolina. Trent had learned about Margaret Walker through a fellow clergyman and invited her to join the faculty of the small Negro liberal arts college. The semester would start in January, and Walker was to report to school soon after the start of the new year. Still dependent upon her family, Walker was not able to buy a ticket to begin her new life and swallowed her pride as she turned to her mother for help. With borrowed money and a small suitcase of clothes, most of which she had brought with her from Chicago and Iowa, Walker again boarded the Jim Crow coach of the Illinois Central, going north. She was in good spirits but, having had teaching jobs disappear no sooner than she learned about them on multiple occasions, she understood there were no guarantees. Walker was coming to the rather startling revelation that who she was and what she wanted to be might have had little meaning in the 1940s within the larger context of an average Black person’s life.